CN109111511B - 超长粒水稻的培育方法 - Google Patents
超长粒水稻的培育方法 Download PDFInfo
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- CN109111511B CN109111511B CN201810206586.5A CN201810206586A CN109111511B CN 109111511 B CN109111511 B CN 109111511B CN 201810206586 A CN201810206586 A CN 201810206586A CN 109111511 B CN109111511 B CN 109111511B
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Abstract
本发明属于水稻分子育种技术领域。具体涉及一种超长粒水稻的培育方法。本发明利用图位克隆的方法,分离克隆了一个新的水稻粒长基因GL3.3(该基因编码的氨基酸序列如SEQ ID NO:1中1‑1275bp所示),该基因与已知粒长基因GS3(该基因编码的氨基酸序列如SEQ ID NO:3中1‑696bp所示)聚合能够形成超长粒长的水稻材料。利用GS3和GL3.3的KASP分子标记引物能够有效的在育种中选择并聚合二者的优势等位基因,选择具有gs3gl3.3基因型组合的超长粒的家系,可以显著提高稻米品质的育种效率。
Description
技术领域
本发明属于水稻分子育种技术领域。具体涉及一种超长粒水稻的培育方法。本发明利用图位克隆的方 法分离克隆了一个新的水稻粒长基因GL3.3,该基因与已知粒长基因GS3聚合能够形成超长粒长的水稻材 料。利用GS3和GL3.3的KASP分子标记引物能够有效的在育种中选择并聚合二者的优势等位基因,选择具 有gs3gl3.3基因型组合的超长粒的家系,可以显著提高稻米品质的育种效率。
背景技术
水稻是我国的主要粮食作物,而水稻的外观品质是决定水稻商品价值的重要指标。长久以来,我国水 稻育种家与种业公司一直将产量作为育种的终极目标,而水稻品质的改良则比较滞后(孔宪琴等,2013)。 我国大部分审定品种的稻米品质较为一般,无法满足国民对品质优良稻米的需求,加工成商品米后价格较 低,一定程度上加深了“稻强米弱”的现象,导致我国稻米进口量的上升(孔宪琴等,2013;于红燕和刘世 义,2016)。因粳稻品质普遍优于籼稻,最近几年,常规粳稻品种在我国水稻主要种植地区种植面积逐年 扩大。我国品质优良的籼稻品种非常少,因此籼稻特别是杂交籼稻的外观品质的遗传改良迫在眉睫。
稻米的外观品质主要由粒形和堊白决定,粒形修长、垩白率低的籼稻受到消费者的青睐(Bao,2014)。 传统育种中改良稻米的外观品质,通常是将产量高的品系与品质优的品系进行杂交,然后不断的同产量高 的品系自交从而得到产量品质都优良的品系。但是,由于粒长、堊白等外观品质都属于数量性状,由多个 基因调控,需要在较大的群体中进行选择,并且性状考察也比较耗时耗力,实际改良过程难度较大。通过 分子育种的方法,利用已克隆粒形、堊白基因的分子标记,将有利的等位基因聚合在一起,只需鉴定基因 型,无需鉴定表型,节省了人力物力,是改良稻米外观品质的有效方法。
分子育种具有许多优势,但是该方法首先要有稳定可靠的基因资源和基因型组合。迄今为止,研究人 员利用不同的群体和方法,克隆一些稻米粒形和堊白的主效基因。品种测序和关联分析的研究结果都表明 GW5和GS3分别是水稻粒宽和粒长最主要和主效的基因(Takanokai等,2009;Duan等,2017;Zhou等,2017)。 而其它的粒形主效基因大多属于稀有变异,如粒宽基因GW2、粒长基因GL3、种子大小基因GS2(Song等, 2007;Qi等,2012;Hu等,2015)。还有一些重要而非主效的粒形基因,如种子大小基因GS5、长宽比基 因GW8和长宽比基因GW7等(Li等,2011;Wang等,2012;Wang等,2015)。而堊白基因目前只有Chalk5 被克隆(Li等,2014)。这些基因为稻米外观品质的改良提供了宝贵的基因资源。虽然克隆的粒形基因已 经不少,但是可供用来改良外观品质的组合很少。Wang等(2012)利用将GS3和GW8无功能的等位型gs3 和gw8聚合到短圆粒材料HJZ74中,成功将该材料改良成修长的粒形。Wang等(2014)后来通过直接研究 具有修长粒形的材料台风优55和台风优208,发现它们因为就有gs3和GW7的基因型组合而表现为修长的粒 形。
因此,从现有材料中直接挖掘有效的基因型组合是更为合理有效的方法。申请人利用自然存在的超长 粒材料与短粒材料进行杂交,然后解析造成超长粒形的原因,最后总结出有效的基因型组合用来改良水稻 粒长。通过开发出有效基因型组合的分子标记,为稻米的粒形改良提供有效的技术支撑。
发明内容
本发明的目的是提供一种培育超长粒水稻的方法,通过试验检测两个粒长基因的功能标记,可以在苗 期就准确预测水稻植株的粒长水平,从而加快超长粒水稻家系的选择进度。
本发明鉴定了两个粒长的基因,并提供了功能性的分子标记或称标记引物。借助这些分子标记辅助选 择技术可以有目的地将柱头外露基因精确导入和聚合,从而高效率快速选育具有超长粒形的家系,节约人 力物力,保持水稻杂交制种的稳产和高产。
本发明通过以下技术方案实现:
申请人通过利用基因GS3(登陆号Os03g0407400)的功能性分子标记引物Kasp-GS3通过PCR扩增,然 后经过荧光定量PCR读带以检测该基因的基因型,所述分子标记引物的DNA序列如下所示:
左端引物序列1(Kasp-GS3F1):GAAGGTGACCAAGTTCATGCTACGCTGCCTCCAGATGCTGC,
左端引物序列2(Kasp-GS3F2):GAAGGTCGGAGTCAACGGATTACGCTGCCTCCAGATGCTGA,
右端引物序列(SF28R):GTAGTACAAAAAGAAACAGC;
申请人又通过另一个基因GL3.3(登陆号Os03g0841800)的功能性分子标记引物Kasp-GL3.3通过PCR 扩增,然后通过荧光定量PCR读带以检测该基因的基因型,所述分子标记引物的DNA序列如下所示:
左端引物序列1(Kasp-GL3.3F1):GAAGGTGACCAAGTTCATGCTTTTTGGGGTTGTATATCAGG,
左端引物序列2(Kasp-GL3.3F2):GAAGGTCGGAGTCAACGGATTTTTTGGGGTTGTATATCAGA,
右端引物序列(Kasp-GL3.3R):CACATAGAGAAATTTTTAC;
申请人通过验证,证明上述两个分子标记引物(即,Kasp-GS3和Kasp-GL3.3)可以应用于选育超长粒 形水稻家系的遗传改良。
申请人提供了一种筛选水稻粒长主效基因GS3的分子标记方法,其步骤包括:利用粒长主效基因GS3 的分子标记引物(Kasp-GS3)扩增待检水稻基因组DNA,并利用荧光定量PCR检测所得的扩增产物,带型 聚类于X轴,读带基因型为Allele X(5016),证明水稻粒长主效基因GS3的增效等位基因gs3的存在。
与此同时,申请人提供了另一种筛选水稻粒长基因GL3.3的分子标记方法,其步骤包括:利用粒长基 因GW5的分子标记(即,Kasp-GL3.3)扩增待检水稻基因组DNA,并利用荧光定量PCR检测所得的扩增产 物,带型聚类于X轴,读带基因型为Allele X(5016),证明水稻长粒主效基因GL3.3的增效等位基因gl3.3 的存在。
申请人提供了一种利用分子标记引物在选育超长粒水稻的辅助选择中的应用,所述的应用步骤包括:
(1)将鉴定为性状优良的短粒和中长粒骨干材料分别与具有高超长粒基因型组合gs3gl3.3的栽培稻 “南洋占”杂交,分别得到F1A和F1B;
(2)以步骤(1)中得到的F1A与短粒骨干材料连续回交5代,每代利用分子标记引物Kasp-GS3和分子 标记引物Kasp-GL3.3鉴定真杂种,直到获得近等基因系BC5F1A;以步骤(1)中得到的F1B与中长粒骨干材 料连续回交5代,每代利用分子标记引物Kasp-GL3.3鉴定真杂种,直到获得近等基因系BC5F1B;
(3)将BC5F1A自交得到BC5F2A,利用分子标记引物Kasp-GS3和分子标记引物Kasp-GL3.3鉴定出基因 型为纯合基因型组合gs3gl3.3的单株,即为改良后的短粒骨干材料;将BC5F1B自交得到BC5F2B,利用分子 标记引物Kasp-GL3.3鉴定基因型为纯合基因型组合gl3.3的单株,
其中:
所述的分子标记引物Kasp-GS3的核苷酸序列如序列表SEQ ID NO:5至SEQ ID NO:7所示所示;
所述的分子标记引物Kasp-GL3.3的核苷酸序列如序列表SEQ ID NO:8至SEQ IDNO:10所示。
本发明的优点在于:
(1)本发明发现了一个新的粒长基因GL3.3,该基因能够提高水稻的粒长。并且GL3.3与已克隆粒长 基因GS3存在上位性互作,二者的聚合能够形成超长的水稻粒形。前人虽然克隆一些粒长基因,但是对于 这些基因的聚合效应没有进行研究。并且一般两个基因的聚合效应会小于两个基因单独效应的累加,而 GL3.3和GS3的聚合效应大于两个基因单独效应的累加。
(2)本发明鉴定的粒长主效基因经过了遗传转化验证。利用GL3.3的转基因材料,申请人验证了该基 因能够有效的提高水稻的粒长。GL3.3通过增加颖壳纵向细胞的长度来提高水稻的粒长而不影响细胞的宽 度。因此GL3.3是一种特殊的类型,与之前发现的粒形基因都不相同,能够更有效的用于粒长的改良。
(3)本发明提供了粒长主效基因GL3.3的功能性分子标记。功能性的分子标记检测水稻植株中的粒长 基因位点,仅在苗期就能快速鉴定出长粒的纯合基因型单株,及时淘汰短粒单株,不仅节约生产成本,而 且大大提高了选择效率,极大地缩短水稻品种的育种周期。而前人研究大多都没有提供基因的功能性分子 标记。
附图说明
序列表SEQ ID NO:1是本发明的粒长基因GL3.3的编码区(CDS)的核苷酸序列及其对应的氨基酸序列。
序列表SEQ ID NO:2是粒长基因GL3.3编码的蛋白质序列。
序列表SEQ ID NO:3是粒长基因GS3的编码区(CDS)的核苷酸序列及其对应的氨基酸序列。
序列表SEQ ID NO:4是粒长基因GS3编码的蛋白质序列。
序列表SEQ ID NO:5是左端引物序列1(即分子标记引物Kasp-GS3的左端引物序列1)。
序列表SEQ ID NO:6是左端引物序列2(即分子标记引物Kasp-GS3的左端引物序列2)。
序列表SEQ ID NO:7是右端引物序列(即分子标记引物Kasp-GS3的右端引物序列)。
序列表SEQ ID NO:8是左端引物序列1(即分子标记引物Kasp-GL3.3的左端引物1)。
序列表SEQ ID NO:9是左端引物序列2(即分子标记引物Kasp-GL3.3的左端引物2)。
序列表SEQ ID NO:10是右端引物序列(即分子标记引物Kasp-GL3.3的右端引物)。
图1:是本发明的总体技术路线图。
图2:本发明粒长基因GL3.3的图位克隆。附图标记说明:图2中的A图是双亲和近等基因系的种子的 外观形态;图2中的B图是重组自交系中粒形QTL初定位的结果;图2中的C图和图2中的D图是GL3.3精细定 位过程;图2中的E图是候选基因在双亲间的等位差异。
图3:本发明的粒长基因GL3.3的遗传转化验证过程。附图标记说明:图3中的A图至E图是水稻品种珍 汕97(ZS97)和两种用CRISPR***敲除材料的种子后代的表型差异:其中,图3中的A图是ZS97与敲除GL3.3 基因的突变体材料的水稻种子;图2中的B图是ZS97与与两种突变体材料的核苷酸序列的差异比较;图3中 的C图是转基因水稻种子粒长的表型差异;图3中的D图是转基因种子粒宽的表型差异;图3中的E图是转基 因水稻种子的千粒重表型差异;图3中F图至图3中的I图为GL3.3基因互补对水稻品种表型差异的检测,其 中:图3中的F图是水稻品种“南阳占”的阳性和阴性材料的种子表型的差异;图3中的G图是“南阳占”的 阳性和阴性材料的种子的粒长;图3中的H图是“南阳占”的阳性和阴性材料的种子的粒宽;图3中的I图是 “南阳占”的阳性和阴性材料的种子的千粒重的表型差异。
图4:本发明的粒长基因GL3.3的表达模式与功能验证结果。附图标记说明:图4中的A图是GL3.3亚细 胞定位;图4中的B图是各种组织的GUS染色;图4中的C图是近等基因系中GL3.3在各个时期的表达量;图4 中的D图是近等基因系的颖壳;图4中E是近等基因系纵向细胞扫描电镜图;图4中F和G分别是近等基因系 纵向细胞数目和细胞长度的比较。
图5:本发明的粒长基因GL3.3的群体遗传学分析。附图标记说明:图5中A图和:图5中的B图分别是 GL3.3在4726种栽培稻中的等位变异和单倍型划分;图5中的C图和图5中的D图是GL3.3不同等位型在不同 亚群中的表型差异;图5中E的图是为GL3.3不同等位型的核酸多态性差异;图5中的F图和G图是GL3.3不同 等位型的延伸性单倍型纯合性分析。
图6:本发明的粒长基因GL3.3的上位性效应测试。附图标记说明:图6中的A图为GS3和GL3.3在粳稻 中组成的四种基因型组合的粒长分布;图6中的B图为GS3和GL3.3在重组自交系群体中的互作分析;图6中 的C图是重组自交系中四种基因型组合家系的种子;图6中的D图至图6中的M图为GL3.3近等基因系各个农 艺性状的表型比较。图中所有的P值都基于两尾t测验。
图7:本发明的粒长基因功能性Kasp标记鉴定方法。附图标记说明:图7中的A图是Kasp-GS3扩增产 物荧光定量PCR读带结果;图7中的B图是Kasp-GL3.3扩增产物荧光定量PCR读带结果。其中:X轴和Y轴分 别代表两种荧光信号的强弱。
图8:本发明的GL3.3基因在栽培稻中粒长改良的分子标记辅助选择方法应用的流程图。
具体实施方式
本发明的总体技术路线:
本发明按照以下总体技术路线来进行:
1、基因精细定位;
2、基因功能验证和效应分析(见图1)。
总体技术步骤1,基因的精细定位是按照遗传学上常用的图位克隆方法实施(具体参考实施例1)。
(1)材料的选择。选择目标性状差异明显的双亲构建遗传群体更有可能定位效应大的QTL。初步定 位的群体一般为双亲杂交产生的F2群体或者重组自交系(RIL)群体(方宣钧等,2000;Yano and Sasaki, 1997)。所述的RIL群体由于接近纯系,能够重复多代多环境考察表型,能够有效而稳定的检测和验证QTL。
(2)构建近等基因系。为了实现对QTL的精细定位,需要通过与亲本之间进行回交,构建近等基因 系(NIL),从而消除背景的影响,使目标QTL的效应呈现为单一孟德尔因子的变化(Tuinstra et al.,1997)。 一般回交到BC3代或者BC4代,背景比较纯净,即可选择目标区段杂合的单株进行自交获得大量的BC3F2或 BC4F2用于筛选重组单株,实现QTL的精细定位。
(3)利用初定位时双侧标记筛选重组单株,然后通过在该区间加密标记,采用染色体步移的方法来 缩小定位区间。如果无法根据当代表型确认重组某些组单株的基因型,则需要对这些单株进行后代测验来 确认它们的基因型。后代测验即种植某个重组单株的自交F2群体,然后考察群体的表型是否发生分离。如 发生分离则确认该重组单株基因型为杂合型;如未发生分离则确认该重组单株的基因型为纯合型。利用上 述方法可将QTL定位到足够小的区间,通常只包含一个候选基因。如果含有多个候选基因,可以结合生物 信息学的方法和表达量分析方法进行排除。另外,通过对双亲中候选基因进行测序来寻找等位变异也是确 认和验证候选基因的有效方法。
总体技术步骤2,即基因的功能验证采用常规遗传转化的方法实施(具体参考实施例2)。
遗传转化的准备工作分为两步同时进行:第一步是受体细胞的培养;第二步是目的基因的制备。
图位克隆过程中的遗传转化,一般选择受体亲本作为转化对象。在水稻中,粳稻的转化效率远高于籼 稻,所以在很多情况下申请人都是选择粳稻材料作为转化对象。首先对受体材料即糙米按常规方法进行组 织培养,待诱导分化得到愈伤组织后进行常规继代培养。与此同时构建表达载体和将目的片段克隆到表达 载体上。接下来选择优质的愈伤组织进行预培养,这样就可以利用纯化后的载体进行农杆菌转化或其他转 化。转化后的细胞首先要通过筛选,选择阳性的进行植株再生培养。对再生植株进行表型鉴定和基因型鉴 定,直到获得后代分离出的单拷贝的阳性和阴性植株。通过对阳性阴性材料的随机区组种植和表型考察确 定目的基因的效应。
实施例1:粒长主效基因GL3.3的定位
1.重组自交系群体的构建
利用超长粒粳稻品种南阳占(NYZ)和短粒籼稻品种珍汕97(ZS97)进行杂交获得F1(双亲种子形态 参见图2中的A图),然后再进行自交,共获得190株F2群体。这190个单株的F2群体,可以按照“一粒传”的 方法(方宣钧等,2000),进行不断自交直到F7代(图1)。
2.基因型鉴定和遗传图谱构建
基因型的鉴定方法为常规SSR分析方法。具体步骤,首选是筛选多态性SSR引物。本发明共筛选了574 对SSR引物,其中RM系列的引物为452对,MRG系列的引物为118对。RM系列引物在水稻品种南阳占和珍 汕97间有多态性的标记为185对,MRG系列引物在珍汕97为54对。由于多态性标记比较充足,遗传连锁图 谱主要由RM系列引物构建,MRG系列引物主要用来填补缺失(GAP)。利用SSR分析获得190个标记的基 因型后,申请人利用MAPMAKER/Exp3.0软件的“Kosambi”作图函数绘制遗传连锁图。最终获得的遗传图 谱全长1362.1cM,标记间的平均距离为7.77cM(王令强,2007)。
3.粒长QTL的初步定位
将190份RILs材料于2001年和2002年5月到10月连续两年种植于湖北省武汉市华中农业大学试验田。每 个家系种植2行,每行10株,株行距为16.5cm×26.4cm。每个家系考察中间的8株的粒长,8株的均值作为该 家系的粒长表型值。QTL的鉴定基于基因型、表型和遗传连锁图,利用WinQTLCart2.5软件(Zeng,1994) 的复合区间作图法,以2cM为步长在全基因组检测粒长相关的QTL。QTL检测的阈值为LOD>2.5,即认为 该区间存在影响粒长的QTL。QTL扫描的峰形图利用R软件绘制(Ihaka and Gentleman,1996)。总共检 测到6个粒长的QTL,其中位于第三染色体的qGS3和qGL3.3效应最为显著(见图2中的B图)。
4.GL3.3的精细定位
为了精细定位GL3.3,申请人构建了ZS97背景的BC4代近等基因系(NIL)。NIL-NYZ具有显著高于 NIL-ZS97的粒长(图2中的A图和图6中的G图)。在5950株BC4F2单株中,申请人鉴定到了187个在标记D3-3 和RM442间发生交换的重组单株。利用这些重组单株,申请人将GL3.3定位到D3-8和D3-9之间,约为15kb 的区间(见图2中的C图至图2中的E图)。这个区间包含两个开放阅读框,Os03g0841800和Os03g0841900。 通过双亲比较测序发现,后者在双亲间无功能性变异。而Os03g0841800在第三外显子后有一个G到A的变 异,该变异导致南阳占(NYZ)中该基因的转录产物缺少第三和第四外显子(见图2中的E图)。因此,申 请人初步确认Os03g0841800为GL3.3的候选基因
实施例2:GL3.3的功能验证和效应分析
1、GL3.3的功能验证
Os03g0841800编码一个6281kb的开放阅读框(ORF),该ORF包含12个外显子和11个内含子,在粳稻 “日本晴”参考基因组中注释为GSK5(Kawahara et al.,2013)。为了进一步确认Os03g0841800是否就 是GL3.3,申请人利用CRISPR/Cas9***(Shan et al.,2013)在短粒籼稻珍汕97中敲除了GSK5基因。申请 人获得了两种导致该基因转录提前终止的突变体(图3中的A图至图3中的E图)。两种突变型植株相比野生 型ZS97(非转基因)都具有显著提高的粒长和粒重(见图3中的C图至E图3中的图)。另一方面,申请人 在“NYZ”中互补转化了“ZS97”中的GL3.3的等位型基因(Hiei et al.,1994)。分析结果表明,转基 因阴性植株具有比阳性植株显著更长的粒形和更高的千粒重(见图3中的F图至图3中的I图)。这些结果表 明GSK5就是GL3.3并且该基因为一个负调控水稻粒长和千粒重的基因。
2.GL3.3的表达模式和功能
为了定位GL3.3在细胞中表达的位置,申请人构建了CaMV 35S启动子驱动的GL3.3-黄色荧光蛋白融合 (YFP)表达载体(Hajdukiewicz et al.,1994)。转化水稻原生质体(Xue et al.,2008)的结果表明 GL3.3-YFP定位在细胞核,这表明GL3.3在细胞核内表达(图4中的A图)。申请人利用荧光定量PCR (RT-PCR)(Livak et al.,2001)和常规GUS染色方法来分析GL3.3基因的时空表达特性。GUS染色结 果表明,GL3.3基因在被试验的水稻品种的胚乳、幼苗、茎和花器官中大量表达(图4中的B图)。NIL-NYZ 和NIL-ZS97的RT-PCR,结果表明GL3.3基因的mRNA在水稻品种的幼苗、幼穗、胚乳、茎和根中表达(图 4中的C图)。因此推定GL3.3基因是一个在水稻各个组织时期中组成型表达的基因。由于NIL-NYZ的颖壳 在受精前就比NIL-ZS97长,所以申请人利用扫描电镜分析了两个NILs的颖壳外表面来解析颖壳长度差异的 具体原因(见图4中的D图至图4中的G图)。发现NIL-NYZ的纵向细胞数目显著少于NIL-ZS97的纵向细胞 数目;而NIL-NYZ的纵向细胞长度要显著大于NIL-ZS97纵向细胞的长度。因此,NIL-NYZ颖壳纵向细胞数 目~10%的降低和细胞长度~20%的增加导致了整体颖壳长度的增加。
3.GL3.3的等位型与人工选择
由于GL3.3是一个负调控粒长的基因,因此南阳占(NYZ)含有一种突变型的gl3.3。在4726份栽培稻 材料中,NYZ所含有的这种等位型的比例为1%,并且这种等位型只出现在粳稻中,因此申请人称其为gl3.3Jap (图5中的A图,图5中的B图)。在粳稻中,具有gl3.3Jap这种等位型的品种相比野生型的品种具有显著较长 的粒形(图5中的D图)。通过进一步分析GL3.3的自然变异,申请人发现了另一种功能性的变异:即,在 第6外显子上一个由C到A的转换,导致氨基酸序列从组氨酸到谷氨酰胺的变化。这种等位型在4726份栽培 稻中的比例为5%,并且主要存在于澳洲稻中,因此申请人将其称为gl3.3Aus(图5中的A图,图5中的B图)。 在澳洲稻中,具有这种等位型的品种相比野生型的品种具有显著较长的粒形(图5中的C图)。利用DnaSP 软件(Rozas等,2003)计算两种突变型和野生型的核酸多态性,申请人发现两种突变型都具有显著较低 的多态性(图5中的E图),可能在育种的过程中受到过人工选择。申请人进一步研究在澳洲稻和粳稻中GL3.3 野生型和突变型的延伸性单倍型纯合性,发现野生型的连锁不平衡衰退很快,而突变型具有衰退的比较慢, 表明突变型受到了人工选择(图5中的F图,图5中的G图)。
4.GL3.3与GS3上位性互作形成超长粒形
虽然gl3.3Aus和gl3.3Jap都影响水稻粒长的自然变异,但是相比GL3.3在作图群体中的加性效应 (a=0.35mm),gl3.3Aus的效应偏小(a=0.24mm)而gl3.3Jap的效应显著偏大(a=1.36mm)(见图5中的C图, 图5中的D图)。由于GL3.3在粳稻中的效应过大,超过了已知的任何粒形的主效基因,申请人推测可能GL3.3 在粳稻中和某个粒长基因存在远程的连锁不平衡。通过分析粒形主效基因GS3的基因型,申请人发现92% 具有gl3.3Jap等位型的粳稻品种也具有gs3等位型,表明gs3在粳稻中与gl3.3Jap远程连锁(见图6中的A图)。 前人研究表明gs3在育种过程中受到人工选择(Takanokai等,2009),因此gl3.3Jap与gs3一起在超长粒粳稻 品种中受到选择。其实考虑了GS3的效应,GL3.3在粳稻中的效应(a=0.45mm)依然大于作图群体中的效 应(图6中的A图),因此申请人怀疑GL3.3可能与GS3存在互作。通过重新分析重组自交系群体中GS3和 GL3.3的效应,申请人发现这两个基因存在明显的上位性互作(图6中的B图,图6中的C图)。这种互作使 得GL3.3在GS3无功能的背景下效应的粳稻,即gs3gl3.3会形成一种超长的粒形。GL3.3在“NYZ”互补转基 因材料中的效应大于“ZS97”敲除转基因材料的效应也进一步说明了这一点(见图3)。
实施例3:GL3.3在水稻粒长改良中的应用
本发明定位到的GL3.3为一个稀有且主效的粒长基因,并且能够和GS3互作而发挥更强的功能形成超长 粒表型,能有效地提高现有栽培稻品种的粒长性状。可以在育种过程中利用GL3.3的分子标记进行辅助选 择能够减少种植面积、简化育种流程和节约人力物力,以提高育种效率。因此将水稻种质材料(例如本实 验中的品种“南阳占”)中具有GL3.3无功能等位型(gl3.3Aus和gl3.3Jap)的材料用于水稻粒长性状的改良, 具有十分广泛的应用前景。
本实施例的技术路线可参见图7所述的方法,图7是申请人设计的利用GL3.3优势等位基因改良水稻粒 长的总体技术流程。该技术流程包括:首先选择生产上的短粒或者中长粒骨干水稻品种材料,即简称的“骨 干材料”(这些“骨干材料”都是可以得到的,包括在生产上具有优良性状而粒长有待改良的常规稻品种, 以及不育系和恢复系,鉴定上述骨干材料的方法都是现有报道的方法,不存在探索性劳动,获得不育系和 恢复系的方法也都是现有报道的方法和本领域的公知常识),与具备优势基因型组合gs3gl3.3的栽培稻材 料(例如“南阳占”,但不限于此)进行杂交,可分别得到短粒骨干材料杂交种F1代(或称F1A)和中长粒 骨干材料F1代(或称F1B)。将F1A与短粒骨干材料连续回交5代(这是领域的公知方法)即可获得近等基因 系,每代利用分子标记引物Kasp-GS3和Kasp-GL3.3选择这两个位点的真杂种单株(图7),直到得到BC5F1A。 相对应的,F1B与中长粒骨干材料连续回交5代获得近等基因系,每代都利用分子标记引物Kasp-GS3和 Kasp-GL3.3选择这两个位点的真杂种单株,直到得到BC5F1B。短粒骨干材料和中长粒骨干材料的近等基因 系BC5F1A和BC5F1B分别自交,获得BC5F2A和BC5F2B。再利用分子标记引物Kasp-GS3和Kasp-GL3.3鉴定出 BC5F2A中具有纯合gs3gl3.3基因型组合的单株,即为柱头外露率改良后的短粒骨干水稻材料。再利用分子 标记引物Kasp-GS3和Kasp-GL3.3鉴定出BC5F2B中具有纯合gl3.3基因型组合的单株,即为柱头外露率改良后 的中长粒水稻骨干材料。改良后的水稻短粒骨干材料和水稻中长粒骨干材料粒形已经成为超长粒,故可称 之为水稻超长粒骨干材料。
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Phe Gly Val Val Tyr Gln Ala Lys Cys Arg Glu Thr Gly Glu Ile Val
100 105 110
Ala Ile Lys Lys Val Leu Gln Asp Lys Arg Tyr Lys Asn Arg Glu Leu
115 120 125
Gln Ile Met His Met Leu Asp His Pro Asn Ile Val Gly Leu Lys His
130 135 140
Tyr Phe Phe Ser Thr Thr Glu Arg Asp Glu Leu Tyr Leu Asn Leu Val
145 150 155 160
Leu Glu Tyr Val Pro Glu Thr Val Asn Arg Ile Ala Arg Gln Tyr Ser
165 170 175
Arg Met Asn Gln Arg Val Pro Leu Ile Tyr Val Lys Leu Tyr Thr Tyr
180 185 190
Gln Ile Cys Arg Ala Leu Ala Tyr Ile His Asn Cys Val Gly Ile Cys
195 200 205
His Arg Asp Ile Lys Pro Gln Asn Val Leu Val Asn Pro His Thr His
210 215 220
Gln Leu Lys Ile Cys Asp Phe Gly Ser Ala Lys Val Leu Val Lys Gly
225 230 235 240
Glu Pro Asn Ile Ser Tyr Ile Cys Ser Arg Tyr Tyr Arg Ala Pro Glu
245 250 255
Leu Ile Phe Gly Ala Thr Glu Tyr Thr Thr Ala Ile Asp Leu Trp Ser
260 265 270
Thr Gly Cys Val Met Ala Glu Leu Leu Leu Gly Gln Pro Leu Phe Pro
275 280 285
Gly Glu Ser Gly Val Asp Gln Leu Val Glu Ile Ile Lys Val Leu Gly
290 295 300
Thr Pro Thr Arg Glu Glu Ile Lys Cys Met Asn Pro Asn Tyr Thr Glu
305 310 315 320
Phe Lys Phe Pro Gln Ile Lys Ala His Pro Trp His Lys Val Phe Gln
325 330 335
Lys Arg Leu Pro Pro Glu Ala Val Asp Leu Val Ser Arg Phe Leu Gln
340 345 350
Tyr Ser Pro Asn Leu Arg Cys Thr Ala Met Glu Ala Cys Met His Pro
355 360 365
Phe Phe Asp Glu Leu Arg Asp Pro Asn Thr Arg Leu Pro Asn Gly Arg
370 375 380
Pro Leu Pro Pro Leu Phe Asn Phe Arg Thr Gln Glu Leu Asn Gly Ile
385 390 395 400
Pro Pro Glu Ala Ile Glu Arg Leu Val Pro Glu His Ala Arg Arg Gln
405 410 415
Ser Leu Phe Met Ala Leu Arg Thr
420
<210> 3
<211> 699
<212> DNA
<213> 水稻(Oryza sativa)
<220>
<221> gene
<222> (1)..(699)
<220>
<221> CDS
<222> (1)..(699)
<400> 3
atg gca atg gcg gcg gcg ccc cgg ccc aag tcg ccg ccg gcg ccg ccc 48
Met Ala Met Ala Ala Ala Pro Arg Pro Lys Ser Pro Pro Ala Pro Pro
1 5 10 15
gac cca tgc ggc cgc cac cgc ctc cag ctc gcc gtc gac gcg ctc cac 96
Asp Pro Cys Gly Arg His Arg Leu Gln Leu Ala Val Asp Ala Leu His
20 25 30
cgc gag atc gga ttc ctc gag ggt gaa ata aat tca atc gaa ggg atc 144
Arg Glu Ile Gly Phe Leu Glu Gly Glu Ile Asn Ser Ile Glu Gly Ile
35 40 45
cac gct gcc tcc aga tgc tgc aga gag gtt gac gaa ttc atc gga aga 192
His Ala Ala Ser Arg Cys Cys Arg Glu Val Asp Glu Phe Ile Gly Arg
50 55 60
act cct gat cca ttc ata acg att tca tcg gag aag cga agt cat gat 240
Thr Pro Asp Pro Phe Ile Thr Ile Ser Ser Glu Lys Arg Ser His Asp
65 70 75 80
cat tct cac cac ttc ttg aag aag ttt cgc tgt ttg tgc aga gca agt 288
His Ser His His Phe Leu Lys Lys Phe Arg Cys Leu Cys Arg Ala Ser
85 90 95
gcg tgc tgc ctc agc tac ctc tcc tgg atc tgc tgc tgc agc agc gcc 336
Ala Cys Cys Leu Ser Tyr Leu Ser Trp Ile Cys Cys Cys Ser Ser Ala
100 105 110
gcc ggc ggc tgc tca tcc tcc tcc tcc tcc tcc ttc aac ctc aag agg 384
Ala Gly Gly Cys Ser Ser Ser Ser Ser Ser Ser Phe Asn Leu Lys Arg
115 120 125
ccg agc tgc tgc tgc aac tgc aac tgc aac tgc tgc tcc tcc tcc tcc 432
Pro Ser Cys Cys Cys Asn Cys Asn Cys Asn Cys Cys Ser Ser Ser Ser
130 135 140
tcc tca tgt ggg gcg gcg tta acg aag agt ccg tgt cgc tgc cgc cgc 480
Ser Ser Cys Gly Ala Ala Leu Thr Lys Ser Pro Cys Arg Cys Arg Arg
145 150 155 160
cgc agc tgc tgc tgc cgt cgc tgc tgc tgc ggc ggc gtc ggc gtc cgc 528
Arg Ser Cys Cys Cys Arg Arg Cys Cys Cys Gly Gly Val Gly Val Arg
165 170 175
gcg tgc gcg agc tgc agc tgc tcc ccg ccg tgc gcg tgc tgc gcg ccg 576
Ala Cys Ala Ser Cys Ser Cys Ser Pro Pro Cys Ala Cys Cys Ala Pro
180 185 190
ccg tgc gcg gga tgc tcg tgc cgc tgc acc tgc ccg tgc ccg tgc ccc 624
Pro Cys Ala Gly Cys Ser Cys Arg Cys Thr Cys Pro Cys Pro Cys Pro
195 200 205
ggc ggc tgc tcc tgc gcg tgc ccg gcg tgc agg tgc tgc tgc ggc gtc 672
Gly Gly Cys Ser Cys Ala Cys Pro Ala Cys Arg Cys Cys Cys Gly Val
210 215 220
cct cgt tgc tgc ccc ccc tgc ttg tga 699
Pro Arg Cys Cys Pro Pro Cys Leu
225 230
<210> 4
<211> 232
<212> PRT
<213> 水稻(Oryza sativa)
<400> 4
Met Ala Met Ala Ala Ala Pro Arg Pro Lys Ser Pro Pro Ala Pro Pro
1 5 10 15
Asp Pro Cys Gly Arg His Arg Leu Gln Leu Ala Val Asp Ala Leu His
20 25 30
Arg Glu Ile Gly Phe Leu Glu Gly Glu Ile Asn Ser Ile Glu Gly Ile
35 40 45
His Ala Ala Ser Arg Cys Cys Arg Glu Val Asp Glu Phe Ile Gly Arg
50 55 60
Thr Pro Asp Pro Phe Ile Thr Ile Ser Ser Glu Lys Arg Ser His Asp
65 70 75 80
His Ser His His Phe Leu Lys Lys Phe Arg Cys Leu Cys Arg Ala Ser
85 90 95
Ala Cys Cys Leu Ser Tyr Leu Ser Trp Ile Cys Cys Cys Ser Ser Ala
100 105 110
Ala Gly Gly Cys Ser Ser Ser Ser Ser Ser Ser Phe Asn Leu Lys Arg
115 120 125
Pro Ser Cys Cys Cys Asn Cys Asn Cys Asn Cys Cys Ser Ser Ser Ser
130 135 140
Ser Ser Cys Gly Ala Ala Leu Thr Lys Ser Pro Cys Arg Cys Arg Arg
145 150 155 160
Arg Ser Cys Cys Cys Arg Arg Cys Cys Cys Gly Gly Val Gly Val Arg
165 170 175
Ala Cys Ala Ser Cys Ser Cys Ser Pro Pro Cys Ala Cys Cys Ala Pro
180 185 190
Pro Cys Ala Gly Cys Ser Cys Arg Cys Thr Cys Pro Cys Pro Cys Pro
195 200 205
Gly Gly Cys Ser Cys Ala Cys Pro Ala Cys Arg Cys Cys Cys Gly Val
210 215 220
Pro Arg Cys Cys Pro Pro Cys Leu
225 230
<210> 5
<211> 41
<212> DNA
<213> 水稻(Oryza sativa)
<220>
<221> primer_bind
<222> (1)..(41)
<400> 5
gaaggtgacc aagttcatgc tacgctgcct ccagatgctg c 41
<210> 6
<211> 41
<212> DNA
<213> 水稻(Oryza sativa)
<220>
<221> primer_bind
<222> (1)..(41)
<400> 6
gaaggtcgga gtcaacggat tacgctgcct ccagatgctg a 41
<210> 7
<211> 20
<212> DNA
<213> 水稻(Oryza sativa)
<220>
<221> primer_bind
<222> (1)..(20)
<400> 7
gtagtacaaa aagaaacagc 20
<210> 8
<211> 41
<212> DNA
<213> 水稻(Oryza sativa)
<220>
<221> primer_bind
<222> (1)..(41)
<400> 8
gaaggtgacc aagttcatgc tttttggggt tgtatatcag g 41
<210> 9
<211> 41
<212> DNA
<213> 水稻(Oryza sativa)
<220>
<221> primer_bind
<222> (1)..(41)
<400> 9
gaaggtcgga gtcaacggat tttttggggt tgtatatcag a 41
<210> 10
<211> 19
<212> DNA
<213> 水稻(Oryza sativa)
<220>
<221> primer_bind
<222> (1)..(19)
<400> 10
cacatagaga aatttttac 19
Claims (2)
1.粒长主效基因GS3和GL3.3的超长粒基因型组合gs3gl3.3在培育超长粒水稻中的应用,其特征在于,所述GL3.3基因编码的蛋白质序列如SEQ ID NO:2所示,所述的GS3基因编码的蛋白质序列如SEQ ID NO:4所示。
2.一种分子标记引物Kasp-GL3.3在培育超长粒水稻中的应用,其特征在于,所述分子标记引物Kasp-GL3.3的核苷酸序列如SEQ ID NO:8至SEQ ID NO:10所示。
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CN105602967A (zh) * | 2014-11-24 | 2016-05-25 | 复旦大学 | 水稻qGL3.2基因在用于改良水稻粒型及千粒重性状中的应用 |
CN106244687A (zh) * | 2016-08-01 | 2016-12-21 | 惠州学院 | 一种水稻gs3功能基因分子标记及检测方法 |
CN107012252A (zh) * | 2017-05-19 | 2017-08-04 | 华中农业大学 | 一组用于改良稻米品质的分子标记及水稻改良方法和应用 |
CN107200775A (zh) * | 2017-01-20 | 2017-09-26 | 华中农业大学 | 一种提高水稻柱头外露率的方法 |
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CN105602967A (zh) * | 2014-11-24 | 2016-05-25 | 复旦大学 | 水稻qGL3.2基因在用于改良水稻粒型及千粒重性状中的应用 |
CN106244687A (zh) * | 2016-08-01 | 2016-12-21 | 惠州学院 | 一种水稻gs3功能基因分子标记及检测方法 |
CN107200775A (zh) * | 2017-01-20 | 2017-09-26 | 华中农业大学 | 一种提高水稻柱头外露率的方法 |
CN107012252A (zh) * | 2017-05-19 | 2017-08-04 | 华中农业大学 | 一组用于改良稻米品质的分子标记及水稻改良方法和应用 |
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