Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz)

Sequenced 4 candidate carotenoid genes from 167 cassava accessions representing the diversity of elite breeder lines

Abstract

Cassava is a widely grown staple in Sub-Saharan Africa and consumed as a cheap source of calories, but the crop is deficient in micronutrients including pro-vitamin A carotenoids. This challenge is currently being addressed through biofortification breeding that relies on phenotypic selection. Gene-based markers linked to pro-vitamin A content variation are expected to increase the rate of genetic gain for this critical trait.

The authors sequenced 4 candidate carotenoid genes from 167 cassava accessions representing the diversity of elite breeder lines from International Institute of Tropical Agriculture (IITA). Total carotenoid content was determined using spectrophotometer and total β-carotene was quantified by high-performance liquid chromatography. Storage root yellowness due to carotenoid pigmentation was assessed. We carried out candidate gene association analysis that accounts for population structure and kinship using genome-wide single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing. Significant SNPs were used to design competitive allele-specific PCR assays and validated on the larger population for potential use in marker-assisted selection breeding. Candidate gene sequencing of the genes β-carotene hydroxylase (crtRB), phytoene synthase (PSY2), lycopene epsilon cyclase (lcyE), and lycopene beta cyclase (lcyB) yielded a total of 37 SNPs. Total carotenoid content, total β-carotene, and color parameters were significantly associated with markers in the PSY2 gene. The SNPs from lcyE were significantly associated with color while those of lcyB and crtRB were not significantly associated with carotenoids or color parameters. These validated and breeder-friendly markers have potential to enhance the efficiency of selection for high β-carotene cassava, thus accelerating genetic gain.

This work is an output of the HarvestPlus Programme. The Department for International Development is one of the main donors for HarvestPlus.

Citation

Udoh, Lovina I., Melaku Gedil, Elizabeth Y. Parkes, Peter Kulakow, Adenubi Adesoye, Chiamaka Nwuba, and Ismail Y. Rabbi. 2017. Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) Molecular Breeding 37 (10): 123. https://doi.org/10.1007/s11032-017-0718-5.

Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz)

Published 11 September 2017