Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.)

Key message

This report describes an integrative analysis of seed-oil-content quantitative trait loci (QTL) in Brassica napus , using a high-density genetic map to align QTL among different populations.

Abstract

Rapeseed (Brassica napus) is an important source of edible oil and sustainable energy. Given the challenge involved in using only a few genes to substantially increase the oil content of rapeseed without affecting the fatty acid composition, exploitation of a greater number of genetic loci that regulate the oil content variation among rapeseed germplasm is of fundamental importance. In this study, we investigated variation in the seed-oil content among two related genetic populations of Brassica napus, the TN double-haploid population and its derivative reconstructed-F₂ population. Each population was grown in multiple experiments under different environmental conditions. Mapping of quantitative trait loci (QTL) identified 41 QTL in the TN populations. Furthermore, of the 20 pairs of epistatic interaction loci detected, approximately one-third were located within the QTL intervals. The use of common markers on different genetic maps and the TN genetic map as a reference enabled us to project QTL from an additional three genetic populations onto the TN genetic map. In summary, we used the TN genetic map of the B. napus genome to identify 46 distinct QTL regions that control seed-oil content on 16 of the 19 linkage groups of B. napus. Of these, 18 were each detected in multiple populations. The present results are of value for ongoing efforts to breed rapeseed with high oil content, and alignment of the QTL makes an important contribution to the development of an integrative system for genetic studies of rapeseed.     

Molecular cytogenetic identification of B genome chromosomes linked to blackleg disease resistance in Brassica napus × B. carinata interspecific hybrids

Key message

Provide evidence that the Brassica B genome chromosome B3 carries blackleg resistance gene, and also the B genome chromosomes were inherited several generations along with B. napus chromosomes.

Abstract

Blackleg disease caused by fungus Leptosphaeria maculans causes significant yield losses in Brassica napus. Brassica carinata possesses excellent resistance to this disease. To introgress blackleg resistance, crosses between B. napus cv. Westar and B. carinata were done. The interspecific-hybrids were backcrossed twice to Westar and self-pollinated three times to produce BC₂S₃ families. Doubled haploid lines (DH1) were produced from one blackleg resistant family. SSR markers were used to study the association between B genome chromosome(s) and blackleg resistance. The entire B3 chromosome of B. carinata was associated with blackleg resistance in DH1. A second DH population (DH2) was produced from F₁s of resistant DH1 lines crossed to blackleg susceptible B. napus cv. Polo where resistance was found to be associated with SSR markers from the middle to bottom of the B3 and top of the B8 chromosomes. The results demonstrated that the B3 chromosome carried gene(s) for blackleg resistance. Genomic in situ hybridization (GISH) and GISH-like analysis of the DH2 lines revealed that susceptible lines, in addition to B. napus chromosomes, possessed one pair of B genome chromosomes (2n = 40), while resistant lines had either one (2n = 40) or two pairs (2n = 42) of B chromosomes. The molecular and GISH data suggested that the B chromosome in the susceptible lines was B7, while it was difficult to confirm the identity of the B chromosomes in the resistant lines. Also, B chromosomes were found to be inherited over several generations along with B. napus chromosomes.     

Genetic analyses of bolting in bulb onion (Allium cepa L.)

Key message

We present the first evidence for a QTL conditioning an adaptive trait in bulb onion, and the first linkage and population genetics analyses of candidate genes involved in photoperiod and vernalization physiology.

Abstract

Economic production of bulb onion (Allium cepa L.) requires adaptation to photoperiod and temperature such that a bulb is formed in the first year and a flowering umbel in the second. ‘Bolting’, or premature flowering before bulb maturation, is an undesirable trait strongly selected against by breeders during adaptation of germplasm. To identify genome regions associated with adaptive traits we conducted linkage mapping and population genetic analyses of candidate genes, and QTL analysis of bolting using a low-density linkage map. We performed tagged amplicon sequencing of ten candidate genes, including the FT-like gene family, in eight diverse populations to identify polymorphisms and seek evidence of differentiation. Low nucleotide diversity and negative estimates of Tajima’s D were observed for most genes, consistent with purifying selection. Significant population differentiation was observed only in AcFT2 and AcSOC1. Selective genotyping in a large ‘Nasik Red × CUDH2150’ F₂ family revealed genome regions on chromosomes 1, 3 and 6 associated (LOD > 3) with bolting. Validation genotyping of two F₂ families grown in two environments confirmed that a QTL on chromosome 1, which we designate AcBlt1, consistently conditions bolting susceptibility in this cross. The chromosome 3 region, which coincides with a functionally characterised acid invertase, was not associated with bolting in other environments, but showed significant association with bulb sucrose content in this and other mapping pedigrees. These putative QTL and candidate genes were placed on the onion map, enabling future comparative studies of adaptive traits.     

Construction of an integrative linkage map and QTL mapping of grain yield-related traits using three related wheat RIL populations

Key message

A novel high-density consensus wheat genetic map was obtained based on three related RIL populations, and the important chromosomal regions affecting yield and related traits were specified.

Abstract

A prerequisite for mapping quantitative trait locus (QTL) is to build a genetic linkage map. In this study, three recombinant inbred line populations (represented by WL, WY, and WJ) sharing one common parental line were used for map construction and subsequently for QTL detection of yield-related traits. PCR-based and diversity arrays technology markers were screened in the three populations. The integrated genetic map contains 1,127 marker loci, which span 2,976.75 cM for the whole genome, 985.93 cM for the A genome, 922.16 cM for the B genome, and 1,068.65 cM for the D genome. Phenotypic values were evaluated in four environments for populations WY and WJ, but three environments for population WL. Individual and combined phenotypic values across environments were used for QTL detection. A total of 165 putative additive QTL were identified, 22 of which showed significant additive-by-environment interaction effects. A total of 65 QTL (51.5 %) were stable across environments, and 23 of these (35.4 %) were common stable QTL that were identified in at least two populations. Notably, QTkw-5B.1, QTkw-6A.2, and QTkw-7B.1 were common major stable QTL in at least two populations, exhibiting 11.28–16.06, 5.64–18.69, and 6.76–21.16 % of the phenotypic variance, respectively. Genetic relationships between kernel dimensions and kernel weight and between yield components and yield were evaluated. Moreover, QTL or regions that commonly interact across genetic backgrounds were discussed by comparing the results of the present study with those of previous similar studies. The present study provides useful information for marker-assisted selection in breeding wheat varieties with high yield.     

QTL mapping for salt tolerance and domestication-related traits in Vigna marina subsp. oblonga,a halophytic species

Key message

QTL mapping in F ₂ population [ V. luteola × V. marina subsp. oblonga ] revealed that the salt tolerance in V. marina subsp. oblonga is controlled by a single major QTL.

Abstract

The habitats of beach cowpea (Vigna marina) are sandy beaches in tropical and subtropical regions. As a species that grows closest to the sea, it has potential to be a gene source for breeding salt-tolerant crops. We reported here for the first time, quantitative trait loci (QTLs) mapping for salt tolerance in V. marina. A genetic linkage map was constructed from an F₂ population of 120 plants derived from an interspecific cross between V. luteola and V. marina subsp. oblonga. The map comprised 150 SSR markers. The markers were clustered into 11 linkage groups spanning 777.6 cM in length with a mean distance between the adjacent markers of 5.59 cM. The F_2:3 population was evaluated for salt tolerance under hydroponic conditions at the seedling and developmental stages. Segregation analysis indicated that salt tolerance in V. marina is controlled by a few genes. Multiple interval mapping consistently identified one major QTL which can explain about 50 % of phenotypic variance. The flanking markers may facilitate transfer of the salt tolerance allele from V. marina subsp. oblonga into related Vigna crops. The QTL for domestication-related traits from V. marina are also discussed.     

Novel and major QTL for branch angle detected by using DH population from an exotic introgression in rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.)

Key message

A high-density SNP map was constructed and several novel QTL for branch angle across six environments in Brassica napus were identified.

Abstract

Branch angle is a major determinant for the ideotype of a plant, while the mechanisms underlying this trait in Brassica napus remain elusive. Herein, we developed one doubled haploid population from a cross involving one Capsella bursa-pastoris derived B. napus intertribal introgression line with the compressed branches and wooden stems, and constructed a high-density SNP map covering the genetic distance of 2242.14 cM, with an average marker interval of 0.73 cM. After phenotypic measurements across six environments, the inclusive composite interval mapping algorithm was conducted to analyze the QTL associated with branch angle. In single-environment analysis, a total of 17 QTL were detected and mainly distributed on chromosomes A01, A03, A09 and C03. Of these, three major QTL, qBA.A03-2, qBA.C03-3 and qBA.C03-4 were steadily expressed, each explaining more than 10% of the phenotypic variation in at least two environments. Compared with other results on rapeseed branch angle, these major QTL were newly detected. In QTL by environment interactions (QEI) mapping, 10 QTL were identified, and the QTL average effect and QEI effect were estimated. Of these, 7 QTL were detected in both single-environment analysis and QEI mapping. Based on the physical positions of SNPs and the functional annotation of the Arabidopsis thaliana genome, 27 genes within the QTL regions were selected as candidate genes, including early auxin-responsive genes, small auxin-up RNA, auxin/indoleacetic acid and gretchenhagen-3. These results may pave the way for deciphering the genetic control of branch angle in B. napus.

     

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

Background

The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available.

Results

We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa.

Conclusions

Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.     

Identification of putative quantitative trait loci associated with a flavonoid related to resistance to cabbage seedpod weevil (Ceutorhynchus obstrictus) in canola derived from an intergeneric cross,Sinapis alba × Brassica napus

Key message

Kaempferol 3- O -sinapoyl-sophoroside 7- O -glucoside was putatively identified as the major component of a characteristic HPLC peak previously correlated with the reduction of cabbage seedpod weevil larval infestation in a novel canola genotype.

Abstract

The cabbage seedpod weevil (Ceutorhynchus obstrictus [Marsham]) (CSPW) is a serious pest of brassicaceous oilseed crops such as canola in both Europe and more recently in North America. At present, the only control strategy against CSPW is the application of insecticides. As an alternative more environmentally-friendly control strategy, we developed novel canola germplasm resistant to weevil attack through introgression of Sinapis alba DNA into Brassica napus by making the wide cross followed by embryo rescue and backcrossing to the B. napus parent. We have previously characterized resistant canola lines by metabolic profiling and were able to correlate reduction of larval infestation to the presence of a characteristic HPLC peak. In this study, we have putatively identified the major component in the peak using mass spectrometry as kaempferol 3-O-sinapoyl-sophoroside 7-O-glucoside (KSSG). We have also identified quantitative trait loci (QTL) associated with this HPLC peak in a mapping population consisting of more than 200 individual doubled haploid (DH) lines derived from a cross between CSW428 (the resistant parent) and SC030686 (the susceptible parent). This QTL accounted for approximately 9.5 % of the phenotypic variation in KSSG content. The observation that only one QTL was identified as surpassing the LOD threshold of 3.0 suggests that both parents may possess the positive alleles for other QTL that have not been detected in our study. This finding also indicates a complex regulatory mechanism for KSSG levels and provides an appropriate explanation for the large transgressive segregation observed in the DH lines of the QTL mapping population.     

QTL mapping of domestication and diversifying selection related traits in round-fruited semi-wild Xishuangbanna cucumber (<Emphasis Type="Italic">Cucumis sativus</Emphasis> L. var. <Emphasis Type="Italic">xishuangbannanesis</Emphasis>)

Key message

QTL analysis revealed 11 QTL underlying flowering time and fruit size variation in the semi-wild Xishuangbanna cucumber, of which, FT6.2 and FS5.2 played the most important roles in determining photoperiod-dependent flowering time and round-fruit shape, respectively.

Abstract

Flowering time and fruit size are two important traits in domestication and diversifying selection in cucumber, but their genetic basis is not well understood. Here we reported QTL mapping results on flowering time and fruit size with F₂ and F_2:3 segregating populations derived from the cross between WI7200, a small fruited, early flowering primitive cultivated cucumber and WI7167, a round-fruited, later flowering semi-wild Xishuangbanna (XIS) cucumber. A linkage map with 267 microsatellite marker loci was developed with 138 F₂ plants. Phenotypic data of male and female flowering time, fruit length and diameter and three other traits (mature fruit weight and number, and seedling hypocotyl length) were collected in multiple environments. Three flowering time QTL, FT1.1, FT5.1 and FT6.2 were identified, in which FT6.2 played the most important role in conferring less photoperiod sensitive early flowering during domestication whereas FT1.1 seemed more influential in regulating flowering time within the cultivated cucumber. Eight consensus fruit size QTL distributed in 7 chromosomes were detected, each of which contributed to both longitudinal and radial growth in cucumber fruit development. Among them, FS5.2 on chromosome 5 exhibited the largest effect on the determination of round fruit shape that was characteristic of the WI7167 XIS cucumber. Possible roles of these flowering time and fruit size QTL in domestication of cucumber and crop evolution of the semi-wild XIS cucumber, as well as the genetic basis of round fruit shape in cucumber are discussed.

     

Mapping of days to flower and seed yield in spring oilseed <Emphasis Type="Italic">Brassica napus</Emphasis> carrying genome content introgressed from <Emphasis Type="Italic">Brassica oleracea</Emphasis>

Earliness of flowering and maturity and high seed yield are important objectives of breeding spring Brassica napus canola. Previously, we have introgressed earliness of flowering from Brassica oleracea into spring B. napus canola through interspecific crossing between these two species. In this paper, we report quantitative trait locus (QTL) mapping of days to flower and seed yield by use of publicly available markers and markers designed based on flowering time genes and a doubled haploid population, derived from crossing of the spring canola parent and an early flowering line developed from a B. napus × B. oleracea cross, tested in nine field trials for over 5 years. Five genomic regions associated with days to flower were identified on C1, C2, C3, and C6 of which the single QTL of C1 was detected in all trials; in all cases, the allele introgressed from B. oleracea reduced the number of days to flower. BLASTn search in the Brassica genomes located the physical position of the QTL markers and identified putative flowering time genes in these regions. In the case of seed yield, ten QTL from eight linkage groups were detected; however, none could be consistently detected in all trials. The QTL region of C1 associated with days to flower did not show significant association with seed yield in more than 80% of the field trials; however, in a single trial, the allele introgressed from B. oleracea exerted a negative effect on seed yield. Thus, the genomic regions and molecular markers identified in this research could potentially be used in breeding for the development of early flowering B. napus canola cultivars without affecting seed yield in a majority of the environments.     

QTL for resistance to root lesion nematode (Pratylenchus thornei) from a synthetic hexaploid wheat source

Key message

A whole genome average interval mapping approach identified eight QTL associated with P. thornei resistance in a DH population from a cross between the synthetic-derived wheat Sokoll and cultivar Krichauff.

Abstract

Pratylenchus thornei are migratory nematodes that feed and reproduce within the wheat root cortex, causing cell death (lesions) resulting in severe yield reductions globally. Genotypic selection using molecular markers closely linked to Pratylenchus resistance genes will accelerate the development of new resistant cultivars by reducing the need for laborious and expensive resistance phenotyping. A doubled haploid wheat population (150 lines) from a cross between the synthetic-derived cultivar Sokoll (P. thornei resistant) and cultivar Krichauff (P. thornei moderately susceptible) was used to identify quantitative trait loci (QTL) associated with P. thornei resistance. The resistance identified in the glasshouse was validated in a field trial. A genetic map was constructed using Diversity Array Technology and the QTL regions identified were further targeted with simple sequence repeat (SSR) and single-nucleotide polymorphism (SNP) markers. Six significant and two suggestive P. thornei resistance QTL were detected using a whole genome average interval mapping approach. Three QTL were identified on chromosome 2B, two on chromosome 6D, and a single QTL on each of chromosomes 2A, 2D and 5D. The QTL on chromosomes 2BS and 6DS mapped to locations previously identified to be associated with Pratylenchus resistance. Together, the QTL on 2B (QRlnt.sk-2B.1–2B.3) and 6D (QRlnt.sk-6D.1 and 6D.2) explained 30 and 48 % of the genotypic variation, respectively. Flanking PCR-based markers based on SSRs and SNPs were developed for the major QTL on 2B and 6D and provide a cost-effective high-throughput tool for marker-assisted breeding of wheat with improved P. thornei resistance.     

Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example

Key message

A comprehensive linkage atlas for seed yield in rapeseed.

Abstract

Most agronomic traits of interest for crop improvement (including seed yield) are highly complex quantitative traits controlled by numerous genetic loci, which brings challenges for comprehensively capturing associated markers/genes. We propose that multiple trait interactions underlie complex traits such as seed yield, and that considering these component traits and their interactions can dissect individual quantitative trait loci (QTL) effects more effectively and improve yield predictions. Using a segregating rapeseed (Brassica napus) population, we analyzed a large set of trait data generated in 19 independent experiments to investigate correlations between seed yield and other complex traits, and further identified QTL in this population with a SNP-based genetic bin map. A total of 1904 consensus QTL accounting for 22 traits, including 80 QTL directly affecting seed yield, were anchored to the B. napus reference sequence. Through trait association analysis and QTL meta-analysis, we identified a total of 525 indivisible QTL that either directly or indirectly contributed to seed yield, of which 295 QTL were detected across multiple environments. A majority (81.5%) of the 525 QTL were pleiotropic. By considering associations between traits, we identified 25 yield-related QTL previously ignored due to contrasting genetic effects, as well as 31 QTL with minor complementary effects. Implementation of the 525 QTL in genomic prediction models improved seed yield prediction accuracy. Dissecting the genetic and phenotypic interrelationships underlying complex quantitative traits using this method will provide valuable insights for genomics-based crop improvement.

     

QTL-seq identifies an early flowering QTL located near Flowering Locus T in cucumber

Key message

Next-generation sequencing enabled a fast discovery of a major QTL controlling early flowering in cucumber, corresponding to the FT gene conditioning flowering time in Arabidopsis.

Abstract

Next-generation sequencing technologies are making it faster and more efficient to establish the association of agronomic traits with molecular markers or candidate genes, which is the requirement for marker-assisted selection in molecular breeding. Early flowering is an important agronomic trait in cucumber (Cucumis sativus L.), but the underlying genetic mechanism is unknown. In this study, we identified a candidate gene for early flowering QTL, Ef1.1 through QTL-seq. Segregation analysis in F₂ and BC₁ populations derived from a cross between two inbred lines “Muromskij” (early flowering) and “9930” (late flowering) suggested quantitative nature of flowering time in cucumber. Genome-wide comparison of SNP profiles between the early and late-flowering bulks constructed from F₂ plants identified a major QTL, designated Ef1.1 on cucumber chromosome 1 for early flowering in Muromskij, which was confirmed by microsatellite marker-based classical QTL mapping in the F₂ population. Joint QTL-seq and traditional QTL analysis delimited Ef1.1 to an 890 kb genomic region. A cucumber gene, Csa1G651710, was identified in this region, which is a homolog of the FLOWERING LOCUS T (FT), the main flowering switch gene in Arabidopsis. Quantitative RT-PCR study of the expression level of Csa1G651710 revealed significantly higher expression in early flowering genotypes. Data presented here provide support for Csa1G651710 as a possible candidate gene for early flowering in the cucumber line Muromskij.     

Development of a complete set of monosomic alien addition lines between Brassica napus and Isatis indigotica (Chinese woad)

Key message

A complete set of monosomic alien addition lines of Brassica napus with one of the seven chromosomes of Isatis indigotica and the recombinant mitochondria was developed and characterized.

Abstract

Monosomic alien addition lines (MAALs) are valuable for elucidating the genome structure and transferring the useful genes and traits in plant breeding. Isatis indigotica (Chinese woad, 2n = 14, II) in Isatideae tribe of Brassicaceae family has been widely cultivated as a medicinal and dye plant in China. Herein, the intertribal somatic hybrid (2n = 52, AACCII) between B. napus cv. Huashuang 3 (2n = 38, AACC) and I. indigotica produced previously was backcrossed recurrently to parental B. napus, and 32 MAAL plants were isolated. Based on their phenotype, 5S and 45S rDNA loci and chromosome-specific SSR markers, these MAALs were classified into seven groups corresponding to potential seven types of MAALs carrying one of the seven I. indigotica chromosomes. One of the MAALs could be distinguishable by expressing the brown anthers of I. indigotica, other two hosted the chromosome with 5S or 45S rDNA locus, but the remaining four were identifiable by SSR markers. The simultaneous detection of the same SSR maker and gene locus in different MAALs revealed the paralogs on the chromosomes involved. The recombinant mitochondrial genome in MAALs was likely related with their male sterility with carpellody stamens, while the MAAL with normal brown anthers probably carried the restoring gene for the male sterility. The complete set of MAALs should be useful for exploiting the I. indigotica genome and for promoting the introgression of valuable genes to B. napus.     

Genome-wide QTL and bulked transcriptomic analysis reveals new candidate genes for the control of tuber carotenoid content in potato (Solanum tuberosum L.)

Key message

Genome-wide QTL analysis of potato tuber carotenoid content was investigated in populations of Solanum tuberosum Group Phureja that segregate for flesh colour, revealing a novel major QTL on chromosome 9.

Abstract

The carotenoid content of edible plant storage organs is a key nutritional and quality trait. Although the structural genes that encode the biosynthetic enzymes are well characterised, much less is known about the factors that determine overall storage organ content. In this study, genome-wide QTL mapping, in concert with an efficient ‘genetical genomics’ analysis using bulked samples, has been employed to investigate the genetic architecture of potato tuber carotenoid content. Two diploid populations of Solanum tuberosum Group Phureja were genotyped (AFLP, SSR and DArT markers) and analysed for their tuber carotenoid content over two growing seasons. Common to both populations were QTL that explained relatively small proportions of the variation in constituent carotenoids and a major QTL on chromosome 3 explaining up to 71 % of the variation in carotenoid content. In one of the populations (01H15), a second major carotenoid QTL was identified on chromosome 9, explaining up to 20 % of the phenotypic variation. Whereas the major chromosome 3 QTL was likely to be due to an allele of a gene encoding β-carotene hydroxylase, no known carotenoid biosynthetic genes are located in the vicinity of the chromosome 9 QTL. A unique expression profiling strategy using phenotypically distinct bulks comprised individuals with similar carotenoid content provided further support for the QTL mapping to chromosome 9. This study shows the potential of using the potato genome sequence to link genetic maps to data arising from eQTL approaches to enhance the discovery of candidate genes underlying QTLs.     

Highly efficient genotyping of rice biparental populations by GoldenGate assays based on parental resequencing

Key message

A new time- and cost-effective strategy was developed for medium-density SNP genotyping of rice biparental populations, using GoldenGate assays based on parental resequencing.

Abstract

Since the advent of molecular markers, crop researchers and breeders have dedicated huge amounts of effort to detecting quantitative trait loci (QTL) in biparental populations for genetic analysis and marker-assisted selection (MAS). In this study, we developed a new time- and cost-effective strategy for genotyping a population of progeny from a rice cross using medium-density single nucleotide polymorphisms (SNPs). Using this strategy, 728,362 “high quality” SNPs were identified by resequencing Teqing and Lemont, the parents of the population. We selected 384 informative SNPs that were evenly distributed across the genome for genotyping the biparental population using the Illumina GoldenGate assay. 335 (87.2 %) validated SNPs were used for further genetic analyses. After removing segregation distortion markers, 321 SNPs were used for linkage map construction and QTL mapping. This strategy generated SNP markers distributed more evenly across the genome than previous SSR assays. Taking the GW5 gene that controls grain shape as an example, our strategy provided higher accuracy (0.8 Mb) and significance (LOD 5.5 and 10.1) in QTL mapping than SSR analysis. Our study thus provides a rapid and efficient strategy for genetic studies and QTL mapping using SNP genotyping assays.