Open AccessGenome‐Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content
Author(s) -
Rabbi Ismail Y.,
Udoh Lovina I.,
Wolfe Marnin,
Parkes Elizabeth Y.,
Gedil Melaku A.,
Dixon Alfred,
Ramu Punna,
Jannink JeanLuc,
Kulakow Peter
Publication year - 2017
Publication title -
the plant genome
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.403
H-Index - 41
ISSN - 1940-3372
DOI - 10.3835/plantgenome2016.09.0094
Subject(s) - biology , phytoene synthase , pleiotropy , locus (genetics) , quantitative trait locus , dry matter , genetics , linkage disequilibrium , carotenoid , germplasm , association mapping , biofortification , single nucleotide polymorphism , candidate gene , genetic architecture , botany , gene , phenotype , genotype , micronutrient , chemistry , organic chemistry , lycopene
Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Primary selection objectives in cassava breeding include dry matter content and micronutrient density, particularly provitamin A carotenoids. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering whether linkage and/or pleiotropy were responsible for observed negative correlation. A genome‐wide association mapping using 672 clones genotyped at 72,279 single nucleotide polymorphism (SNP) loci was performed. Root yellowness was used indirectly to assess variation in carotenoid content. Two major loci for root yellowness were identified on chromosome 1 at positions 24.1 and 30.5 Mbp. A single locus for dry matter content that colocated with the 24.1 Mbp peak for carotenoids was identified. Haplotypes at these loci explained 70 and 37% of the phenotypic variability for root yellowness and dry matter content, respectively. Evidence of megabase‐scale linkage disequilibrium (LD) around the major loci of the two traits and detection of the major dry matter locus in independent analysis for the white‐ and yellow‐root subpopulations suggests that physical linkage rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid ( phytoene synthase ) and starch biosynthesis ( UDP‐glucose pyrophosphorylase and sucrose synthase ) occurred in the vicinity of the identified locus at 24.1 Mbp. These findings elucidate the genetic architecture of carotenoids and dry matter in cassava and provide an opportunity to accelerate breeding of these traits.