Genome-Wide Association Study (GWAS) to Identify Salt-Tolerance QTLs Carrying Novel Candidate Genes in Rice During Early Vegetative Stage

Abstract

Background Rice is considered as a salt-sensitive plant, particularly at early vegetative stage, and its production is suffered from salinity due to expansion of salt affected land in areas under cultivation. Hence, significant increase of rice productivity on salinized lands is really necessary. Today genome-wide association study (GWAS) is a method of choice for fine mapping of QTLs involved in plant responses to abiotic stresses including salinity stress at early vegetative stage. In this study using > 33,000 SNP markers we identified rice genomic regions associated to early stage salinity tolerance. Eight salinity-related traits including shoot length (SL), root length (RL), root dry weight (RDW), root fresh weight (RFW), shoot fresh weight (SFW), shoot dry weight (SDW), relative water content (RWC) and TW, and 4 derived traits including SL-R, RL-R, RDW-R and RFW-R in a diverse panel of rice were evaluated under salinity (100 mM NaCl) and normal conditions in growth chamber. Genome-wide association study (GWAS) was applied based on MLM(+Q + K) model. Results Under stress conditions 151 trait-marker associations were identified that were scattered on 10 chromosomes of rice that arranged in 29 genomic regions. A genomic region on chromosome 1 (11.26 Mbp) was identified which co-located with a known QTL region SalTol1 for salinity tolerance at vegetative stage. A candidate gene (Os01g0304100) was identified in this region which encodes a cation chloride cotransporter. Furthermore, on this chromosome two other candidate genes, Os01g0624700 (24.95 Mbp) and Os01g0812000 (34.51 Mbp), were identified that encode a WRKY transcription factor (WRKY 12) and a transcriptional activator of gibberellin-dependent alpha-amylase expression (GAMyb), respectively. Also, a narrow interval on the same chromosome (40.79–42.98 Mbp) carries 12 candidate genes, some of them were not so far reported for salinity tolerance at seedling stage. Two of more interesting genes are Os01g0966000 and Os01g0963000, encoding a plasma membrane (PM) H+-ATPase and a peroxidase BP1 protein. A candidate gene was identified on chromosome 2 (Os02g0730300 at 30.4 Mbp) encoding a high affinity K+ transporter (HAK). On chromosome 6 a DnaJ-encoding gene and pseudouridine synthase gene were identified. Two novel genes on chromosome 8 including the ABI/VP1 transcription factor and retinoblastoma-related protein (RBR), and 3 novel genes on chromosome 11 including a Lox, F-box and Na+/H+ antiporter, were also identified. Conclusion Known or novel candidate genes in this research were identified that can be used for improvement of salinity tolerance in molecular breeding programmes of rice. Further study and identification of effective genes on salinity tolerance by the use of candidate gene-association analysis can help to precisely uncover the mechanisms of salinity tolerance at molecular level. A time dependent relationship between salt tolerance and expression level of candidate genes could be recognized.

Genome-Wide Association Study Reveals Marker–Trait Associations for Early Vegetative Stage Salinity Tolerance in Rice

“…The MTAs qSNC1, qSKC1, and qSNK1 were located in the genomic region reported to be associated with shoot K + concentration (qSKC1:RM8094-RM10825) and shoot and root Na + /K + ratio (qSNK1; qRNK1: RM1287-RM1025) [24]. The MTA, qSKC6 (AX-95937335-3.42 Mb) identified under salt stress conditions was located in the genomic region reported to be associated with RDW and RFW under control conditions (qRFWn6.1; qRDWn6.1 at 3.59 Mb) [47]. The MTAs, qRNK1 was positioned in the genomic region reported to accountable for shoot Na + concentration (qSNC1: RM1287-RM10793), shoot and root K + concentration (qSKC1: RM8094-RM10825; qRKC1: RM1287-RM11300) and root Na + /K + ratio qRNK1: RM1287-RM10825) [24].…”

Genome-wide association study for seedling biomass-related traits in Gossypium arboreum L.

“…Multigenic control and elusive environmental influences make it difficult to understand the genetic control and development of molecular markers for seedling biomass-related traits [ 17 ]. Owing to advances in omics, recent reports suggested the identification of molecular markers concerning seedling biomass-related traits in different species, viz., rice [ 18 ], Brassica [ 19 ], and wheat [ 20 – 22 ].…”

“…Recent advances in sequencing technology have led to extensive Genome-wide association studies (GWAS) in crop plants [ 17 , 18 , 23 – 26 ]. Based on population genetics and genome analysis of natural genetic populations, GWAS has proven to be an efficient tool for understanding the relationship between phenotype and associated genetic variation [ 27 – 29 ].…”

“…Based on population genetics and genome analysis of natural genetic populations, GWAS has proven to be an efficient tool for understanding the relationship between phenotype and associated genetic variation [ 27 – 29 ]. At present, the previously published molecular markers related to seedling biomass-related traits were mainly determined by traditional QTL methods utilizing F2 populations and RIL populations [ 18 – 20 , 22 ]. Furthermore, diploid Gossypium arboreum , which is the ancestors of the modern cultivated allotetraploid cotton should be an ideal model for basic research in cotton [ 30 ].…”

Genome-wide association analysis for rice salt tolerance at seedling and reproductive stages

“…By using 708 rice accessions and high-density SNPs within genes, Liu et al (2019) detected 2255 SNPs that were signi cantly associated with ST-related traits at both seedling stage in greenhouse and reproductive stage at saline elds. In total, although a lot of ST related QTLs/genes have been reported, few of them, especially for those at reproductive stage, were characterized and successfully used in breeding (Li et al, 2020;Theerawitaya et al, 2020;Nayyeripasand et al, 2021).…”