Peach (Prunus persica (L.) Batsch) is one of the most produced and studied stone fruits. Many genetic and genomic resources are available for this species, including a high-quality genome. More recently, a new high-density Illumina peach Single Nucleotide Polymorphism (SNP) chip (9+9K) has been developed by an international consortium as an add-on to the previous 9K array. In the current study, this new array was used to study the genetic diversity and population structure of the National Peach Germplasm Collection of the Agrifood Research and Technology Centre of Aragon (CITA), located in Zaragoza (northern Spain). To accomplish this, 90 peach accessions were genotyped using the new peach SNP chip (9+9K). A total of 9796 SNPs were finally selected for genetic analyses. Through Identity-By-Descent (IBD) estimate analysis, 15 different groups with genetically identical individuals were identified. The genetic diversity and population structure elucidated a possible exchange of germplasm material among regions, mainly in the northern regions of Spain. This study will allow for more efficient management of the National Peach Germplasm Collection by classifying valuable individuals for genetic diversity preservation and will benefit forthcoming Genome-Wide Association Studies (GWAS) of commercially important fruit traits in peach.

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.

Expression quantitative trait loci (eQTL), are associations between genetic variants, such as Single Nucleotide Polymorphisms (SNPs), and gene expression. eQTLs are an important tool to understand the genetics of gene expression of complex phenotypes. eQTLs analysis are common in human studies and in model species such as mice, rats and yeast but are very scarce in wood crop species such as fruit trees or grapevines. In this study a comprehensive bioinformatic pipeline has been carried out using genomics and expression data from 10 genotypes of grape, which has been used as model species. As a result of this study a total of 10618 genetic variants that regulate gene expression levels of 525 genes were detected. A 78% of them, 411, received a functional annotation from UniProtKB or DAVID, some of the annotated protein-coding genes are Germin-like proteins (GLPs), auxin-regulatory factors, GRFS, ANK_REP_REGION domain-containing protein, Kinesin motor domain-containing protein and RPP13like protein 2(LOC100852873). This new inventory of cis eQTLs influencing gene expression during the ripening of fruits of Vitis vinifera L. will be an important resource for future research to understand the mechanistic basis for variation in gene regulation in this species. In the future, this methodology may be applied to other woody species, once the necessary databases are generated.

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