Genetic Diversity and Genome-Wide Association Study of Morphological and Quality Traits in Peach Using Two Spanish Peach Germplasm Collections

Abstract

Peach [Prunus persica (L.) Batsch] is one of the most important stone fruits species in world production. Spanish peach production is currently the second largest in the world and the available cultivars in Spain includes a great source of genetic diversity with variability in fruit quality traits and postharvest disorders tolerance. In order to explore the genetic diversity and single nucleotide polymorphism (SNP)-trait associations in the Spanish germplasm, the new peach 18K SNP v2 array was used to genotype 287 accessions belonging to the two National Peach Germplasm Collections placed at the Agrifood Research and Technology Centre of Aragon (CITA) and at the Experimental Station of Aula Dei (EEAD)-CSIC. The high density of the new SNP array allowed the identification of 30 groups of synonymies, which had not been identified before using low-density markers. In addition, a possible large-scale molecular event in ‘Starcrest’, a sport of ‘Springcrest’, was detected showing a possible chromosome replacement of a 13.5 Mb region. Previous suggestions about Spanish diversification regions agreed with our genetic diversity and linkage disequilibrium (LD) decay results using high-density markers. A genome-wide association study (GWAS) detected 34 significant SNP-trait association with the type of leaf glands (TLG), fruit hairiness (FH), and flesh texture (FT). The impact of the significant SNPs was studied with SnpEff. Candidate genes encode several important family proteins involved in trichome formation and powdery mildew resistance (linked to TLG in peach). The genetic distance among cultivars obtained, together with SNP-trait associations found, provide new knowledge for marker-assisted selection and crossing approaches in peach breeding programmes.

ddRAD-seq-derived SNPs reveal novel association signatures for fruit-related traits in peach

“…For this reason, SNP arrays are widely used, reducing the cost and enabling the detection of thousands of SNPs in a single assay 9 . In peach, commercially available arrays IPSC peach 9K 10 and IPSC peach 18K 11 have been used to explore the genetic diversity and to assist the breeding process 1,12 . Despite their utility, the major drawback of SNP genotyping arrays consists in their ascertainment bias 13 .…”

“…Genotype-to-phenotype associations for agronomic and fruit-related traits have been widely tested in peach using different genotyping methods like SSRs 15 , 9K SNP array 1,4,16 , 18K SNP array 3,12 and high-throughput resequencing technology 17 . However, to the best of our knowledge this is the first report characterizing the genetic architecture of peach traits using ddRADseq-derived SNPs.…”