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.

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.

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Single nucleotide polymorphism (SNP) represent a change in a single nucleotide within the genome. This can alter the phenotype of an individual within the same species if it occurs in a coding region of the gene. The change in nucleotide can produce desirable characteristic in plants and can become an object for selection. New SNPs have been discovered and subsequently converted to molecular markers using various non-gel based and next generation sequencing platforms. Considering that SNP markers are based on target genes, its abundance in the genome, high automation and multiplexability, has made it a marker of choice and an effective tool for screening plant germplasm for desirable traits. This chapter considers SNP as molecular marker, their discovery and different SNP genotyping methods was documented. A few case studies of SNP as allele specific markers and their association with traits of interest was considered. Thus, highlighting their efficacy as useful tool for marker assisted selection and plant germplasms screening.

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Cassava is produced globally and consumed as an important staple in Africa for its calories, but the crop is deficient in micronutrients such as vitamin A. Pro-vitamin A carotenoids including β-carotene are precursors of vitamin A in the human body. Carotenoids are generally associated with colors of fruits and vegetables. Although most cassava varieties have white tuberous roots and generally accepted, naturally; some cassava roots are colored yellow and contain negligible amounts of vitamin A. Several genes have been identified in the carotenoids biosynthesis pathway of plants, but studies show that Phytoene synthase 2 (PSY2), lycopene epsilon cyclase, and β-carotene hydroxylase genes have higher expression levels in yellow cassava roots. So far, the PSY2 gene has been identified as the key gene associated with carotenoids in cassava. Some initiatives are implementing conventional breeding to increase pro-vitamin A carotenoids in cassava roots, and much success has been achieved in this regard. This chapter highlights various prediction tools employed for carotenoid content in fresh cassava roots, including molecular marker-assisted strategies developed to fast-track the conventional breeding for increased carotenoids in cassava.