Construction of genetic linkage map of cassava from Nachinyaya × ar37-80 mapping population using DNA markers

Abstract

Cassava brown streak disease (CBSD) is the major constraint in Cassava (Manihot esculenta) production in Eastern Africa including Tanzania. Genetic linkage map is a pre-requisite for QTL analysis; marker assisted breeding and map-based gene cloning. It is also a prerequisite for the study of inheritance of qualitative and quantitative traits and the molecular information can be applied in marker-assisted selection (MAS).Objectives of this study were to (I) determine heterozygosity of an F1 population from a cross between Nachinyaya (CBSD tolerant) and AR37-80 (CBSD susceptible) using DNA markers and (ii) develop a SNP-based genetic linkage map of F1 hybrid derived from a cross between Nachinyaya and AR37-80 to be used in marker-assisted selection (MAS). The leaf samples were obtained from 271 F1genotypes planted at Makutupora, Tanzania. Genotyping was done at Biosciences Eastern and Central Africa (BecA) laboratory, Nairobi, by screening 26 SSR markers to identify polymorphic markers against the parental genotypes. The F1hybrid integrity was verified to eliminate selfs and off-types using ABI 3730 sequencer and the data analyzed using GeneMapper 4.0 software. Fifteen SSR markers were polymorphic and more informative; however, only 14 markers were used to screen the F1 genotypes. After ABI 3730 sequencing, 257 F1 genotypes were found to be true crosses from the two parents. DNA from the 257 F1 genotypes and the two parents were genotyped at KBioscience using 514 SNP markers. The SNP based genotypic data were used to develop genetic linkage maps using JoinMap ®4.1 computer software. Twenty linkage groups that spanned 1697cM with an average distance between the markers of 3.98cM were developed. A total of 217 new SNP markers were mapped for the first time; the markers were not evenly distributed across the linkage groups. However, the number of markers ranged from one (LG20) to 26 (LG8). The results obtained in this research could be useful to identify QTL in Nachinyaya that is associated with CBSD resistance. Key words: Cassava brown streak disease, Simple sequence repeats, Single nucleotide polymorphism and linkage map.