Construction of two genetic linkage maps of taro using single nucleotide polymorphism and microsatellite markers

Abstract

Linkage maps are needed for genetic studies and molecular breeding of taro (Colocasia esculenta). In this study, we used genotyping-by-sequencing (GBS) to identify single nucleotide polymorphism (SNP) loci on two mapping populations: F31 (HLB11 × VU006) composed of 266 progenies and F32 [HLB01 × (VU370×ID316)] composed of 292 progenies. SNP calling generated an initial set of 22,734 SNPs for F31 and 16,744 for F32. A large proportion of individuals and loci were later removed by filtering on the proportion of missing data and segregation distortions. Linkage maps were constructed with filtered SNPs in association with 14 simple sequence repeat (SSR) markers, using the maximum likelihood method. In both populations, loci were successfully grouped into 14 linkage groups (LGs) with an independence logarithm of odds (LOD) threshold of 11.0 and 8.0 for F31 and F32, respectively. LGs ranged in size from 90 to 15 markers for F31 and from 92 to 12 markers for F32. Bridge markers (459 SNPs and 9 SSRs) were identified and revealed homologous groups between families. Although our maps presented unprecedented chromosome coverage, the colinearity between homologous groups was low (except for LG07), and map lengths were globally inflated. Putative effects of missing data, segregation distortion, and genotyping errors on map accuracy are discussed. This research work led to the identification of a reliable set of SNPs potentially useful as a tool for a wide range of genetic studies in taro.