CN113186198A - 一种抗褐飞虱基因Bph41及其编码蛋白质和应用 - Google Patents
一种抗褐飞虱基因Bph41及其编码蛋白质和应用 Download PDFInfo
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- CN113186198A CN113186198A CN202110391033.3A CN202110391033A CN113186198A CN 113186198 A CN113186198 A CN 113186198A CN 202110391033 A CN202110391033 A CN 202110391033A CN 113186198 A CN113186198 A CN 113186198A
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- brown planthopper
- bph41
- resistant gene
- rice
- gene
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Abstract
本发明涉及一种抗褐飞虱基因Bph41及其编码蛋白质和应用。所述抗褐飞虱基因Bph41包括如下任一所示的核苷酸序列:i)SEQ IDNO:1所示的核苷酸序列;或ii)SEQ ID No.1所示核苷酸序列经取代、缺失和/或增加一个或几个核苷酸编码相同功能蛋白的核苷酸序列。本发明研究发现了一种抗褐飞虱基因Bph41,将该基因转入普通水稻品种中,可以显著提高水稻对于褐飞虱的抗性,从而减轻褐飞虱产生的危害,达到增产和稳产的目的。
Description
技术领域
本发明涉及植物基因工程领域,尤其涉及一种抗褐飞虱基因Bph41及其编码蛋白质和应用。
背景技术
水稻是一种重要的粮食作物,世界上有超过一半的人以其为主食。由于水稻基因组精细遗传图和物理图谱已完成,其转基因技术相对容易,并且与其它禾本科作物基因组具有共线性,因而被视做模式植物。随着包括水稻在内的多种生物基因组测序的完成,人类开始进入后基因组时代。全面开展功能基因组研究已成为生命科学的前沿领域。因此水稻功能基因的研究对社会经济发展和生物学研究具有重大意义。
粮食安全问题,是全世界人民面临的挑战。50、60年代的矮化育种和70年代的杂交水稻培育两次科技革命使水稻产量大幅度提高。矮化高产水稻的推广导致飞虱为害开始严重起来。尤其是进入21世纪整个亚洲水稻产区飞虱爆发的频率和规模有逐渐扩大的趋势,目前已经成为了水稻生产上最大的威胁。
长期以来,褐飞虱的防治主要是依靠施用化学杀虫剂。由于褐飞虱爆发多发生在水稻成熟灌浆期,此时稻株长势旺盛,将杀虫剂施到稻株基部的操作非常困难。事实上由于化学杀虫剂的连年大量施用,褐飞虱抗药性成倍增加,使药剂防治的效果有限。同时使用化学杀虫剂防治褐飞虱,一方面增加了农民的生产成本,另一方面化学杀虫剂还造成对非目标生物的毒杀、对环境和粮食污染等环境和生态问题。
利用抗褐飞虱基因培育抗虫水稻品种是褐飞虱综合防治中最为经济有效的方法。国际水稻研究所(IRRI)的研究结果和东南亚的水稻生产实践证明,即使是只有中等抗性水平的水稻品种,也足以将褐飞虱的群体控制在造成危害的水平以下,不至于对水稻造成实际的危害和产量损失。因此,挖掘水稻抗褐飞虱基因并在水稻育种项目中应用是防治水稻褐飞虱的根本措施。
水稻抗褐飞虱基因的研究始于上世纪70年代初。至今已经在普通栽培稻和野生稻资源中鉴定和定位了三十多个水稻抗褐飞虱的主效抗虫基因(具体见Du等,2020.Currentunderstanding of the genomic,genetic,and molecular control of insectresistance in rice.Mol Breeding2020,40:24)。8个基因(Bph14,Bph26,Bph3,Bph29,Bph9,Bph18,Bph32和Bph6)已经被克隆,这些基因都是利用图位克隆法得到(Du et al.,2009;Tamura et al.2014;Liu et al.2014;Wang et al.2015b;Zhao et al.2016;Ji etal.2016;Ren et al.2016;Guo et al.2018)。
全基因组关联分析(Genome-wide association study,GWAS)最早应用于人类疾病的遗传分析。近年来,随着基因组技术的快速发展,特别是测序技术手段的提高,许多动植物的全基因组测序已经完成,GWAS成为研究作物复杂性状的有力工具。与传统的图位克隆发掘基因相比,关联分析法具有无需构建专门的作图群体、节省时间,可实现精细定位等优点。同时,GWAS突破了图位克隆法一般适合于较小基因组物种的局限,只需全基因组SNPs标记和表型性状即可。近几年,GWAS分析方法也得到较快的发展。我国科学家和国际同行的研究结果表明,GWAS方法在作物形态性状、生理性状和产量相关性状等方面均发掘到目的基因。例如,控制水稻抽穗天数的基因LOC_Os01g62780、控制水稻株高和穗长基因LOC_Os11g08410以及分蘖数基因NAL1(Yano等2016,Genome-wide association study usingwhole-genome sequencing rapidly identifies new genes influencing agronomictraits in rice.Nature Genetics,48:927-934),控制水稻粒型基因OsSPL13(Si等2016,OsSPL13 controls grain size in cultivated rice.Nature Genetics,48:447-456)。
发明内容
为了解决现有技术存在的问题,本发明提供一种抗褐飞虱基因Bph41及其编码蛋白质和应用。将该基因转入普通水稻品种中,可以显著提高水稻对于褐飞虱的抗性。
第一方面,本发明提供一种抗褐飞虱基因Bph41,包括如下任一所示的核苷酸序列:
i)SEQ ID NO:1所示的核苷酸序列;或
ii)SEQ ID No.1所示核苷酸序列经取代、缺失和/或增加一个或几个核苷酸编码相同功能蛋白的核苷酸序列。
本发明进一步提供由所述抗褐飞虱基因Bph41编码得到的蛋白质,所述蛋白质包括如下任一所示的氨基酸序列:
i)如SEQ ID No.2所示的氨基酸序列;或
ii)SEQ ID No.2所示的氨基酸序列经一个或多个氨基酸的替换、***或缺失得到的具有相同功能蛋白的氨基酸序列。
本发明进一步提供检测所述抗褐飞虱基因Bph41的分子标记的引物对,所述引物对包括:
正向引物序列:5’-ATGGCGACGACGACCGGCAG-3’,
反向引物序列:5’-TCATAATAATGTACAAGAGAGTATAGC-3’。
进一步地,所述分子标记为rs4_11033430、rs4_11033910和rs4_11034040中的一种或多种;其中,rs4_11033430的多态性为C/G、rs4_11033910的多态性为T/C,rs4_11034040的多态性为A/C。
本发明进一步提供一种包含所述抗褐飞虱基因Bph41的生物材料,所述生物材料为载体、表达盒或转基因细胞中的一种或多种。
本发明进一步提供所述抗褐飞虱基因Bph41或其编码蛋白,或所述引物对,或所述生物材料在鉴定植物的褐飞虱抗性中的应用。
本发明进一步提供所述抗褐飞虱基因Bph41或其编码蛋白,或所述引物对,或所述生物材料在抗褐飞虱植物育种中的应用。
进一步地,所述应用为:将所述抗褐飞虱基因Bph41在所述植物中过表达,或将过表达抗褐飞虱基因Bph41的植物与其他植物杂交,培育抗褐飞虱株系。
进一步地,所述植物为水稻。
本发明进一步提供一种检测抗褐飞虱基因Bph41的方法,包括:
获得待测植物的基因组DNA,通过权利要求3所述引物对进行扩增;
若扩增结果中,rs4_11033430、rs4_11033910和rs4_11034040的碱基分别是C、T和A,则表明待测植物包含抗褐飞虱基因Bph41。
本发明具备如下有益效果:
(1)本发明利用全基因组关联性分析成功克隆了水稻抗褐飞虱基因Bph41。
(2)本发明克隆的Bph41基因具有明显的抗褐飞虱性能,这对全面理解水稻抗褐飞虱基因类型的多样性有重要意义。
(3)本发明提供的抗褐飞虱基因Bph41使水稻抗褐飞虱性能提高,通过遗传转化或杂交将Bph41应用于水稻育种中,可以改善水稻品种的抗褐飞虱性,从而减轻褐飞虱的为害,达到增产和稳产的目的。
(4)刺吸式昆虫是农业生产中的一大类虫害,抗褐飞虱基因Bph41克隆和抗褐飞虱功能证实,对于其他植物的抗刺吸式昆虫研究具有重要参考作用。
附图说明
图1为本发明实施例1提供的1520份水稻品种进化树。
图2为本发明实施例1提供的1520份水稻品种抗褐飞虱鉴定结果;图中横坐标WG表示褐飞虱体重增加率,纵坐标表示水稻品种个数;虫源为褐飞虱生物型I。
图3为本发明实施例1提供的全基因组关联分析的曼哈顿图。
图4为本发明实施例提供的单倍型A和B对褐飞虱抗性结果。
图5为基本发明实施例提供的转基因水稻抗褐飞虱的鉴定结果。
图6为本发明实施例提供的根据Bph41基因组序列开发的功能性分子标记68-75示例。
具体实施方式
以下实施例用于说明本发明,但不用来限制本发明的范围。
实施例1Bph41基因的克隆及分子标记开发
1.全基因组关联性分析
从中国农业科学院作物科学研究所取得1520份水稻品种,位于世界范围的74个国家,主要包括籼稻和粳稻,这些水稻品种的进化树如图1所示,其中不同灰度的区域代表不同亚群,不同的分支代表不同的类型。
本发明对1520份水稻品种进行了褐飞虱抗性测定,方法是测定褐飞虱雌成虫取食前和取食48小时后的体重,进而获得褐飞虱的体重增加率(WG)。对每个水稻品种,用12只褐飞虱的平均体重增加率来指示抗性水平。得到如图2所示结果,图示为褐飞虱取食1520水稻品种48小时的体重增加率直方图;图中横坐标WG表示褐飞虱体重增加率,纵坐标表示水稻品种个数;虫源为褐飞虱生物型I。结果显示:1520份水稻品种对褐飞虱的抗性水平呈现左偏态分布,即感虫品种远多于抗虫品种。
本发明进一步用Plink软件从3K水稻基因组数据(Li,Z.等,2014The 3,000ricegenomes project.GigaScience 3,7)提取出次要等位基因频率大于0.01、缺失率小于0.2的全基因组SNPs数据。用前7个主成分(Q)作为固定效应,每个个体间的亲缘矩阵(K)作为随机效应进行种群结构修正。利用EMMAX软件中的混合线性模型进行GWAS分析。用公式p=0.05/N(N为SNPs数目)确定全基因组显著性阈值。显著性p值阈值约为1.0×10-8。p值小于阈值(-log10(p)超过8)的SNP认为是显著SNP。显著SNP物理位置的上下游各150kb区域确定为显著区域,重叠的多个显著区域合并为一个显著区域。
2.确定候选基因
全基因组关联性分析分析得到如图3所示的结果,图3为为全基因组关联分析的曼哈顿图;每个点代表一个SNP标记与褐飞虱抗性的关联程度,p值越小(-log10(p)越大),与褐飞虱抗性关联程度越高;-log10(p)超过阈值8的位点认为是显著关联位点;第6号染色体0.8-1.57Mb是全基因组关联程度最高的区域,-log10(p)远超过阈值8;所用模型为EMMAX软件的混合线性模型。结果显示:第4号染色体存在一个显著区域10.48-12.47Mbp,说明该区域含有抗褐飞虱基因,作为候选区域。候选区域内的一个显著SNP rs4_11033430位于LOC_Os04g19750的外显子区并预测引起氨基酸改变。结合日本晴参考基因组基因功能注释信息(http://rice.plantbiology.msu.ed u/),LOC_Os04g19750编码一个F-box-LRR蛋白。拟南芥中的cpr30编码F-box蛋白并对丁香假单胞菌保持抗性(Gou et al,2019),LOC_Os04g19750是cpr30在水稻中的同源蛋白,作为候选基因。根据显著SNP rs4_11033430在1520份材料中的不同碱基形式,将1520份材料分成单倍型A和单倍型B,其中单倍型A有1470份材料,单倍型B有36份。单倍型B的材料对褐飞虱抗性显著高于单倍型A的材料(如图4所示,单倍型A的褐飞虱增重率(WG)显著高于单倍型B)。选择单倍型B中的G68作为扩增LOC_Os04g19750的材料。
3.获得Bph41全长DNA
以抗褐飞虱亲本G68叶片DNA为模板,根据日本晴参考基因组序列在NCBI上Primer-BLAST设计引物,扩增出涵盖候选基因的多段重叠的DNA序列,并拼接出涵盖该基因的基因组序列。根据拼接的基因组序列重新合成引物,扩增获得Bph41的全长DNA,其核苷酸序列如序列表SEQ ID NO.1所示。
4.抗褐飞虱基因Bph41分子标记
相比感性材料,Bph41外显子区域存在3个SNPs,这3个SNPs的物理位置分别是rs4_11033430、rs4_11033910和rs4_11034040。在抗性亲本中,rs4_11033430、rs4_11033910和rs4_11034040的碱基分别是C、T和A,即单倍型G68;在感性亲本中,3个SNPs的碱基分别是G、C和C,即单倍型Nipponbare。因此,分子标记即是用:
68-75标记引物:
正向引物序列ATGGCGACGACGACCGGCAG,如SEQ ID NO.3所示;
反向引物序列TCATAATAATGTACAAGAGAGTATAGC,如SEQ ID NO.4所示;
扩增水稻抗褐飞虱品种或者育种材料DNA,如果用引物68-75能够扩增出单倍型G68的扩增片段,标志着水稻抗褐飞虱基因Bph41的存在。因此,利用本发明提供的上述分子标记方法来鉴定Bph41抗性基因的存在具有非常高的效率,可以预测水稻植株的褐飞虱抗性,加快抗褐飞虱水稻品种育种进程。
实施例2Bph41基因的功能验证和应用
1.遗传转化载体的构建
Bph41基因过表达载体的构建。所用载体为pCXUN(由美国Ohio State University的王国梁教授提供),采用XcmI酶切pCXUN载体,将外源片段加A后可以直接连入。
采用PCR的方法直接扩增Bph41基因,经加A后连入载体。测序验证无误后,所得载体即为Bph41基因过表达载体,将其转入农杆菌EHA105中。挑取单克隆扩大培养,进行PCR验证无误后,加等体积的50%甘油混匀,-70℃保存备用。
2.遗传转化
采用农杆菌EHA105介导的遗传转化方法(Hiei等,1994,Efficienttransformation of rice(Oryza sativa L.)mediated by Agrobacterium and sequenceanalysis of the boundaries of the T-DNA.Plant Journal 6:271-282)将上述Bph41基因过表达载体导入褐飞虱感性的普通水稻品种Kasalath。
3.Bph41基因转基因功能验证
Bph41基因过表达转化载体获得阳性转基因植株20株。收获种子后,用T2代Bph41转基因植株,采用苗期集团法进行了抗虫鉴定。如图5所示,对转基因阳性株系8-2、11-12和8-9进行了抗褐飞虱鉴定。鉴定结果如图5所示,接入褐飞虱7天后,感虫对照品种Kasalath整株全部死亡,转基因阳性植株生长健康,无叶片受害,抗虫级别为2-4级,证实Bph41基因具有抗褐飞虱的功能。因此,抗褐飞虱基因Bph41可以在水稻中应用也可以在水稻种子中应用,培育具有抗褐飞虱性能的水稻品种。
实施例3分子标记的验证
1、材料和方法
1.1材料:抗褐飞虱亲本G68(含抗褐飞虱基因Bph41)、褐飞虱感性水稻品种日本晴(Nipponbare)及3K水稻中的549份品种。
分子标记引物:68-75,其核苷酸序列分别如SEQ ID No.3-4所示。
1.2方法
CTAB抽提法提取水稻样品基因组DNA。用引物68-75扩增样品DNA。50μl体系。50μl反应体系包括:2×Phanta Max Buffer,25.0μl;10mM dNTP,1.0μl;ddH2O,9.0μl;10μM引物,2.0μl;Phanta Max Super-F DNA Polymerase,1.0μl,和50ng DNA模板。扩增反应在Bioer PCR仪上进行:95℃3min;95℃15s,72℃60s,30个循环;72℃5min。68-75的扩增产物通过Sanger测序检测G68和Nipponbare在rs4_11033430、rs4_11033910和rs4_11034040碱基形式。3K水稻中的549份品种在rs4_11033430、rs4_11033910和rs4_11034040碱基通过软件Plink从3K水稻SNPs数据集提取。
2、结果:用上述方法,分别对水稻品种G68、Nipponbare进行扩增,以及提取549份品种的SNPs。结果表明,利用68-75分子标记引物在rs4_11033430、rs4_11033910和rs4_11034040能扩增出C、T和A的品种和549份水稻中提取出C、T和A的品种(单倍型G68)对褐飞虱均表现出抗虫性。而不能扩出或者提取出上述碱基的品种(单倍型Nipponbare)对褐飞虱均表现出感虫性(图6)。
由此说明,本发明提供的分子标记方法能够准确筛选出含有抗褐飞虱基因Bph41,从而大大提高育种效率。
虽然,上文中已经用一般性说明及具体实施方案对本发明作了详尽的描述,但在本发明基础上,可以对之作一些修改或改进,这对本领域技术人员而言是显而易见的。因此,在不偏离本发明精神的基础上所做的这些修改或改进,均属于本发明要求保护的范围。
序列表
<110> 武汉大学 袁隆平农业高科技股份有限公司 武汉禾泰青生物科技有限公司
<120> 一种抗褐飞虱基因Bph41及其编码蛋白质和应用
<130> KHP211112399.9
<160> 4
<170> SIPOSequenceListing 1.0
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<211> 1461
<212> DNA
<213> 人工序列(Artificial Sequence)
<400> 1
atggcgacga cgaccggcag gcaccgacac gaccggctga gcgctctccc ggacggaata 60
ctagtgcgcg tcctctctca cctcggctcc gtcgacgcgg ctagcaccgc cgcgctgtcc 120
caccggtggc gccacatcca cgcagccgtc cccgtcgtcg acctcgtcga ccccgagagc 180
gaccagatct caagcgccat cgtcgccaag aactcggcgg cgcccatccg cacgctccgg 240
ctcgtcgatc tctggccgcc gcacgacgcg ctccaccagg cggtcgccac cgccaccgcc 300
gccggcctcc aggagttcga cgtcaagctc aggcacgggg actgctccaa ccgcaagctc 360
tgccccttcc gccgccaccc cgatgcctcc gccgacttcg acgactccat gcgcggctcg 420
ttcaccgcca cgccgccaca catcttccgg tgcgacacgc tgcgccgcct gcggctcacc 480
aacttccagc tcgacgtgcc ggagggcggc gtctccatgc cgtcgctgga gatcctctcc 540
ctcaagagga tcatggcgac gacggacgag gcggtgcagc agctcgtctc cggctgcccg 600
aacctcgccg acctgacgct ggagcagtgc cccagcgtgg cggacctcgt cgttgccagc 660
ccgcgcctcg agagcttcgc catgatctgc tgccacaacg ccgcccacgt cgtgctccac 720
acccaacgcc tccggacgct gcgctacaag ggcggccttc ccgccggcga gaacttcttg 780
atgatcgccg actgcaccaa cgtcctggcc atgacgatcg acatctgaga gagcctcgtc 840
gggaaatccg cccccgccgt cgtgcccatc acgaagctca tcacccggtg cgccagcctc 900
accttcctcc acctccacct ccgcccggcg atggcgtacc acagcggcgc cttcacgtgc 960
gccctccgcc accatcccca cctccggcag ctcgcgctca agggcctcct caaggacgac 1020
cagaccatcc gctcagtctc cacattgctc cgcaacacgc cggagctcga cgtgctctcg 1080
ctgttccctc tccgtcctca gcctgcaaag ccatactacc tcggcgtcga ctccgacgac 1140
gactacgact ccgaggagga ggaggaggag gaggacggcg gcgcctcgga tgataaccaa 1200
ggtgtgcgtg tgccgctgag cttgtgggag agcaacatcg agtgcttgca caagctgagg 1260
aagatcaaat tgcacaacta caaagggaag cccaacgaga gattgctcgc aaagtatctt 1320
ctatccaagg caacatcttt ggagcaattc ttcgttaccc taccagctaa aaccacggca 1380
gatcgtcaat tgaagttgac caacgagctt aaatactggc gtgccaacaa acgcgctata 1440
ctctcttgta cattattatg a 1461
<210> 2
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Pro Asp Gly Ile Leu Val Arg Val Leu Ser His Leu Gly Ser Val Asp
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Ala Val Pro Val Val Asp Leu Val Asp Pro Glu Ser Asp Gln Ile Ser
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Ser Ala Ile Val Ala Lys Asn Ser Ala Ala Pro Ile Arg Thr Leu Arg
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Leu Val Asp Leu Trp Pro Pro His Asp Ala Leu His Gln Ala Val Ala
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Thr Ala Thr Ala Ala Gly Leu Gln Glu Phe Asp Val Lys Leu Arg His
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Gly Asp Cys Ser Asn Arg Lys Leu Cys Pro Phe Arg Arg His Pro Asp
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Ala Ser Ala Asp Phe Asp Asp Ser Met Arg Gly Ser Phe Thr Ala Thr
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Pro Pro His Ile Phe Arg Cys Asp Thr Leu Arg Arg Leu Arg Leu Thr
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Asn Phe Gln Leu Asp Val Pro Glu Gly Gly Val Ser Met Pro Ser Leu
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Glu Ile Leu Ser Leu Lys Arg Ile Met Ala Thr Thr Asp Glu Ala Val
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Gln Gln Leu Val Ser Gly Cys Pro Asn Leu Ala Asp Leu Thr Leu Glu
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Gln Cys Pro Ser Val Ala Asp Leu Val Val Ala Ser Pro Arg Leu Glu
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Ser Phe Ala Met Ile Cys Cys His Asn Ala Ala His Val Val Leu His
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Glu Asn Phe Leu Met Ile Ala Asp Cys Thr Asn Val Leu Ala Met Thr
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His Leu Arg Pro Ala Met Ala Tyr His Ser Gly Ala Phe Thr Cys Ala
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Pro Glu Leu Asp Val Leu Ser Leu Phe Pro Leu Arg Pro Gln Pro Ala
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atggcgacga cgaccggcag 20
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<212> DNA
<213> 人工序列(Artificial Sequence)
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tcataataat gtacaagaga gtatagc 27
Claims (10)
1.一种抗褐飞虱基因Bph41,其特征在于,包括如下任一所示的核苷酸序列:
i)SEQ ID NO:1所示的核苷酸序列;或
ii)SEQ ID No.1所示核苷酸序列经取代、缺失和/或增加一个或几个核苷酸编码相同功能蛋白的核苷酸序列。
2.一种蛋白质,其特征在于,所述蛋白质由权利要求1所述抗褐飞虱基因Bph41编码得到;所述蛋白质包括如下任一所示的氨基酸序列:
i)如SEQ ID No.2所示的氨基酸序列;或
ii)SEQ ID No.2所示的氨基酸序列经一个或多个氨基酸的替换、***或缺失得到的具有相同功能蛋白的氨基酸序列。
3.一种引物对,其特征在于,所述引物对用于检测如权利要求1所述的抗褐飞虱基因Bph41的分子标记;所述引物对包括:
正向引物序列:5’-ATGGCGACGACGACCGGCAG-3’,
反向引物序列:5’-TCATAATAATGTACAAGAGAGTATAGC-3’。
4.根据权利要求3所述的引物对,其特征在于,所述分子标记为rs4_11033430、rs4_11033910和rs4_11034040中的一种或多种;其中,rs4_11033430的多态性为C/G、rs4_11033910的多态性为T/C,rs4_11034040的多态性为A/C。
5.一种生物材料,其特征在于,所述生物材料包括如权利要求1所述的抗褐飞虱基因Bph41;所述生物材料为载体、表达盒或转基因细胞中的一种或多种。
6.权利要求1所述抗褐飞虱基因Bph41或其编码蛋白,或权利要求3或4所述引物对,或权利要求5所述生物材料在鉴定植物的褐飞虱抗性中的应用。
7.权利要求1所述抗褐飞虱基因Bph41或其编码蛋白,或权利要求3或4所述引物对,或权利要求5所述生物材料在抗褐飞虱植物育种中的应用。
8.根据权利要求7所述的应用,其特征在于,所述应用为:将所述抗褐飞虱基因Bph41在所述植物中过表达,或将过表达抗褐飞虱基因Bph41的植物与其他植物杂交,培育抗褐飞虱株系。
9.根据权利要求6-8任一项所述的应用,其特征在于,所述植物为水稻。
10.一种检测如权利要求1所述抗褐飞虱基因Bph41的方法,其特征在于,包括:
获得待测植物的基因组DNA,通过权利要求3所述引物对进行扩增;
若扩增结果中,rs4_11033430、rs4_11033910和rs4_11034040的碱基分别是C、T和A,则表明待测植物包含抗褐飞虱基因Bph41。
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