Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios.
Infinium 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.
Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy. giorgiotumino@hotmail.it.|Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands. giorgiotumino@hotmail.it.
Giorgio
G
Tumino
Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
Roeland E
RE
Voorrips
Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
Fulvia
F
Rizza
Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
Franz W
FW
Badeck
Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
Caterina
C
Morcia
Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
Roberta
R
Ghizzoni
Julius Kühn Institut, Federal Research Centre for Cultivated Plants, Institute for Breeding Research on Agricultural Crops, 06484, Quedlinburg, Germany.
Christoph U
CU
Germeier
Biometris, Wageningen UR, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
Maria-João
MJ
Paulo
Council for Agricultural Research and Economics, Genomics Research Centre, Via San Protaso 302, 29017, Fiorenzuola d'Arda, PC, Italy.
Valeria
V
Terzi
Wageningen UR Plant Breeding, Droevendaalsesteeg 1, NL-6708 PB, Wageningen, The Netherlands.
Marinus J M
MJ
Smulders
D018554:Avena / Q000235:genetics*; D002874:Chromosome Mapping; D005615:Freezing; D056726:Genetic Association Studies; D005828:Genetics, Population; D005838:Genotype; D008957:Models, Genetic; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci