Identification and Molecular Analysis of Pro-vitamin A Carotenoid Genes in Cassava ( Manihot esculenta Crantz)

Cassava is one of the most important sources of calories in the tropics and consumed as a staple food. Several cassava varieties are deficient in vitamin A. The present work is envisaged towards the genetic improvement of carotenoid content in cassava, by identifying single nucleotide polymorphism (SNP) attributed to variation in carotenoid concentration among some cassava genotypes. Phytoene synthase (PSY), β-carotene hydroxylase (HYD), lycopene β and e cyclase (LYCB and LYCE), have been found to play a role in increasing levels of β-carotene in plants. A total of 40 lines with varying total carotene content were drawn from a cassava recurrent selection breeding program.  Primers for HYD, LYCB, LYCE, and PSY genes designed from cassava ESTs were used to genotype the cassava lines. Amplified PCR products were purified and sequenced. A total of 169 polymorphisms were detected among the sequences under study both in the coding and non-coding regions of the genes. Analysis of SNPs in relation to carotene content of each accession revealed a variation G/T at 1295 th position of the LYCE reference gene that caused an amino acid exchange from tryptophan (Trp) to leucine (leu) in a high carotene line 07/0593. High total carotene lines recorded the highest number of polymorphism with 42%of entire polymorphisms observed. This indicates that if the whole gene is sequenced unique polymorphisms associated with high carotene cassava can be retrieved for marker development to aid selection for high carotenoid containing cassava germplasm.