Browsing by Subject "Molecular markers"
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Item IDENTIFICATION OF DROUGHT-RELATED QUANTITATIVE TRAIT LOCI (QTLs) IN SUGARCANE (Saccharum spp.) USING GENIC MARKERS(2011-08-08) Sharma, VivekPopulation 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.Item Ontogenic Morphometry and Genetic Diversity of Lygus hesperus (Hemiptera: Miridae)(2011-05) Shrestha, Ram B.; Parajulee, Megha N.; Francisco, Michael J. D. S.; Densmore, Llewellyn D.; Holaday, A. Scott; Strauss, Richard E.; Burow, Mark D.Lygus hesperus Knight (Hemiptera: Miridae) is an economically important pest of many field crops, including cotton, in the United States. Lygus hesperus is commonly found in the western United States, hence, it is commonly known as Western Tarnished Plant Bug. Lygus hesperus populations from different geographic regions respond differently to the identical pest management practices. Population-specific pest management strategy is required for successful management of this pest. Morphological or molecular techniques or biological assays could be used to differentiate these Lygus populations. But scientific information on ontogenic morphometry and genetic diversity of this species is mostly lacking. Therefore, ontogenic morphometry, and genetic diversity studies were conducted in the cotton entomology laboratory at Texas AgriLife Research Center, Lubbock, Texas. Lygus hesperus has allometric ontogenic growth patterns and there was no significant difference between ontogenic shape and size trajectories between male and female. The discriminant function analysis revealed significant differences in pattern of ontogenic shape and size between Lygus hesperus and Lygus lineolaris. Thus, the morphometric technique can be used to differentiate nymphal stages of two species when they are hard to differentiate by visual observation of their morphology. Ten polymorphic microsatellite markers were developed and used in a genetic diversity study of eight Lygus hesperus populations from the Texas High Plains. Lygus hesperus population from this region showed a high degree of genetic diversity. Lygus hesperus from the Texas high Plains showed significant genetic population structure and they were differentiated into three genetically distinct populations. The molecular marker comparison study showed Simple Sequence Repeat (SSR) and Amplified Fragment Length Polymorphism (AFLP) markers are potential markers for genetic diversity study of this species when the capillary electrophoresis facility is available but Inter Simple Sequence Repeat (ISSR) markers can be next alternative when the capillary electrophoresis facility is not available. Morphometric and molecular biology knowledge and techniques developed in these studies will be useful in identification of pest management units and development of population specific precision pest management technology for Lygus hesperus.