Nayyeripasand Leila, Garoosi Ghasem Ali, Ahmadikhah Asadollah
Agricultural Biotechnology Department, Faculty of Agriculture, Imam Khomeini International University, Qazvin, Iran.
Department of Plant Sciences and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshi University, G.C. Velenjak, Tehran, Iran.
Rice (N Y). 2021 Jan 9;14(1):9. doi: 10.1186/s12284-020-00433-0.
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.
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.
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.
水稻被认为是一种对盐敏感的植物，尤其是在营养生长早期，由于种植区域盐渍化土地的扩大，其产量受到盐分的影响。因此，提高盐渍化土地上水稻的生产力非常必要。如今，全基因组关联研究（GWAS）是精细定位参与植物对非生物胁迫（包括营养生长早期的盐胁迫）响应的QTL的首选方法。在本研究中，我们使用超过33000个SNP标记，鉴定了与水稻早期耐盐性相关的基因组区域。在生长室中，在盐胁迫（100 mM NaCl）和正常条件下，对一个多样化的水稻群体中的八个与盐相关的性状，包括地上部长度（SL）、根长度（RL）、根干重（RDW）、根鲜重（RFW）、地上部鲜重（SFW）、地上部干重（SDW）、相对含水量（RWC）和TW，以及四个衍生性状，包括SL-R、RL-R、RDW-R和RFW-R进行了评估。基于MLM(+Q+K)模型进行全基因组关联研究（GWAS）。
在胁迫条件下，鉴定出151个性状-标记关联，它们分布在水稻的10条染色体上，排列在29个基因组区域。在1号染色体上鉴定出一个基因组区域（11.26 Mbp），该区域与已知控制营养生长阶段耐盐性的QTL区域SalTol1共定位。在该区域鉴定出一个候选基因（Os01g0304100），其编码一种阳离子氯转运蛋白。此外，在该染色体上还鉴定出另外两个候选基因，Os01g0624700（24.95 Mbp）和Os01g0812000（34.51 Mbp），它们分别编码一个WRKY转录因子（WRKY 12）和一个赤霉素依赖性α-淀粉酶表达的转录激活因子（GAMyb）。同样，在同一染色体上的一个狭窄区间（40.79-42.98 Mbp）包含12个候选基因,其中一些基因在苗期耐盐性方面尚未见报道。两个更有趣的基因是Os01g0966000和Os01g0963000，分别编码质膜（PM）H-ATPase和过氧化物酶BP1蛋白。在2号染色体上鉴定出一个候选基因（30.4 Mbp处的Os02g0730300），其编码一个高亲和力钾转运蛋白（HAK）。在6号染色体上鉴定出一个编码DnaJ的基因和一个假尿苷合酶基因。在8号染色体上还鉴定出两个新基因，包括ABI/VP1转录因子和视网膜母细胞瘤相关蛋白（RBR），在11号染色体上鉴定出3个新基因，包括一个脂氧合酶、一个F-box和一个Na/H反向转运蛋白。
本研究鉴定出了已知或新的候选基因，可用于水稻分子育种计划中耐盐性的改良。通过使用候选基因关联分析进一步研究和鉴定耐盐性有效基因，有助于在分子水平上精确揭示耐盐机制。可以识别耐盐性与候选基因表达水平之间的时间依赖关系。
