Targeted improvement of the wheat genome by marker-assisted selection and understanding its homoeologous gene evolution and expression balance

Jasdeep Singh Mutti

doi:10.7273/000005741

Increasing global demand for wheat, due to burgeoning human population, increased use in feed, and ethanol production requires improved cultivars to substantially increase its productivity. The objectives of this study were to: i) understand mechanism(s) controlling the unique gene expression balance in the polyploid wheat that may have led to its adaptation and success as a major crop plant, and ii) to make cultivar improvement more targeted, precise, and fast through marker-assisted selection. In silico analysis, confirmed by single stranded conformation polymorphism (SSCP), revealed that more than 91% of the hexaploid wheat genes are expressed from two or more homoeologues. Expression of only 9% of the genes was from one of the three homoeologues. In general, the proportion of expressed copies decreased with the increase in structural copy number. Homoeologous gene expression was further influenced by the physical location of the genes on the chromosomes. Short arms of wheat chromosomes appear to be functionally different from long arms. Expresion of all three homoeologues was favored in the proximal regions of the short arms but in the long arms, the terminal regions were favored. The most significant observation was that tissue specific expression patterns for 87% of the wheat genes were different for different homoeologues. More genes and more homoeologues/gene were expressed in the root tissue and the least number were expressed in meiosis and early stages of flowering. The maximum tissue-specific homoeologous gene expression was observed during flowering and seed development stages and the least was observed in roots. About 30% of the genes showed altered methylation or expression pattern in response to homoeologue copy number change, suggesting that expression of these genes is interdependent among homoeologues. Sequence changes among homoeologues showed a distinct pattern that was common to all genes studied. The middle of the coding region exhibited the least proportion of sequence changes. Accounting for codon usage, the ratio of synonymous to non-synonymous changes did not show any increase in synonymous changes which would be expected due to selection pressure. We therefore postulated that wheat and perhaps other higher eukaryotes possess a mechanism to protect translated parts of the genes from sequence change(s), irrespective of their function. The applied part of my research focused on targeted use of marker-assisted selection for rapid introgression of single genes into popular cultivars. Using marker assisted backcross breeding; we individually transferred seven pest resistance genes into seven winter wheat lines to develop 28 advanced breeding lines. We also optimized a marker-assisted background selection based method of gene introgressions. After testing various approaches by simulations, we incorporated the available information on the distribution of genes and recombination on wheat chromosomes to develop a marker-assisted background selection method to accomplish ≥96% recovery of recurrent parent genome (RPG) in two backcrosses.

Targeted improvement of the wheat genome by marker-assisted selection and understanding its homoeologous gene evolution and expression balance

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