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.
| Identifer | oai:union.ndltd.org:tamu.edu/oai:repository.tamu.edu:1969.1/ETD-TAMU-2009-05-595 |
| Date | 2009 May 1900 |
| Creators | Sharma, Vivek |
| Contributors | Da Silva, Jorge A., Rooney, William L. |
| Source Sets | Texas A and M University |
| Language | en_US |
| Detected Language | English |
| Type | thesis, text |
| Format | application/pdf |
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