Identification of a key locus, qNL3.1, associated with seed germination under salt stress via a genome-wide association study in rice

Abstract

Key message Two causal OsTTL and OsSAPK1genes of the key locus qNL3.1 significantly associated with seed germination under salt stress were identified via a genome-wide association study, which could improve rice seed germination under salt stress. Abstract Rice is a salt-sensitive crop, and its seed germination determines subsequent seedling establishment and yields. In this study, 168 accessions were investigated for the genetic control of seed germination under salt stress based on the germination rate (GR), germination index (GI), time at which 50% germination was achieved (T50) and mean level (ML). Extensive natural variation in seed germination was observed among accessions under salt stress. Correlation analysis showed significantly positive correlations among GR, GI and ML and a negative correlation with T50 during seed germination under salt stress. Forty-nine loci significantly associated with seed germination under salt stress were identified, and seven of these were identified in both years. By comparison, 16 loci were colocated with the previous QTLs, and the remaining 33 loci might be novel. qNL3.1, colocated with qLTG-3, was simultaneously identified with the four indices in two years and might be a key locus for seed germination under salt stress. Analysis of candidate genes showed that two genes, the similar to transthyretin-like protein OsTTL and the serine/threonine protein kinase OsSAPK1, were the causal genes of qNL3.1. Germination tests indicated that both Osttl and Ossapk1 mutants significantly reduced seed germination under salt stress compared to the wild type. Haplotype analysis showed that Hap.1 of OsTTL and Hap.1 of OsSAPK1 genes were excellent alleles, and their combination resulted in high seed germination under salt stress. Eight accessions with elite performance of seed germination under salt stress were identified, which could improve rice seed germination under salt stress.

Genome-wide association studies identified OsTMF as a gene regulating rice seed germination under salt stress

“…To accurately measure seed germination in such a manner, we did the germination experiments on water- or NaCl solution-immersed filter paper in petri dishes (with a cover, but without seal), and refreshed the solutions in every two days. After counting germinated seeds, germination rate and germination index were calculated to evaluate seed germination status under salt stress ( Shi et al., 2017 ; Ju et al., 2022 ; Li et al., 2022 ; Mei et al., 2022 ; Zhan et al., 2023 ). In this study, we established germination grades (1 to 11) using the GR3, GR4 and GI ratios of salt stress condition to the control condition.…”

Endophyte-mediated enhancement of salt resistance in Arachis hypogaea L. by regulation of osmotic stress and plant defense-related genes

“…Additionally, salt stress has been shown to impede seed germination, cell signaling, and lipid metabolism in plants ( Gupta et al, 2022 ). Furthermore, salt stress hindered seed germination, cell signaling, and lipid metabolism of the plant ( Pan et al, 2023 ; Ravi et al, 2023 ; Zhan et al, 2023 ). Nonetheless, the application of microorganisms has been identified as a potential protective measure, offering a means by which plants can defend against various biotic and abiotic stresses ( Khan et al, 2021 ).…”