Identifying quantitative trait loci for the general combining ability of yield-relevant traits in maize

Maize is the most important staple crop worldwide. Many of its agronomic traits present with a high level of heterosis. Combining ability was proposed to exploit the rule of heterosis, and general combining ability (GCA) is a crucial measure of parental performance. In this study, a recombinant inbred line population was used to construct testcross populations by crossing with four testers based on North Carolina design II. Six yield-relevant traits were investigated as phenotypic data. GCA effects were estimated for three scenarios based on the heterotic group and the number of tester lines. These estimates were then used to identify quantitative trait loci (QTL) and dissect genetic basis of GCA. A higher heritability of GCA was obtained for each trait. Thus, testing in early generation of breeding may effectively select candidate lines with relatively superior GCA performance. The GCA QTL detected in each scenario was slightly different according to the linkage mapping. Most of the GCA-relevant loci were simultaneously detected in all three datasets. Therefore, the genetic basis of GCA was nearly constant although discrepant inbred lines were appointed as testers. In addition, favorable alleles corresponding to GCA could be pyramided via marker-assisted selection and made available for maize hybrid breeding.     

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.     

Co-localization of quantitative trait loci for foliar disease resistance in sorghum

Quantitative trait loci (QTL) analysis of resistance to three foliar diseases, viz. target leaf spot, zonate leaf spot and drechstera leaf blight was undertaken in sorghum using 168 F₇ recombinant inbred lines derived from a cross between '296B' (resistant) and 'IS18551' (susceptible) parents. The genomic region flanked by plant colour locus ( Plcor ) and simple sequence repeat marker Xtxp95 on chromosome SBI-06 harboured disease-response QTL for all the three diseases caused by different fungal pathogens. It is hypothesized that this region on sorghum chromosome SBI-06 could harbour a cluster of disease-response loci to different pathogens as observed in the syntenic regions on rice chromosome 4 and maize chromosome 2. The information gained in this study can be used in deploying marker-assisted selection for foliar resistance and map-based isolation of important disease resistance genes in sorghum.     

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.     

Novel quantitative trait loci for yield and yield related traits identified in Basmati rice (Oryza sativa)

Increasing crop productivity is one of the prime goals of crop breeding research. Rice grain yield is a complex quantitative trait governed by polygenes. Although several QTLs governing grain yield traits have been reported and limited attempts have been made to map QTLs for grain yield parameters in Basmati rice. A population from the cross Sonasal and Pusa Basmati 1121 comprising 352 RILs was generated through the single seed descent method. A total of 12 QTLs governing yield and yield-related traits were mapped on six chromosomes, namely, 1, 2, 3, 7, 8 and 9, of which five QTLs were novel. We identified a novel and robust epistatic QTL (qPH1.1 and qPL1.1) governing plant height and panicle length, flanked by the markers RM5336-RM1 on chromosome 1. The gene encoding brassinosteroid insensitive 1-associated receptor kinase 1 precursor is the putative candidate gene underlying this epistatic QTL. Another novel QTL, qNT3.1, governing tiller number was bracketed to a region of .77 Mb between the markers RM15247 and RM15281 on chromosome 3. Of the 57 annotated gene models, Os03g0437600 encoding alpha/beta-fold hydrolase, a homologous to AtKai2 is a putative candidate gene underlying the novel QTL qNT3.1. The other QTLs such as qDFF1.1 governing days to 50% flowering co-localizes with the gene Ghd7, QTL for plant height qPH1.2 co-localizes with the gene sd1, the QTLs for panicle length co-localizes with FUWA and DEP2, the QTL for tiller number co-localizes with OsRLCK57 and QTLs for thousand-grain weight co-localize with the major gene GS3. The QTLs identified in the current study can be effectively used in marker-assisted selection for developing Basmati rice varieties with a higher yield.     

Mapping quantitative trait loci for salt tolerance at germination and the seedling stage in barley (Hordeum vulgare L.)

Quantitative trait loci (QTLs) controlling salt tolerance at germination and the seedling stage in barley (Hordeum vulgare L.) were identified by interval mapping analysis using marker information from two doubled haploid (DH) populations derived from the crosses, Steptoe/Morex and Harrington/TR306. Interval mapping analysis revealed that the QTLs for salt tolerance at germination in the DH lines of Steptoe/Morex were located on chromosomes 4 (4H), 6(6H), and 7(5H), and in the DH lines of Harrington/TR306 on chromosomes 5(1H) and 7(5H). In both DH populations, the most effective QTLs were found at different loci on chromosome 7(5H). Genetic linkage between salt tolerance at germination and abscisic acid (ABA) response was found from QTL mapping. The QTLs for the most effective ABA response at germination were located very close to those for salt tolerance on chromosome 7 (5H) in both crosses. The QTLs for salt tolerance at the seedling stage were located on chromosomes 2(2H), 5(1H), 6(6H), and 7(5H) in the DH lines of Steptoe/Morex, and on chromosome 7(5H) in the DH lines of Harrington/TR 306. Their positions were different from those of QTLs controlling salt tolerance at germination, indicating that salt tolerance at germination and at the seedling stage were controlled by different loci. This revised version was published online in July 2006 with corrections to the Cover Date.     

Genetic variation in barley of crossability with wheat and its quantitative trait loci analysis

To study genetic variation in crossability, 80 barley accessions of diverse geographic origin consisting of 50 wild barleys (H. vulgare ssp. spontaneum or ssp. agriocrithon) and 30 cultivated barleys (H. vulgare ssp. vulgare) were crossed as the male parent with a highly crossable wheat variety, Shinchunaga. Crossabilities, expressed as the percentage of pollinated florets giving embryo-containing caryopses, ranged from 0% to 68.6%. Barley accessions from East Asia had generally a low crossability, while barley accessions from other regions exhibited a wider range of crossability including highly crossable genotypes. No significant difference in mean crossability was found between wild and cultivated barleys. To estimate the number and location of barley genes controlling the crossability, doubled haploid lines derived from the cross between the barley varieties Steptoe and Morex were crossed as the male parent with wheat. Quantitative trait loci (QTL) analysis using molecular markers identified four QTL. These were mapped to the centromeric regions of chromosomes 2H, 3H and 5H and the short arm of chromosome 7H. The QTL on chromosomes 3H and 5H had larger effects than those on chromosomes 2H and 7H. The four QTL collectively explained 35.4% of the total variance under a multiple QTL model. Relationships of the QTL identified in the present study with previously reported crossability genes of barley and wheat are discussed. This revised version was published online in August 2006 with corrections to the Cover Date.     

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 of quantitative trait loci associated with rice black‐streaked dwarf virus disease and its insect vector in rice (Oryza sativa L.)

Rice black‐streaked dwarf virus disease (RBSDVD), transmitted by small brown planthopper (SBPH, Laodelphax striatellus), causes serious loss in rice production. Breeding resistant cultivars are one of the most effective strategies to control the virus disease and its vector. By both natural inoculations in the field and modified seedling‐box screening test in the glasshouse, an indica variety WR24 showed high resistance to RBSDVD and SBPH. An F_2:3 population consisting of 153 lines derived from a cross between WR24 and a susceptible japonica variety Suyunuo was used for quantitative trait loci (QTL) analysis of RBSDVD and SBPH resistance. The linkage map consisting of 130 SSR markers was constructed with an average marker interval of 13.90 cM, spanning a total of 1890.9 cM. Totally, five QTLs for RBSDV resistance, viz. qRBSDV3^WR24, qRBSDV6^WR24, qRBSDV7^WR24, qRBSDV9^WR24 and qRBSDV11^WR24, were detected on chromosomes 3, 6, 7, 9 and 11, with LOD scores of 2.7, 3.08, 3.13, 5.28 and 3.7, respectively. Meanwhile, three QTLs for SBPH resistance, including qSBPH5^WR24, qSBPH7^WR24 and qSBPH10^WR24, were mapped on chromosomes 5, 7 and 10, with LOD scores of 2.18, 3.5 and 3.57, respectively. All resistant alleles were from WR24. Among these QTLs, qRBSDV7^WR24, qSBPH5^WR24 and qSBPH10^WR24 were newly reported, and qSBPH10^WR24 showed major effect that explained 17.9% of total phenotypic variance. The RBSDVD and SBPH resistance QTLs and the tightly linked DNA markers can be utilized in RBSDV and SBPH resistance breeding in rice.     

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.     

Mapping of quantitative trait loci for resistance to race 1 of Pyrenophora tritici‐repentis in synthetic hexaploid wheat

Tan spot, caused by a necrotrophic fungus Pyrenophora tritici‐repentis (Ptr), has become an important foliar disease of wheat worldwide. Effective control of tan spot can be achieved by deployment of resistant wheat cultivars. An F_2:3 population derived from a cross between synthetic hexaploid wheat (SHW), TA4161‐L1 (moderately resistant) and susceptible winter wheat cultivar, ‘TAM105’ was evaluated with race 1 of Ptr under controlled conditions. The population was genotyped using Diversity Arrays Technology (DArT). Presence of transgressive segregants indicated contribution of positive alleles from both parents. Two major QTLs were located on the short arm of chromosomes 1A and 6A and designated as QTs.ksu‐1A and QTs.ksu‐6A, respectively. Two additional QTLs were identified on chromosome 7A. Resistant alleles of all the QTLs were contributed by TA4161‐L1. Novel QTLs on 6A and 7A can be a valuable addition to known resistance genes and utilized in breeding programmes to produce highly resistant cultivars.     

Detection of epistatic and environmental interaction QTLs for leaf orientation‐related traits in maize

Leaf architecture traits in maize are quantitative and have been studied by quantitative trait loci (QTLs) mapping. However, additional QTLs for these traits require mapping and the interactions between mapped QTLs require studying because of the complicated genetic nature of these traits. To detect common QTLs and to find new ones, we investigated the maize traits of leaf angle, leaf flagging‐point length, leaf length and leaf orientation value using a set of recombinant inbred line populations and single nucleotide polymorphism markers. In total, 19 QTLs contributed 4.13–13.52% of the phenotypic effects to the corresponding traits that were mapped, and their candidate genes are provided. Common and major QTLs have also been detected. All of the QTLs showed significant additive effects and non‐significant additive × environment effects in combined environments. The majority showed additive × additive epistasis effects and non‐significant QTL × environment effects under single environments. Common and major QTLs provided information for fine mapping and gene cloning, and SNP markers can be used for marker‐assisted selection breeding.     

Quantitative trait loci mapping for yield-related traits under low and high planting densities in maize (Zea mays)

Average maize yield per hectare has increased significantly because of the improvement in high-density tolerance, but little attention has been paid to the genetic mechanism of grain yield response to high planting density. Here, we used a population of 301 recombinant inbred lines (RILs) derived from the cross YE478 × 08–641 to detect quantitative trait loci (QTLs) for 16 yield-related traits under two planting densities (57,000 and 114,000 plants per ha) across four environments. These yield-related traits responded differently to high-density stress. A total of 110 QTLs were observed for these traits: 33 QTLs only under low planting density, 50 QTLs under high planting density and 27 QTLs across both densities. Only two major QTLs, qCD6 and qWKEL2-2, were identified across low- and high-density treatments. Seven environmentally stable QTLs were also observed containing qED6, qWKEL3, qRN3-3, qRN7-2, qRN9-2 and qRN10 across both densities, as well as qRN9-1 under low density. In addition, 16 and eight pairs of loci with epistasis interaction (EPI) were detected under low and high planting densities, respectively. Additionally, nine and 17 loci showed QTL × environment interaction (QEI) under low- and high-density conditions, respectively. These interactions are of lesser importance than the main QTL effects. We also observed 26 pleiotropic QTL clusters, and the hotspot region 3.08 concentrated nine QTLs, suggesting its great importance for maize yield. These findings suggested that multiple minor QTLs, loci with EPI and QEI, pleiotropy and the complex network of “crosstalk” among them for yield-related traits were greatly influenced by plant density, which increases our understanding of the genetic mechanism of yield-related traits for high-density tolerance.     

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.     

Root‐lodging resistance in maize as an example for high‐throughput genetic mapping via single nucleotide polymorphism‐based selective genotyping

Large‐scale selective genotyping and high‐throughput analysis are two important strategies for low‐cost and high‐effective genetic mapping. In this study, selective genotyping was applied to four maize F₂ populations. Thirty plants were selected from each of the two tails of the original F₂ populations to represent extreme resistant and susceptible plants to root lodging, and genotyped individually with 1536 single nucleotide polymorphisms (SNPs). A quantitative trait locus (QTL) was declared when at least three closely linked SNPs showed significant allele frequency difference between the two tails. Nine QTL were identified for root lodging across the four populations, which were located on chromosomes 2, 4, 5, 7, 8 and 10 and one of them was shared between two populations. A total of 20 segregation distortion regions (SDRs) were identified across the four populations, one of which was co‐localized with a QTL on chromosome 4. The tightly linked SNPs identified in this study can be used for marker‐assisted selection for root lodging. Selective genotyping, when combined with pooled DNA analysis, can be used to develop strategies for high‐throughput genetic mapping for all crops.     

Identification of salt tolerance‐improving quantitative trait loci alleles from a salt‐susceptible rice breeding line by introgression breeding

To improve salt tolerance of two elite rice varieties, Ce258 and Zhongguangxiang1 (ZGX1), two sets of introgression lines (ILs) each comprising 200 BC₁F₁₀ lines derived from a common donor, IR75862, and two recipient parents, Ce258 and ZGX1, were used for mapping of QTLs for four salt tolerance‐related traits at the seedling stage. Although the three parents were susceptible to salt, the two IL populations showed transgressive segregations for salt tolerance with 12 and 8 salt tolerance ILs in the Ce258‐ILs and ZGX1‐ILs. Eighteen main‐effect QTLs were identified for the four traits in the two IL populations, and the IR75862 alleles at most loci showed increased and decreased salt tolerance in the ZGX1 and Ce258 backgrounds, suggesting overwhelming genetic background effects on QTL detection for salt tolerance. The qDSS11 simultaneously detected in the two backgrounds was validated in a F₂ population derived from a salt tolerance line and ZGX1. Our results indicated that salt tolerance‐enhancing allele could be identified in the elite susceptible breeding lines and that introgression of the favourable alleles could facilitate the development of superior lines with greater salt tolerance levels.     

Genomewide association study reveals novel quantitative trait loci associated with resistance towards Septoria tritici blotch in North European winter wheat

Fungal diseases are a major constraint for wheat production. Effective disease resistance is essential for ensuring a high production quality and yield. One of the most severe fungal diseases of wheat is Septoria tritici blotch (STB), which influences wheat production across the world. In this study, genomewide association mapping was used to identify new chromosomal regions on the wheat genome conferring effective resistance towards STB. A winter wheat population of 164 North European varieties and breeding lines was genotyped with 15K single nucleotide polymorphism (SNP) wheat array. The varieties were evaluated for STB in field trials at three locations in Denmark and across 3 years. The association analysis revealed four quantitative trait loci, on chromosomes 1B, 2A, 5D and 7A, highly associated with STB resistance. By comparing varieties containing several quantitative trait loci (QTL) with varieties containing none of the found QTL, a significant difference was found in the mean disease score. This indicates that an effective resistance can be obtained by pyramiding several QTL.