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.

中文翻译：

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全基因组关联研究（GWAS）鉴定早期营养期水稻中携带新候选基因的耐盐QTL

背景

水稻被认为是对盐敏感的植物，特别是在营养早期，由于耕地地区受盐影响的土地的扩大，水稻的生产受到盐碱化的困扰。因此，确实有必要在盐碱化的土地上大幅度提高稻米的生产率。如今，全基因组关联研究（GWAS）是精细定位QTL的一种选择方法，该QTL参与植物对植物早期非生物胁迫（包括盐分胁迫）的反应。在使用> 33,000 SNP标记的这项研究中，我们鉴定了与早期盐度耐受性相关的水稻基因组区域。与盐度有关的8个性状包括枝长（SL），根长（RL），根干重（RDW），根鲜重（RFW），茎鲜重（SFW），茎干重（SDW），相对含水量（ RWC）和TW，以及4个衍生性状，包括SL-R，RL-R，在盐度（100 mM NaCl）和生长室内正常条件下，评估了不同水稻品种中的RDW-R和RFW-R。基于MLM（+ Q + K）模型应用了全基因组关联研究（GWAS）。

结果

在胁迫条件下，鉴定出151个性状标记关联，这些关联散布在排列在29个基因组区域中的水稻的10条染色体上。鉴定了1号染色体上的一个基因组区域（11.26 Mbp），该区域与已知的QTL区域SalTol1位于同一位置，以营养期耐盐度。在该区域中鉴定出编码阳离子氯化物共转运蛋白的候选基因（Os01g0304100）。此外，在这条染色体上，还鉴定了另外两个候选基因Os01g0624700（24.95 Mbp）和Os01g0812000（34.51 Mbp），它们编码WRKY转录因子（WRKY 12）和赤霉素依赖性α-淀粉酶表达的转录激活因子（GAMyb）。同样，在同一条染色体上的一个狭窄区间（40.79–42.98 Mbp）带有12个候选基因，到目前为止，还没有报道其中一些在苗期耐盐度。两个更有趣的基因是Os01g0966000和Os01g0963000，它们编码质膜（PM）H ⁺ -ATPase和过氧化物酶BP1蛋白。在2号染色体（30.4 Mbp的Os02g0730300）上鉴定了一个候选基因，该基因编码高亲和力K ⁺转运蛋白（HAK）。在6号染色体上，鉴定了DnaJ编码基因和假尿苷合酶基因。8号染色体上的两个新基因包括ABI / VP1转录因子和视网膜母细胞瘤相关蛋白（RBR），11号染色体上的3个新基因包括一个还确定了Lox， F-box和Na ⁺ / H ⁺反向转运蛋白。

结论

鉴定了本研究中已知或新颖的候选基因，可用于提高水稻分子育种程序的耐盐性。通过使用候选基因关联分析对耐盐性有效基因进行进一步的研究和鉴定，可以在分子水平上准确揭示耐盐性的机制。耐盐性与候选基因表达水平之间存在时间依赖性。