Sharma, Vivek (2009-05). IDENTIFICATION OF DROUGHT-RELATED QUANTITATIVE TRAIT LOCI (QTLs) IN SUGARCANE (Saccharum spp.) USING GENIC MARKERS. Doctoral Dissertation. Thesis uri icon

abstract

  • 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.
  • 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.

publication date

  • May 2009