Genomic selection for fruit quality traits in apple (Malus×domestica Borkh.).

PloS One
Satish KumarCharmaine Carlisle

Abstract

The genome sequence of apple (Malus×domestica Borkh.) was published more than a year ago, which helped develop an 8K SNP chip to assist in implementing genomic selection (GS). In apple breeding programmes, GS can be used to obtain genomic breeding values (GEBV) for choosing next-generation parents or selections for further testing as potential commercial cultivars at a very early stage. Thus GS has the potential to accelerate breeding efficiency significantly because of decreased generation interval or increased selection intensity. We evaluated the accuracy of GS in a population of 1120 seedlings generated from a factorial mating design of four females and two male parents. All seedlings were genotyped using an Illumina Infinium chip comprising 8,000 single nucleotide polymorphisms (SNPs), and were phenotyped for various fruit quality traits. Random-regression best liner unbiased prediction (RR-BLUP) and the Bayesian LASSO method were used to obtain GEBV, and compared using a cross-validation approach for their accuracy to predict unobserved BLUP-BV. Accuracies were very similar for both methods, varying from 0.70 to 0.90 for various fruit quality traits. The selection response per unit time using GS compared with the traditio...Continue Reading

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Citations

Apr 5, 2014·PloS One·David ChagnéRiccardo Velasco
Dec 19, 2013·TheScientificWorldJournal·Abhishek Bohra
Jun 14, 2013·BMC Genomics·Satish KumarRichard K Volz
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Apr 8, 2020·Horticulture Research·Satish KumarClaire Molloy

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Methods Mentioned

BETA
genotyping
chip
Assay

Software Mentioned

GOLD
RR
BEAGLE
Illumina® GenomeStudio software
LASSO
BLR package
ClusterSep
BLUP
ASReml
R

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