Genetic dissection for zinc deficiency tolerance in rice using bi-parental mapping and association analysis.

KEY MESSAGE: Zinc deficiency is a widespread soil constraint in rice production. Here, we present QTL/candidate genes associated with Zn deficiency tolerance identified through bi-parental QTL mapping and genome-wide association analysis. Zinc (Zn) deficiency is a widespread soil constraint in rice production. Despite several physiological studies elucidating Zn deficiency tolerance mechanisms, little is known about genetic factors conferring tolerance. To identify QTL associated with root development, biomass accumulation, and grain yield under Zn deficiency, we combined bi-parental QTL mapping in a population of 200 backcross inbred (BC1F6) lines and genome-wide association analysis using 247 k SNP markers across 140 accessions of an indica diversity panel. Three QTLs for Zn deficiency tolerance on chromosomes 3, 6, and 12 co-localized in both approaches and the association analysis detected two additional strong QTL on chromosomes 1 and 9 not present in the bi-parental population. Based on haplotype analysis of the indica panel, biomass consistently increased due to the minor 'tolerance' haplotypes, which had frequencies between 13 and 34%. By utilizing the previous transcript data collected from the same Zn-deficient field, we identified one putative candidate gene within the chromosome 6-QTL, which was associated with all traits in both analyses. Gene Os06g44220 was barely expressed under +Zn conditions but strongly upregulated in both root and shoot under stress and consistently more so in the tolerant genotype. Os06g44220 is an uncharacterized gene with expression previously detected only under salinity stress. Four SNP alterations within the promoter region distinguish the two alleles identified and a genotype tolerant to Zn deficiency shares the same allele as salinity tolerant varieties, lending support to the hypothesis that this gene may confer tolerance to both stresses.

Systems genomics of salinity stress response in rice.

Populations can adapt to stressful environments through changes in gene expression. However, the role of gene regulation in mediating stress response and adaptation remains largely unexplored. Here, we use an integrative field dataset obtained from 780 plants of Oryza sativa ssp. indica (rice) grown in a field experiment under normal or moderate salt stress conditions to examine selection and evolution of gene expression variation under salinity stress conditions. We find that salinity stress induces increased selective pressure on gene expression. Further, we show that trans-eQTLs rather than cis-eQTLs are primarily associated with rice's gene expression under salinity stress, potentially via a few master-regulators. Importantly, and contrary to the expectations, we find that cis-trans reinforcement is more common than cis-trans compensation which may be reflective of rice diversification subsequent to domestication. We further identify genetic fixation as the likely mechanism underlying this compensation/reinforcement. Additionally, we show that cis- and trans-eQTLs are under different selection regimes, giving us insights into the evolutionary dynamics of gene expression variation. By examining genomic, transcriptomic, and phenotypic variation across a rice population, we gain insights into the molecular and genetic landscape underlying adaptive salinity stress responses, which is relevant for other crops and other stresses.