Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice ( Oryza sativa L.)

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (R_d) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with R_d. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that R_d shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. R_d also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of R_d collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high R_d. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% R_d of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of R_d in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

Keywords: CRISPR/CAS9; GWAS; LRK1; dark respiration; molecular genetics; rice population.