Identification and validation of quantitative trait loci associated with seed yield in soybean

In soybean [Glycine max (L.) Merrill], the genetic analysis of seed yield is important to aid in the breeding of high-yielding cultivars. Seed yield is a complex trait, and the number of quantitative trait loci (QTL) involved in seed yield is high. The aims of this study were to identify QTL associated with seed yield and validate their effects on seed yield using near-isogenic lines. The QTL analysis was conducted using a recombinant inbred line population derived from a cross between Japanese cultivars ‘Toyoharuka’ and ‘Toyomusume’, and eight seed yield-associated QTL were identified. There were significant positive correlations between seed yield and the number of favorable alleles at QTL associated with seed yield in the recombinant inbred lines for three years. The effects of qSY8-1, a QTL promoting greater seed yield, was validated in the Toyoharuka background. In a two-year yield trial, the 100-seed weight and seed yield of Toyoharuka-NIL, the near-isogenic line having the Toyomusume allele at qSY8-1, were significantly greater than those of Toyoharuka (106% and 107%, respectively) without any change for days to flowering and maturity. Our results suggest that qSY8-1 was not associated with maturity genes, and contributed to the 100-seed weight.     

Quantitative trait loci for agronomic and seed quality traits in an F2 and F4:6 soybean population

Molecular breeding is becoming more practical as better technology emerges. The use of molecular markers in plant breeding for indirect selection of important traits can favorably impact breeding efficiency. The purpose of this research is to identify quantitative trait loci (QTL) on molecular linkage groups (MLG) which are associated with seed protein concentration, seed oil concentration, seed size, plant height, lodging, and maturity, in a population from a cross between the soybean cultivars ‘Essex’ and ‘Williams.’ DNA was extracted from F₂ generation soybean leaves and amplified via polymerase chain reaction (PCR) using simple sequence repeat (SSR) markers. Markers that were polymorphic between the parents were analyzed against phenotypic trait data from the F₂ and F_4:6 generation. For the F₂ population, significant additive QTL were Satt540 (MLG M, maturity, r² = 0.11; height, r² = 0.04, seed size, r²= 0.06], Satt373 (MLG L, seed size, r² = 0.04; height, r² = 0.14), Satt50 (MLG A1, maturity r² = 0.07), Satt14 (MLG D2, oil, r² = 0.05), and Satt251 (protein r² = 0.03, oil, r² =0.04). Significant dominant QTL for the F₂ population were Satt540 (MLG M,height, r² = 0.04; seed size, r² = 0.06) and Satt14 (MLG D2, oil, r² = 0.05). In the F_4:6 generation significant additive QTL were Satt239 (MLGI, height, r² = 0.02 at Knoxville, TN and r² = 0.03 at Springfield, TN), Satt14 (MLG D2, seed size, r² = 0.14 at Knoxville, TN), Satt373 (MLG L, protein, r² = 0.04 at Knoxville, TN) and Satt251 (MLG B1, lodging r² = 0.04 at Springfield, TN). Averaged over both environments in the F_4:6 generation, significant additive QTL were identified as Satt251 (MLG B1, protein, r² = 0.03), and Satt239 (MLG I, height, r² = 0.03). The results found in this study indicate that selections based solely on these QTL would produce limited gains (based on low r² values). Few QTL were detected to be stable across environments. Further research to identify stable QTL over environments is needed to make marker-assisted approaches more widely adopted by soybean breeders. This revised version was published online in July 2006 with corrections to the Cover Date.     

Dynamic quantitative trait loci underlies isoflavone accumulation in soybean seed

Most of quantitative trait loci (QTL) underlying soybean seed isoflavone contents were derived from the harvest stage of plant development, which uncover the genetic effects that were expressed in earlier seed developmental stages. The aim of this study was to detect conditional QTL associated with isoflavone accumulation during the entire seed development. A total of 112 recombinant inbred lines developed from the cross between ‘Zhongdou 27’ (higher seed isoflavone content) and ‘Jiunong 20’ (lower seed isoflavone content) were used for the conditional QTL analysis of daidzein (DZ), genistein (GT), glycitein (GC) and total isoflavone (TI) accumulations through composite interval mapping with mixed genetic model. The results indicated that the number and type of QTL and their additive effects for individual and total isoflavone accumulations were different among R3 to R8 developmental stages. Three unconditional QTL and six conditional QTL for DZ, four unconditional QTL and five conditional QTL for GT, six unconditional QTL and five conditional QTL for GC, six unconditional QTL and seven conditional QTL for TI were identified at different developmental stages, respectively. Unconditional and conditional QTL that affect individual and total isoflavone accumulations exhibited multiple expression patterns, implying that some QTL are active for long period and others are transient. Two genomic regions, Satt144‐Satt569 in linkage group F (LG F; chromosome 13, chr 13) for DZ, GC, GT and TI accumulations and Satt540‐Sat_240 in LG M (chr 07) for TI and GC accumulations, were found to significantly affect individual and total isoflavone accumulations in multiple developmental stages, suggesting that the accumulation of soybean seed isoflavones is governed by time‐dependent gene expression.     

Identification of quantitative trait loci (QTLs) for seed protein concentration in soybean and analysis for additive effects and epistatic effects of QTLs under multiple environments

Soybean protein concentration is a key trait driver of successful soybean quality. A recombination inbred lines derived from a cross between ‘Charleston’ and ‘Dongnong594’, were planted in three environments across four years in China. Then, the genetic effects were partitioned into additive main effects, epistatic main effects and their environment interaction effects by using composite interval mapping, multiple interval mapping and composite interval mapping in a mixed linear model. Forty‐three quantitative trait loci QTLs were identified on 17 of 20 soybean chromosomes excluding Ch 7, Ch 8 and Ch 17. Two QTLs showed a good stability across multiple environments, qPRO20‐1 was detected under four environments, which explained 4.4–9.95% phenotypic variances and the allele was from ‘Charleston’ among four environments. qPRO7‐5 was detected under three environments, which explained 7.2–14.5% phenotypic variances and the allele was from ‘Dongnong 594’, three pathway genes of protein biosynthesis were detected in the interval of qPRO7‐5. The additive main‐effect QTLs contributed more phenotypic variation than the epistasis and environmental interaction. This indicated that it is feasible by marker‐assisted selection to improve soybean protein concentration.     

Identification of quantitative trait loci underlying resistance of soybean to Fusarium graminearum

Fusarium graminearum could cause serious yield loss of soybean. Host resistance could offer an economical and effective way to control F. graminearum. The aims of this study were to identify and confirm quantitative trait loci (QTLs) underlying resistance to F. graminearum, and to analyse the genetic effects of pyramid resistance QTL on resistance level. A total of 140 F_2:14 recombinant inbred lines (RILs) were constructed via the cross between 'Hefeng 25' (moderate resistance to F. graminearum) and 'Conrad' (resistance to F. graminearum). The molecular genetic linkage map was constructed based on 164 simple sequence repeat (SSR) markers. A total of seven QTLs underlying F. graminearum resistance, located on six chromosomes, were identified. Among these seven identified QTLs, beneficial allele of qFG-1, qFG-2 and qFG-3 derived from 'Hefeng 25' and beneficial allele of qFG-4, qFG-5, qFG-6, qFG-7 derived from 'Conrad'. Of these seven identified QTLs, qFG-1, qFG-3, qFG-4 and qFG-5 were novel for F. graminearum resistance. Four pairs of QTLs with significant epistatic effects were found. The accumulation of resistance QTL was positively correlated with decreases in disease severity index, which was valuable for improving efficiency of marker-assistant breeding in F. graminearum resistance.     

Identification and confirmation of quantitative trait loci for stachyose content in soybean seed

Stachyose is an unfavorable sugar in soybean meal that causes flatulence for non‐ruminant animals. Understanding the genetic control of stachyose in soybean will facilitate the modification of stachyose content at the molecular level. The objective of this study was to identify quantitative trait loci (QTL) associated with seed stachyose content using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. A normal stachyose cultivar, ‘Osage’, was crossed with a low stachyose line, V99‐5089, to develop a QTL mapping population. Two parents were screened with 33 SSR and 37 SNP markers randomly distributed on chromosome 10, and 20 SSR and 19 SNP markers surrounding a previously reported stachyose QTL region on chromosome 11. Of these, 5 SSR and 16 SNP markers were used to screen the F_3:4 lines derived from ‘Osage’ x V99‐5089. Seed samples from F_3:5 and F_3:6 lines were analyzed for stachyose content using high‐performance liquid chromatography (HPLC). Composite interval mapping analysis indicated that two stachyose QTL were mapped to chromosome 10 and 11, explaining 11% and 79% of phenotypic variation for stachyose content, respectively. The SSR/SNP markers linked to stachyose QTL could be used in breeding soybean lines with desired stachyose contents. Chi‐square tests further indicated that these two QTL probably represent two independent genes for stachyose content. Therefore, a major QTL was confirmed on chromosome 11 and a novel QTL was found on chromosome 10 for stachyose content.     

An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts

Recognizing the enormous potential of DNA markers in plant breeding, many agricultural research centers and plant breeding institutes have adopted the capacity for marker development and marker-assisted selection (MAS). However, due to rapid developments in marker technology, statistical methodology for identifying quantitative trait loci (QTLs) and the jargon used by molecular biologists, the utility of DNA markers in plant breeding may not be clearly understood by non-molecular biologists. This review provides an introduction to DNA markers and the concept of polymorphism, linkage analysis and map construction, the principles of QTL analysis and how markers may be applied in breeding programs using MAS. This review has been specifically written for readers who have only a basic knowledge of molecular biology and/or plant genetics. Its format is therefore ideal for conventional plant breeders, physiologists, pathologists, other plant scientists and students.     

Identification of quantitative trait loci underlying seed protein and oil contents of soybean across multi‐genetic backgrounds and environments

Seed protein and oil contents are important quantitative traits in soybean. Previously, quantitative trait loci (QTL) associated with seed protein and oil were mostly identified in single genetic background. The objective of this work was to identify QTL and their epistatic effects underlying seed protein and oil contents in three recombinant inbred line populations (two of them used one common female parent) across eight environments by composite interval mapping. Forty QTL underlying protein content and 35 QTL underlying oil content were identified. Among them, nine were universal QTL underlying protein content and four were universal QTL underlying oil content. Epistatic interactions between QTL underlying seed protein/oil and different genetic backgrounds were detected. Different pairs of epistatic interactions were observed in diverse genetic backgrounds across multi‐environments. Common marker intervals were observed to simultaneously underlie seed protein and oil contents with different epistatic interactions. The results in this study suggested that a specific genotype with high oil content and low protein content might significantly affect the selection of soybean lines for high seed protein.     

Mapping major genes and quantitative trait loci controlling agronomic traits in almond

Six tree traits (self-compatibility, blooming date, blooming density, productivity, leafing date and ripening time) and five pomological traits (kernel taste, in-shell weight, shell hardness, kernel weight and double kernel) were studied in an F₁ almond progeny of 167 seedlings from the cross between the French cultivar 'R1000' and the Spanish cultivar 'Desmayo Largueta'. In addition, a set of 135 codominant microsatellites or simple-sequence repeat (SSR) markers developed from peach, cherry and almond were used for the molecular characterization of the progeny. A genetic linkage map was constructed with 56 of these SSRs. Cosegregation analysis allowed the identification of the map positions of two major genes to be confirmed for kernel taste ( Sk ) in linkage group five (G5) and for self-incompatibility ( S ) in G6. QTLs mapped include two for leafing date ( Lf-Q1 and Lf-Q2 ) in G1 and G4, one for shell hardness ( D-Q ) in G2, one each for double kernel ( Dk-Q ) and productivity ( P-Q ) in G4, one for blooming date ( Lb-Q ) in G4, two for kernel weight ( Kw-Q1 and Kw-Q2 ) in G1 and G4, and two for in-shell weight ( Shw-Q1 and Shw-Q2 ) in G1 and G2. Four SSR loci (BPPCT011, UDP96-013, UDP96-003 and PceGA025) were linked to the important agronomic traits of leafing date, shell hardness, blooming date and kernel taste. Finally, the development of efficient marker-assisted selection strategies applied to almond and other Prunus breeding programmes was also discussed.     

Identification of quantitative trait loci underlying soybean (Glycine max) 100-seed weight under different levels of phosphorus fertilizer application

The “100-seed weight (100-SW)” trait is an important component of soybean quality and yield. Phosphorus (P) deficiency induces a wide array of metabolic effects that limits plant growth, especially in soybean. In this study, the 100-SW values of a recombinant inbred line (RIL) population constructed by a cross between “Zhongdou27” and “Jiunong20” were evaluated in three tested environments under regular P and low P level conditions. We detected 12 additive quantitative trait loci (QTL) on nine linkage groups, explaining 8.11%–17.21% of the total phenotype variations. Two of these identified QTLs, qSW2-3 and qSW17-2, were identified in multi-environments both under regular and low P level conditions, and explained 10.10%–14.11% and 10.12%–12.06% of the observed variations, respectively. One QTL, qSW17-2, was novel which has been reported for the first time. Additionally, three QTLs (qSW10-1, qSW13-1 and qSW17-1) were detected under low P conditions and the other QTLs were detected specifically under regular P levels. These particular QTLs improve our understanding of the genetic basis of P efficiency in soybean.     

Genetic analysis of net-like cracking in soybean seed coats

Cracking of seed coats in soybean (Glycine max (L.) Merr.) deteriorates the external appearance of seeds and reduces their commercial value. Two types of cracking have been reported that occur in some cultivars: Type I with irregular cracks and Type II with net-like cracks. This study was conducted to determine the genetic basis of net-like cracking. Genetic analysis was performed using F₁ plants produced by crossing Uzuramame, a Japanese landrace with black seed coats having net-like cracking and a Clark mutant with black seed coats, their F₂ population and F₃ lines. Degree of cracking in individual plants was calculated by averaging cracking index (no cracking: 0 to severe cracking: 4) of total or 100-seed samples (average cracking index, ACI). Uzuramame exhibited intense cracking, whereas the Clark mutant showed slight cracking. Intermediate degree of cracking in F₁ plants suggested incomplete dominance. ACI of F₂ plants was continuously distributed. Gene number involved was estimated to be 1.4 by Wright's method. All F₃ lines derived from F₂ plants with ACI more than 2.8 displayed severe cracking phenotypes. In contrast, F₃ lines derived from F₂ plants with ACI less than 2.8 segregated from low to high ACI (0.5 to 3.2). When F₂ plants were classified as slight (ACI<2.8) or severe (ACI>2.8) cracking, the frequency distribution of the F₂ plants fitted to a 3:1 ratio. Genotypes of SSR marker Satt264 that is closely linked to SoyPRP1 locus for proline-rich cell wall protein had a minor effect on ACI. Further, seed weight was positively associated with ACI (r =0.46^**). Our results suggest that net-like cracking is controlled primarily by a major gene, and SoyPRP1 and gene(s) contributing to seed weight may have minor effects on the intensity of cracking. This revised version was published online in July 2006 with corrections to the Cover Date.     

Identification of quantitative trait loci for grain yield, seed protein concentration and maturity in field pea (Pisum sativum L.)

Breeding efforts to improve grain yield, seed protein concentration and early maturity in pea (Pisum sativum L.) have proven to be difficult. The use of molecular markers will improve our understanding of the genetic factors conditioning these traits and is expected to assist in selection of superior genotypes. This study was conducted to identify genetic loci associated with grain yield, seed protein concentration and early maturity in pea. A population of 88 recombinant inbred lines (RILs) that was developed from a cross between 'Carneval' and 'MP1401' was evaluated at 13 environments across the provinces of Alberta, Manitoba and Saskatchewan, Canada in 1998, 1999 and 2000. A linkage map consisting of 193 AFLPs (amplified fragment length polymorphism), 13 RAPDs (random amplified polymorphic DNA) and one STS (sequence tagged site) marker was used to identify putative quantitative trait loci (QTL) for grain yield, seed protein concentration and early maturity. Four QTL were identified each for grain yield and days to maturity, and three QTL were identified for seed protein concentration. A multiple QTL model for each trait showed that these genomic regions accounted for 39%, 45% and 35% of the total phenotypic variation for grain yield, seed protein concentration and days to maturity, respectively. The consistency of these QTL across environments and their potential for marker-assisted selection are discussed in this report.     

Quantitative trait loci analysis of soluble sugar contents in soybean

The soluble sugar content in soybean seeds, mainly sucrose, stachyose, raffinose and trace amounts of glucose and fructose, is important for the increasing global market demand for various soyfoods including tofu, soymilk, natto, bean sprouts and edamame due to their nutritional value and health benefits. The objective of this study was to conduct quantitative trait loci (QTL) analysis and identify molecular markers for soluble sugar content in soybean seeds for marker‐assisted selection (MAS) in soybean breeding. The content of the five previously mentioned sugars were measured and associated QTLs were mapped based on a F₂ population that was derived from a cross between V97‐3000 and V99‐5089. Eleven QTLs were detected for the five sugar contents: one for glucose, three each for fructose and sucrose, and two each for raffinose and stachyose. However, only one QTL for sucrose, one QTL for raffinose, and two QTLs for stachyose were identified with LOD > 3.0 and R² > 10% from this research. The QTL on chromosome 11 [linkage group (LG) B1] was identified as associated with sucrose, raffinose and stachyose in the same region as previously reported for sucrose and stachyose. The SSR marker, Satt359, on the QTL B1 region had an significant association with sucrose (LOD = 5.192; R² = 0.134), raffinose (LOD = 3.95; R² = 0.104), and stachyose (LOD = 13.572; R² = 0.314); therefore it can be used to assist breeding selection for sucrose, raffinose and stachyose contents simultaneously.     

Identification of quantitative trait loci for seed traits and floral morphology in a field-grown Lolium perenne × Lolium multiflorum mapping population

Lolium perenne L. (perennial ryegrass), and Lolium multiflorum Lam. (annual or Italian ryegrass), differ in several traits related to seed yield. Generally, L. multiflorum spikes are larger than L. perenne spikes, and have more spikelets, more florets per spikelet, larger seeds and awns. The greater number of spikelets and florets and larger seeds are associated with higher seed yield in L. multiflorum . Ryegrass ( Lolium sp.) cultivars are produced by seed multiplication and understanding the genetics of seed production traits would aid in plant improvement. A total of 30 QTL for seed production related traits were identified in this study. The QTLs were primarily located on linkage groups 2 and 4 which appear to be the most important for distinguishing L.   multiflorum and L. perenne . These QTL will be used to develop molecular markers for marker-assisted breeding and screening of L. perenne seed lots to detect seed contamination with L. multiflorum .     

Quantitative trait loci for agronomic traits in soybean

There continues to be improvement in seed yields of soybean by conventional breeding, but molecular techniques may provide faster genetic gains. The objective of this study was to identify quantitative trait loci (QTL) associated with the agronomic traits seed yield, lodging, plant height, seed filling period and plant maturity in soybean. To achieve this objective, 101 F₆‐derived recombinant inbred lines (RIL) from a population developed from a cross of N87‐984‐16 × TN93‐99 were used. Experiments were conducted in six environments during 2002–2003. Heritability estimates on an entry mean basis from data combined across environments ranged from 0.12 to 0.65 for seed yield and seed filling period, respectively. Composite interval mapping detected one QTL for yield (near Satt076), two for lodging (near Satt225 and Satt593) and four for maturity (near Satt263, Satt292, Satt293 and Satt591) in this population. Additional environmentally sensitive QTL for these traits, and for seed filling period and plant height are also reported. The QTL associated with agronomic traits that we report and the recently released germplasm (PI 636460) from this population may be useful in soybean breeding programmes.     

Mapping and validation of PCR-based markers associated with a major QTL for seed dormancy in wheat

Seed dormancy is one of the important factors controlling pre-harvest sprouting (PHS) resistance in wheat. We identified a major quantitative trait locus (QTL) for seed dormancy on the long arm of wheat chromosome 4A (4AL) via simple sequence repeat (SSR)-based genetic mapping using doubled haploid lines from a cross between Japanese PHS resistant variety ‘Kitamoe’ and the Alpine non-resistant variety “Münstertaler” (K/M). The QTL explained 43.3% of total phenotypic variation for seed dormancy under greenhouse conditions. SSR markers flanking the QTL were assigned to the chromosome long arm fraction length 0.59–0.66 on the basis of chromosome deletion analysis, suggesting that the gene(s) controlling seed dormancy are probably located within this region. Under greenhouse conditions, the QTL explained 28.5 and 39.0% of total phenotypic variation for seed dormancy in Haruyutaka/Leader (HT/L) and OS21-5/Haruyokoi (O/HK) populations, respectively. However, in field conditions, the effect was relatively low or not significant in both the K/M and HT/L populations. These markers were considered to be widely useful in common with various genetic backgrounds for improvement of seed dormancy through the use of marker-assisted selection. Further detailed research using near isogenic lines will be needed to define how this major QTL interacts with environmental conditions in our area.     

Analysis of quantitative trait loci associated with leaflet types in two recombinant inbred lines of soybean

Leaf area, length and width affect the photosynthetic capability of a plant and so increasing the photosynthetic rate per unit leaf area may improve seed yield in soybean. In this study, simple sequence repeat (SSR) markers were used to identify the genomic regions significantly associated with the quantitative trait locus (QTL) that controls length, width and the length/width ratio of the terminal and lateral leaflet in two segregating F_2:10 recombinant inbred line (RIL) populations, ‘Keounolkong’ × ‘Shinpaldalkong’ (K/S) and ‘Keounolkong’ × ‘Iksan10’ (K/I). In the K/S population, one QTL was identified for terminal leaflet length (TLL), two for lateral leaflet length (LLL), four for terminal leaflet width (TLW), four for lateral leaflet width (LLW), two for terminal leaflet length/width ratio (TLR) and four for lateral leaflet length/width ratio (LLR), with total phenotypic variations of 7.43, 10.9, 26.57, 23.46, 20.25 and 23.31%, respectively. In the K/I population, two QTLs were identified for TLL, two for LLL, three for TLW, and two for LLW, four for TLR and two for LLR with total phenotypic variations of 29.89, 22.77, 18.5, 12.15, 22.96 and 17.85%, respectively. Only a few QTLs coincided among the leaflet traits and no relationships were observed between the two populations. Many QTLs were associated with leaflet traits but each single QTL made only a minimal contribution. Thus, pyramiding the favourable alleles for leaflet traits in soybean breeding programmes may accelerate vegetative growth and perhaps lead to higher yields by maximizing total photosynthetic performance.     

Molecular loci associated with seed isoflavone content may underlie resistance to soybean pod borer (Leguminivora glycinivorella)

Soybean pod borer (SPB) (Leguminivora glycinivorella (Mats.) Obraztsov) causes severe loss of soybean (Glycine max L. Merr.) seed yield and quality in some regions of the world, especially in north‐eastern China, Japan and Russia. Isoflavones in soybean seed play a crucial role in plant resistance to diseases and pests. The aim of this study was to find whether SPB resistance QTL are associated with soybean seed isoflavone content. A cross was made between ‘Zhongdou 27’ (higher isoflavone content) and ‘Jiunong 20’ (lower isoflavone content). One hundred and twelve F_5:10 recombinant inbred lines were derived through single‐seed descent. A plastic‐net cabinet was used to cover the plants in early August, and thirty SPB moths per square metre were put in to infest the soybean green pods. The results indicated that the percentage of seeds damaged by SPB was positively correlated with glycitein content (GC), whereas it was negatively correlated with genistein (GT), daidzein (DZ) and total isoflavone content (TI). Four QTL underlying SPB damage to seeds were identified and the phenotypic variation for SPB resistance explained by the four QTL ranged from 2% to 14% on chromosomes Gm7, 10, 13 and 17. Moreover, eleven QTL underlying isoflavone content were identified, and ten of them were encompassed within the same four marker intervals as the SPB QTL (BARC‐Satt208‐Sat292, Satt144‐Sat074, Satt540‐Sat244 and Satt345‐Satt592). These QTL could be useful in marker‐assisted selection for breeding soybean cultivars with both SPB resistance and high seed isoflavone content.     

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.