Pedigree-Based Analysis in a Multiparental Population of Octoploid Strawberry Reveals QTL Alleles Conferring Resistance to Phytophthora cactorum

• Published in: G3 : genes - genomes - genetics Vol. 7; no. 6; pp. 1707 - 1719
• Main Authors: Mangandi, Jozer, Verma, Sujeet, Osorio, Luis, Peres, Natalia A, van de Weg, Eric, Whitaker, Vance M
• Format: Journal Article
• Language: English
• Published: England Genetics Society of America 01-06-2017; Oxford University Press
• Subjects: Alleles; Breeding; Chromosome Mapping; disease resistance; Disease Resistance - genetics; FaRPc2; FlexQTL; Fragaria; Fragaria - genetics; Fragaria - microbiology; Genetic Linkage; Genotype; haplotype; Haplotype quantitative trait locus; Haplotypes; Host-Pathogen Interactions - genetics; Linkage Disequilibrium; MPP; Multiparental Population; Multiparental Populations; Pedigree; Phenotype; Phytophthora; Plant Diseases - genetics; Plant Diseases - microbiology; Polymorphism, Single Nucleotide; Quantitative Trait Loci; quantitative trait locus; Quantitative Trait, Heritable; Reproducibility of Results; Fragaria; haplotype; disease resistance; FlexQTL; FaRPc2; quantitative trait locus; MPP; Multiparental Populations
• ISSN: 2160-1836; 2160-1836
• DOI: 10.1534/g3.117.042119

Understanding the genetic architecture of traits in breeding programs can be critical for making genetic progress. Important factors include the number of loci controlling a trait, allele frequencies at those loci, and allele effects in breeding germplasm. To this end, multiparental populations offer many advantages for quantitative trait locus (QTL) analyses compared to biparental populations. These include increased power for QTL detection, the ability to sample a larger number of segregating loci and alleles, and estimation of allele effects across diverse genetic backgrounds. Here, we investigate the genetic architecture of resistance to crown rot disease caused by
in strawberry (
×
), using connected full-sib families from a breeding population. Clonal replicates of > 1100 seedlings from 139 full-sib families arising from 61 parents were control-inoculated during two consecutive seasons. Subgenome-specific single nucleotide polymorphism (SNP) loci were mapped in allo-octoploid strawberry (2
= 8 × = 56), and FlexQTL software was utilized to perform a Bayesian, pedigree-based QTL analysis. A major locus on linkage group (LG) 7D, which we name
, accounts for most of the genetic variation for resistance. Four predominant SNP haplotypes were detected in the
region, two of which are strongly associated with two different levels of resistance, suggesting the presence of multiple resistance alleles. The phenotypic effects of
alleles across trials and across numerous genetic backgrounds make this locus a highly desirable target for genetic improvement of resistance in cultivated strawberry.