Abstract
Potato is the fourth most important food crop in the world. Although with a long history for breeding approaches, genomic information and association between genes and agronomic traits remain largely unknown particularly in autotetraploid potato cultivars, which limit the molecular breeding progression. By resequencing the genome of 108 main cultivar potato accessions with rich genetic diversity and population structure from International Potato Center, with approximate 20-fold coverage, we revealed more than 27 million Single Nucleotide Polymorphisms and ~ 3 million Insertion and Deletions with high quality and accuracy. Domestication analysis and genome-wide association studies (GWAS) identified candidate loci related to photoperiodic flowering time and temperature sensitivity as well as disease resistance, providing informative insights into the selection and domestication of cultivar potato. In addition, GWAS with GWASploy for 25 agronomic traits identified candidate loci by association signals, especially those related to tuber size, small-sized tuber weight and tuber thickness that was also validated by transcriptome analysis. Our study provides a valuable resource that facilitates the elucidation of domestication process as well as the genetic studies and agronomic improvement of autotetraploid potato.
Highlights
Potato (Solanum tuberosum L.) is the predominant vegetable crop in the global food system and a critical food crop (Birch et al 2012)
Trimmed reads were mapped to the S. tuberosum group Phureja DM reference genome (Pham et al 2020; Xu et al 2011) for alignment, and GATK (McKenna et al 2010) was used to detect the population SNP (Single Nucleotide Polymorphisms) and InDel (Insertion and Deletion) (Table S2)
We identified 27,565,997 SNPs and 2,961,770 InDels by analyzing these CIP accessions, which lays a good foundation for the selective interval analysis and genome-wide association studies (GWAS) analysis
Summary
Potato (Solanum tuberosum L.) is the predominant vegetable crop in the global food system and a critical food crop (Birch et al 2012). We resequenced 108 core cultivated germplasms of autotetraploid potato from International Potato Center by whole-genome sequencing and revealed the loci associated with the rich genetic diversity by analyzing 25 agronomic traits with GWASploy analysis.
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