Genome-wide association mapping of correlated traits in cassava: dry matter and total carotenoid content

Authors: RABBI, ISMAIL - International Institute Of Tropical Agriculture (IITA); UDOH, LOVINA - International Institute Of Tropical Agriculture (IITA); WOLFE, MARNIN - Cornell University; PARKES, ELIZABETH - International Institute Of Tropical Agriculture (IITA); GEDIL, MELAKU - International Institute Of Tropical Agriculture (IITA); DIXON, ALFRED - International Institute Of Tropical Agriculture (IITA); PUNNA, RAMU - Cornell University; Jannink, Jean-Luc; KULAKOW, PETER - International Institute Of Tropical Agriculture (IITA)

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/12/2017
Publication Date: 11/28/2017
Citation: Rabbi, I., Udoh, L., Wolfe, M., Parkes, E., Gedil, M., Dixon, A., Punna, R., Jannink, J., Kulakow, P. 2017. Genome-wide association mapping of correlated traits in cassava: dry matter and total carotenoid content. The Plant Genome. 10(3):1-14.

Interpretive Summary: Cassava is a starchy root crop cultivated in the tropics for fresh consumption and commercial processing. Dry matter content and provitamin A carotenoids are important food quality components. These traits are negatively correlated in the African germplasm. This study aimed at identifying genetic markers associated with these traits and uncovering the mechanism for the observed negative correlation. A genome-wide association mapping using 672 clones genotyped at 72,279 single nucleotide polymorphism (S NP) loci was performed. Root yellowness was used to assess variation in carotenoid content. Two major loci for root yellowness were identified, one of colocated with a locus for dry matter content. Markers at these loci explained 70 and 37% of the phenotypic variability for root yellowness and dry matter content, respectively. We found extensive association between loci in the region suggesting that physical link age rather that pleiotropy is more likely to be the cause of the negative correlation between the target traits. Moreover, candidate genes for carotenoid) and starch biosynthesis occurred in the vicinity of the identified locus. These findings provide an opportunity to accelerate breeding of these traits.

Technical 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 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.