GENOMICS ENABLED GENE DISCOVERY IN DIPLOID AND POLYPLOID WHEAT

Abstract

Hexaploid bread wheat (Triticum aestivum) is one of the most important staple food crops for humans. Sustainable genetic improvement in wheat is critical for ensuring global food security and requires the introduction of new genes and alleles into elite wheat cultivars. The progenitor species and wild wheat relatives are a reservoir of genetic diversity for wheat improvement. This doctoral thesis demonstrates the application of genomic resources and bioinformatics pipelines to characterize the wild germplasm and to streamline the gene discovery pipeline using five diverse species involving wheat progenitor, wild, and related species. Genomics-assisted characterization of the genetic diversity present in gene banks is a major step towards the systematic utilization of unexploited germplasm to ensure the sustainable development of new varieties. Toward this end, we used genomics datasets to curate wild and related accessions of tetraploid wheat from two distinct species Triticum turgidum and Triticum timopheevii. Using Genotyping by sequencing (GBS) data and a unique similarity matrix and powercore analysis, a set of 102 accessions were identified as the core set accessions that represent 20 and 35 percent of the total accessions of the WGRC tetraploid wheat collection of T. turgidum and T. timopheevii, respectively. Further, three distinct centers of rich genetic diversity were identified for wild and domesticated emmer and T. timopheevii in the Fertile Crescent. GWAS analysis of the genotypic and phenotypic dataset identified a novel QTL for leaf rust resistance on chromosome 2B in T. timopheevii. Triticale is a man-made cereal derived from a cross between tetraploid and hexaploid wheat with diploid rye. There are large numbers of triticale germplasm available in different gene banks; however, in many cases, the ploidy information is not accurate and affects the quality of work with large triticale germplasm. In this work, using the low-cost GBS datasets, a pipeline was developed to detect contamination in the UMD triticale collection and facilitated the accurate classification of ploidy, ensuring the purity of the triticale germplasm. This approach identified contamination of 11 wheat accessions and enabled the correct classification of 236 hexaploid and 12 octoploid triticale, these results were further confirmed through GISH experiments. Wild and related germplasms are considered as the goldmine of genetic diversity for wheat improvement. The modern wheat cultivars have gone through several rounds of heavy selections for yield related traits and have lost the genetic diversity against several abiotic and biotic stresses. On the other hand, wild relatives of wheat have been growing naturally without any substantial artificial selection pressure and it allowed them to preserve their genetic diversity. This study investigates the genetic diversity of a selected set of genes to visualize the differences in wild wheat relatives and polyploid wheat cultivars. To study these differences, group 5 chromosome of Aegilops geniculata and Aegilops umbellulata, belonging to the tertiary gene pool, were assembled. Comparative analysis revealed a higher rate of pseudogenization in bread wheat compared to these two wild relatives, primarily due to the difference in exon/intron length between the genes, rendering these genes non-functional. Diploid einkorn wheat (Triticum monococcum), with inherent disease resistance, offers a valuable resource for wheat improvement. To facilitate its proper utilization, two of the reference genomes-one wild (T. monococcum ssp. aegilopoides) and one domesticated (T. monococcum ssp. monococcum) were assembled in the study. Kmer-GWAS identified seven novel QTLs associated with powdery mildew resistance, three for leaf rust resistance, and two for stem rust resistance. These QTLs harbor diverse gene classes encoding for resistance gene analogs, cysteine-rich receptor kinases, transcription factors, and G-type lectins. Overall, the knowledge and resources developed in this research would contribute to the characterization of vast germplasm and the development of climate-resilient wheat.