Summary Soya bean is a major source of edible oil and protein for human consumption as well as animal feed. Understanding the genetic basis of different traits in soya bean will provide important insights for improving breeding strategies for this crop. A genome‐wide association study (GWAS) was conducted to accelerate molecular breeding for the improvement of agronomic traits in soya bean. A genotyping‐by‐sequencing (GBS) approach was used to provide dense genome‐wide marker coverage (>47 000 SNPs) for a panel of 304 short‐season soya bean lines. A subset of 139 lines, representative of the diversity among these, was characterized phenotypically for eight traits under six environments (3 sites × 2 years). Marker coverage proved sufficient to ensure highly significant associations between the genes known to control simple traits (flower, hilum and pubescence colour) and flanking SNPs. Between one and eight genomic loci associated with more complex traits (maturity, plant height, seed weight, seed oil and protein) were also identified. Importantly, most of these GWAS loci were located within genomic regions identified by previously reported quantitative trait locus (QTL) for these traits. In some cases, the reported QTLs were also successfully validated by additional QTL mapping in a biparental population. This study demonstrates that integrating GBS and GWAS can be used as a powerful complementary approach to classical biparental mapping for dissecting complex traits in soya bean.

Molecular mapping of cultivated oats was conducted to update the previous reference map constructed using a recombinant inbred (RI) population derived from Avena byzantina C. Koch cv. Kanota x Avena sativa L. cv. Ogle. In the current work, 607 new markers were scored, many on a larger set of RI lines (133 vs. 71) than previously reported. A robust, updated framework map was developed to resolve linkage associations among 286 markers. The remaining 880 markers were placed individually within the most likely framework interval using chi2 tests. This molecular framework incorporates and builds on previous studies, including physical mapping and linkage mapping in additional oat populations. The resulting map provides a common tool for use by oat researchers concerned with structural genomics, functional genomics, and molecular breeding.

Oat (Avena sativa L.) genotypes differ in their patterns of growth and development in response to vernalization (cold temperatures applied to germinating seeds). Genomic regions controlling vernalization response in heading date, plant height, and tiller number were mapped in a recombinant inbred (RI) population derived from the cross of oat cultivars ‘Kanota’ (vernalization‐responsive) and ‘Ogle’ (vernalization‐insensitive).Seventy‐one F6‐derived RI lines were subjected to vernalization and no‐vernalization treatments, and then grown in growth chambers. A genetic linkage map of 561 (primarily RFLP) loci was used to identify quantitativet rait loci (QTLs) affecting the traits in vernalized and non‐vernalized plants. Nine to 16 linkage groups and unlinked loci were associated with each trait assessed herein. Individual loci explained up to 37% of the phenotypic variation. Three to five significant loci were included in multiple locus linear models which explained up to 66% of phenotypic variation for each trait. One to 14 interactions between loci were found for each trait. The interactions explained up to 30% of the phenotypic variation not accounted for by the main effects of loci involved in the interactions. Inclusion of epistatic interactions tended to improve the fit of multiple locus models. As much as 83% of phenotypic variation was explained by multiple locus models including epistasis. Numerous epistatic interactions involving at least one locus with no significant main effect were detected.

In spring-type oat ( Avena sativa L.), quantitative trait loci (QTLs) detected in adapted populations may have the greatest potential for improving germplasm via marker-assisted selection. An F(6) recombinant inbred (RI) population was developed from a cross between two Canadian spring oat varieties: 'Terra', a hulless line, and 'Marion', an elite covered-seeded line. A molecular linkage map was generated using 430 AFLP, RFLP, RAPD, SCAR, and phenotypic markers scored on 101 RI lines. This map was refined by selecting a robust set of 124 framework markers that mapped to 35 linkage groups and contained 35 unlinked loci. One hundred one lines grown in up to 13 field environments in Canada and the United States between 1992 and 1997 were evaluated for 16 agronomic, kernel, and chemical composition traits. QTLs were localized using three detection methods with an experiment-wide error rate of approximately 0.05 for each trait. In total, 34 main-effect QTLs affecting the following traits were identified: heading date, plant height, lodging, visual score, grain yield, kernel weight, milling yield, test weight, thin and plump kernels, groat beta-glucan concentration, oil concentration, and protein. Several of these correspond to QTLs in homologous or homoeologous regions reported in other oat QTL studies. Twenty-four QTL-by-environment interactions and three epistatic interactions were also detected. The locus controlling the covered/hulless character ( N1) affected most of the traits measured in this study. Additive QTL models with N1 as a covariate were superior to models based on separate covered and hulless sub-populations. This approach is recommended for other populations segregating for major genes. Marker-trait associations identified in this study have considerable potential for use in marker-assisted selection strategies to improve traits within spring oat breeding programs.