Identification of drought-related quantitative trait loci (QTLs) in sugarcane (Saccharum spp.) using genic markers.

摘要

Population based association studies in crops that were established by domestication and early breeding can be a valuable basis for the identification of QTLs. A case control design in a population is an ideal way to identify maximum candidate sites contributing to a complex polygenic trait such as drought. In the current study, marker loci associated with drought related QTLs were identified in sugarcane (Saccharum spp), one of the most complex crop genomes, with its polyploid nature (>8), chromosome number (>100) and interspecific origin. The objectives of this investigation were: (1) development of genic markers, which can be used for marker-assisted selection of drought tolerant genotypes of sugarcane. (2) genotypic characterization of sugarcane population at drought related loci using EST-SSR markers. Using 55 microsatellite markers, 56 polymorphisms were scored among 80 modern sugarcane genotypes. Homogeneity of the population was confirmed by determining the distribution of allele frequencies obtained by random genomic microsatellite markers. This analysis was conducted in the STRUCTURE program and the population was divided in 3 subgroups based on the allelic distribution. Phenotypic data to evaluate drought tolerance among the genotypes was collected by measuring chlorophyll content, chlorophyll fluorescence, leaf temperature and leaf relative water content. A generalized linear model in SPSS was used to find association between marker loci and phenotypic data. Markers with significant association (P≤0.001 level) with the trait were subjected to linear regression to screen the spurious associations. Based on the results, 21 EST-SSR markers and 11 TRAP markers related to drought-defining physiological parameters were considered as genuine associations in this study. Fifty-six polymorphisms produced by 13 EST-SSR primers were used to produce genetic similarity matrix for 80 genotypes. Dendrogram prepared from this genetic similarity matrix will be useful in selecting parents carrying diversity at drought specific loci.