Identification of quantitative trait loci associated with boiled seed hardness in soybean

Boiled seed hardness is an important factor in the processing of soybean food products such as nimame and natto. Little information is available on the genetic basis for boiled seed hardness, despite the wide variation in this trait. DNA markers linked to the gene controlling this trait should be useful in soybean breeding programs because of the difficulty of its evaluation. In this report, quantitative trait locus (QTL) analysis was performed to reveal the genetic factors associated with boiled seed hardness using a recombinant inbred line population developed from a cross between two Japanese cultivars, ‘Natto-shoryu’ and ‘Hyoukei-kuro 3’, which differ largely in boiled seed hardness, which in ‘Natto-shoryu’ is about twice that of ‘Hyoukei-kuro 3’. Two significantly stable QTLs, qHbs3-1 and qHbs6-1, were identified on chromosomes 3 and 6, for which the ‘Hyoukei-kuro 3’ alleles contribute to decrease boiled seed hardness for both QTLs. qHbs3-1 also showed significant effects in progeny of a residual heterozygous line and in a different segregating population. Given its substantial effect on boiled seed hardness, SSR markers closely linked to qHbs3-1, such as BARCSOYSSR_03_0165 and BARCSOYSSR_03_0185, could be useful for marker-assisted selection in soybean breeding.     

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.     

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.     

利用PyBSASeq算法挖掘大豆百粒重相关位点与候选基因

基于量化染色体区间上与目标性状相关多态性位点的富集程度这一原理开发的PyBSASeq算法,被证实更适合进行基于BSA-seq技术的复杂数量性状遗传解析。本研究采用该算法,以‘滑皮豆’和‘齐黄26’为亲本杂交所衍生的包含149个RILs为材料,挖掘与大豆百粒重相关位点,共获得11个与目标性状紧密关联的候选区域,分别位于1号、2号、4号、7号、9号、14号和16号染色体,其中qSW4-1、qSW9-1、qSW9-2和qSW7-1与已报道大豆百粒重QTL位置一致。候选区域共包含218个编码基因,根据基因表达特性和单倍型分析结果,最终获得2个与目标性状相关的候选基因Glyma.02G075000和Glyma.04G082500,分别参与蔗糖的运输和维生素E的生物合成。研究结果将有助于大豆百粒重遗传机制的阐释,并为基于BSA-Seq技术的数量性状研究提供参考。     

Identification of quantitative trait loci underlying soybean (Glycine max [L.] Merr.) seed weight including main,epistatic and QTL × environment effects in different regions of Northeast China

Seed weight (SW) is the important soybean (Glycine max [L.] Merr.), yield component and also affected the quality of soybean‐derived foods. The aim of this study was to identify the quantitative trait loci (QTL) underlying SW through 112 recombinant inbred lines (RILs) derived from the cross between “Zhongdou27” (G. max, designated by its bigger seed size, 21.9 g/100 seeds) and “Jiunong 20” (G. max, smaller seed size, 17.5 g/100 seeds). Phenotypic data were collected from this RIL population after it was grown in the sixteen tested environments. A total of eight QTL (QSW1‐1, QSW2‐1, QSW2‐2, QSW5‐1, QSW15‐1, QSW17‐1, QSW19‐1 and QSW20‐1) were identified, and they could explain 4.23%–14.65% of the phenotypic variation. Among these eight QTL, three QTL (QSW1‐1 located on the interval of Sat_159‐Satt603 of chromosome (Chr) 1 (LGD1a), QSW19‐1 located on the interval of Sat_340‐Satt523 of Chr 19 (LGL) and QSW20‐1 located on Sat_418‐Sat_105 of Chr 20 (LGI)) were newly identified and could explain 4.235%–10.08%, 8.45%–13.49% and 8.08%–10.18% of the phenotypic variation, respectively. Six of the eight identified QTL including QSW2‐2, QSW5‐1, QSW15‐1, QSW17‐1, QSW19‐1 and QSW20‐1 exhibited a significant additive (a) effect, while two QTL (QSW2‐1 and QSW19‐1) only displayed significant additive‐by‐environment (ae) effects. A total of four epistatic pairwise QTL for SW were identified in the different environments. These eight QTL and their genetic information obtained here were valuable for molecular marker‐assisted selection and the realization of a reasonable SW breeding programme in soybean.     

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.     

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.     

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.     

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.     

The presence or absence of the soybean Kunitz trypsin inhibitor as a quantitative trait locus for seed protein content

Numerous quantitative trait loci (QTL) for various characters have recently been reported in different crop plants. However, information is limited about the molecular mechanisms behind QTL, because most of them have only been detected at a statistical level. Therefore, progeny from a cross between two soybean genotypes segregating for the presence vs. absence of the Kunitz trypsin inhibitor, a 21.5 kDa protein, have been analysed for possible effects of that protein on agronomic and seed quality characters. Protein content was reduced by, on average, 4.5 g/kg in segregants lacking the Kunitz protein, whereas oil content and other characters remained unaffected. This finding can be interpreted as a ‘model QTL’ for variation in seed protein content, because the molecular and genetic backgrounds of the soybean Kunitz trypsin inhibitor are well understood.     

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.     

Mapping quantitative trait loci for yield-related traits in soybean (Glycine max L.)

Development of soybean cultivars with high seed yield is a major focus in soybean breeding programs. This study was conducted to identify genetic loci associated with seed yield-related traits in soybean and also to clarify consistency of the detected QTLs with QTLs found by previous researchers. A population of 135 F_2:3 lines was developed from a cross between a vegetable soybean line (MJ0004-6) and a landrace cultivar from Myanmar ({"type":"entrez-nucleotide","attrs":{"text":"R18500","term_id":"772110","term_text":"R18500"}}R18500). They were evaluated in the experimental field of Kasetsart University, Kamphaeng Saen, Nakhon Pathom, Thailand in a randomized complete block design with two replications each in 2011 and 2012 growing seasons. The two parents exhibited contrasting characteristics for most of the traits that were mapped. Analysis of variance showed that the main effects of genotype and environment (year) were significant for all studied traits. Genotype by environment interaction was also highly significant for all the traits. The population was genotyped by 149 polymorphic SSR markers and the genetic map consisted of 129 SSR loci which converged into 38 linkage groups covering 1156 cM of soybean genome. There were 10 QTLs significantly associated with seed yield-related traits across two seasons with single QTLs explaining between 5.0% to 21.9% of the phenotypic variation. Three of these QTLs were detected in both years for days to flowering, days to maturity and 100 seed weight. Most of the detected QTLs in our research were consistent with earlier QTLs reported by previous researchers. However, four novel QTLs including SF1, SF2 and SF3 on linkage groups L and N for seed filling period and PN1 on linkage group D1b for pod number were identified in the present study.     

Analysis of contributors to grain yield in wheat at the individual quantitative trait locus level

In wheat, strong genetic correlations have been found between grain yield (GY) and tiller number per plant (TN), fertile spikelet number per spike (FSN), kernel number per spike (KN) and thousand‐kernel weight (TKW). To investigate their genetic relationships at the individual quantitative trait locus (QTL) level, we performed both normal and multivariate conditional QTL analysis based on two recombinant inbred lines (RILs) populations. A total of 79 and 48 normal QTLs were identified in the International Triticeae Mapping Initiative (ITMI)/SHW‐L1 × Chuanmai 32 (SC) populations, respectively, as well as 55 and 35 conditional QTLs. Thirty‐two QTL clusters in the ITMI population and 18 QTL clusters in the SC population explained 0.9%–46.2% of phenotypic variance for two to eight traits. A comparison between the normal and conditional QTL mapping analyses indicated that FSN made the smallest contribution to GY among the four GY components that were considered at the QTL level. The effects of TN, KN and TKW on GY were stronger at the QTL level.     

Detection and validation of QTLs associated with seed longevity in rice (Oryza sativa L.)

Seed longevity in rice is a major determinant in seed production and germplasm preservation. In this paper, a recombinant inbred line (RIL) population consisting of 172 lines derived from the cross between Xiang743 and ‘Katy’ was used to map quantitative trait loci (QTLs) for seed longevity (SL) after seed storage for 18 and 30 months under ambient conditions. Two putative QTLs, qSL‐2 and qSL‐8, were detected and located on chromosomes 2 and 8, respectively. qSL‐2 is an allele from Xiang743 allele and increases seed longevity. qSL‐8 was a novel QTL from ‘Katy’ allele and increases seed longevity. qSL‐8 explained 15.29% and 17.35% of the phenotypic variance after seed storage for 18 and 30 months, respectively. Furthermore, qSL‐8 was validated in a secondary population developed by self‐pollination of a residual heterozygous line (RHL) selected from the RIL population, which explained 25.93% of the phenotypic contribution. These results provide an opportunity for map‐based cloning of qSL‐8. Furthermore, qSL‐8 may be a target for improving seed longevity by marker‐assisted selection (MAS) in rice.     

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.     

Identification of quantitative trait loci controlling grain size and shape in the D genome of synthetic hexaploid wheat lines

Synthetic hexaploid wheat is an effective genetic resource for transferring agronomically important genes from Aegilops tauschii to common wheat. Wide variation in grain size and shape, one of the main targets for wheat breeding, has been observed among Ae. tauschii accessions. To identify the quantitative trait loci (QTLs) responsible for grain size and shape variation in the wheat D genome under a hexaploid genetic background, six parameters related to grain size and shape were measured using SmartGrain digital image software and QTL analysis was conducted using four F₂ mapping populations of wheat synthetic hexaploids. In total, 18 QTLs for the six parameters were found on five of the seven D-genome chromosomes. The identified QTLs significantly contributed to the variation in grain size and shape among the synthetic wheat lines, implying that the D-genome QTLs might be at least partly functional in hexaploid wheat. Thus, synthetic wheat lines with diverse D genomes from Ae. tauschii are useful resources for the identification of agronomically important loci that function in hexaploid wheat.     

Mapping and validation of the quantitative trait loci for leaf stay‐green‐associated parameters in maize

Functional stay‐green is generally regarded as a desirable trait of varieties in major crops including maize. In this study, we used an F_3:4 recombinant inbred line population with 165 lines from a cross between a stay‐green inbred line (Zheng58) and a model inbred line (B73) using 211 polymorphic simple sequence repeat markers to map quantitative trait loci for three stay‐green‐associated parameters, chlorophyll content, photosystem II photochemical efficiency and stay‐green area, at maturity stage, detected a total of 23 quantitative trait loci (QTL) on nine chromosomes. Single QTL explained 3.7–13.5% of the phenotypic variance. Additionally, we validated some important stay‐green QTL using a heterogeneous inbred family approach and found that the stay‐green‐associated parameters were significantly correlated with the plant yield. This study may contribute to a better insight into the regulatory mechanism behind leaf stay‐green in maize and a novel development of elite maize varieties with delayed leaf senescence through molecular marker‐assisted selection.     

Identification and comparative analysis of quantitative trait loci associated with parthenocarpy in processing cucumber

Parthenocarpy (seedless fruit) is an economically important yield‐related trait in cucumber (Cucumis sativus L.; 2n = 2x = 14). However, the genomic locations of factors controlling parthenocarpic fruit development in this species are not known. Therefore, an F_{2 : 3} mating design was utilized to map quantitative trait loci (QTL) for parthenocarpy using a narrow cross employing two gynoecious, indeterminate and normal leaf lines [2A (parthenocarpic) and Gy8 (non‐parthenocarpic)]. QTL detection was performed employing 2A‐ and Gy8‐coupling phase data using the parthenocarpic yield of 126 F₃ families grown at two locations at Hancock, WI in 2000. The QTLs detected in this study were compared with the map locations of QTLs conditioning first‐harvest yield of seeded cucumber characterized in a previous study. There were 10 QTLs for parthenocarpy detected defining four genomic regions, in which three QTLs also mapped to the same genomic regions as QTLs detected for fruit yield at first‐harvest as reported in a previous study. The eight fluorescence amplified fragment length polymorphism (AFLP) markers linked to parthenocarpy through QTL mapping defined herein (four each in linkage groups 1 and 4) are candidates for use in marker‐assisted selection programmes where breeding for increased levels of parthenocarpy is an objective in the elite‐processing cucumber populations.