Whole genome approaches to identify early meiotic gene candidates in cereals

Early events during meiotic prophase I underpin not only viability but the variation of a species from generation to generation. Understanding and manipulating processes such as chromosome pairing and recombination are integral for improving plant breeding. This study uses comparative genetics, quantitative trait locus (QTL) analysis and a transcriptomics-based approach to identify genes that might have a role in genome-wide recombination control. Comparative genetics and the analysis of the yeast and Arabidopsis sequenced genomes has allowed the identification of early meiotic candidates that are conserved in wheat, rice and barley. Secondly, scoring recombination frequency as a phenotype for QTL analysis across wheat, rice and barley mapping populations has enabled us to identify genomic regions and candidate genes that could be involved in genome-wide recombination. Transcriptome data for candidate genes indicate that they are expressed in meiotic tissues. Candidates identified included a non-annotated expressed protein, a DNA topoisomerase 2-like candidate, RecG, RuvB and RAD54 homologues.William D. Bovill, Priyanka Deveshwar, Sanjay Kapoor, Jason A. Abl

Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice

Water-deficit stress is detrimental for rice growth, development, and yield. Transcriptome analysis of 1-week-old rice (Oryza sativa L. var. IR64) seedling under water-deficit stress condition using Affymetrix 57 K GeneChip® has revealed 1,563 and 1,746 genes to be up- and downregulated, respectively. In an effort to amalgamate data across laboratories, we identified 5,611 differentially expressing genes under varying extrinsic water-deficit stress conditions in six vegetative and one reproductive stage of development in rice. Transcription factors (TFs) involved in ABA-dependent and ABA-independent pathways have been found to be upregulated during water-deficit stress. Members of zinc-finger TFs namely, C2H2, C2C2, C3H, LIM, PHD, WRKY, ZF-HD, and ZIM, along with TF families like GeBP, jumonji, MBF1 and ULT express differentially under water-deficit conditions. NAC (NAM, ATAF and CUC) TF family emerges to be a potential key regulator of multiple abiotic stresses. Among the 12 TF genes that are co-upregulated under water-deficit, salt and cold stress conditions, five belong to the NAC TF family. We identified water-deficit stress-responsive genes encoding key enzymes involved in biosynthesis of osmoprotectants like polyols and sugars; amino acid and quaternary ammonium compounds; cell wall loosening and structural components; cholesterol and very long chain fatty acid; cytokinin and secondary metabolites. Comparison of genes responsive to water-deficit stress conditions with genes preferentially expressed during panicle and seed development revealed a significant overlap of transcriptome alteration and pathways

Whole genome approaches to identify early meiotic gene candidates in cereals

Early events during meiotic prophase I underpin not only viability but the variation of a species from generation to generation. Understanding and manipulating processes such as chromosome pairing and recombination are integral for improving plant breeding. This study uses comparative genetics, quantitative trait locus (QTL) analysis and a transcriptomics-based approach to identify genes that might have a role in genome-wide recombination control. Comparative genetics and the analysis of the yeast and Arabidopsis sequenced genomes has allowed the identification of early meiotic candidates that are conserved in wheat, rice and barley. Secondly, scoring recombination frequency as a phenotype for QTL analysis across wheat, rice and barley mapping populations has enabled us to identify genomic regions and candidate genes that could be involved in genome-wide recombination. Transcriptome data for candidate genes indicate that they are expressed in meiotic tissues. Candidates identified included a non-annotated expressed protein, a DNA topoisomerase 2-like candidate, RecG, RuvB and RAD54 homologues.William D. Bovill, Priyanka Deveshwar, Sanjay Kapoor, Jason A. Abl