Identification of the QTL underlying the vitamin E content of soybean seeds

Vitamin E (VE) is an important antioxidant supplement for human health. Soybean seed extracts are the main source of VE supplements. Therefore, increasing the VE content of soybean seeds is important issue in breeding programmes. To detect quantitative trait loci (QTL) associated with VE in soybean seeds, 238 F_6:7 recombinant inbred lines (RILs) were created by crossing a high VE cultivar, ‘Beifeng 9’, with a low VE cultivar, ‘Freeborn’. A genetic map was constructed using 218 polymorphic simple sequence repeat (SSR) markers. Composite interval mapping analysis detected 66 QTLs for contents of individual and total VE, 21 for α‐tocopherol, seventeen for γ‐tocopherol, thirteen for δ‐tocopherol and fifteen for total VE. The QTLs were located on chromosomes 9, 10, 15, 18 and 19. Phenotypic variance underlain by each QTL ranged from 2.4% to 32.6%. Two major QTLs (BARCSOYSSR_10_1140–BARCSOYSSR_10_1188 and BARCSOYSSR_15_0855 to BARCSOYSSR_15_0887) associated with α‐Toc, γ‐Toc, δ‐Toc and total VE contents were mapped on chromosomes 10 and 15. They explained 12.0% and 32.6% of phenotypic variance for α‐Toc; 5.5% and 13.0% for γ‐Toc; 6.6% and 23.6% for δ‐Toc; and 19.6% and 21.8% for total VE. QTL intervals BARCSOYSSR_15_0790–BARCSOYSSR_15_0855 (Qα15_1, Qγ15_1), BARCSOYSSR_15_1113–BARCSOYSSR_15_1159 (Qα15_3, Qδ15_2, QTVE15_4) and BARCSOYSSR_15_1159–BARCSOYSSR_15_1190 (Qα15_4, Qγ15_5, QTVE15_5) were associated with α‐Toc and explained 22.2%, 23.8% and 24.4% of the phenotypic variation in multiple environments. BARCSOYSSR_09_1098–BARCSOYSSR_09_1128 (QTVE9_1) and BARCSOYSSR_15_0887–BARCSOYSSR_15_0935 (QTVE15_2, Qγ15_3) associated with total VE content explained 21.8% and 16.4% of the phenotypic variation in two environments. These QTLs allow for marker‐assisted selection for cultivars with high VE contents.     

Identification of quantitative trait loci controlling soybean seed weight in recombinant inbred lines derived from PI 483463 (Glycine soja) × ‘Hutcheson’ (G. max)

The objective of this study was to identify quantitative trait loci (QTLs) controlling 100‐seed weight in soybean using 188 recombinant inbred lines (RIL) derived from a cross of PI 483463 and ‘Hutcheson’. The parents and RILs were grown for 4 years (2010–2013), and mature, dry seeds were used for 100‐seed weight measurement. The variance components of genotype (a), environment (e) and a × e interactions for seed weight were highly significant. The QTL analysis identified 14 QTLs explaining 3.83–12.23% of the total phenotypic variation. One of the QTLs, qSW17‐2, was found to be the stable QTL, being identified in all the environments with high phenotypic variation as compared to the other QTLs. Of the 14 QTLs, 10 QTLs showed colocalization with the seed weight QTLs identified in earlier reports, and four QTLs, qSW5‐1, qSW14‐1, qSW15‐1 and qSW15‐2, found to be the novel QTLs. A two‐dimensional genome scan revealed 11 pairs of epistatic QTLs across 11 chromosomes. The QTLs identified in this study may be useful in genetic improvement of soybean seed weight.     

Quantitative trait loci underlying soybean seed tocopherol content with main additive,epistatic and QTL × environment effects

Soybean (Glycine max [L.] Merrill) seeds are a major source of tocopherols (Toc), which could significantly improve immune system health of human and prevent or treat many serious diseases. Selection for higher Toc contents of seeds could increase nutritional value of soybean‐derived food, laying on an important breeding goal for many soybean breeders. The present objectives of the work were to evaluate various genetic effects of QTL associated with individual and total Toc content based on a RIL population (“Beifeng 9” × “Freeborn”) in six environments to improve the efficiency of molecular marker‐assisted selection (MAS) for high‐Toc breeding. The results described that eighteen, thirteen, eleven and thirteen QTL were associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc content, respectively, and have additive main effects (a) and/or additive × environment interaction effects (ae) in certain environments. Among them, four QTL for α‐Toc, two QTL for γ‐Toc, one QTL for δ‐Toc and four QTL for total Toc could increase α‐Toc, γ‐Toc, δ‐Toc and total Toc content via significant a effect, respectively, which have stronger stability in different years and locations. It implied a value for MAS. Additionally, twenty‐five, fifteen, eleven and twenty epistatic pairwise QTL associated with α‐Toc, γ‐Toc, δ‐Toc and total Toc contents, respectively, were detected. The genetic information of the QTL effects obtained here would be beneficial for breeding soybean variety with high‐Toc content by MAS.     

Identification of quantitative trait loci and candidate genes controlling the tocopherol synthesis pathway in soybean (Glycine max)

A recombinant inbred line (RIL) population was used to identify quantitative trait loci (QTLs) and their candidate genes controlling the tocopherol (Toc) synthesis pathway. The RIL population was cultivated in field conditions in 3 years. A genetic map constructed using 1624 DNA markers was used for QTL analysis. We identified 22 QTLs for seed tocopherol contents and their ratios, of which two QTL clusters on chromosomes (Chr) 9 and 14 exerted consistent large effects on tocopherol composition across the 3 years. The QTL cluster localized on Chr 9 might correspond to γ-TMT3, which controls the conversion of γ-Toc into α-Toc. The QTL cluster localized on Chr 14 was novel, which might regulate the conversion of MPBQ (a precursor of δ-Toc) into DMPBQ (the precursor of γ-Toc). The effect of the QTL cluster on Chr 14 was validated in a pair of near isogenic lines, and its candidate gene was mined. The identified QTLs and their candidate genes might be used in breeding programmes to improve α-Toc content in soybean seeds.     

Molecular mapping of soybean seed tocopherols in the cross ‘OAC Bayfield’ × ‘OAC Shire’

Soybean (Glycine max [L.] Merr.) is cultivated primarily for its protein and oil in the seed. In addition, soybean seeds contain nutraceutical compounds such as tocopherols (vitamin E), which are powerful antioxidants with health benefits. The objective of this study was to identify molecular markers linked to quantitative trait loci (QTL) that affect accumulation of soybean seed tocopherols. A recombinant inbred line (RIL) population derived from the cross ‘OAC Bayfield’ × ‘OAC Shire’ was grown in three locations over 2 years. A total of 151 SSR markers were polymorphic of which a one‐way analysis of variance identified 42 markers whereas composite interval mapping identified 26 markers linked to tocopherol QTL across 17 chromosomes. Individual QTL explained from 7% to 42% of the total phenotypic variation. Significant two‐locus epistatic interactions were identified for a total of 122 combinations in 2009 and 152 in 2010. The multiple‐locus models explained 18.4–72.2% of the total phenotypic variation. The reported QTL may be used in marker‐assisted selection (MAS) to develop high tocopherol soybean cultivars.     

Impact of epistasis and QTL × environmental interaction on the oil filling rate of soybean seed at different developmental stages

The oil accumulation in the developing soybean seed has been shown to be a dynamic process with different rates and activities at different phases affected by both genotype and environment. The objective of the present study was to investigate additive, epistatic and quantitative trait loci (QTL) × environment interaction (QE) effects of the QTL controlling oil filling rate in soybean seed. A total of 143 recombinant inbred lines (RILs) derived from the cross of Charleston and Dongnong 594 were used in this study to obtain 2 years of field data (2004 and 2005). A total of 26 QTL with significantly unconditional and conditional additive (a) effect and/or additive × environment interaction (ae) effect at different filling stages were identified on 14 linkage groups. Among the QTL with significant a effects, 18 QTL showed positive effects and 6 QTL had negative effects on seed filling rate of oil content during seed development. A total of 29 epistatic pairwise QTL underlying seed filling rate were identified at different filling stages. About 28 pairs of the QTL showed additive × additive epistatic (aa) effects and 14 pairs of the QTL showed aa × environment interaction (aae) effects at different filling stages. QTL with aa and aae (additive × additive × environment) effects appeared to vary at different filling stages. Our results demonstrated that oil filling rate in soybean seed were under genetic, developmental and environmental control.     

Quantitative trait loci with additive and epistatic effects underlying resistance to two HG types of soybean cyst nematode

The resistance of soybean (Glycine max L. Merr.) cultivars varies with the different races of the soybean cyst nematode (SCN), Heterodera glycines, referred to as HG types (biotypes). Resistant cultivars with durable resistance are emphasized in recent years. The aim here was to identify quantitative trait loci (QTLs) for resistance to two SCN HG types (HG type 2.5.7, race 1; and HG type 1.2.3.5.7, race 4) in resistant cultivar ‘L‐10’ and to analyse the additive and epistatic effects of the identified QTLs. A total of 140 F₅‐derived F₁₀ recombinant inbred lines (F_5:10 RILs) were advanced via single‐seed‐descent from the cross between ‘L‐10’ (broadly resistant to SCN) and “Heinong 37” (SCN‐susceptible). For SCN HG type 2.5.7 and HG type 1.2.3.5.7 resistance, three and six QTLs for resistance to SCN HG type 2.5.7 and HG type 1.2.3.5.7 were identified, respectively, most of which could explain <10% of the phenotypic variation. Among these QTLs, five were identified over 2 years, while the other QTLs were detected in either 2009 or 2010. QSCN1‐2, located near the SSR marker Sat_069 of linkage group D1b (Chromosome, 2), was responsible for the largest proportion of phenotypic variation (16.01% in 2009 and 18.94% in 2010), suggested that it could effectively be used as a candidate QTL for the marker‐assisted selection (MAS) of soybean lines resistant to SCN. Additionally, for SCN HG type 2.5.7 and HG type 1.2.3.5.7 resistance, two and four QTLs showed an additive effect (a), respectively. One epistatic pair of QTLs (QSCN1‐1‐QSCN1‐3) for SCN HG type 2.5.7 resistance and eight epistatic pairs of QTLs for SCN HG type 1.2.3.5.7 resistance were found to have significant aa effects, among which one pair of QTLs (QSCN4‐4 and QSCN4‐5) contributed a large proportion of aa effects (3%). The results indicated that additive and epistatic effects could significantly affect SCN resistance. Therefore, both of a and aa effects should be considered in MAS programmes.     

Identification and validation of an over‐dominant QTL controlling soybean seed weight using populations derived from Glycine max × Glycine soja

Heterosis, or hybrid vigour, has been used to improve seed yield in several important crops for decades and it has potential applications in soybean. The discovery of over‐dominant quantitative trait loci (QTL) underlying yield‐related traits, such as seed weight, will facilitate hybrid soybean breeding via marker‐assisted selection. In this study, F₂ and F_2 : 3 populations derived from the crosses of ‘Jidou 12’ (Glycine max) × ‘ZYD2738’ (Glycine soja) and ‘Jidou 9’ (G. max) × ‘ZYD2738’ were used to identify over‐dominant QTL associated with seed weight. A total of seven QTL were identified. Among them, qSWT_13_1, mapped on chromosome 13 and linked with Satt114, showed an over‐dominant effect in two populations for two successive generations. This over‐dominant effect was further examined by six subpopulations derived from ‘Jidou12’ × ‘ZYD2738’. The seed weight for heterozygous individuals was 1.1‐ to 1.6‐fold higher than that of homozygous individuals among the six validation populations examined in different locations and years. Therefore, qSWT_13_1 may be a useful locus to improve the yield of hybrid soybean and to understand the molecular mechanism of heterosis in soybean.     

Molecular genetic analysis of flour color using a doubled haploid population in bread wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Flour color is an important trait in the assessment of flour quality for the production of many end products. In this study, quantitative trait loci (QTLs) with additive effects, epistatic effects, and QTL × environment (QE) interactions for flour color in bread wheat (Triticum aestivum L.) were studied, using a set of 168 doubled haploid (DH) lines derived from a Huapei 3 × Yumai 57 cross. A genetic map was constructed using 283 simple sequence repeats (SSR) and 22 expressed sequence tags (EST)-SSR markers. The DH and parents were evaluated for flour color in three environments. QTL analyses were performed using QTLNetwork 2.0 software based on a mixed linear model approach. A total of 18 additive QTLs and 24 pairs of epistatic QTLs were detected for flour color, which were distributed on 19 of the 21 chromosomes. One major QTL, qa1B, closely linked to barc372 0.1 cM, could account for 25.64% of the phenotypic variation of a* without any influence from the environments. So qa1B could be used in the molecular marker-assisted selection (MAS) in wheat breeding programs. The results showed that both additive and epistatic effects were important genetic basis for flour color, and were also sometimes subject to environmental modifications. The information obtained in this study should be useful for manipulating the QTLs for flour color by MAS in wheat breeding programs. Kun-Pu Zhang and Guang-Feng Chen contributed equally to this study.     

Mapping QTLs for salt tolerance with additive,epistatic and QTL × treatment interaction effects at seedling stage in wheat

Quantitative trait loci (QTLs) for salt tolerance with additive, epistatic and QTL × treatment interaction effects at seedling stage in wheat were identified. A set of 131 recombinant inbred lines derived from cross Chuan 35050 × Shannong 483 were evaluated under salt stress and normal conditions. Wide variation was found for all studied traits. A total of 18 additive and 16 epistatic QTLs were detected, among which five and 11 were with significant QTL × treatment effects. Ten QTL clusters were identified, and each may represent a single gene or closely linked genes. The locus controlling shoot K⁺/Na⁺ concentration ratio and shoot Na⁺ concentration on chromosome 5A may be identical to Nax2. The interval Xgwm6‐Xgwm538 on chromosome 4B for total dry weight was also identified in a previous study, both near the marker Xgwm6. The marker Xgwm6 may be useful for marker‐assisted selection. Six pairs of homoeologous QTLs were detected, showing synteny among the A, B and D genomes. These results facilitate understanding the mechanisms and the genetic basis of salt tolerance in wheat.     

Genetic dissection of vitamin E content in rice (Oryza sativa) grains using recombinant inbred lines derived from a cross between 'Zhenshan97B' and 'Nanyangzhan'

Vitamin E (VE) is an important nutritional trait in rice grains. In order to dissect the genetic basis underlying VE content, a recombinant inbred lines population derived from 'Zhenshan 97B' and 'Nanyangzhan' was used for quantitative trait locus (QTL) analysis. Totally, 29 QTLs for six VE traits were identified in 2 consecutive years. Among those, five QTLs repeatedly detected in two years formed a cluster on chromosome 2, which was responsible for all five VE isomers. OsγTMT, the gene encoding γ‐tocopherol methyltransferase in rice, was located to the same region and treated as the candidate gene. Sequence analysis of alleles from two parents revealed many polymorphisms, including 19 single nucleotide polymorphisms (SNPs) and two insert/deletions (Indels) in the promoter region, two nonsynonymous SNPs in exons, and 25 SNPs and an Indel in introns. Besides, a QTL for δ‐tocotrienol and two QTLs for α‐tocopherol were repeatedly detected on chromosome 5 and 8, respectively, all three regions carrying no homologous genes involved in VE biosynthesis. These results could be useful in development of rice lines displaying desirable VE content.     

Identification and genetic characterization of a safflower mutant with a modified tocopherol profile

Safflower (Carthamus tinctorius L.) seeds have a tocopherol fraction dominated by α‐tocopherol, which accounts for more than 95% of the tocopherols. α‐Tocopherol exerts a high vitamin E activity, but a low in vitro antioxidant action. For non‐food applications, replacement of high α‐tocopherol by γ‐tocopherol is preferred. Because of the limited variability found in germplasm of cultivated safflower, the objective of the present research was to search for variability for tocopherol profile in germplasm of wild safflower species. Bulk seed samples of 77 accessions from six species were analysed for total tocopherol content and profile. One accession of C. oxyacanthus showed increased γ‐tocopherol content (36%). Single‐seed analysis showed the existence of a bimodal distribution, which included high α‐tocopherol (>90%) and high γ‐tocopherol (HGT) seeds (>85%). Plants from the HGT seeds bred true for the trait and showed introgression of cultivated safflower, which allowed a rapid selection for cultivated safflower traits. Genetic analysis revealed that the HGT trait was controlled by partially recessive alleles at a single locus Tph1, which will facilitate the transference of the novel trait to diverse safflower germplasms.     

Independent selection for seed free tryptophan content and vernalization response in chickpea domestication

Chickpea shows a distinct domestication trajectory vis‐a‐vis pod dehiscence and growth cycle mediated by vernalization insensitivity compared with its companion Near Eastern legumes. Our objectives were: (i) to map the quantitative trait loci (QTLs) associated with vernalization response and seed free tryptophan in domesticated × wild chickpea progeny and (ii) estimate the genetic correlation between vernalization response and free tryptophan content. A domesticated × wild chickpea cross was used to document phenotypic segregation in both traits and to construct a skeletal genetic map for QTL detection. A number of vernalization response and seed free tryptophan content QTLs were documented in both F₂ and F₃ generations. No significant genetic correlation between these two traits was observed. Epistatic relationship between two free tryptophan loci was documented. It is evident that selection for high seed tryptophan is easier to accomplish relative to selection for vernalization insensitivity. This suggests that the two traits were selected independently in antiquity, thereby corroborating earlier claims for conscious selection processes associated with chickpea domestication.     

Selection for contrasting tocopherol content and profile in Ethiopian mustard

Tocopherols are compounds present in oilseeds with major effect on nutritional and technological properties of seed oils. Brassica spp. mainly contain varying concentrations of α‐tocopherol, with high vitamin E value, and γ‐tocopherol, which contributes to oil stability. The objective of this research was to select for contrasting tocopherol content and profile in Ethiopian mustard (Brassica carinata A. Braun). A collection of 211 F_4:5 lines was evaluated for tocopherol content and profile, and divergent selection was conducted till the S_3:4 generation. Selection resulted in two lines with increased tocopherol content (244 and 243 mg/kg seed as average of four environments), one line with reduced tocopherol content (117 mg/kg), two lines with reduced α/γ‐tocopherol ratio (0.22 and 0.28) and two lines with increased α/γ‐tocopherol ratio (3.74 and 3.34). Control line C‐101 averaged 196 mg/kg with α/γ‐tocopherol ratio of 1.10. Reduced α/γ‐tocopherol ratio was controlled by recessive alleles at a single locus. Seed to plant correlation was high (r = 0.92), which suggests the feasibility of selecting at the single‐seed level.     

Fine mapping of a QTL for the number of spikelets per panicle by using near‐isogenic lines derived from an interspecific cross between Oryza sativa and Oryza minuta

We constructed a high‐resolution physical map for the qSPP7 QTL for spikelets per panicle (SPP) on rice chromosome 7 across a 28.6‐kb region containing four predicted genes. Using a series of BC₇F₄ near‐isogenic lines (NILs) derived from a cross between the Korean japonica cultivar ‘Hwaseongbyeo’ and Oryza minuta (IRGC Acc. No. 101144), three QTLs for the number of SPP, grains per panicle and primary branches were identified in the cluster (P ≤ 0.01). All three QTLs were additive, and alleles from the O. minuta parent were beneficial in the ‘Hwaseongbyeo’ background. qSPP7 was mapped to a 28.6‐kb region between the two simple sequence repeat (SSR) markers RM4952 and RM21605. The additive effect of the O. minuta allele at qSPP7 was 23 SPP, and 43.6% of the phenotypic variance was explained by the segregation of the SSR marker RM4952. Colocalization of the three QTLs suggested that this locus was associated with panicle structure and had pleiotropic effects. The NIL populations and molecular markers are useful for cloning qspp7.     

多种环境下大豆单株粒重QTL的定位与互作分析

定位大豆单株粒重QTL、分析QTL间的上位效应及QTL与环境互作效应, 有利于大豆单株粒重遗传机理的深入研究。利用147个F_2:14~F_2:18 RIL群体, 5年2点多环境下以CIM和MIM方法同时定位大豆单株粒重QTL, 检测到17个控制单株粒重的QTL, 分别位于D1a、B1、B2、C2、F、G和A1连锁群上, 贡献率为6.0%~47.9%;用2种方法同时检测到3个QTL, 即qSWPP-DIa-3、qSWPP-F-1和qSWPP-D1a-5, 贡献率为6.3%~38.3%;2年以上同时检测到4个QTL, 即qSWPP-DIa-1、qSWPP-DIa-2、qSWPP-B1-1和qSWPP-G-1, 贡献率为8.1%~47.9%;利用QTLMapper分析QE互作效应和QTL间上位效应, 7种环境下的数据联合分析得到1个QE互作QTL和4对上位效应QTL, 贡献率和加性效应都较小。在分子标记辅助育种中应该同时考虑主效QTL及各微效QTL之间的互作。     

Genetic dissection of seed vigour under artificial ageing conditions using two joined maize recombinant inbred line populations

Seed vigour plays an important role in agricultural production, and seeds with high sowing quality are necessary for improving agriculture production. In our study, two connected maize recombinant inbred line (RIL) populations derived from Yu82 × Shen137 and Yu537A × Shen137 crosses were evaluated for the mean germination time (MGT) and other related traits under three artificial ageing treatments. We used meta‐analysis to integrate genetic maps and identify quantitative trait loci (QTLs) across the two populations. In total, 74 QTLs and 20 meta‐QTLs (mQTLs) were identified. Four key mQTLs, mQTL2‐2, mQTL5‐4, mQTL6 and mQTL8, which contained initial QTLs with R² values >10% and included 5–9 initial QTLs, may be hot spots of important QTLs for the associated traits. Twenty‐two key candidate genes associated with four seed vigour‐related traits mapped to 14 mQTLs. In particular, the GRMZM2G163749, GRMZM2G122172/GRMZM2G554885/GRMZM2G122871 and GRMZM2G150367 genes mapped within the important mQTL5–4, mQTL6 and mQTL8 regions, respectively. Fine mapping for the genetic regions of these three mQTLs merits further study and could be utilized for marker‐assisted breeding.     

Analysis of quantitative trait loci underlying the period of reproductive growth stages in soybean (<Emphasis Type="Italic">Glycine max</Emphasis> [L.] Merr.)

Quantitative trait loci (QTLs) underlying reproductive growth stages are important for molecular breeding of soybeans [Glycine max (L.) Merr.]. Most of these QTLs identified so far derived from a single environment, and thus may be influenced by specific environmental conditions. In this study (from 2004 to 2005), analysis of QTLs underlying the period to reach a given reproductive growth stage was performed in three different environments (Harbin, Heilongjiang Province, China). QTL analysis was achieved with a recombination inbred line (RIL) population consisting of 153 lines. The RIL population derived from a cross between an American semi-dwarf cultivar (cv. Charleston) and a Chinese line with a short growth stage (cv. Dongnong 594). The growth stage data of soybean was recorded for each day. QTLs for all eight reproductive growth stages of soybean (R1 to R8) were analyzed by a composite interval mapping method combined with a mixed genetic model. Fifty-four QTLs displayed main effects and 56 QTL pairs showed epistatic effects. Two marker intervals (Satt173–Satt581, Satt402–Satt267), located on the linkage group O and D1a respectively, strongly influenced plant developmental processes during reproductive growth stages. The findings of this study open the possibility to modulate the structure of soybean growth stages by marker-assisted selection and pyramiding QTL analysis. H.-M. Qiu and D.-W. Xin contributed equally to this work.     

大豆产量及主要农艺性状QTL的上位性互作和环境互作分析

以栽培大豆晋豆23为母本,半野生大豆灰布支黑豆ZDD2315为父本杂交衍生的F2:15和F2:16的447个RIL家系为遗传群体,绘制SSR遗传图谱,采用混合线性模型方法,对2年大豆小区产量及主要农艺性状进行加性QTL、加性×加性上位互作及环境互作分析。结果检测到9个与小区产量、茎粗、有效分枝、主茎节数、株高、结荚高度相关的QTL,分别位于J_2、I、M连锁群上,其中小区产量、茎粗、株高、有效分枝和主茎节数QTL的加性效应为正值,说明增加这些性状的等位基因来源于母本晋豆23。同时,检测到7对影响小区产量、茎粗、株高和结荚高度的加性×加性上位互作效应及环境互作效应的QTL,共发现14个与环境存在互作的QTL。上位效应和QE互作效应对大豆小区产量及主要农艺性状的遗传影响较大。大豆分子标记辅助育种中,既要考虑起主要作用的QTL,又要注重上位性QTL,才有利于性状的稳定表达和遗传。