Understanding expression dynamics and sequence variability of genes regulating nutritional and cooking quality related traits in rice Oryza sativa L

Abstract

Targeted genetic studies have been undertaken for grain quality-related traits in rice (Oryza sativa L.). However, there are only a few reports to understand the concerted sequence variations, haplotype diversity and expression dynamics analysis for genes governing the grain quality traits. In the present study, 80 functionally characterized genes governing the rice nutritional and cooking quality related traits were selected. Their expression dynamics across various developmental stages and tissues were also observed. Moreover, we have generated co-expression networks to understand the positive and negative correlations and identification of genes at the hotspots of interactions. Regulatory gene analysis revealed a number of potential transcription factors influencing the gene expressions. In addition to the identification of SNPs and their functional impact, the heritable genetic patterns of SNPs viz. haplotypes were generated and associated with relevant phenotypic traits such as grain chalkiness and pericarp color. Haplotypic networks spanning across nine rice isozyme classification groups have provided an insight to the evolutionary patterns within the sequence variations. A comparative nucleotide diversity analysis between cultivated and wild Oryza rufipogon cultivars revealed the selection pressures on these genes. In addition, genetic loci significantly associated with chalkiness and pericarp color traits were identified based on the GWAS analysis across a core panel of 325 diverse rice accessions. The sequence variations observed across the original ~4700 rice accessions dataset has also enabled the development of allele specific and SSR markers for the selected 80 genes. Subsequently, a genomics and transcriptomics resource has been developed using these results. newline