A Whole Genome Association Study in Mandarin Hybrids
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AuthorTerol, Javier; Borredá, Carles; Pérez-Román, Estela; González-Ibeas, Daniel; Ibanez, Victoria; Tadeo, Francisco R.; Talón, Manuel
Cita bibliográficaTerol, J., Borredá, C., Pérez-Román, E., Gonzalez-Ibeas, D., Ibaņez, V., Tadeo, F. R., & Talon, M. (2020). A Whole Genome Association Study in Mandarin Hybrids. In: Plant and Animal Genome XXVIII Conference (January 11-15, 2020).
A segregating population of 667 hybrids from a cross between Clemenules x Nadorcott has been established in three different locations in Spain. The population has been genotyped by sequencing (GBS) and phenotyping is in its second year. The data will be used to obtain markers useful for marker assisted breeding. This phenotyping protocol will focus in the main traits related to vegetative and reproductive stages, with special attention to fruit quality and productivity, as well as efficiency in the use of water, resistance to heat waves or the presence of symptoms of biotic and abiotic stresses. We will use these data to perform genome wide association studies, that will include the following steps: definition of phenotypes (quantitative vs. presence/absence), filtering of samples with Low Call Rate, studies of stratification of the population (Structure), quality of the SNPs (call rate, frequency of the minor allele), statistical analysis (Additive Model, Mixed Linear Model, Multi-Locus Model Analysis), correlation studies, Manhattan plots (P value), selection of significant SNPs, and study of genomic regions and nearby genes. The GBS has produced a total of 11103 SNPs useful for GWAS and some phenotyping data are already available. Some preliminary results will be shown.