Allelic variations of LcyE and crtRB1 genes in tropical adapted yellow endosperm maize inbred lines

Abstract

Maize is an important staple cereal crop in sub-Saharan Africa. Tropical-adapted yellow endosperm maize varieties in Africa have low amounts of pro-vitamin A. Use of molecular markers that detect alleles associated with high level of pro-vitamin A can help to improve the pro-vitamin A content in maize through conventional breeding. In this study polymerase chain reaction (PCR) based markers were used to characterize two sets of tropical-adapted yellow endosperm maize inbred lines for allelic variants, present in two carotenoid biosynthesis genes encoding lycopene epsilon cyclase (LcyE) and  -carotene hydroxylase 1 (crtRB1). Frequency of the favourable allele at LcyE 3’TE polymorphism is 29% in Set 1 and 67% in Set 2, and the 5TE was present at frequencies of 24% in S1 and 3.3% in 2. The frequency of the favourable allele at the LcyE SNP216 polymorphism was more than 95% in both the sets of inbred lines. None of the lines included in Set 1 had favourable alleles for crtRB1. On the other hand, in Set 2 the favourable allele in the crtRB1 5TE insertion, had a frequency of 14% whereas the favourable allele-frequency was 11% for crtRB1 3TE and was 1% for InDel4. Twelve maize inbred lines (9.8%) had favourable alleles for crtRB1 3’TE and 5TE in Set 2. None of the maize inbred lines carried favourable alleles for all three crtRB1 polymorphisms. Favourable haplotypes of LcyE and crtRB1 were found together in fifteen (12%) inbred lines.