Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding

Abstract

SummaryUpland rice is a distinctive drought‐aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought‐aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high‐quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought‐resistant rice and the “blue revolution” in agriculture.

Progress in Rice Breeding Based on Genomic Research

“…Wei et al, studied eight genome-wide association-based research cohorts (QTNs), mapped rice quantitative trait nucleotides (QTNs) and inferred QTN effects, which illustrated that molecular markers can be used to resolve the genetic drag caused by uneven genome distribution when QTGs are mapped [76]. Wang et al, also conducted a comprehensive study integrating the genome, transcriptome, and population analysis of rice, identified key candidate genes for drought adaptation in upland rice (UR), and constructed a genomic navigation map for drought-resistant breeding in rice, revealing the crucial role of accumulated highland-specific variations in enhancing drought tolerance [77]. The application of molecular navigation breeding significantly enhances the efficiency of rice breeding, optimizes the cultivation of new varieties, and provides scientifically effective guidance for rice-breeding design.…”