Chapter 19 - Deciphering the genomic hotspots in wheat for key breeding traits using comparative and structural genomics

Abstract

Wheat (Triticum aestivum L.) is a staple crop, contributing about a fifth of total calories intake by humans. The objective of worldwide wheat breeding program is to meet the global food demand for projected 9.8 billion populations by 2050. Therefore breeders need to accelerate the genetic gain, increase production, enhance protection, and improve quality traits. The completion of wheat-genome sequencing project and availability of the well-annotated wheat reference genome with advanced comparative and structural bioinformatics tools widens the scope of understanding of wheat biology and the molecular basis of important agronomic traits. Wheat has A, B, and D homologous subgenome, each having seven chromosomes encoding 107,891 high-confidence genes. The comparative analysis of wheat genome with rice, maize, sorghum, barley, Brachypodium, and two diploid wheat progenitor species genome revealed blocks of orthologous and paralogous genes consisting of approximately 22,000–28,000 orthologous genes and about 6000–18,000 paralogous genes. The agronomically important genes of rice, barley, or maize breeding program could be prioritized based on synteny and homologous block study on the specific wheat chromosomes. The functional characterization of these blocks is attained through marker–trait association studies. Advancements in high-throughput sequence-based genotyping, field phenotyping, and genome-wide association studies provide information about the regions of interest on wheat chromosomes, referred to as genomic hotspots. The physical position of the gene sequences and the position of markers flanking such regions are also important in pyramiding of genes. In this chapter, we discussed the wheat hotspots for recent agronomic, stress tolerance, and wheat quality traits. We also discussed the pipelines, tools, and web resources used for identification and analysis of homologous blocks and hotspot regions in wheat that might be useful for students and early career wheat researchers.