Abstract
Key messageInfinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option.Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward’s clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2734-y) contains supplementary material, which is available to authorized users.
Highlights
Hexaploid oat (Avena sativa L.) is an important crop grown on nearly 10 million hectares worldwide (FAOSTAT 2015) mostly in temperate regions in a wide range of environmental conditions
The objectives of the work were: (1) to study genetic diversity in European oat germplasm, (2) to show the feasibility of Genome-Wide Association Study (GWAS) based on continuous SNP signal ratios in a collection including heterogeneous samples for simple traits such as lemma color and hullessness, whose phenotypic variation is explained by few major genes, (3) to use GWAS and chlorophyll fluorescence data for identifying QTLs affecting frost tolerance in oat
Five diploid A. strigosa accessions were included in a first Principal Component Analysis (PCA) and removed from the following analyses, as they clearly clustered far from hexaploid oat samples
Summary
Hexaploid oat (Avena sativa L.) is an important crop grown on nearly 10 million hectares worldwide (FAOSTAT 2015) mostly in temperate regions in a wide range of environmental conditions. Gene banks preserve about 80,000 accessions of cultivated oats and more than 20,000 wild oats. This germplasm can be considered a reservoir of potentially useful genes, to be exploited in pre-breeding and breeding programs (Lipman et al 2005). An important trait for oat, to which much (pre-) breeding is devoted, is tolerance to frost. Oat is the most frost sensitive and its insufficient level of winter hardiness. Theor Appl Genet (2016) 129:1711–1724 is one of the most important factors limiting the cultivation of winter oat in cold areas. Winter oats have a long growth cycle and early maturity, and give higher yields
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