Identification of quantitative trait loci and candidate genes associated with ABA sensitivity in common wild rice (Oryza rufipogon Griff,)

Abscisic acid （ABA）, as one of the foremost signaling molecules in plants, is an important hormone which plays versatile functions in regulating developmental process and adaptive stress process. A set of introgression lines were previously generated via a backcrossing program using an elite indica cultivar rice Teqing （O. sativa L.） as recipient and an accession of Yuanjiang common wild rice （O. rufipogon Griff.） as donor. In this study, the previously developed introgression lines were evaluated for ABA sensitivity. Here we reported that a total of 14 quantitative trait loci （QTLs） associated with ABA sensitivity were identified. An ABA sensitive introgression line, YIL53, was identified and characterized. Physiological characterization, including chlorophyll content, malondialdehyde content, soluble sugar content, and stomata movement, demonstrated that YIL53 exhibited the characteristics associated with ABA sensitivity. Genotypic analysis revealed that YIL53 harbored one QTL related to ABA sensitivity, qASS1-2, which was located on chromosome 1 within one introgressed segment derived from the Yuanjiang common wild rice. Furthermore, the qASS1-2 was finally narrowed down to a 441-kb region between simple sequence repeats （SSR） marker RM212 and single nucleotide polymorphism （SNP） marker M3 using the segregation population derived from the cross between Teqing and YIL53, and three candidate genes associated with ABA sensitivity were identified using a strategy combined gene expression analysis with QTL mapping. Identification of the QTLs related to ABA sensitivity and characterization of the ABA sensitive line YIL53 would provide a helpful basis for isolating novel genes related to ABA sensitivity.

Genome-wide association study revealed genetic variations of ABA sensitivity controlled by multiple stress-related genes in rice

Abscisic acid(ABA)is a critical phytohormone that regulates multiple physiological processes including plant growth and stress tolerance.The core ABA signaling pathway has been well established,but genetic variations mediating ABA responses remain largely unknown.In this study,we performed genome-wide association study(GWAS)to identify loci and genes associated with ABA sensitivity(reflected by seed germination inhibition by ABA)in a panel of 425 rice accessions.The seed germination assay revealed that Aus and indica rice had stronger ABA sensitivity than japonica rice.A total of 48 non-redundant association loci were detected in the indica subpopulation and whole population,and 386 genes in these loci were responsive to ABA or abiotic stresses.Eight association loci were overlapped with previously reported loci for yield under drought stress or for droughtindicative image traits.Haplotype analyses of important candidate genes such as OsSAPK6,a key component in the ABA signaling core,were performed to identify key SNPs/InDels that may affect gene functions through promoter activity regulation,amino acid variation,or gene splicing.These results provide insights into the genetic basis of ABA sensitivity related to stress responses.