Identifying SNP markers tightly associated with six major genes in peach [Prunus persica (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS)

Publication Overview
TitleIdentifying SNP markers tightly associated with six major genes in peach [Prunus persica (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS)
AuthorsN/A
TypeJournal Article
Journal NameTree Genetics & Genomes
Volume12
Year2016
Page(s)121
CitationLambert P, Campoy JA, Pacheco I, Mauroux JB, Linge CDS, Micheletti D, Bassi D, Rossini L, Dirlewanger E, Pascal T, Troggio M, Aranzana MJ, Patocchi A, Arús P. Identifying SNP markers tightly associated with six major genes in peach [Prunus persica (L.) Batsch] using a high-density SNP array with an objective of marker-assisted selection (MAS). Tree Genetics & Genomes (2016) 12: 121.

Abstract

One of the applications of genomics is to identify genetic markers linked to loci responsible for variation in phenotypic traits, which could be used in breeding programs to select individuals with favorable alleles, particularly at the seedling stage. With this aim, in the framework of the European project FruitBreedomics, we selected five main peach fruit characters and a resistance trait, controlled by major genes with Mendelian inheritance: fruit flesh color Y, fruit skin pubescence G, fruit shape S, sub-acid fruit D, stone adhesion-flesh texture F-M, and resistance to green peach aphid Rm2. They were all previously mapped in Prunus. We then selected three F1 and three F2 progenies segregating for these characters and developed genetic maps of the linkage groups including the major genes, using the single nucleotide polymorphism (SNP) genome-wide scans obtained with the International Peach SNP Consortium (IPSC) 9K SNP array v1. We identified SNPs co-segregating with the characters in all cases. Their positions were in agreement with the known positions of the major genes. The number of SNPs linked to each of these, as well as the size of the physical regions encompassing them, varied depending on the maps. As a result, the number of useful SNPs for marker-assisted selection varied accordingly. As a whole, this study establishes a sound basis for further development of MAS on these characters. Additionally, we also discussed some limitations that were observed regarding the SNP array efficiency.
Features
This publication contains information about 8 features:
Feature NameUniquenameType
mesocarp colormesocarp color-Yheritable_phenotypic_marker
Non-acid fruitnon-acid fruit-Dheritable_phenotypic_marker
flesh adhesionflesh adhesion-Fheritable_phenotypic_marker
resistance to Myzus persicaeresistance to Myzus persicae-Rm2heritable_phenotypic_marker
fruit hairinessfruit hairiness-Gheritable_phenotypic_marker
fruit shapefruit shape-Sheritable_phenotypic_marker
CPPCT059CPPCT059genetic_marker
EPPISF025EPPISF025genetic_marker
Featuremaps
This publication contains information about 6 maps:
Map Name
Peach-BN-F1
Peach-WB-F2
Peach-JF-F2-2016
Peach-BO-F1
Peach-MR028-F1
Peach-PR-F2