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ThesisItem Restricted Association mapping for grain micronutrient density, grain size and grain weight in Aegilops tauschii species(Punjab Agricultural University, Ludhiana, 2016) Arora, Sanu; Chunneja, ParveenBread wheat is the most important cereal being consumed worldwide. However, due to expanding world‟s population size, the problem of nutritional deficiencies is increasingly affecting the health of people with predominant cereal-based diet. This poses the futuristic demands of both increasing the yield and producing nutritionally enriched wheats on the wheat breeding programmes. However, the hexaploid wheat exhibits limited genetic diversity, which can be broadened by exploiting the wild relatives of wheat by introgression of novel genes/alleles. Aegilops tauschii, the diploid D-genome progenitor of hexaploid wheat, can be used to increase the genetic diversity both for improving grain yield and nutritional quality of bread wheat. To identify the new sources of improving grain yield and nutritional quality, we performed genome wide association study (GWAS) using a collection of 190 Ae. tauschii accessions. The Ae. tauschii germplasm was assessed for grain micronutrients concentration (Fe, Zn, Cu, Mn), grain size (length and width) and 50-grain weight. Quantitative distribution and low to medium heritabilities were observed for grain phenotypes. Ae. tauschii was found to have two to three fold more variation for these phenotypic traits compared to hexaploid wheat cultivars. The accessions were genotyped using SSR markers and SNP markers through genotyping by sequencing (GBS) approach. A total of 59,830 SNPs were mined from the GBS reads of 190 Ae. tauschii accessions and after filtering for more than 30% missing data and minimum allele frequencies of 0.05, a total of 24,567 SNPs were obtained. These filtered GBS SNP tags were aligned to wheat POPSEQ data for assigning the genetic positions. A total of 11489 SNPs mapped to seven Ae. tauschii chromosomes. Genetic diversity was assessed using STRUCTURE software and by conducting phylogeny as well as principal component analysis (PCA). These analysis revealed presence of two distinct lineages (lineage 1 and lineage 2) in Ae. tauschii germplasm. The two lineages broadly corresponded to ssp. tauschii and ssp. strangulata. Both the lineages differed significantly for grain micronutrient concentrations (Fe, Cu and Mn), grain width and grain weight. High mean values for grain micronutrients concentration (Fe, Zn and Cu) and grain weight was observed for lineage 2 (except for Mn concentration). The majority of the accessions identified for higher grain micronutrients from lineage 2 had their origin from Azerbaijan and Iran. Since Ae. tauschii depicted strong structure, GWAS was conducted separately for the two lineages. Linkage disequilibrium across whole Ae. tauschii genome was assessed and observed to be widespread with LD decay to 50% at 9.7 cM and 2.8 cM for lineage 1 and 2, respectively. GWAS was conducted for grain phenotypes using 78 (non-redundant) accessions of lineage 2. Three, six and two significant marker trait associations were found for grain length, width and 50-grain weight, respectively with –log10 (P) >3 with most of the associations located on chromosomes 5D and 7D. For grain Fe concentration only one significant association was observed for –log10 (P) >3 and for grain Zn concentration, SNP marker associations were detected at –log10 (P) 2.5. The study demonstrated the existence of high genetic variation for grain micronutrient concentration and grain size in Ae. tauschii germplasm and utility of GWAS to identify new loci that will be useful to diversify the D-genome of hexaploid wheat for improving both the grain yield and nutritional quality.