UNDERSTANDING ALLELIC DIVERSITY AND STRUCTURAL VARIATION OF RUBISCO ACTIVASE GENES IN WHEAT

Usama Sheraz

Wheat (Triticum aestivum L.) is one of the world’s most important cereal crops, but its productivity is increasingly threatened by high temperature stress. Heat stress reduces photosynthetic efficiency, accelerates senescence, disrupts grain filling and ultimately limits yield. Improving wheat performance under heat stress requires a better understanding of both the genetic variation associated with heat-responsive traits and the molecular systems that help maintain photosynthesis under stressful environments. This project investigates wheat heat tolerance from genetic and molecular perspectives which combine mapping-based analysis of heat-responsive traits with a detailed characterization of allelic and structural diversity in Rubisco activase TaRca genes.Wheat is an allohexaploid species (2n = 6x = 42) composed of three related subgenomes, A, B and D, that arose through two distinct polyploidization events. This genome structure is important for the study of Rubisco activase (RCA) because TaRca genes occur as related copies across the homoeologous chromosome groups rather than as a single gene. In wheat, the TaRca gene reflects both ancient tandem duplication in grasses and subsequent polyploidization which resulted in six TaRca copies, two. Each on the three homoeologous chromosomes. Hence, it is important to study sequence variation that may occur between the tandemly arranged TaRca1 and TaRca2 copies, and among their three A-, B- and D-subgenome homeologs. Therefore, it is important to accurately characterize RCA diversity in wheat and its relationship to its function. To explore this diversity, chromosome-specific TaRca genomic regions on wheat chromosomes 4A, 4B and 4D were analyzed across a diverse panel of wheat and related germplasm. Approximately 8.4-kb TaRca contigs were aligned independently for each chromosome and examined for SNPs, indels, haplotype structure, and coding effects in TaRca1, TaRca2α and TaRca2β. The TaRca region showed clear subgenome and accession-specific patterns of diversity. The 4A copies carried the highest level of sequence and structural variation, and the 4B copies were the most conserved. The 4D showed intermediate level of variation with a distinct contribution from Aegilops tauschii-related haplotypes. Most of the larger structural variations and SNPs were in the non-coding part of the gene, mapping to intergenic, promoter-proximal, UTR, and intronic regions. Significant number of protein-altering SNPs were observed in the validated coding sequences of the gene as well. Between the two copies of the gene, coding part of TaRca1 showed approximately 45% higher variation than that in TaRca2. This thesis contributes to a genetic framework for understanding wheat heat tolerance. Findings of the study provide a foundation for future work linking wheat heat-tolerance loci, RCA haplotypes, transcript regulation, protein function and photosynthetic performance under high temperature stress.

UNDERSTANDING ALLELIC DIVERSITY AND STRUCTURAL VARIATION OF RUBISCO ACTIVASE GENES IN WHEAT

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