
==== Front
PeerJ
PeerJ
peerj
PeerJ
2167-8359
PeerJ Inc. San Diego, USA

17778
10.7717/peerj.17778
Agricultural Science
Plant Science
QTL mapping for seed vigor-related traits under artificial aging in common wheat in two introgression line (IL) populations
Yang Zhenrong 1
Wu Jirong 1
Wang Qiyu 1
Chen Weiguo 2
Shi Huawei 1
Shi Yugang 1
Yang Jinwen 1
Li Ning 1
Sun Daizhen sundaizhen@sxau.edu.cn
1
Jing Ruilian jingruilian@caas.cn
3
1 College of Agriculture, Shanxi Agricultural University, Key Laboratory of Sustainable Dryland Agriculture (Co-construction by Ministry and Province), Jinzhong, China
2 College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
3 State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
Kutlu Imren
16 9 2024
2024
12 e1777828 10 2023
28 6 2024
©2024 Yang et al.
2024
Yang et al.
https://creativecommons.org/licenses/by-nc/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits using, remixing, and building upon the work non-commercially, as long as it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.

Background

Seed vigor recognized as a quantitative trait is of particular importance for agricultural production. However, limited knowledge is available for understanding genetic basis of wheat seed vigor.

Methods

The aim of this study was to identify quantitative trait loci (QTL) responsible for 10 seed vigor-related traits representing multiple aspects of seed-vigor dynamics during artificial aging with 6 different treatment times (0, 24, 36, 48, 60, and 72 h) under controlled conditions (48 °C, 95% humidity, and dark). The mapping populations were two wheat introgression lines (IL-1 and IL-2) derived from recipient parent (Lumai 14) and donor parent (Shaanhan 8675 or Jing 411).

Results

A total of 26 additive QTLs and 72 pairs of epistatic QTLs were detected for wheat seed-vigor traits. Importantly, chromosomes 1B and 7B contained several co-located QTLs, and chromosome 2A had a QTL-rich region near the marker Xwmc667, indicating that these QTLs may affect wheat seed vigor with pleiotropic effects. Furthermore, several possible consistent QTLs (hot-spot regions) were examined by comparison analysis of QTLs detected in this study and reported previously. Finally, a set of candidate genes for wheat seed vigor were predicted to be involved in transcription regulation, carbohydrate and lipid metabolism.

Conclusion

The present findings lay new insights into the mechanism underlying wheat seed vigor, providing valuable information for wheat genetic improvement especially marker-assisted breeding to increase seed vigor and consequently achieve high grain yield despite of further investigation required.

Wheat
Seed
Vigor
Artificial aging introgression lines
QTL mapping
Key Research and Development Program Project in Shanxi Province202102140601001 Science and Technology Innovation Foundation of Shanxi Agricultural University2020BQ42 This work was supported by the Key Research and Development Program Project in Shanxi Province (202102140601001), and by the Science and Technology Innovation Foundation of Shanxi Agricultural University (2020BQ42). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
==== Body
pmcIntroduction

Seed vigor is an important agronomic traits in determining wheat (Triticum aestivum) yields as in other crops (Reed, Bradford & Khanday, 2022). Generally, high-vigor seeds exhibit a high germination rate, leading to uniform seedlings and ultimately large yields. In contrast, low-vigor seeds show a low germination rate, resulting in unhealthy seedlings and eventually the reduced production (Shi et al., 2020). Therefore, it is so significant to elucidate the genetic basis of crop seed vigor and timely monitor the change of seed viability over the period of storage for ensuring stable and high yields of crops, maintaining economic benefits of agricultural production (Rajjou et al., 2008; Schwember & Bradford, 2010; Ahmed, Yang & Fu, 2016; Zuo et al., 2018).

For assessing seed vigor, the natural aging (NA) under normal conditions usually takes a long time complete, whereas artificial aging (AA) under high temperature and humidity is easily conducted for quicker examination of seed vigor-related traits (Bentsink et al., 2000; Murthy, Kumar & Sun, 2003; Landjeva, Lohwasser & Börner, 2010; Zuo et al., 2018). Thus, AA method is recommended for measuring seed vigor by the International Seed Testing Association (Zheng et al., 2017). Increasing reports showed that seed aging/deterioration is a complex biological trait involving a network consisted of biochemical, physiological, molecular, and metabolic processes (Mcdonald, 1999; Rajjou et al., 2012). The reported causes for seed deterioration during storage in various plant species include the loss of cellular membrane integrity, weak energy metabolism, production of reactive oxygen species (ROS) and their counter balance, lipid peroxidation, impaired RNA and protein synthesis, enzyme inactivation, and damage to DNA integrity (Corbineau et al., 2002; Kibinza et al., 2006; Ahmed, Yang & Fu, 2016; Shi et al., 2020). A number of genes were identified to be related to seed vigor. For instance, the increase of lipoxygenase (LOX) activity promoted oxidization of lipids, ROS burst, and seed deterioration (Corbineau et al., 2002). Overexpression of ZmGOLS2 and ZmRS in Arabidopsis and maize increased seed vigor (Li et al., 2017). A rice small heat shock protein OsHSP18.2 was found to enhance seed vigor by eliminating ROS in seeds under biotic stress (Kaur et al., 2015). Moreover, overexpression of Heat Shock Factor A9 encoding a seed-specific transcription factor resulted in extension of seed longevity by enhancing levels of heat shock proteins in transgenic tobacco (Nicotiana tabacum) plants (Prieto-Dapena et al., 2006; Kotak et al., 2007). A lectin-like receptor protein kinase (LecRK) was also detected to contribute to innate immunity and seed germination in rice by upregulating α-amylase gene (Cheng et al., 2013). Mutation of SNL1/2 (SWI-INDEPENDENT3 (SIN3)-LIKE) in Arabidopsis resulted in the decrease of seed dormancy and a shortened seed longevity (Wang et al., 2013). These data demonstrated the complex genetic nature of seed vigor.

Phenotypic variations of seed vigor were detected among different crops and varieties (TeKrony & Hunter, 1995; Soltani, 2001; Sun, Wang & Sun, 2007), which were quantitative traits controlled by multiple genes (Dickson, 1980; Arif & Börner, 2020) and affected by environmental factors (Arif et al., 2012). A number of traits were measured to examine seed vigor, including germination rate (GR), germination energy (GE), germination index (GI), seedling length (SL), root length (RL), seed wet weight (SWW) and dry weight (SDW) as well as vigor index (VI). In view of quantitative heredity of those traits, QTL (quantitative trait loci) analysis was employed as an effective approach to dissect the genetic basis of seed vigor-related traits of crops in recent years (Miura et al., 2002; Zeng et al., 2006; Singh et al., 2008; Xue et al., 2008; Nagel et al., 2009; Revilla et al., 2009; Nagel et al., 2011; Agacka-Moldoch et al., 2015).

In wheat, QTLs were also identified for seed vigor. For example, 24 QTLs related to seed vigor were mapped to chromosomes 1D, 2D, 4D, 5D, and 7D using a set of common wheat lines carrying known D genome introgression segments (Landjeva, Lohwasser & Börner, 2010). 94 QTLs related to seed vigor traits in wheat were detected using 246 recombinant inbred lines derived from the cross between Zhou 8425B and Chinese Spring, with one of the stable QTL-rich regions on chromosome 2D flanked by IWB21991 and IWB11197 as a pleiotropic locus strongly affecting seed vigor-related traits after accelerated aging treatment (Zuo et al., 2018). QTLs of seed longevity in durum wheat were detected with a bi-parental mapping population consisited of 114 recombinant inbred lines, with four QTLs for germination energy on chromosomes 4B, 5A (2 QTLs), and 6B, and three significant QTLs for germination rate on chromosomes 5A and 7B (2 QTLs) under artificial aging (Arif & Börner, 2019). 24 QTLs related to wheat seed longevity were identified by a SNP based GWAS analysis (Arif & Börner, 2020). A total of 49 additive QTLs for seed vigor-related traits were mapped in wheat genome, with each accounted for 6.01–17.18% of the phenotypic variations (Shi et al., 2020). More recently, a total of 46 additive QTLs and 29 pairs of epistatic QTLs related to seed longevity and dormancy in bread wheat were identified using 7584 high-quality SNPs (Arif et al., 2022). Despite of such increasing reports on QTL analysis of wheat seed vigor-relate traits (Ter Steege et al., 2005; Landjeva et al., 2008; Czyczyło-Mysza et al., 2014; Li et al., 2014; Moore & Rebetzke, 2015; Ayalew et al., 2018; Batool et al., 2018; Li et al., 2018a; Li et al., 2018b; Blackburn et al., 2021), the genetic analysis of wheat seed vigor is still required (Arif et al., 2012; Arif & Börner, 2020) because it is hard to detect the same QTLs even within the same population under multiple conditions.

Different from other mapping populations, introgression line (IL) populations were more powerful in QTL mapping specially for small QTL detection by eliminating interference from the genetic background and improving the accuracy of mapping (Kaeppler, 1997; Landjeva, Lohwasser & Börner, 2010). Here, two IL populations and their parents were employed to identify QTLs related to seed vigor in wheat by AA method so as to better understand the genetic mechanism of wheat seed vigor.

Materials & Methods

Wheat materials

The test plant materials were two wheat IL populations (IL-1 and IL-2), and each of them contained 160 lines (BC3F9). IL-1 and IL-2 populations were derived from wheat cultivars Lumai 14 (recipient and recurrent parent) and Shaanhan 8675 (donor parent) or Jing 411 (donor parent), respectively. Lumai 14 is a winter wheat variety with better disease resistance, high yield, wide adaptability and early maturity (Ge et al., 2013). Shaanhan 8675 is a dryland wheat variety, which has strong stress resistance, wide adaptability, stable and high yield (Dai et al., 2009). Jing 411 is a wheat variety developed in the early 1990s, which has the advantages of strong cold and disease resistance, great tillering ability, high and stable yield, and wide adaptability (Chen et al., 2009). The IL-1 population was developed through an initial cross between Lumai 14 (female parent) and Shaanhan 8675 (male parent) to produce the F1 generation. Then, Lumai 14 was backcrossed with the F1 for three generations to obtain the BC3F1, and then self-cross for many years. Similarly, the IL-2 population was constructed using the same approach, but with the male parent material being Jing 411 instead of Shaanhan 8675. The details of IL populations construction were described previously by Chen et al. (2020) and Yan et al. (2019). These two IL populations were planted in the wheat experiment field (37°25′N, 112°25′E) of Shanxi Agricultural University (Taigu, China) in the growing season of 2019–2020. The field management was the same as used in the local production practice. The soil fertility of the test field before planting was as follows: total nitrogen 1.19 g/kg; total phosphorus 1.07 g/kg; total potassium 14.92 g/kg; available nitrogen 52.37 mg/kg; available phosphorus 13.39 mg/kg; available potassium 88.80 mg/kg. The application amount of nitrogen fertilizer in the experimental field was N 270 kg/hm (urea), with 50% applied as base fertilizer and 50% applied as topdressing during the greening jointing period. Water management was carried out in pre-wintering period, jointing period and mid-grouting period respectively, with irrigation volume of 650 m3/hm2 each time. The wheat seeds were collected in batches from each plant line at wax ripening stage for follow-up test.

Genetic background of IL populations

We use GGT2.0 (Graphical Genotype) software (https://ggt.software.informer.com/2.0/) to analyze the number, length, and proportion of imported fragments in each line’s genome. In IL-1, some segments of the donor parent Shaanhan 8675 were introgressed into 160 lines. The number of introgressed segments ranged from 1 to 46, with an average of 8.04 cM, and the length of introgressed segments ranged from 12.80 cM-994.2 cM, with an average length of 133.70 cM. Within the 160 lines, the proportion of the donor parent’s genome ranged from 0.50 to 38.70% (Chen et al., 2020). In IL-2, all 160 lines introgressed partial segments of the donor parent Jing 411. The number of introgressed segments ranged from 2 to 25, with an average of 6.85 cM, and the length of introgressed segments ranged from 23.12 cM–516.37 cM, with an average length of 155.68 cM. Within the 160 lines, the proportion of the donor parent’s genome ranged from 0.90 to 20.10% (Yan et al., 2019).

Artificial accelerated aging test and standard seed germination test

An artificial aging (AA) test was carried out based on the method described by Shi et al. (2020). In brief, after three months of storage at room temperature, the harvested wheat seeds were used for AA test. 950 healthy seeds from each wheat plant line were placed into the kraft paper bag, and then laid on the grid. 1,000 mL of distilled water was added at the bottom of the aging basin (30 cm in diameter). The basin was sealed with a cover and then placed on the grid, followed by putting the aging basin in an artificial climate incubator with a temperature of 48 °C and a relative humidity of 100% for artificial aging. Then, the seeds were respectively aged for 0 h (as the control), 24 h, 36 h, 48 h, 60 h, and 72 h, under dark conditions. After naturally drying at room temperature for three days, the seeds were used for the standard seed germination test. The treatment for each wheat plant line was conducted with three biological replicates.

The aged seeds were germinated according to the standard germination method. 50 seeds were selected for each treatment, with three replicates. Firstly, the seeds were disinfected with 0.1% NaClO solution for 20 min, and washed with distilled water for 4 times, followed by immersion in a culture dish for 18 h (at this time point, 0 h-aged seeds (control) started to appear white). Secondly, the seeds were evenly placed on a seedling tray (31 cm long, 23 cm wide and 4.5 cm thick), and 1,000 ml distilled water were added into the tray. Thirdly, the seeds were placed in an artificial climate box, and then cultured under the conditions of temperature 25 °C, relative humidity 75%, light intensity 12000 LX, and a photoperiod of 16 h-light and 8 h-dark. An appropriate amount of distilled water was regularly added to ensure the humidity of seedling tray. Fourthly, after the seeds were immersed for three days, the normal seed germination was recognized when the protruding part of seed radicle reached to the half of seed length. Finally, on the seventh day of cultivation, five seedlings per treatment were randomly selected to measure the seedling lengh (SL), root length (RL), seedling fresh weight (SFW) and root fresh weight (RFW).

Calculation of traits related to wheat seed vigor

The calculation formulas were as follows: (Shi et al., 2020)

Germation energy (GE) = (n3/50) ×100%

Germination rate (GR) = (n7/50) ×100%

Germination index (GI) = ΣGt/Dt

Germination pace (GP) =n7/ Σ(n × g) ×100

Vigor index (VI) = GI × SL

Simple vigor index (SVI) = GR × SL

In these formulas, n3 is the number of germinated seed on 3 d of culture while n7 is the number of germinated seed on 7 d of culture. Gt means the number of germinated seed per day, and Dt refers to the corresponding germination days of Gt.

Data analysis and QTL mapping

Phenotypic data were statistically analyzed by Excel 2016 (Microsoft Corp., Redmond, USA), SPSS 25 (SPSS Inc., Chicago, USA), and Origin 2021 (OriginLab Corp., Northampton, MA, USA). The genetic map of the populations was integrated by our lab (Yan et al., 2019; Chen et al., 2020). The genetic linkage maps of the two IL populations were constructed using MapDraw software based on the integrated map of wheat high density SSR markers published by Somers (Somers, Isaac & Edwards, 2004). There were 187 polymorphic SSR markers in IL-1 population and 156 in IL-2 population. SSR amplicon sizes for these markers were detected using polyacrylamide gel electrophoresis (Yan et al., 2019). The total length of the linkage maps was 2569 cM for both two IL populations, and the mean distance between the markers was 13.73 cM for IL-1 population and 16.47 cM for IL-2 population.

QTLs were described by the nomenclature q trait-processing time-chromosome. QTL detection was performed using IciMapping 4.2 (http://www.isbreeding.net/) (Permutation times = 1,000, P < 0.05).

Results

Phenotypic analysis of seed-vigor traits in two IL populations after artificial aging

After aging treatments, a total of 10 traits related to seed vigor were measured including GE, GR, GI, GP, SL, RL, SFW, RFW, VI and SVI. The results showed that there was progressive decline in all the 10 traits with the prolongation of aging time. In most cases, the absolute values of skewness and kurtosis coefficients of the traits in those two IL populations were less than one, representing the characteristic of normal distribution of the traits tested among these populations (Fig. 1 and Fig. S1). As evident from Tables S1 and S2, the variation of these seed vigor traits in the two mapped populations showed a continuous distribution. In the IL-1, the phenotypic value of both parents under different aging conditions were all within the range of variation of the genetic population for mapping, and in the IL-2, except for 72 h of aging, the traits of both parents under other aging conditions were all within the variation range of the population. The results indicated that these seed vigor traits were quantitative traits controlled by a few minor-polygenes, and the genes controlling these traits were effectively recombined. Therefore, these two wheat IL populations are suitable for QTL mapping of these seed vigor traits.

10.7717/peerj.17778/fig-1 Figure 1 Frequency distributions and differences for wheat seed vigor-related traits under six different aging treatments in IL - 1 population.

IL, introgression line, GE, gemination energy, GR, gemination rate, GI, germination index, GP, germination pace, SL, seedling lengh; RL, Root Length, SFW, seedling fresh weight, RFW, root fresh weight, VI, vigor index, SVI, simple vigor index. The same below. For the frequency distribution histogram, the X-axis represents the distribution range (interval) of phenotypic for each trait in IL-1 population, while the Y-axis corresponds to the number of lines in each intervals under 6 different treatments, The fitting curves of different colors reflect the distribution of phenotypic under the different aging treatment. For a boxpLot, the X-axis represents the six aging treatment for each trait, while the Y-axis corresponds to the phenotype. Different colors represent aging for 0 h, 24 h, 36 h, 48 h, 60 h and aging 72 h, respectively. Different lowercase letters showed significant difference (P < 0.05).

10.7717/peerj.17778/table-1 Table 1 Additive-effect QTLs for seed vigor traits detected in wheat IL-1 population.

Trait	Aging time	QTL	Chr.	Marker	LOD	Additive effect	PVE (%)	
GR	0 h	qGR-0h-3D	3D	Xwmc418	3.26	−0.03	9.84	
72 h	qGR-72h-5A	5A	Xwmc524	3.23	0.13	9.02	
GI	72 h	qGI-72h-5A	5A	Xwmc524	3.09	1.88	10	
GP	48 h	qGP-48h-7A	7A	Xcfa2019	3.58	−1.5	11.47	
60 h	qGP-60h-6A	6A	Xwmc807	2.94	1.45	9.29	
RL	0 h	qRL-0h-1B	1B	Xwmc830	2.89	0.88	7.47	
24 h	qRL-24h-1B	1B	Xwmc830	3.57	0.88	10.59	
VI	36 h	qVI-36h-7B	7B	Xgwm400	2.78	−15.41	9.05	
60 h	qVI-60h-6A	6A	Xwmc807	3.09	17.59	10.07	
SVI	36 h	qSVI-36h-7B	7B	Xgwm400	3.05	−0.83	9.65	
Notes.

Positive values in additive effect indicate that ‘Shaanhan 8675’ alleles increase the corresponding trait, and, conversely, negative values indicate that ‘Shaanhan 8675’ alleles decrease the trait.

10.7717/peerj.17778/table-2 Table 2 Additive-effect QTLs for seed vigor traits detected in wheat IL-2 population.

Trait	Aging time	QTL	Chr	Marker	LOD	Additive effect	PVE (%)	
GE	60 h	qGE-60h-7B	7B	Xwmc396	4.85	0.14	21.35	
GI	0 h	qGI-0h-4B	4B	Xwmc47	2.94	−0.51	9.38	
	72 h	qGI-72h-1B	1B	Xwmc406	4.76	2.62	10.89	
GP	36 h	qGP-36h-5B	5B	Xwmc616	4.19	1.14	9.91	
	36 h	qGP36h-6D	6D	Xbarc96	3.51	0.92	8.27	
	36 h	qGP-36h-7D	7D	Xwmc671	3.39	−1.79	7.98	
SL	36 h	qSL-36h-2A	2A	Xwmc667	3.27	0.54	10.02	
48 h	qSL-48h-2A-1	2A	Xwmc667	4.99	0.82	13.16	
48 h	qSL-48h-2A-2	2A	Xgwm359	2.73	−0.49	6.8	
60 h	qSL-60h-2A	2A	Xwmc667	2.82	0.93	10.01	
RL	0 h	qRL-0h-1D	1D	Xgdm126	2.59	0.46	7.49	
	24 h	qRL-24h-1D	1D	Xgdm126	3.05	0.48	8.56	
SFW	48 h	qSW-48h-2A	2A	Xwmc667	3.27	3.99	10.16	
	60 h	qSW-60h-2A	2A	Xwmc667	2.8	5.11	10.12	
VI	24 h	qVI-24h-1D	1D	Xgwm458	3.44	−10.55	12.58	
	72 h	qVI-72h-1B	1B	Xwmc406	3.65	20.89	21.89	
Notes.

Positive values in additive effect indicate that ‘Jing 411’ alleles increase the corresponding traits, and, conversely, negative values indicate that ‘Jing 411’ alleles decrease the trait.

In addition, we also noticed that the donor parent Shaanhan 8675 was treated with 0 h aging except for SL and FRW, the other eight traits were lower than that of recipient parent Lumai 14, and the other nine traits of donor parent Jing 411 were lower than that of Lumai 14 except SFW, which indicated that the seed vigor of Lumai 14 was better than that of other two parents without aging treatment. After 72 h of aging, except for SL, the decline degree of the traits was lower in the Jing 411 than that in the Lumai 14, indicating a relatively good storability of the Jing 411. In the Shaanhan 8675, the decline degree of the six vigor traits including GE, GR, GI, GP, VI and SVI was lower than that in the Lumai 14, but the decline degree of SL, RL, SFW and RFW in the Shaanhan 8675 was higher than that in Lumai 14. This showed that Shaanhan 8675 was superior to Lumai 14 in seed germination vigor after extreme aging, but seedling vigor was weaker in Shaanhan 8675 than in Lumai 14 (Tables S1 and S2). Additionally, a correlation analysis was conducted for those 10 seed-vigor traits (Fig. 2 and Fig. S2). Consistently, a significant or extremely significant correlation was detected between seed-vigor traits among these two IL populations under the same aging condition.

10.7717/peerj.17778/fig-2 Figure 2 Heatmap of the correlations between wheat seed vigor-related traits in IL - 1 population.

(A–F) Aging for 0 h, 24 h, 36 h, 48 h, 60 h and aging 72 h, respectively. Asterisks (*, **, ***) indicate that correlation is significant at P < 0.05, P < 0.01, and P < 0.001, respectively.

Detection of additive QTLs for wheat seed-vigor traits

Under six different aging treatments (six different lengths of aging time), a total of 26 additive QTLs for all the traits except RFW were identified from those two IL populations (Tables 1 and 2, Figs. 3 and 4). In IL-1 population, 10 additive QTLs were detected, with the LOD values of 2.78−3.58 and their phenotypic contribution rates from 7.47 to 11.47%. These additive QTLs were distributed on chromosomes 1B, 3D, 5A, 6A, 7A and 7B of wheat (Table 1), respectively. In IL-2 population, 16 additive QTLs were detected, with the LOD values of 2.59−4.99 and their phenotypic contribution rates were from 6.80% to 21.89%, as well as their distribution on chromosomes 1B, 1D, 2A, 4B, 5B, 6D, 7B and 7D (Table 2), respectively.

10.7717/peerj.17778/fig-3 Figure 3 Distribution of additive QTLs for wheat seed-vigor traits detected in IL - 1 population.

Different colors represent different aging time.

10.7717/peerj.17778/fig-4 Figure 4 Distribution of additive QTLs for wheat seed-vigor traits detected in IL - 2 population.

Different colors represent different aging time.

Additive QTL of seed germination energy (GE)

One additive QTL (qGE-60h-7B) of seed GE was identified in IL-2 population after 60 h of aging. This GE QTL was located near the marker Xwmc396 on chromosome 7B, with its favorable allele coming from Jing 411. This QTL contributed 21.35% of the phenotypic variation, with the additive effect of 0.14 and the LOD value of 4.85, indicating a high potential in wheat breeding to increase seed vigor.

Additive QTL of seed germination rate (GR)

In IL-1 population, one additive QTL of GR was identified at 0 h and 72 h of aging, respectively. qGR-0h-3D detected at 0 h of aging was located near the marker Xwmc418 on chromosome 3D, with its synergetic alleles from Shaanhan 8675 and the additive effect of 0.13. qGR-72h-5A detected at 72 h of aging was mapped near the marker Xwmc524 on wheat chromosome 5A. The contribution rate of qGR-0h-3D and qGR-72h-5A was 9.84% and 9.02% of the phenotypic variation, respectively.

Additive QTL of seed germination index (GI)

Three additive QTLs of GI were detected using these two IL populations, with their locations on chromosomes 1B, 4B and 5A. At 0 h of aging, an additive QTL of GI (qGI-0h-4B) was detected near the marker Xwmc47 on chromosome 4B using IL-2 population. After 72 h of extreme aging, an additive QTL of GI was detected, respectively, in the two populations, with qGI-72h-5A in IL-1 and qGI-72h-1B in IL-2. For these two loci, the synergistic alleles were Shaanhan 8675 and Jing 411, respectively. The additive effect was 1.88 and 2.62 for qGI-72h-5A and qGI-72h-1B, respectively.

Additive QTL of seed germination pace (GP)

In IL-1 population, an additive QTL of seed GP was detected at 48 h and 60 h of aging, respectively. qGP-48h-7A was mapped near the marker Xcfa2019 on chromosome 7A at 48 h of aging. This QTL was recognized as a major QTL responsible for wheat seed GP since it contributed 11.47% of phenotypic variation and its synergetic alleles were come from Lumai 14, with the additive effect of −1.50. For IL-2 population, three additive QTLs of GP were detected at 36 h of aging, locating on chromosomes 5B, 6D and 7D, respectively. With just 7.98%–9.91% of contribution to the phenotypic variation, they were minor QTLs for GP.

Additive QTL of wheat seedling length (SL)

Four additive QTLs for this trait were detected in IL-2 population. qSL-36h-2A, qSL-48h-2A-1 and qSL-60h-2A were located near the marker Xwmc667 on chromosome 2A. Interestingly, these three QTLs are likely the same QTL locus, named qSL-2A detected under the three different aging treatments. Moreover, their contributions to the phenotypic variation were greater than 10, indicating that qSL-2A is the major QTL responsible for wheat SL under those three aging treatments. qSL-48h-2A-2 was another additive QTL of SL on chromosome 2A, having its synergetic alleles provided by Lumai 14 and the additive effect of −0.49 as well as only accounting for 6.80% of phenotypic variation.

Additive QTL of root length (RL) of wheat seedling

Two additive QTLs for RL of wheat seedling were detected at 0 h and 24 h of aging, respectively. In IL-1 population, qRL-0h-1B and qRL-24h-1B were all located near the marker Xwmc830 on chromosome 1B. Their synergetic alleles were all derived from Shaanhan 8675, and the additive effect was 0.88. Thus, it’s likely that they were located at the same QTL locus named as qRL-1B responsible for wheat seedling RT trait at 0 h and 24 h of aging. Similarly, in IL-2 population, qRL-0h-1D and qRL-24h-1D were mapped near the marker Xgdm126 on chromosome 1D. Their synergetic alleles were all derived from Jing 411 and their additive effects were 0.46 and 0.48, respectively. Therefore, these two QTLs were likely located at the same QTL locus named as qRL-1D. Since the QTLs of RL were detected in both IL populations under 0 h and 24 h of aging treatments, these two additive QTLs, qRL-1B and qRL-1D only affected the root length of wheat seedling under no aging or slightly aging, but had no significant impact on the root length after a long period of aging.

Additive QTL of seedling fresh weight (SFW)

One additive QTL for this trait was detected in IL-2 population at 48 h and 60 h of aging, repectively. qSFW-48h-2A and qSFW-60h-2A had the LOD value of 3.27 and 2.80, respectively. Since these two QTLs were located near the marker Xwmc667 on chromosome 2A, and their synergistic alleles were all derived from Jing 411, they should be the same QTL named as qSFW-2A responsible for this trait under the two aging treatments. This QTL accounted for the phenotypic variation by more than 10% and thus, qSFW-2A was a major QTL for this trait under two kinds of aging treatment, showing a certain utilization value in wheat breading to achieve stronger seed vigor.

Additive QTL of seed vigor index (VI)

After the wheat seeds were aged, two additive QTLs of seed VI trait were, respectively, detected in the two IL populations under aging treatments. In IL-1 population, qVI-60h-6A and qVI-36h-7B were detected to locate on chromosomes 6A and 7B, respectively, at 60 h and 36 h of aging. With the synergistic alleles derived from Shaanhan 8675 and the additive effect of 17.59, qVI-60h-6A was a major QTL for wheat VI trait due to its high contribution to the phenotypic variation (10.07%). Conversely, qVI-36h-7B was a minor QTL for this trait, with the synergistic alleles derived from Lumai 14 and the additive effect of −15.41, as well as a small contribution to the phenotypic variation (9.05%). In IL-2 population, two additive QTLs (qVI-72h-1B and qVI-24h-1D) of seed VI were located on chromosomes 1B and 1D, respectively. qVI-24h-1D had the synergistic alleles derived from Lumai 14 and the additive effect of −15.41 as well as a high contribution to the phenotypic variation (12.58%). qVI-72h-1B had the synergistic alleles derived from Jing 411 and the additive effect up to 20.89 as well as a much higher contribution to the phenotypic variation (21.80%) Collectively, both qVI-24h-1D and qVI-72h-1B were the major QTLs responsible for wheat seed VI under aging, with qVI-72h-1B having much greater impact and high value for use in wheat breeding program to enhance seed VI.

Additive QTL of simple vigor index (SVI) of seeds

In the IL-1 population, one additive QTL of SVI (qSVI-36h-7B) was detected after 36 h of aging. This QTL was located near the marker Xgwm400 on chromosome 7B, with its synergistic alleles provided by Lumai 14, the additive effect of −0.83, the LOD value of 3.05 and accounting for 9.65% of the phenotypic variation.

Detection of epistatic QTLs for wheat seed-vigor traits

A total of 72 pairs of epistatic QTLs responsible for eight seed-vigor traits (GR, GI, GP, SL, RL, SFW, VI and SVI) were detected using the two wheat IL population, with distribution on chromosomes 1A, 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4D, 5A, 5B, 5D, 6A, 7A and 7B of wheat, respectively. 47 pairs of them were located on chromosome 4D (Tables S3 and S4). The LOD value of these epistatic QTLs ranged from 4.89 to 7.74. Their contributions to the phenotypic variation were from 0.20% to 15.92%, and their epistatic effects ranged from −16.42 to 16.57. Remarkably, there were 25 pairs of epistatic QTLs with parental effect greater than recombination effect (the interaction effect was greater than 0) and 47 pairs of epistatic QTLs with parental effect less than recombination effect (the interaction effect was less than 0). Moreover, 6 QTLs for wheat seed-vigor traits exhibited additive effect and epistatic effect, including qGE-48h-7A, qSL-48h-2A-1, qSL-48h-2A-2, qSL-60h-2A, qRL-24h-1D, and qSW-48h-2A.

In addition, several pairs of epistatic QTLs with pleiotropy were simultaneously mapped to two markers, conditionally designated marker 1 and marker 2. As shown in Tables S3 and S4, in wheat IL-1 population, five pairs of epistatic QTLs concurrently linked to SL, VI and SVI were located near the marker1 (Xwmc720) and marker2 (Xwmc752, Xgwm583, Xgwm63, Xwmc758 and Xwmc696), respectively. Likewise, ten pairs of epistatic QTLs located near the marker1 (Xwmc720) and the marker2 (Xwmc705, Xbarc56, Xgwm400, Xgwm46, Xwmc662, Xwmc76, Xwmc766, Xwmc819, Xgwm148 and Xwmc41), respectively, were also simultaneously linked to VI and SVI. Another three epistatic QTLs located near the marker1 (Xwmc331) and the marker2 (Xgwm148, Xwmc41, Xgwm63), respectively, were all detected to affect VI and SVI traits. In wheat IL-2 population, three epistatic QTLs were detected near the marker1 (Xcfd9) and the marker2 (Xgwm261 and Xwmc112), respectively, with all of them affecting SL and SFW traits synchronously.

Prediction of candidate genes within QTLs responsible for wheat seed vigor

Five QTLs were detected near marker Xwmc667 on chromosome 2A in IL-2 population (Table 2, Fig. 4), including qSL-36h-2A, qSL-48h-2A-1, qSL-60h-2A, qSW-48h-2A and qSW-60h-2A. These five QTLs were detected to affect SL and SFW under different aging treatments with large contribution to the phenotypic variation (>10%).

The co-located region of these five QTLs on chromosome 2A was considered as an important hotspot region in association with wheat seed vigor. Based on the WheatOmics (http://202.194.139.32/jbrowse.html), marker Xwmc667 was located between 7,961,478 bp-7,961,536 bp on chromosome 2A. This physical region was then extended 1 Mb on the left and right sides, respectively, to be used as the target genome region (6,961,478 bp–8,961,536 bp) for mining the candidate genes. Based on the Chinese Wheat Complete Genome Reference Sequence (IWGSC RefSeqv1.0), a total of 37 genes (Table S5) were found in this region and gene annotation was performed by referring to the website (https://plants.ensembl.org/index.html). Of them, five genes Cytochrome P450 family protein (TraesCS2A01G015800), Pectate lyase (TraesCS2A01G016500), F-box family protein (TraesCS2A01G017300), FACT complex subunit SPT16 (TraesCS2A01G017400) and Cytochrome P450 (TraesCS2A01G018800) were found to be highly associated with seed vigor possibly (Table 3).

10.7717/peerj.17778/table-3 Table 3 Genetic information of additive QTL hotspots in IL population.

Gene ID	Chr.	Interval (bp)	Gene Annotation	
TraesCS2A01G015800	2A	6997999..7000883	Cytochrome P450 family protein	
TraesCS2A01G016500	2A	7687810..7692604	Pectate lyase	
TraesCS2A01G017300	2A	8141118..8143112	F-box family protein	
TraesCS2A01G017400	2A	8147731..8150606	FACT complex subunit SPT16	
TraesCS2A01G018800	2A	8755966..8757713	Cytochrome P450	

GO analysis was performed for these 37 candidate genes (Table S6). All the candidate genes were significantly enriched in two categories of GO function clustering, with seven terms in biological processes (BP) and three terms in molecular functions (MF) (Fig. 5). Importantly, two candidate genes Cytochrome P450 family protein (TraesCS2A01G015800) and Cytochrome P450 (TraesCS2A02G018800) were functionally clustered into four terms including single-organism process, metabolic process, catalytic activity, and binding. The candidate gene pectate lyase (TraesCS2A01G016500) was grouped into metabolic process, catalytic activity, and binding.

10.7717/peerj.17778/fig-5 Figure 5 GO annotation clustering map of the candidate genes.

KEGG analysis was employed to predict the pathways involved by the candidate genes (Table S7). Most of the candidate genes were enriched in metabolic pathway and biosynthesis of secondary metabolites (Fig. 6). Notably, Cytochrome P450 (TraesCS2A02G018800) was significantly enriched in five metabolic pathways including glucosinolate biosynthesis, 2-Oxocarboxylic acid metabolism, cyanoamino acid metabolism, metabolic pathways and biosynthesis of secondary metabolites. Pectate lyase (TraesCS2A02G016500) was significantly enriched in pentose and glucuronate interconversions, and metabolic pathways.

10.7717/peerj.17778/fig-6 Figure 6 Pathway distribution map of the candidate genes.

Discussion

Phenotypic variation and genetic basis of seed-vigor traits

The level of seed vigor is mainly affected by genetic basis and environmental factors during seed development and seed storage (Sun, Wang & Sun, 2007). In order to effectively examine seed vigor, artificial aging is usually employed, which makes it possible to evaluate seed vigor in short time (Rajjou et al., 2008). During seed aging, a lot of physiological and biochemical processes occurred, which made it extremely complicated to measure seed vigor after artificial aging (Corbineau et al., 2002; Ahmed, Yang & Fu, 2016). Thus, it is required to determine appropriate parameters to measure the dynamics of seed vigor during seed aging. In the present study, 10 parameters representing different aspects of seed vigor were adopted to fully and precisely characterize the level of wheat seed vigor under six different aging conditions (0, 24, 36, 48, 60, and 72 h of aging), which is different from the previous reports where a few traits reflecting wheat seed vigor were measured under only one aging treatment (Agacka-Moldoch et al., 2016; Arif et al., 2017; Zuo et al., 2018). Our findings suggest that the numerical values obtained for these ten parameters (GE, GR, GI, GP, SL, RL, SRW, RFW, VI, and SVI) decreased with the extension of aging time with a continuous variation pattern (Figs. 1 and 2, Tables S1 and S2). Moreover, the absolute values of skewness and kurtosis coefficient of each trait in the two wheat IL populations evidenced the normal distribution of phenotypes of the traits examined (Fig. 1). This indicate that the ten parameters, together with two IL populations and six aging treatments tested here were very suitable for detecting QTLs responsible for wheat seed vigor.

In this study, a total of 26 additive QTLs and 72 pairs of epistatic QTLs were detected in two introgression lines under six different periods of aging, which affected the GE, GR, GP, GI, SL, RL, VI, SVI and other vigor traits in wheat. It shows that the traits could be improved by artificial selection effectively, thus achieving the target of improving seed vigor as well as the final yield increase. In addition to the RFW, additive QTLs were detected for the rest 9 seed vigor traits. As qRL-0h-1B and qRL-24h-1B were located near the marker Xwmc830 on chromosome 1B, qRL-0h-1D and qRL-24h-1D were located near the marker Xgdm126 on chromosome 1D, qSW-48h-2A and qSW-60h-2A were located near the marker Xwmc667 on chromosome 2A, qSL-36h-2A, qSL-48h-2A-1 and qSL-60h-2A were located near the marker Xwmc667 on chromosome 2A (Tables S1, S2), they were the same QTL affected the corresponding traits at different aging periods, which suggested that these QTLs had longer action period than other QTLs during seed storage or aging process, and should be paid more attention to in breeding practice.

A significant correlation was detected between the parameters tested here for assessing wheat seed vigor (Fig. 2), which is consistent with a previous reports (Shi et al., 2020). This suggests that the genetic loci controlling seed vigor may be pleiotropic and interacted with each other. Correspondingly, several chromosome regions (hotspots) were identified to contain multiple QTLs of wheat seed vigor in the present study. For example, qGE-60h-6A and qVI-60h-6A were detected near the marker Xwmc807 on chromosome 6A. qVI-36h-7B and qSVI-36h-7B located near the marker Xgwm400 on chromosome 7B. qGI-72h-1B and qVI-72h-1B were mapped near the marker Xwmc406 on chromosome 1B. Particularly, qSL-36h-2A, qSL-48h-2A-1, qSL-60h-2A, qSW-48h-2A and qSW-60h-2A were identified near the marker Xwmc667 (Tables 1 and 2). Clearly, these closely-located QTLs may have the pleiotropism on wheat seed vigor. Furthermore, a number of epistatic QTLs were also detected for wheat seed vigor here. For example, in IL-1 population, five pairs of epistatic QTLs were detected to simultaneously affect the SL, VI and SVI, while 13 pairs of epistatic QTLs were identified to synergistically influence VI and SVI. In IL-2 population, the epistatic QTLs located between the marker Xcfd9 and Xgwm261 or Xwmc112 were interacted in controlling the SL and SFW at the same time of aging (Tables S3 and S4). These additive QTLs with one cause and multiple effects, as well as epistatic QTLs with multiple effects, provide good molecular genetic evidence for significant phenotypic correlations between seed vigor traits.

Comparison of QTLs detected between the two IL populations of wheat

Theoretically, quantitative traits like seed vigor are controlled by minor-polygenes (Bewley & Black, 1994; Zuo et al., 2018), which makes it difficult to identify the same QTL even using the same population (Schwember & Bradford, 2010; Arif et al., 2012). Hence, it is necessary to identify QTL using different mapping populations, multiple traits and different aging treatments. In this study, QTL mapping was performed on 10 vigor traits of two wheat IL populations under six different aging times. The 10 traits represented different aspects in wheat seed germination and seedling morphogenesis, the six different aging times represented different degrees of seed aging/deterioration. It is useful to understand the vigor regulation of wheat seed in aging process. In order to precisely detect the real QTLs for wheat seed vigor, two IL populations derived from the cross between the common receptor parent Lumai 14 and different donor parents Jing 411 or Shaanhan 8675. Such populations have the common genetic background with difference in introgressive fragments, which makes it convenient to do comparative analysis of QTL effects.

Here, a total of 10 additive QTLs and 17 pairs of epistatic QTLs responsible for the seed vigor traits were identified using IL-1 population, with the additive QTLs mapped on chromosomes 1B, 3D, 5A, 6A, 7A and 7B of wheat (Table 1 and Table S3). Moreover, 16 additive QTLs and 55 pairs of epistatic QTLs were detected by IL-2 population, with the additive QTLs distributed on chromosomes 1B, 1D, 2A, 4B, 5B, 6D, 7B and 7D (Table 2 and Table S4). Most of these additive QTLs were found in A subgenome (11), followed by B (nine) and D (six) subgenomes. However, consistent QTLs for seed-vigor traits were only detected on chromosomes 1B and 7B. The causes for just a few consistent QTLs detected could be due to genotype difference of donor parents, population size, introductions of donor fragments, molecular marker density and other factors of the two mapping populations. Therefore, it is still necessary to further use linkage or association mapping to analyze more diverse populations or germplasm so as to discover the stable QTLs related to seed vigor for wheat breeding to increase seed vigor or predict seed life under the multi-genetic background.

Comparison of QTLs detected with the QTLs reported previously in wheat

In view of importance of wheat seed vigor, some genetic loci related to seed germination or seedling vigor were identified by QTL analysis in recent years through different mapping populations (Batool et al., 2018; Li et al., 2018a; Li et al., 2018b; Blackburn et al., 2021). Notably, among the 26 QTLs detected in the present study, six QTLs were located in the same or adjacent areas on the chromosome as the seed-vigor related QTLs reported previously. In this study, our data showed that two QTLs of root length (qRL-0h-1B and qRL-24h-1B) were closely located at the marker Xwmc830 on chromosome 1B. Similarly, Shi et al. (2020) detected a QTL of SL (QSLe1B) between Xwmc44 and AX-108745931 on chromosome 1B using a doubled haploid population of wheat. According to the integrated genetic map of SSR molecular markers in wheat (Somers, Isaac & Edwards, 2004), the distance between Xwmc830 and Xwmc44 was only 2 cM. Thus, qRL-0h-1B and qRL-24h-1B detected here and QSLe1B obtained by Shi et al. (2020) may be the same QTL or co-located in a QTL cluster region responsible for wheat seed-vigor traits. Another example is that a QTL (qVI-24h-1D) of wheat seed vigor index was mapped near the marker Xgwm458 on chromosome 1D in our study. Coincidently, two QTLs (QLi-mgt.ipk-1D for the average germination time, and QMgr.ipk-1D for the average germination rate) were also detected near this marker on chromosome 1D by Landjeva, Lohwasser & Börner (2010)), with accounting for 15.3% and 16.2% of phenotypic variation, respectively. The third example is that a QTL (qSL-48h-2A) for wheat seedling length was detected near the marker Xgwm359 on chromosome 2A. Interestingly, a QTL (QNDVIs-caas-2A.1) controlling the vigor of wheat seedlings was detected near the marker Xwmc177 just having 0.96 cM apart from the marker Xgwm359 site on chromosome 2A (https://shigen.nig.ac.jp/wheat/komugi/maps/markerMap.jsp) by Li et al. (2014). Therefore, qSL-48h-2A and QNDVIs-caas-2A.1 were probably the same QTL for wheat seed-vigor related traits. The fourth example is that two QTLs (qVI-60h-6A and qGP-60h-6A for seed vigor index and germination pace, respectively) were detected at marker Xwmc807 on chromosome 6A. Consistently, Li et al. (2014) reported that QGCs-caas-6A and QNDVIs-caas-6A for wheat seedling vigor were detected at marker Xwmc256 within just 1 cM distance to the maker Xwmc807 on chromosome 6A (Somers, Isaac & Edwards, 2004). This indicates that qVI-60h-6A, qGP-60h-6A, QGCs-caas-6A and QNDVIs-caas-6A may be the same QTL locus (or form a QTL cluster). The fifth example is that a QTL (qGP-36h-6D) for seed germination rate was detected near marker Xbarc96 on chromosome 6D in our study, while two QTLs (QGCw-caas-6D and QGCs-caas-6D) of wheat seedling vigor were also detected at this marker loci on chromosome 6D by Li et al. (2014), representing that this locus plays a major role in the vigor of wheat seeds and seedlings. Collectively, the above six QTLs detected in the current study and previous reports were located in the same genome area (or hot-spot region), functioning importantly for wheat seed vigor though each of them affected one or more specific traits related to seed vigor. Compared to the known reports of QTLs for wheat seed vigor, the other 20 additive QTLs for wheat seed vigor detected in the present study might be all new loci.

High vigor seeds always have better field performance and higher yield (Sun, Wang & Sun, 2007). Seed vigor is also related to other agronomic traits (Aparicio et al., 2002; Czyczyło-Mysza et al., 2014; Capo-chichi et al., 2021). Correspondingly, QTLs of seed vigor may co-locate in the same genome area or adjacent region with QTLs for other traits. In agreement with this, six QTLs for wheat seed vigor detected in the present study were found to be co-located in the region adjacent to the QTLs for grain and other agronomic traits of wheat detected in our previous studies (Chen et al., 2019; Yan et al., 2019; Chen et al., 2020) using the same mapping population. Such co-located QTLs formed pleiotropic loci or gene cluster, functioning coordinately. For example, qGP-36h-5B for GP was mapped to the marker Xwmc616 on chromosome 5B in this study, while at the same locus, three QTLs were detected, including qKL-5B-1 for grain length, qKT-5B for grain thickness, and qLTR-5B-1 for the length-thickness ratio of grain by Chen et al. (2019). Near the marker Xbarc96 on chromosome 6D, qGP-36h-6D responsible for wheat seed GP in this study were located together with qKW-6D for grain width (Chen et al., 2019) and QTgw-6D for thousand seed weight (Yan et al., 2019). Near the marker Xwmc671 on chromosome 7D, qGP-36h-7D for wheat seed GP in this study were co-located with QHd-7D for wheat heading stage identified by Yan et al. (2019). Moreover, both qSL-48h-2A-2 for wheat seedling length by this study and QSl-2A for wheat spike length by Yan et al. (2019) were mapped near Xgwm359 on chromosome 2A. Near the marker Xgdm126 on chromosome 1D, there exist two QTLs (qRL-0h-1D and qRL-24h-1D) for root length in this study, and three QTLs (QNt-1D for effective tillers, Gwp-1D-2 for yield per plant and QFsn-1D for fertile spikelets) detected by Yan et al. (2019). Furthermore, qGP-60h-6A for wheat seed GP in this study was located near the marker Xwmc807 on chromosome 6A, together with other five QTLs detected by Chen et al. (2020) including qPH-6A for plant height, qSL-6A for spike length, qTGW-6A-1 for thousand seed weight, qNT-6A for the number of effective tillers and qFSN-6A for the number of fertile spikelets on the left and right side of Xwmc807 (within a 4 cM region). Clearly, these six QTLs formed a QTL cluster, affecting not only wheat seed germination pace, but also other agronomic traits of wheat. In addition to QTL mapping results by our lab, Batool et al. (2018) detected a QTL affecting wheat GR, GI, VI and RL located between Xwmc177 and xbarc19 on chromosome 1B using a RIL population derived from a cross of wheat Pasban 90 × Frontana. This QTL was co-located with another QTL of seedling length detected in the present study near the marker Xgwm359 closely linked to Xwmc177 (within a distance of 4 cM), revealing that this genomic region may play an important role for wheat seed vigor and seedling growth.

From the point of wheat breeding, several major QTLs or hot-spot genome region described above can be used in molecular marker-assisted breeding for pyramiding excellent agronomy traits to develop new wheat varieties with stronger stress resistance and storage tolerance. In this regard, priority should be given to the use of those pleiotropic loci or gene clusters identified during the breeding practices, also paying attention to the coordination between the traits controlled by the QTL-rich regions.

Candidate genes related to wheat seed vigor

Seed vigor is a quantitative trait involved in multiple metabolite processes such as carbohydrates, lipids, proteins, and secondary substances. Here, 37 genes were mined from the genomic region (6,961,478 bp–8,961,536 bp) of five QTL-colocation on wheat chromosome 2A (Table S5). Five candidate genes were screened to be closely related to seed vigor according to the function annotation by GO and KEGG (Figs. 5 and 6).

Two candidate genes Cytochrome P450 family protein (TraesCS2A01G015800) and Cytochrome P450 (TraesCS2A01G018800) were functionally annotated as encoding cytochrome P450 family proteins. CYP450 family have multiple functions invlovled in biosynthesis and catabolism (Xu, Wang & Guo, 2015; Pandian et al., 2020; Singh et al., 2021). For example, a rice P450 (CYP724B1) functioning crucially in plant architecture, panicle development, and seed germination (Tong et al., 2018). Rice CYP96b4 mutant exhibited pleiotropic-unusual phenotype such as dwarft plant, delayed seed germination and enhanced drought resistance (Tamiru et al., 2015). An Arabidopsis, CYP77A4, was examined to catalyze epoxidation of fatty acids during seed germination (Xiang et al., 2023). Soybean GmCYP78A10 regulated seed size and weight as well as pod number (Xiang et al., 2023). According these reports, we speculate that Cytochrome P450 family protein (TraesCS2A01G015800) and Cytochrome P450 (TraesCS2A01G018800) may function importantly in wheat seed vigor. The candidate gene pectate lyase (TraesCS2A01G016500) was annotated to encode a pectate lyase. This enzyme regulated cell relaxation and expansion through controlling pectate content in cell wall, and thus, affected plant development process (Wagner & Kohorn, 2001; Peaucelle et al., 2011; Xu et al., 2022). The increased expression of pectate lyase family genes in the auxin-treated Arabidopsis roots resulted benefiting lateral root regeneration (Laskowski et al., 2006). A rice dwarf and early-senescence leaf1 (del1) was identified to encode a pectate lyase (PL) precursor, with its high expression in elongating tissues (Leng et al., 2017). Another example for pectate lyase function is that inhibition of pectate lyase gene expressions in strawberry and tomato fruits altered peel cell size, number and thickness, leading to enhancement of fruit firmness and storage capacity (Benítez-Burraco et al., 2003; Sesmero, Quesada & Mercado, 2007; Santiago-Doménech et al., 2008; Posé et al., 2015; Uluisik et al., 2016). These examples provide some evidences that pectate lyase (TraesCS2A01G016500) may involve in wheat seed vigor since cell division and elongation affected by pectate lyase are the typical features during seed germination. The candidate gene FACT complex subunit SPT16 (TraesCS2A01G017400) was annotated to encode the subunits (SSRP1 and SPT16) of FACT (facilitates chromatin transcription) (Lolas et al., 2010) Arabidopsis mutant plants of AtSSRP1 or AtSPT16 displayed various defects in vegetative and reproductive development including early bolting and less seed production (Grasser, 2020). AtSSRP1 was also identified to modulate the transition from seed dormancy to germination and from vegetative to reproductive development by focilitating expression of DOG1 and FLC genes, respectively (Michl-Holzinger, Mortensen & Grasser, 2019; Grasser, 2020). The candidate gene F-box family protein (TraesCS2A01G017300) was annotated to encode a F-box family protein. Several members of F-box family proteins were detected to mediate phytohormone signaling pathway, flower development, seed germination, and lateral branching (Saxena, Negi & Sharma, 2023). For example, AtFOA2 (AT3G16740) controlled seed germination by regulating biosynthesis of GA and ABA (He et al., 2016). Overexpression of rice F-box protein gene OsFBK12 delayed seed germination, and enlarged grains (Chen et al., 2013). Remarkably, one of wheat F-box proteins was found to be related to seed germination and other processes. Over expression of a F-box protein gene TaFBA1 in tobacco plants resulted in the reduced sensibility to ABA treatment during seed germination but increase of tolerance against abiotic stresses including drought, salt, heat and oxidative stress, and this wheat protein could regulated multiple target genes to adjust plant growth and development (Zhou et al., 2014; Kong et al., 2016; Zhao et al., 2017; Li et al., 2018a; Li et al., 2018b).

Collectively, five wheat genes mined from the QTL region in this study might function importantly for wheat seed vigor. In future investigation, the candidate genes among all the major QTLs identified here should be mined and then functionally characterized in detail, including transgenic assays and mutant examinations so as to comprehensively elucidate the complex gene network underlying the regulation of seed vigor in wheat.

Conclusions

In the present study, a total of 26 additive QTLs and 72 pairs of epistatic QTLs for 10 seed-vigor traits were detected under six AA treatments using two wheat introgression line populations derived from cultivars Lumai 14 (recipient/recurrent parent) and Shaanhan 8675 (donor parent) or Jing 411 (donor parent), respectively. Of them, 10 additive QTLs distributed on chromosomes 1B, 1D, 2A, 3D, 4B, 5A, 5B, 6A, 6D, 7A, 7B and 7D were identified as new QTLs for wheat seed vigor. Importantly, several major QTLs were identified to control multiple seed-vigor traits such as qSL-2A responsible for both wheat seedling length and weight at 36 h, 48 h and 60 h of aging treatments. Particularly, five QTLs (qSL-36h-2A, qSL-48h-2A-1, qSL-60h-2A, qSW-48h-2A and qSW-60h-2A) near the marker Xwmc667 on chromosome 2A formed a closely-located QTL-rich region, exhibiting pleiotropic effects on wheat seed vigor. Moreover, several QTL clusters detected here were, respectively, located in the same genomic regions as QTLs for wheat seed-vigor traits detected previously using other populations, indicating that they might be the consistent/stable QTLs for wheat seed vigor. A number of candidate genes mined from the co-located region of the five QTLs were predicted to mediate carbohydrate and lipid metabolism, transcription regulation and cell division, with Cytochrome P450 family protein (TraesCS2A01G015800), Cytochrome P450 (TraesCS2A01G018800), Pectate lyase (TraesCS2A01G016500), FACT complex subunit SPT16 (TraesCS2A01G017400) and F-box family protein (TraesCS2A01G017300) functing importantly in wheat seed vigor. The present findings including stable QTLs, related molecular markers and candidate genes provide valuable scientific reference for molecular marker-assisted selection in wheat breeding to improve seed vigor and storage life. The epistatic QTLs detected here should be also considered in wheat breeding towards high grain yield and excellent quality despite epistasis is so complicated and remains to be further investigation.

Supplemental Information

10.7717/peerj.17778/supp-1 Supplemental Information 1 The descriptive statistics and analysis of seed vigor traits in IL-1 population

Note: GE, GR, GI, GP, SL, RL, SFW, RFW, VI, SVI = Germinating Energy, Germination Rate, Germination Index, Germination pace, Seedling Length, Root Length, Seedling Fresh Weight, Root Fresh Weight, Vigor Index, and Simple Vigor Index, respectively. 0 h, 24 h, 36 h, 48 h,60 h, and 72 h represent aging time respectively. Seedling and Root length is measured in centimeters, Seedling and Root weight is measured in milligram. * and ** represent the significance level at P < 0.05 and P < 0.01, respectively.

10.7717/peerj.17778/supp-2 Supplemental Information 2 The descriptive statistics and analysis of seed vigor traits in IL-2 population

Note: GE, GR, GI, GP, SL, RL, SFW, RFW, VI, SVI = Germinating Energy, Germination Rate, Germination Index, Germination pace, Seedling Length, Root Length, Seedling Fresh Weight, Root Fresh Weight, Vigor Index, and Simple Vigor Index, respectively. 0 h, 24 h, 36 h, 48 h, 60 h, and 72 h represent aging time respectively. Seedling and Root length is measured in centimeters, Seedling and Root weight is measured in milligram. * and ** represent the significance level at P < 0.05 and P < 0.01, respectively.

10.7717/peerj.17778/supp-3 Supplemental Information 3 Epistatic-effect QTLs for seed vigor traits detected in wheat IL-1 population

Note: Positive value means parent type effect > recombinant type effect while negative value means recombinant type effect > parent type effect.

10.7717/peerj.17778/supp-4 Supplemental Information 4 Epistatic-effect QTLs for seed vigor traits detected in wheat IL-2 population

Note: Positive value means parent type effect > recombinant type effect while negative value means recombinant type effect > parent type effect.

10.7717/peerj.17778/supp-5 Supplemental Information 5 Annotated genes within the identified QTL region

10.7717/peerj.17778/supp-6 Supplemental Information 6 GO enrichment analysis of the genes in candidate region

10.7717/peerj.17778/supp-7 Supplemental Information 7 Enrichment analysis of candidate genes by KEGG

10.7717/peerj.17778/supp-8 Supplemental Information 8 Frequency distributions and differences for wheat seed vigor-related traits under six different aging treatments in IL-2 population

GE, gemination energy; GR, gemination rate; GI, germination index; GP, germination pace; SL, seedling lengh; RL, Root Length; SFW, seedling fresh weight; RFW, root fresh weight; VI, vigor index; SVI, simple vigor index. For the frequency distribution histogram, the X-axis represents the distribution range (interval) of phenotypic for each trait in IL-2 population, while the Y-axis corresponds to the number of lines in each intervals under 6 different treatments. The fitting curves of different colors reflect the distribution of phenotypic under the different aging treatment. For a boxpLot, the X-axis represents the six aging treatment for each trait, while the Y-axis corresponds to the phenotype. Different colors represent aging for 0 h, 24 h, 36 h, 48 h, 60 h and aging 72 h, respectively.

10.7717/peerj.17778/supp-9 Supplemental Information 9 Heatmap of the correlations between seed vigor-related traits in IL-2 population

a, b, c, d, e, and f represent aging for 0 h, 24 h, 36 h, 48 h, 60 h and aging 72 h, respectively. *, **, and *** indicate significant at P < 0.05, P < 0.01, and P < 0.001, respectively.

10.7717/peerj.17778/supp-10 Supplemental Information 10 Phenotypic of the parents for the seed vigor-related traits in IL-1 population in wheat

10.7717/peerj.17778/supp-11 Supplemental Information 11 Phenotypic of the parents for the seed vigor-related traits in IL-2 population in wheat

10.7717/peerj.17778/supp-12 Supplemental Information 12 Phenotypic of the seed vigor-related traits for 160 lines in IL-1 population in wheat

10.7717/peerj.17778/supp-13 Supplemental Information 13 Phenotypic of the seed vigor-related traits for 160 lines in IL-2 population in wheat

10.7717/peerj.17778/supp-14 Supplemental Information 14 Adding an author

10.7717/peerj.17778/supp-15 Supplemental Information 15 Removing author

Additional Information and Declarations

Competing Interests

Author Contributions

Data Availability

The authors declare there are no competing interests.

Zhenrong Yang conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Jirong Wu performed the experiments, prepared figures and/or tables, and approved the final draft.

Qiyu Wang conceived and designed the experiments, performed the experiments, prepared figures and/or tables, and approved the final draft.

Weiguo Chen conceived and designed the experiments, performed the experiments, analyzed the data, prepared figures and/or tables, authored or reviewed drafts of the article, and approved the final draft.

Huawei Shi performed the experiments, prepared figures and/or tables, and approved the final draft.

Yugang Shi analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Jinwen Yang analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Ning Li analyzed the data, authored or reviewed drafts of the article, and approved the final draft.

Daizhen Sun conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

Ruilian Jing conceived and designed the experiments, authored or reviewed drafts of the article, and approved the final draft.

The following information was supplied regarding data availability:

The raw measurements are available in the Supplementary Files.
==== Refs
References

Agacka-Moldoch et al. (2016) Agacka-Moldoch M Arif MAR Lohwasser U Doroszewska T Qualset CO Börner A 2016 The inheritance of wheat grain longevity: a comparison between induced and natural ageing Journal of Applied Genetics 57 477 481 10.1007/s13353-016-0348-3 27085344
Agacka-Moldoch et al. (2015) Agacka-Moldoch M Nagel M Doroszewska T Lewis RS Börner A 2015 Mapping quantitative trait loci determining seed longevity in tobacco (Nicotiana tabacum L.) Euphytica 202 479 486 10.1007/s10681-015-1355-x
Ahmed, Yang & Fu (2016) Ahmed Z Yang H Fu YB 2016 The associative changes in scutellum nuclear content and morphology with viability loss of naturally aged and accelerated aging wheat (Triticum aestivum) seeds Frontiers in Plant Science 7 1474 10.3389/fpls.2016.01474 27729925
Aparicio et al. (2002) Aparicio N Villegas D Araus JL Blanco R Royo C 2002 Seedling development and biomass as affected by seed size and morphology in durum wheat The Journal of Agricultural Science 139 143 150 10.1017/S0021859602002411
Arif et al. (2022) Arif MAR Agacka-Mołdoch M Qualset CO Börner A 2022 Mapping of additive and epistatic QTLs linked to seed longevity in bread wheat (Triticum aestivum L.) Cereal Research Communications 50 709 715 10.1007/s42976-021-00240-3
Arif & Börner (2019) Arif MAR Börner A 2019 Mapping of QTL associated with seed longevity in durum wheat (Triticum durum Desf.) Journal of Applied Genetics 60 33 36 10.1007/s13353-018-0477-y 30414053
Arif & Börner (2020) Arif MAR Börner A 2020 An SNP based GWAS analysis of seed longevity in wheat Cereal Research Communications 48 149 156 10.1007/s42976-020-00025-0
Arif et al. (2017) Arif MAR Nagel M Lohwasser U Börner A 2017 Genetic architecture of seed longevity in bread wheat (Triticum aestivum L.) Journal of Biosciences 42 81 89 10.1007/s12038-016-9661-6 28229967
Arif et al. (2012) Arif MAR Nagel M Neumann K Kobiljski B Lohwasser U Börner A 2012 Genetic studies of seed longevity in hexaploid wheat using segregation and association mapping approaches Euphytica 186 1 13 10.1007/s10681-011-0471-5
Ayalew et al. (2018) Ayalew H Liu H Liu C Yan G 2018 Identification of early vigor QTLs and QTL by environment interactions in wheat (Triticum eastivum L.) Plant Molecular Biology Reporter 36 399 405 10.1007/s11105-018-1093-z
Batool et al. (2018) Batool N Ilyas N Shahzad A Hauser BA Arshad M 2018 Quantitative trait loci (QTLs) mapping for salt stress tolerance in wheat at germination stage Pakistan Journal of Agricultural Sciences 55 47 55 10.21162/PAKJAS/18.5426
Benítez-Burraco et al. (2003) Benítez-Burraco A Blanco-Portales R Redondo-Nevado J Bellido ML Moyano E Caballero JL Muñoz Blanco J 2003 Cloning and characterization of two ripening-related strawberry (Fragaria × ananassa cv. Chandler) pectate lyase genes Journal of Experimental Botany 54 633 645 10.1093/jxb/erg065 12554706
Bentsink et al. (2000) Bentsink L Alonso-Blanco C Vreugdenhil D Tesnier K Groot SP Koornneef M 2000 Genetic analysis of seed-soluble oligosaccharides in relation to seed storability of Arabidopsis Plant Physiology 124 1595 1604 10.1104/pp.124.4.1595 11115877
Bewley & Black (1994) Bewley JD Black M 1994 Seeds: physiology of development and germination Springer New York New York
Blackburn et al. (2021) Blackburn A Sidhu G Schillinger WF Skinner D Gill K 2021 QTL mapping using GBS and SSR genotyping reveals genomic regions controlling wheat coleoptile length and seedling emergence Euphytica 217 45 10.1007/s10681-021-02778-z
Capo-chichi et al. (2021) Capo-chichi LJA Eldridge S Elakhdar A Kubo T Brueggeman R Anyia AO 2021 QTL mapping and phenotypic variation for seedling vigour traits in barley (Hordeum vulgare L.) Plants 10 6 1149 10.3390/plants10061149 34200109
Chen et al. (2020) Chen W Sun D Li R Wang S Shi Y Zhang W Jing R 2020 Mining the stable quantitative trait loci for agronomic traits in wheat (Triticum aestivum L.) based on an introgression line population BMC Plant Biology 20 275 10.1186/s12870-020-02488-z 32539793
Chen et al. (2019) Chen W Sun D Yan X Li R Wang S Shi Y Jing R 2019 QTL analysis of wheat kernel traits, and genetic effects of qKW-6A on kernel width Euphytica 215 11 10.1007/s10681-018-2333-x
Chen et al. (2009) Chen X He Z Wang D Zhuang Q Zhang Y Zhang Y Zhang Y Xia X 2009 Developing hight yielding wheat varieties from core parentJing 411’ Crops 4 1 5 10.16035/j.issn.1001-7283.2009.04.008
Chen et al. (2013) Chen Y Xu Y Luo W Li W Chen N Zhang D Chong K 2013 The F-box protein OsFBK12 targets OsSAMS1 for degradation and affects pleiotropic phenotypes, including leaf senescence, in rice Plant Physiology 163 1673 1685 10.1104/pp.113.224527 24144792
Cheng et al. (2013) Cheng X Wu Y Guo J Du B Chen R Zhu L He G 2013 A rice lectin receptor-like kinase that is involved in innate immune responses also contributes to seed germination Plant Journal 76 687 698 10.1111/tpj.12328
Corbineau et al. (2002) Corbineau F Gay-Mathieu C Vinel D Côme D 2002 Decrease in sunflower (Helianthus annuus) seed viability caused by high temperature as related to energy metabolism, membrane damage and lipid composition Physiologia Plantarum 116 489 496 10.1034/j.1399-3054.2002.1160407.x
Czyczyło-Mysza et al. (2014) Czyczyło-Mysza I Marcińska I Skrzypek E Cyganek K Juzoń K Karbarz M 2014 QTL mapping for germination of seeds obtained from previous wheat generation under drought Central European Journal of Biology 9 374 382 10.2478/s11535-013-0273-y
Dai et al. (2009) Dai J Jing J Li Z Li H 2009 Molecular mapping and analysis of a resistance gene to stripe rust (Puccinia striiformis f. sp. tritici) in common wheat cultivar Shaanhan 8675 Acta Phytopathologica Sinica 39 420 424 10.13926/j.cnki.apps.2009.04.013
Dickson (1980) Dickson MH 1980 Genetic aspects of seed quality HortScience 15 771 774 10.21273/HORTSCI.15.6.771
Ge et al. (2013) Ge H Li Y Wang R Li Z Wang S Gao J Zhang X 2013 Genetic contribution of Lumai 14 to novel wheat varieties developed in shandong province Acta Agronomica Sinica 38 954 961 10.3724/SP.J.1006.2012.00954
Grasser (2020) Grasser KD 2020 The FACT histone chaperone: tuning gene transcription in the chromatin context to modulate plant growth and development Frontiers in Plant Science 11 85 10.3389/fpls.2020.00085 32140163
He et al. (2016) He R Yu D Li X Duan G Zhang Y Tang D Zhao X Liu X 2016 F-box gene FOA2 regulates GA- and ABA- mediated seed germination in Arabidopsis Science China Life Sciences 59 1192 1194 10.1007/s11427-016-0098-3 27612866
Kaeppler (1997) Kaeppler SM 1997 Quantitative trait locus mapping using sets of near-isogenic lines: relative power comparisons and technical considerations Theoretical and Applied Genetics 95 384 392 10.1007/s001220050574
Kaur et al. (2015) Kaur H Petla BP Kamble NU Singh A Rao V Salvi P Ghosh S Majee M 2015 Differentially expressed seed aging responsive heat shock protein OsHSP18.2 implicates in seed vigor, longevity and improves germination and seedling establishment under abiotic stress Frontiers in Plant Science 6 713 10.3389/fpls.2015.00713 26442027
Kibinza et al. (2006) Kibinza S Vinel D Côme D Bailly C Corbineau F 2006 Sunflower seed deterioration as related to moisture content during ageing, energy metabolism and active oxygen species scavenging Physiologia Plantarum 128 496 506 10.1111/j.1399-3054.2006.00771.x
Kong et al. (2016) Kong X Zhou S Yin S Zhao Z Han Y Wang W 2016 Stress-inducible expression of an F-box gene TaFBA1 from wheat enhanced the drought tolerance in transgenic tobacco plants without impacting growth and development Frontiers in Plant Science 7 1295 10.3389/fpls.2016.01295 27656187
Kotak et al. (2007) Kotak S Larkindale J Lee U Von Koskull-Döring P Vierling E Scharf KD 2007 Complexity of the heat stress response in plants Current Opinion in Plant Biology 10 310 316 10.1016/j.pbi.2007.04.011 17482504
Landjeva, Lohwasser & Börner (2010) Landjeva S Lohwasser U Börner A 2010 Genetic mapping within the wheat D genome reveals QTL for germination, seed vigour and longevity, and early seedling growth Euphytica 171 129 143 10.1007/s10681-009-0016-3
Landjeva et al. (2008) Landjeva S Neumann K Lohwasser U Börner A 2008 Molecular mapping of genomic regions associated with wheat seedling growth under osmotic stress Biologia Plantarum 52 259 266 10.1007/s10535-008-0056-x
Laskowski et al. (2006) Laskowski M Biller S Stanley K Kajstura T Prusty R 2006 Expression profiling of auxin-treated Arabidopsis roots: toward a molecular analysis of lateral root emergence Plant and Cell Physiology 47 788 792 10.1093/pcp/pcj043 16621846
Leng et al. (2017) Leng Y Yang Y Ren D Huang L Dai L Wang Y Chen L Tu Z Gao Y Li X Zhu L Hu J Zhang G Gao Z Guo L Kong Z Lin Y Qian Q Zeng D 2017 A rice pectate lyase-like gene is required for plant growth and leaf senescence Plant Physiology 174 1151 1166 10.1104/pp.16.01625 28455404
Li et al. (2018a) Li J Wan H Wei H-T Wang Q Zhou Y Yang W 2018a QTL mapping for early vigor related traits in an elite wheat-breeding parent Chuanmai 42 derived from synthetic hexaploid wheat Agricultural and Food Sciences 55 1 33 45 10.21162/PAKJAS/18.4488
Li et al. (2018b) Li Q Wang W Wang W Zhang G Liu Y Wang Y Wang W 2018b Wheat F-box protein gene TaFBA1 is involved in plant tolerance to heat stress Frontiers in Plant Science 9 521 10.3389/fpls.2018.00521 29740462
Li et al. (2017) Li T Zhang Y Wang D Liu Y Dirk LMA Goodman J Downie AB Wang J Wang G Zhao T 2017 Regulation of seed vigor by manipulation of raffinose family oligosaccharides in maize and Arabidopsis thaliana Molecular Plant 10 1540 1555 10.1016/j.molp.2017.10.014 29122666
Li et al. (2014) Li X Chen X Xiao Y Xia X Wang D He Z Wang H 2014 Identification of QTLs for seedling vigor in winter wheat Euphytica 198 199 209 10.1007/s10681-014-1092-6
Lolas et al. (2010) Lolas IB Himanen K Grønlund JT Lynggaard C Houben A Melzer M Van Lijsebettens M Grasser KD 2010 The transcript elongation factor FACT affects Arabidopsis vegetative and reproductive development and genetically interacts with HUB1/2 Plant Journal 61 686 697 10.1111/j.1365-313X.2009.04096.x
Mcdonald (1999) Mcdonald MB 1999 Seed deterioration: physiology, repair and assessment Seed Science and Technology 27 177 237 10.1007/BF01288216
Michl-Holzinger, Mortensen & Grasser (2019) Michl-Holzinger P Mortensen SA Grasser KD 2019 The SSRP1 subunit of the histone chaperone FACT is required for seed dormancy in Arabidopsis Journal of Plant Physiology 236 105 108 10.1016/j.jplph.2019.03.006 30947026
Miura et al. (2002) Miura K Lin S Yano M Nagamine T 2002 Mapping quantitative trait loci controlling seed longevity in rice (Oryza sativa L.) Theoretical and Applied Genetics 104 981 986 10.1007/s00122-002-0872-x 12582603
Moore & Rebetzke (2015) Moore C Rebetzke G 2015 Genomic regions for embryo size and early vigour in multiple wheat (Triticum aestivum L.) populations Agronomy 5 152 179 10.3390/agronomy5020152
Murthy, Kumar & Sun (2003) Murthy UM Kumar PP Sun WQ 2003 Mechanisms of seed ageing under different storage conditions for Vigna radiata (L.) Wilczek: lipid peroxidation, sugar hydrolysis, Maillard reactions and their relationship to glass state transition Journal of Experimental Botany 54 1057 1067 10.1093/jxb/erg092 12598575
Nagel et al. (2011) Nagel M Rosenhauer M Willner E Snowdon RJ Friedt W Börner A 2011 Seed longevity in oilseed rape (Brassica napus L.)—genetic variation and QTL mapping Plant Genetic Resources 9 260 263 10.1017/S1479262111000372
Nagel et al. (2009) Nagel M Vogel H Landjeva S Buck-Sorlin G Lohwasser U Scholz U Börner A 2009 Seed conservation in ex situ genebanks—genetic studies on longevity in barley Euphytica 170 5 14 10.1007/s10681-009-9975-7
Pandian et al. (2020) Pandian BA Sathishraj R Djanaguiraman M Prasad PVV Jugulam M 2020 Role of Cytochrome P450 enzymes in plant stress response Antioxidants 9 5 454 10.3390/antiox9050454 32466087
Peaucelle et al. (2011) Peaucelle A Braybrook Siobhan A Le Guillou L Bron E Kuhlemeier C Höfte H 2011 Pectin-induced changes in cell wall mechanics underlie organ initiation in Arabidopsis Current Biology 21 1720 1726 10.1016/j.cub.2011.08.057 21982593
Posé et al. (2015) Posé S Kirby AR Paniagua C Waldron KW Morris VJ Quesada MA Mercado JA 2015 The nanostructural characterization of strawberry pectins in pectate lyase or polygalacturonase silenced fruits elucidates their role in softening Carbohydrate Polymers 132 134 145 10.1016/j.carbpol.2015.06.018 26256334
Prieto-Dapena et al. (2006) Prieto-Dapena P Castaño R Almoguera C Jordano J 2006 Improved resistance to controlled deterioration in transgenic seeds Plant Physiology 142 1102 1112 10.1104/pp.106.087817 16998084
Rajjou et al. (2012) Rajjou L Duval M Gallardo K Catusse J Bally J Job C Job D 2012 Seed germination and vigor Annual Review of Plant Biology 63 507 533 10.1146/annurev-arplant-042811-105550
Rajjou et al. (2008) Rajjou LC Lovigny Y Groot SPC Belghazi M Job C Job D 2008 Proteome-wide characterization of seed aging in Arabidopsis: a comparison between artificial and natural aging protocols Plant Physiology 148 620 641 10.1104/pp.108.123141 18599647
Reed, Bradford & Khanday (2022) Reed RC Bradford KJ Khanday I 2022 Seed germination and vigor: ensuring crop sustainability in a changing climate Heredity 128 450 459 10.1038/s41437-022-00497-2 35013549
Revilla et al. (2009) Revilla P Butrón A Rodríguez VM Malvar RA Ordás A 2009 Identification of genes related to germination in aged maize seed by screening natural variability Journal of Experimental Botany 60 4151 4157 10.1093/jxb/erp249 19684106
Santiago-Doménech et al. (2008) Santiago-Doménech N Jiménez-Bemúdez S Matas AJ Rose JK Muñoz Blanco J Mercado JA Quesada MA 2008 Antisense inhibition of a pectate lyase gene supports a role for pectin depolymerization in strawberry fruit softening Journal of Experimental Botany 59 2769 2779 10.1093/jxb/ern142 18522930
Saxena, Negi & Sharma (2023) Saxena H Negi H Sharma B 2023 Role of F-box E3-ubiquitin ligases in plant development and stress responses Plant Cell Reports 42 1133 1146 10.1007/s00299-023-03023-8 37195503
Schwember & Bradford (2010) Schwember AR Bradford KJ 2010 Quantitative trait loci associated with longevity of lettuce seeds under conventional and controlled deterioration storage conditions Journal of Experimental Botany 61 4423 4436 10.1093/jxb/erq248 20693410
Sesmero, Quesada & Mercado (2007) Sesmero R Quesada MA Mercado JA 2007 Antisense inhibition of pectate lyase gene expression in strawberry fruit: characteristics of fruits processed into jam Journal of Food Engineering 79 194 199 10.1016/j.jfoodeng.2006.01.044
Shi et al. (2020) Shi H Guan W Shi Y Wang S Fan H Yang J Chen W Zhang W Sun D Jing R 2020 QTL mapping and candidate gene analysis of seed vigor-related traits during artificial aging in wheat (Triticum aestivum) Science Report 10 22060 10.1038/s41598-020-75778-z
Singh et al. (2021) Singh A Panwar R Mittal P Hassan MI Singh IK 2021 Plant Cytochrome P450s: role in stress tolerance and potential applications for human welfare International Journal of Biological Macromolecules 184 874 886 10.1016/j.ijbiomac.2021.06.125 34175340
Singh et al. (2008) Singh R Raipuria R Bhatia VS Rani A Pushpendra Husain SM Chauhan DK Chauhan GS Mohapatra T 2008 SSR markers associated with seed longevity in soybean Seed Science and Technology 36 162 167 10.15258/sst.2008.36.1.17
Soltani (2001) Soltani A 2001 Genetic variation for and interrelationships among seed vigor traits in wheat from the Caspian Sea coast of Iran Seed Science and Technology 29 2001 653 662
Somers, Isaac & Edwards (2004) Somers DJ Isaac P Edwards K 2004 A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.) Theoretical and Applied Genetics 109 1105 1114 10.1007/s00122-004-1740-7 15490101
Sun, Wang & Sun (2007) Sun Q Wang J Sun B 2007 Advances on seed vigor physiological and genetic mechanisms Agricultural Sciences in China 6 1060 1066 10.1016/S1671-2927(07)60147-3
Tamiru et al. (2015) Tamiru M Undan JR Takagi H Abe A Yoshida K Undan JQ Natsume S Uemura A Saitoh H Matsumura H Urasaki N Yokota T Terauchi R 2015 A Cytochrome P450, OsDSS1, is involved in growth and drought stress responses in rice (Oryza sativa L.) Plant Molecular Biology 88 85 99 10.1007/s11103-015-0310-5 25800365
TeKrony & Hunter (1995) TeKrony DM Hunter JL 1995 Effect of seed maturation and genotype on seed vigor in maize Crop Science 35 857 862 10.2135/cropsci1995.0011183X003500030037x
Ter Steege et al. (2005) Ter Steege MW Den Ouden FM Lambers H Stam P Peeters AJM 2005 Genetic and physiological architecture of early vigor in aegilops tauschii, the D-genome donor of hexaploid wheat. A quantitative trait loci analysis Plant Physiology 139 1078 1094 10.1104/pp.105.063263 16183848
Tong et al. (2018) Tong X Wang Y Sun A Bello BK Ni S Zhang J 2018 Notched belly grain 4, a novel allele of dwarf 11, regulates grain shape and seed germination in rice (Oryza sativa L.) International Journal of Molecular Sciences 19 4069 10.3390/ijms19124069 30558382
Uluisik et al. (2016) Uluisik S Chapman NH Smith R Poole M Adams G Gillis RB Besong TMD Sheldon J Stiegelmeyer S Perez L Samsulrizal N Wang D Fisk ID Yang N Baxter C Rickett D Fray R Blanco-Ulate B Powell ALT Harding SE Craigon J Rose JKC Fich EA Sun L Domozych DS Fraser PD Tucker GA Grierson D Seymour GB 2016 Genetic improvement of tomato by targeted control of fruit softening Nature Biotechnology 34 950 952 10.1038/nbt.3602
Wagner & Kohorn (2001) Wagner TA Kohorn BD 2001 Wall-associated kinases are expressed throughout plant development and are required for cell expansion The Plant Cell 13 303 318 10.1105/tpc.13.2.303 11226187
Wang et al. (2013) Wang Z Cao H Sun Y Li X Chen F Carles A Li Y Ding M Zhang C Deng X Soppe WJJ Liu Y 2013 Arabidopsis paired amphipathic helix proteins SNL1 and SNL2 redundantly regulate primary seed dormancy via abscisic acid–ethylene antagonism mediated by histone deacetylation The Plant Cell 25 149 166 10.1105/tpc.112.108191 23371947
Xiang et al. (2023) Xiang F Liu W Liu X Song Y Zhang Y Zhu X Wang P Guo S Song C 2023 Direct balancing of lipid mobilization and reactive oxygen species production by the epoxidation of fatty acid catalyzed by a Cytochrome P450 protein during seed germination New Phytologist 237 2104 2117 10.1111/nph.18669 36495066
Xu, Wang & Guo (2015) Xu J Wang X Guo W 2015 The Cytochrome P450 superfamily: key players in plant development and defense Journal of Integrative Agriculture 14 1673 1686 10.1016/S2095-3119(14)60980-1
Xu et al. (2022) Xu Z Dai J Kang T Shah K Li Q Liu K Xing L Ma J Zhang D Zhao C 2022 PpePL1 and PpePL15 are the core members of the pectate lyase gene family involved in peach fruit ripening and softening Frontiers in Plant Science 13 844055 10.3389/fpls.2022.844055 35401624
Xue et al. (2008) Xue Y Zhang S Yao Q R-h Peng Xiong A-S Li X Zhu W Zhu YY Zha D 2008 Identification of quantitative trait loci for seed storability in rice (Oryza sativa L.) Euphytica 164 739 744 10.1007/s10681-008-9696-3
Yan et al. (2019) Yan X Sun D Li R Wang S Ma G Cao Y Yang B Jing R 2019 Mapping quantitative trait loci for important agronomic traits and developing potential near-isogenic lines in wheat International Journal of Agriculture and Biology 22 20 28 10.17957/IJAB/15.1028
Zeng et al. (2006) Zeng DL Guo LB Xu YB Yasukumi K Zhu LH Qian Q 2006 QTL analysis of seed storability in rice Plant Breeding 125 57 60 10.1111/j.1439-0523.2006.01169.x
Zhao et al. (2017) Zhao Z Zhang G Zhou S Ren Y Wang W 2017 The improvement of salt tolerance in transgenic tobacco by overexpression of wheat F-box gene TaFBA1 Plant Science 259 71 85 10.1016/j.plantsci.2017.03.010 28483055
Zheng et al. (2017) Zheng Y Xue X Yongkang C Zheng J Zhang L Wang J Niu N Zhang G Ma S 2017 Comparative study on determination methods of wheat seed vigor Jiangsu Agricultural Science 45 61 64 10.15889/j.issn.1002-1302.2017.15.015
Zhou et al. (2014) Zhou S Sun X Yin S Kong X Zhou S Xu Y Luo Y Wang W 2014 The role of the F-box gene TaFBA1 from wheat (Triticum aestivum L.) in drought tolerance Plant Physiology and Biochemistry 84 213 223 10.1016/j.plaphy.2014.09.017 25299612
Zuo et al. (2018) Zuo J Liu J Gao F Yin G Wang Z Chen F Li X Xu J Chen T Li L Li Y Xia X Cao H Liu Y 2018 Genome-wide linkage mapping reveals QTLs for seed vigor-related traits under artificial aging in common wheat (Triticum aestivum) Frontiers in Plant Science 9 1101 10.3389/fpls.2018.01101 30100918
