Genome‐Wide Association Mapping of Correlated Traits in Cassava: Dry Matter and Total Carotenoid Content

Abstract

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 megabasescale 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.

Introgressed Manihot glaziovii Alleles in Modern Cassava Germplasm Benefit Important Traits and Are Under Balancing Selection

“…We know from previous studies in cassava, and confirm here (Fig. S9, Table S21), that the introgression regions on chromosomes 1 and 4 are characterized by strong, relatively long-range LD (29, 32). We computed the cumulative genetic size in centimorgans in one megabase windows along each chromosome (Table S21).…”

“…1 (Fig. 5; (32)) seem to explain the higher frequency of those introgression segments in W. Africa, given the breeding emphasis placed there on that trait as well as yield. The chr.…”

“…Though we do not know whether an inversion or other structural variant underlies M. glaziovii introgressions in cassava, we estimated that recombination is clearly reduced in the introgressed regions on chr. 1 and 4 by 14% and 71%, respectively compared to the rest of the genome ((29, 32); Figs. S6 & S9, Table S21).…”

“…Large genome-segments derived from M. glaziovii were recently discovered in a sample of African genotypes, suggesting that historical introgressions remain important today (29). Several other studies have identified QTL in these regions, leading us to hypothesize that M. glaziovii alleles confer CBSD resistance (29–31) and possibly increased storage root dry matter content (32).…”

Genome‐Wide Association Study of Resistance to Cassava Green Mite Pest and Related Traits in Cassava

“…This approach has been particularly useful for mapping major loci for various other traits in cassava. Some of the studied traits include genetic architecture of cassava mosaic disease, which is caused by cassava mosaic geminiviruses in the family Geminiviridae and the genus Begomovirus (Wolfe et al, 2016), b-carotene and dry matter content (Esuma et al, 2016;Rabbi et al, 2017), shoot weight, fresh root yield, starch fraction amylose content, dry matter content, and starch yield (de Oliveira et al, 2012). The current study was conducted aiming to identify genomic regions and single-nucleotide polymorphism (SNPs) linked to CGM resistance and other CGM-related traits in a GWAS panel of 845 advanced breeding lines.…”