Abstract
Multiple stress tolerance at the seed germination stage is crucial for better crop establishment in the direct-seeded rice ecosystem. Therefore, identifying rice genes/quantitative trait loci (QTLs) associated with salinity and anaerobic tolerance at the germination stage is a prerequisite for adaptive breeding. Here, we studied 498 highly diverse rice accessions Xian (Indica) and Geng (Japonica), and six traits that are highly associated with salinity and anaerobic tolerance at germination stage were measured. A high-density 2.8M Single Nucleotide Polymorphisms (SNP) genotype map generated from the 3,000 Rice Genomes Project (3KRGP) was used for mapping through a genome-wide association study. In total, 99 loci harboring 117 QTLs were detected in different populations, 54, 21, and 42 of which were associated with anaerobic, salinity, and combined (anaerobic and salinity) stress tolerance. Nineteen QTLs were close to the reported loci for abiotic stress tolerance, whereas two regions on chromosome 4 (qSGr4a/qCL4c/qRI4d and qAGr4/qSGr4b) and one region on chromosome 10 (qRI10/qCL10/ qSGr10b/qBM10) were associated with anaerobic and salinity related traits. Further haplotype analysis detected 25 promising candidates genes significantly associated with the target traits. Two known genes (OsMT2B and OsTPP7) significantly associated with grain yield and its related traits under saline and anaerobic stress conditions were identified. In this study, we identified the genes involved in auxin efflux (Os09g0491740) and transportation (Os01g0976100), whereas we identified multistress responses gene OsMT2B (Os01g0974200) and a major gene OsTPP7 (Os09g0369400) involved in anaerobic germination and coleoptile elongation on chromosome 9. These promising candidates provide valuable resources for validating potential salt and anaerobic tolerance genes and will facilitate direct-seeded rice breeding for salt and anaerobic tolerance through marker-assisted selection or gene editing.
Highlights
As the staple food for most Asian people, rice productivity has more than doubled since the “Green Revolution” in 1960s, when the global breeding efforts have been largely focused on improving yields under irrigated lands in Asia and rest of the world (Khush, 2001; Jena and Nissila, 2017)
ANOVA showed that the genotypic differences among the accessions explained 97.2%, 32%, and 97.5% of the total phenotypic variances of GR under anaerobic condition (AGr), coleoptile lengths (CLs), and response index (RI) contributing to AGT (Supplementary Table S1), and 97.4%, 90.3%, and 97.1% of the total phenotypic variances of GR under salinity condition (SGr), and BM contributing to SGT, respectively (Supplementary Table S1)
Highly positive correlation was observed between the three AGT traits, with r = 0.82 between AGr and CL, 0.82 between AGr and RI, and 0.99 between CL and RI, indicating that CL was the primary determinant of AGT
Summary
As the staple food for most Asian people, rice productivity has more than doubled since the “Green Revolution” in 1960s, when the global breeding efforts have been largely focused on improving yields under irrigated lands in Asia and rest of the world (Khush, 2001; Jena and Nissila, 2017). DSR can be exposed to combined stress of salinity in nonanoxic conditions during tidal in lowlands of coastal areas of many Asian countries (Ray et al, 2016; Naveed et al, 2018). Under this kind of scenario, flooding decelerates seed germination and delays seedling establishment (Ismail et al, 2008), whereas shoot growth of rice seedlings can be simultaneously arrested under salt stress due to osmotic stress and high accumulation of Na+ in shoot tissues (Munns and Tester, 2008), because rice plants could not maintain their normal energy level under hypoxia (low O2 concentration) (Kurniasih et al, 2013).
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
