CN110628936B - 水稻成株期耐盐基因LOC_Os03g28300的分子标记方法及应用 - Google Patents
水稻成株期耐盐基因LOC_Os03g28300的分子标记方法及应用 Download PDFInfo
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Abstract
本发明公开了水稻成株期耐盐基因LOC_Os03g28300的分子标记方法，用一对特异的PCR引物RM15177，PCR扩增待检测水稻育种材料基因组DNA，如果引物对RM15177能够扩增出150bp大小的片段，则该育种材料带有耐盐基因LOC_Os03g28300，RM15177正向引物序列如SEQ ID No.1所示，反向引物序列如SEQ ID No.2所示。该分子标记方法可用于水稻耐盐分子标记辅助选择育种。
Description
技术领域
本发明涉及一种水稻成株期耐盐基因LOC_Os03g28300及其分子标记方法，属于水稻抗逆育种和分子遗传学领域。
背景技术
盐胁迫是影响全球作物产量的主要非生物逆境因子之一。我国盐碱耕地面积约有1亿亩，盐害已引起作物大量减产。水稻是世界上最重要的粮食作物之一，对盐害敏感，当土壤中可溶性盐浓度达到0.3％时即表现出受害症状，最终导致显著减产。培育耐盐水稻品种对解决粮食安全问题有重要的意义。
分子遗传学研究表明，水稻耐盐表现为受多基因控制的数量性状。迄今为止，已有多个影响水稻耐盐性的主效QTL被鉴定出来，其中Saltol等基因已被精细定位，SKC1已被克隆。水稻不同基因型之间的耐盐性差异巨大，拓宽遗传变异进而鉴定和挖掘有利基因是开展突破性育种的先决条件。种质资源是人们在长期生产实践中培育和保留的自然群体材料，它们携带有多种有利变异的基因，是进行遗传改良的宝库。实践证明，通过对核心种质的鉴定和遗传改良是获得农作物主栽品种有利变异的有效途径。随着生物学技术的发展，利用二代测序技术得到的高密度SNPs标记进行目标性状的全基因组关联分析可有效促进目标性状候选基因的高效挖掘。目前，水稻芽期，幼苗期及生殖期等不同时期耐盐相关QTL都有报道并精细定位了部分候选基因。但迄今尚未有成株期耐盐性相关候选基因精细定位的报道。
发明内容
本发明所要解决的技术问题为：如何提供一个影响水稻成株期耐盐性的新型耐盐基因的分子标记方法，可以有效的进行水稻苗期耐盐性的辅助选择，应用于水稻抗逆育种。
本发明的技术方案为：
水稻成株期耐盐基因LOC_Os03g28300，是在水稻基因组第3染色体存在一个与水稻成株期耐盐相关的基因位点，该基因能显著提高盐逆境下水稻产量。
水稻成株期耐盐基因LOC_Os03g28300的分子标记方法，用一对特异的PCR引物RM15177，PCR扩增待检测水稻育种材料基因组DNA，如果引物对RM15177能够扩增出150bp大小的片段，则该育种材料带有耐盐基因LOC_Os03g28300，RM15177正向引物序列如SEQ IDNo.1所示(TCCTGTGTTGGACGGAGTATGC)，反向引物序列如SEQ ID No.2所示(GCCTCAGAGGTTAGAAGACAGACAGC)。
检测水稻是否含有水稻成株期耐盐基因LOC_Os03g28300的方法，用一对特异的PCR引物RM15177，PCR扩增待检测水稻育种材料基因组DNA，如果引物对RM15177能够扩增出150bp大小的片段，则该育种材料带有耐盐基因LOC_Os03g28300，RM15177正向引物序列如SEQ ID No.1所示(TCCTGTGTTGGACGGAGTATGC)，反向引物序列如SEQ ID No.2所示(GCCTCAGAGGTTAGAAGACAGACAGC)。
本发明的水稻成株期耐盐基因LOC_Os03g28300的分子标记方法或检测水稻是否含有水稻成株期耐盐基因LOC_Os03g28300的方法在水稻耐盐分子标记辅助选择育种中的应用。
本发明利用来自包括中国，印度，美国，菲律宾等在内的77个国家的具有广泛差异的708份水稻核心种质资源，系统分析了其在成株期盐胁迫条件下的耐盐性表现，结合高密度SNP标记及单倍体分析，筛选到一个影响盐胁迫下水稻苗期生长及产量的耐盐基因LOC_Os03g28300。同时，通过根据与目标基因紧密连锁的SNP标记设计PCR引物RM15177，为进一步的分子标记辅助选择育种提供有效的分子标记。耐盐新基因LOC_Os03g28300及其紧密连锁的分子标记RM15177有望应用于水稻耐盐标记辅助选择育种。
与现有技术相比，本发明具有以下有益效果：
1、LOC_Os03g28300是利用具有广泛差异性的来自全球不同国家的700多个种质资源，通过耐盐表型及SNP关联分析，检测到的一个新基因。该基因与成株期盐胁迫条件下水稻产量显著相关。
2、与耐盐基因紧密关联分子标记的确定为分子标记辅助选择耐盐水稻提供了有效信息，能够获得在盐胁迫条件下保持高产的水稻材料。本发明的分子标记可用于筛选水稻成株期盐逆境下育种群体的有利基因型，有效鉴别带有该基因的耐盐个体，加快育种进程。
附图说明
图1感盐品种IR29(P1)与耐盐品种DA DAO TOU(P2)杂交F2群体成株期个体耐盐性表现与RM15177标记基因型图谱。感盐品种IR29与耐盐品种DA DAO TOU杂交的F2群体，经SSR标记RM15177的PCR扩增产物在5％聚丙烯酰胺凝胶电泳的带型图谱及其对应的表型(1-30为随机选取的F2代单株；M为DNA Ladder；P1为170bp，P2为150bp)。
具体实施方式
下面结合具体实施例对本发明作进一步说明，其中所用的方法如无特别说明均为常规方法。
一、耐盐新基因的挖掘
1、供试材料
实验材料为分别来自包括中国，印度，美国，菲律宾等在内的77个国家的708份水稻核心种质资源(包括，400份籼稻，247份粳稻，39份籼粳稻中间型，16份Aus，和6份Basmati)。
2、实验材料的耐盐性表型鉴定
本实验对708份水稻材料进行了连续两年的耐盐表型鉴定，确保表型数据的可靠性。具体操作方法：708份水稻材料在稻田直播，生长到2叶期后，用淡水与海水按一定比例调配好的0.5％浓度的盐水灌溉，该盐水浓度一直保持到水稻成熟。播种1个月后统计出苗数，记载抽穗期，成熟后考查小区产量和小区有效穗数，随机从每小区中选择10穗，考查穗总粒数，穗实粒数、结实率和千粒重等产量相关指标性状。
3、基因型数据处理及全基因组关联分析(GWAS)
利用3K水稻重测序项目构建的Rice SNP-Seek Database(http://snp-seek.irri.org/)中的32M SNP原始基因型数据，按照以下原则处理原始数据：1)同一SNP位点有2个以上等位基因的，只保留频率最高的两个等位基因，其余均按缺失处理；2)当MAF(最小等位基因频率)≤0.05或者缺失率＞20％时，SNP数据删除按缺失处理，共获得3,455,952个高质量SNP标记；3)随机选取部分SNP数据利用R软件包GAPIT程序进行Kinship和主成分分析，剖析群体结构；4)根据Rice Genome Annotation Project(http://rice.plantbiology.msu.edu/)产生的IRGSP-1.0版本的日本晴基因组基因功能注释，提取位于44,332个注释基因上的1,101,404个SNP基因型，与盐胁迫条件下的小区产量及考种的产量相关性状如穗总粒数、穗实粒数、结实率、千粒重等表型，分籼、粳亚群体和整个群体利用软件包中GAPIT程序进行候选基因的全基因组关联分析(GWAS)，关联统计学分析达到P<1.0×10-4水平的SNP定义为与目标性状显著关联的SNP，获得与各个性状显著关联的SNP标记如表1。
表1 与考查性状关联的SNP汇总
SN:出苗数，HD:抽穗期，GY:小区产量，PN:小区穗数，TSN:穗总穗数，FGN:穗实粒数，SSR:结实率，TGW:千粒重
4、耐盐候选基因鉴定
从funRiceGenes数据库(https://funricegenes.github.io/)和QTARO数据库(http://qtaro.abr.affrc.go.jp)中筛选到230个已知盐应答响应相关基因。将检测到与耐盐相关性状关联的903个基因与230个耐胁响应基因进行对比，选择具有相同功能注释和代谢路径的43个关联基因进一步进行单倍型分析。如果目标基因的主要单倍型对应的表型存在显著差异(P<0.001)，我们定义该基因为耐盐候选基因。研究共鉴定出影响成株期耐盐相关性状的15个候选基因(表2)，其中LOC_Os03g28300显著影响盐胁迫条件下水稻结实率进而影响产量，可以解释粳稻亚群中水稻结实率变异的10.6％和产量变异的11.5％。进一步分析发现，LOC_Os03g28300编码含有蛋白质的蛋白激酶结构域。在粳稻类群中鉴定出该基因存在7个SNP变异，其中一个位于外显子上的SNP S3_16283872，由C变T将原来的脯氨酸变成丝氨酸，导致耐盐性增强，而其他SNP均位于UTR区和内含子区。通过鉴定与LOC_Os03g28300紧密连锁的PCR引物RM15177(其中正向引物序列为：TCCTGTGTTGGACGGAGTATGC，反向引物序列为：GCCTCAGAGGTTAGAAGACAGACAGC)，可以进一步为分子标记辅助选择育种提供有效的分子标记。耐盐新基因LOC_Os03g2830及其紧密连锁的分子标记RM15177有望应用于水稻耐盐标记辅助选择育种。
表2 鉴定出与成株期耐盐相关性状关联的15个耐盐候选基因
a从MSU Rice Genome Annotation Project数据库获取的基因；b基因内关联分析峰值SNP对应的统计值；c基因单倍型方差分析；d性状名称同表1；e 2016(Y16)and 2017(Y17).
二、耐盐F2分离群体耐盐基因LOC_Os03g2830的标记验证分析
1、供试材料盐胁迫处理
利用感盐品种IR29与带有耐盐候选基因LOC_Os03g2830的品种DADAO TOU配组构建F2分离群体，该群体计300株在正常水田育秧，单本移栽于0.5％盐胁环境，成熟后考查产量及结实率等产量相关性状。
2、DNA提取、PCR扩增及凝胶电泳
参考Temnykh等(2000年)的DNA提取方法，对各单株分别提取基因组DNA。以各个单株的基因组DNA为模板对RM15177标记进行聚合酶链式(PCR)反应。PCR反应的产物通过聚丙烯酰胺凝胶电泳进行分离，溴化乙啶染色后，在凝胶成像系统下成像。参考双亲的扩增条带，对后代单株的带型进行判别记录。
3、标记辅助选择效果分析和t测验分析
根据后代单株的RM15177标记扩增条带所表示的基因型，将F2群体耐盐和感盐个体与基因型对应情况如图1所示，带有感盐亲本IR29(P1)纯合基因型个体的单株的结实率和产量都较低，带有耐盐亲本DA DAO TOU(P2)纯合基因型个体的结实率和单株产量一般较高，而杂合基因型个体的单株的结实率和产量居中偏向耐盐亲本，表明RM15177对耐盐基因LOC_Os03g2830具有比较理想的辅助选择效果。将F2群体中的个体分成两组，其中一组是RM15177位点基因型为IR29纯合基因型的个体(称为感盐组)，共计71株；另一组是RM15177位点基因型为DA DAO TOU纯合基因型的个体(称为耐盐组)，共计68株。将两组个体考察所得的平均结实率和单株产量进行t测验(表3)，结果表明，两组个体间的结实率和单株产量均达到极显著差异水平，表明RM15177标记附近确实存在一个影响盐胁迫下产量的主效基因LOC_Os03g2830，而且与RM15177标记紧密连锁。
表3 感盐亲本IR29与耐盐亲本DADAO TOU杂交F2群体在RM15177标记位点耐盐和感盐亲本纯合基因型两组个体的单株产量和结实率表现
**表示差异达到0.01水平显著。
序列表
<110> 中国农业科学院作物科学研究所
<120> 水稻全生育期耐盐基因LOC_Os03g28300的分子标记方法及应用
<160> 2
<170> SIPOSequenceListing 1.0
<210> 1
<211> 22
<212> DNA
<213> Oryza sativa
<400> 1
tcctgtgttg gacggagtat gc 22
<210> 2
<211> 26
<212> DNA
<213> Oryza sativa
<400> 2
gcctcagagg ttagaagaca gacagc 26
Claims (2)
1.检测水稻是否含有水稻成株期耐盐基因LOC_Os03g28300的方法，用一对特异的PCR引物对，PCR扩增待检测水稻基因组DNA，如果引物对能够扩增出150bp大小的片段，则该水稻带有耐盐基因LOC_Os03g28300，所述引物对正向引物序列如SEQ ID No.1所示，反向引物序列如SEQ ID No.2所示；所述待检测水稻为感盐品种IR29与耐盐品种DA DAO TOU杂交F2群体。
2.权利要求1所述的检测水稻是否含有水稻成株期耐盐基因LOC_Os03g28300的方法在水稻耐盐分子标记辅助选择育种中的应用。
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