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Assessment of genetic diversity and genetic framework/structure in chickpea crop has important effects on plants breeding programs and preservation of inherited resources. New types of markers have improved our ability to quickly and cost effectively uncover potentially useful variations in large chickpea germplasm collections in gene banks. Single nucleotide polymorphism (SNP) are recently developed markers, which are very effective in discovering inherited diversity. Little is known about the level of genetic diversity in these accessions to advance elite varieties. Chickpea production is predominant in arid & semiarid regions, such as in Pakistan, faces immense challenges of drought and heat stress. Addressing these challenges has made more difficult outstanding to lack of genetic and phenotypic characterization of available cultivated varieties and breeding materials. Genotyping-by-sequencing offers a rapid and cost-effective means to identify genome-wide nucleotide variation in crop germplasm.In this study, we have compared genetic variations and population structure of a previously uncharacterized collection of chickpea cultivated germplasm. Here, we used 31,995 SNP markers to estimate the genetic diversity and population structure in collection of 952 landraces and elite cultivars from the second centers of diversity and Fertile Crescent (Ethiopia, India, Pakistan & Turkey). For Pakistani accessions, we used 8,113 SNP markers to determine genetic variations and compare population structure within 77 landraces and 5 elite cultivars, currently grown in situ on farms throughout the chickpea growing regions of Pakistan. The compiled landraces span a striking aridity gradient into the Thal desert of the Punjab Province, Pakistan. Despite low levels of variations across the collection and limited genetic structure, we found some differentiation among accessions from arid, semi-arid, irrigated, and coastal areas. In a subset of 232 markers, we discovered evidence of differentiation along gradients of elevation and isothermality. Our results highlighted the utility of exploring large germplasm collections for nucleotide variation associated with environmental extremes. And further to use this data to nominate germplasm accessions with potential to improve crop drought tolerance and other environmental traits.To investigate the basis of genetic factors controlling flower color in chickpea, molecular and genetic characterization of colored flower and white flower chickpea accessions were performed. This unique white flowered color RS11 Chickpea accession lacking the anthocyanin in flower tissues. The genetic constitution of this accession is different to other white flower chickpea accessions because when it was crossed to another white flower color accession, they produced colored F1. None of white flower chickpea can synthesize mRNA corresponding to Leucoanthocyanidin dioxygenase (LDOX) gene, also called anthocyanidin synthase (ANS) on B and C locus. Molecular analysis of white chickpea revealed the presence of full deletion Intron, spanning both exon with in coding region of LDOX gene. Phenotyping and genotyping of F2 generations from cross between RS 11 (white flower) and 96029 (color flower) revealed segregation for flower color according to the Mendel’s pattern of segregation. Color and white flower phenotype demonstrated its complete linkage with the deletion in LDOX gene inherited as a recessive gene trait. Taken together the findings indicated that mutation in LDOX genes which is present on C locus here in RS 11 is responsible for white flower color in this chickpea accession.
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