Genome-wide association mapping to identify genetic loci governing agronomic traits and genomic prediction prospects in tetraploid potatoes

Abstract

Genome-wide association studies (GWAS) and Genomic Prediction (GP) have become powerful tools for examining genetically complex traits in crops. The present study was undertaken on a diverse potato panel of 222 tetraploid potato cultivars and breeding lines, genotyped using genotyping with a sequencing approach to identify 120,622 high-quality single nucleotide polymorphism (SNP) markers. The phenotype data was observed on 12 agronomic traits, including morphological (qualitative) and tuber yield traits (quantitative). The population structure showed three different sub-populations with varying levels of admixtures in them. The LD decay was observed at ∼5Mb distance and GWAS using the Q+K model identified 46 marker-trait associations (MTAs), including 20 associations for tuber morphological traits and rest 26 for tuber yield traits. The average phenotypic variance captured by the associated SNPs was around 10 % for most traits. The putative candidate genes identified for different traits were cytochrome P450 71A4 for flesh color, phytochrome-B and ATP synthase subunit for tuber number, and receptor-like kinases and MYB transcription factor for tuber yield. We did not get any marker trait association for tuber skin color and chip score. The GP accuracy was moderate (0.3–0.5) to high (>0.5) for most of the traits except crisp score, tuber shape and marketable tubers, which recorded low GP accuracy. The reduced marker density did not show any decline in the GP accuracy of different traits. Overall, the study presents the genetic analysis of a diverse panel with information on genetic control and genomic predictions of complex traits for use in genomics-assisted breeding and genomic selection in potatoes.