不同环境基于高密度遗传图谱的稻米外观品质QTL定位
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摘要
为解析稻米外观品质遗传基础,挖掘稳定存在的控制稻米外观品质性状的QTL,本研究以籼稻品种V20B和爪哇稻品种CPSLO17作为亲本,构建包含150个重组自交家系(recombinantion inbred line,RIL)的RIL作图群体,进行外观品质性状QTL定位分析。利用特定位点扩增长度测序(SLAF-seq)技术,构建了一个由12个连锁群包含8602个标记,平均间距为0.29 cM的高密度遗传图谱。采用Ici Mapping 4.0软件的ICIM-ADD方法在3种环境(贵阳、贵定、三亚)对4个外观品质性状(粒长、粒宽、垩白度和垩白粒率)进行QTL(quantitative trait locus)定位分析。结果表明:3种环境共检测到9个粒长QTL、6个粒宽QTL、3个垩白度QTL和4个垩白粒率QTL;有5个QTL在多个环境被重复检测到,其中3种环境都定位到的粒宽QTL q GW5-1和垩白度QTL qCha5-1为同一定位区间(第5染色体的Marker1642127-Marker1514505);此外,垩白度QTL qCha5-2的定位区间(Marker1554573-Marker1554589)和垩白粒率QTL qCGP5-2也是一样的。序列比对发现QTL qCha5-1定位区间仅51.5 kb,是新的垩白性状主效QTL。本研究结果不仅为挖掘新的外观品质性状基因奠定基础,也有助于开发新的分子标记进行水稻外观品质性状遗传改良。
To analyze the genetic basis of appearance quality of rice, explore QTL which controlled rice appearance quality related traits stably existing, a mapping population of 150 lines(recombination inbred lines, RIL), derived from a cross between rice varieties V20 B and CPSLO17, was applied to analysis QTL location of appearance quality trait. The specific locus amplified fragment sequencing(SLAF-seq) technology was employed to construct a high-density genetic map in rice(Oryza sativa L.). A genetic map included 8602 markers on the 12 linkage groups was successfully constructed, which with an average distance of 0.29 cM between adjacent markers. The ICIM-ADD method of Ici Mapping 4.0 software was used to analyze QTL location for four appearance quality traits, including grain length(GL), grain width(GW), chalky grain rate, and chalkiness degree in three environmental conditions(Guiyang, Guiding, and Sanya). A total of nine QTLs for grain length(GL), six QTLs for grain width(GW), four QTLs for chalkiness size, three QTLs for chalkiness degree traits were detested in three environments. Five QTLs were repeatedly detected in multiple environments, of which the QTL q GW5-1 and qCha5-1 with the same localization interval(Marker1642127-Marker1514505 on chromosome 5) were repeatedly located in all three environments. In addition, the positioning interval of chalkiness QTL qCha5-2(Marker1554573-Marker1554589) is the same as the chalkiness size QTL qCGP5-2. The sequence alignment found that the location interval of QTL qCha5-1 was only 51.5 kb, which was a new main effect QTL for chalkiness trait. These results lay the foundation for further exploiting candidate gene of appearance quality, which also contribute to the development of new molecular markers for rice appearance quality traits genetic improvement.
To analyze the genetic basis of appearance quality of rice, explore QTL which controlled rice appearance quality related traits stably existing, a mapping population of 150 lines(recombination inbred lines, RIL), derived from a cross between rice varieties V20 B and CPSLO17, was applied to analysis QTL location of appearance quality trait. The specific locus amplified fragment sequencing(SLAF-seq) technology was employed to construct a high-density genetic map in rice(Oryza sativa L.). A genetic map included 8602 markers on the 12 linkage groups was successfully constructed, which with an average distance of 0.29 cM between adjacent markers. The ICIM-ADD method of Ici Mapping 4.0 software was used to analyze QTL location for four appearance quality traits, including grain length(GL), grain width(GW), chalky grain rate, and chalkiness degree in three environmental conditions(Guiyang, Guiding, and Sanya). A total of nine QTLs for grain length(GL), six QTLs for grain width(GW), four QTLs for chalkiness size, three QTLs for chalkiness degree traits were detested in three environments. Five QTLs were repeatedly detected in multiple environments, of which the QTL q GW5-1 and qCha5-1 with the same localization interval(Marker1642127-Marker1514505 on chromosome 5) were repeatedly located in all three environments. In addition, the positioning interval of chalkiness QTL qCha5-2(Marker1554573-Marker1554589) is the same as the chalkiness size QTL qCGP5-2. The sequence alignment found that the location interval of QTL qCha5-1 was only 51.5 kb, which was a new main effect QTL for chalkiness trait. These results lay the foundation for further exploiting candidate gene of appearance quality, which also contribute to the development of new molecular markers for rice appearance quality traits genetic improvement.
引文
[1]张昌泉,赵冬生,李钱峰,顾铭洪,刘巧泉.稻米品质性状基因的克隆与功能研究进展.中国农业科学,2016,49:4267–4283Zhang C Q,Zhao D S,Li Q F,Gu M H,Liu Q Q.Progresses in research on cloning and functional analysis of key genes involving in rice grain quality.Sci Agric Sin,2016,49:4267–4283(in Chinese with English abstract)
[2]李一博,赵雷.水稻品质性状的遗传改良及其关键科学问题.生命科学,2016,28:1168–1179Li Y B,Zhao L.Genetic improvement and key scientific questions of grain quality traits in rice.Chin Bull Life Sci,2016,28:1168–1179(in Chinese with English abstract)
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[5]Qiu X,Chen K,Lv W,Ou X,Zhu Y,Xing D,Yang L,Fan F,Yang J,Xu J,Zheng T,Li Z.Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice(Oryza sativa L.).Theor Appl Genet,2017,130:951–967
[6]Wan X Y,Wan J M,Weng J F,Jiang L,Bi J C,Wang C M,Zhai H Q.Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments.Theor Appl Genet,2005,110:1334–1346
[7]杨亚春,倪大虎,宋丰顺,李泽福,易成新,杨剑波.不同生态地点下稻米外观品质性状的QTL定位分析.中国水稻科学,2011,25:43–51Yang Y C,Ni D H,Song F S,Li Z F,Yi C X,Yang J B.Identification of QTLs for rice appearance quality traits across different ecological sites.Chin J Rice Sci,2011,25:43–51(in Chinese with English abstract)
[8]Fan C C,Xing Y Z,Mao H L,Lu T T,Han B,Xu C G,Li X H,Zhang Q F.GS3,a major QTL for grain length and weight and minor QTL for grain width and thickness in rice,encodes a putative transmembrane protein.Theor Appl Genet,2006,112:1164–1171
[9]Mao H,Sun S,Yao J,Wang C,Yu S,Xu C,Li X,Zhang Q.Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.Proc Natl Acad Sci USA,2010,107:19579–19584
[10]Shomura A,Izawa T,Ebana K,Ebitani T,Kanegae H,Konishi S,Yano M.Deletion in a gene associated with grain size increased yields during rice domestication.Nat Genet,2008,40:1023–1028
[11]Weng J F,Gu S H,Wan X Y,Gao H,Guo T,Su N,Lei C L,Zhang X,Cheng Z J,Guo X P,Wang J L,Jiang L,Zhai H Q,Wan J M.Isolation and initial characterization of GW5,a major QTL associated with rice grain width and weight.Cell Res,2008,18:1199–1209
[12]Che R,Tong H,Shi B,Liu Y,Fang S,Liu D,Xiao Y,Hu B,Liu L,Wang H,Zhao M,Chu C.Control of grain size and rice yield by GL2-mediated brassinosteroid responses.Nat Plants,2015,2:15195
[13]Hu J,Wang Y,Fang Y,Zeng L,Xu J,Yu H,Shi Z,Pan J,Zhang D,Kang S,Zhu L,Dong G,Guo L,Zeng D,Zhang G,Xie L,Xiong G,Li J,Qian Q.A rare allele of GS2 enhances grain size and grain yield in rice.Mol Plant,2015,8:1455–1465
[14]Song X J,Huang W,Shi M,Zhu M Z,Lin H X.A QTL for rice grain width and weight encodes a previously unknown RING type E3 ubiquitin ligase.Nat Genet,2007,39:623–630
[15]Wang S K,Li S,Liu Q,Wu K,Zhang J Q,Wang S S,Wang Y,Chen X B,Zhang Y,Gao C X,Wang F,Huang H X,Fu X D.The Os SPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality.Nat Genet,2015,47:949–954
[16]Wang Y X,Xiong G S,Hu J,Jiang L,Yu H,Xu J,Fang Y X,Zeng L J,Xu E B,Xu J,Ye W J,Meng X B,Liu R F,Chen H Q,Jing Y H,Wang Y H,Zhu X D,Li J Y,Qian Q.Copy number variation at the GL7 locus contributes to grain size diversity in rice.Nat Genet,2015,47:944–948
[17]Wang S K,Wu K,Yuan Q B,Liu X Y,Liu Z B,Lin X Y,Zeng R Z,Zhu H T,Dong G J,Qian Q,Zhang G Q,Fu X D.Control of grain size,shape and quality by Os SPL16 in rice.Nat Genet,2012,44:950–954
[18]Peng B,Wang L,Fan C,Jiang G,Luo L,Li Y,He Y.Comparative mapping of chalkiness components in rice using five populations across two environments.BMC Genet,2014,15:49
[19]Zhao X,Daygon V D,Mc Nally K L,Hamilton R S,Xie F,Reinke R F,Fitzgerald M A.Identification of stable QTLs causing chalk in rice grains in nine environments.Theor Appl Genet,2016,129:141–153
[20]邱先进,袁志华,陈凯,杜斌,何文静,杨隆维,徐建龙,邢丹英,吕文恺.用全基因组关联分析解析籼稻垩白的遗传基础.作物学报,2015,41:1007–1016Qiu X J,Yuan Z H,Chen K,Du B,He W J,Yang L W,Xu J L,Xing D Y,Lyu W K.Genetic dissection of grain chalkiness in indica mini-core germplasm using genome-wide association method.Acta Agron Sin,2015,41:1007–1016(in Chinese with English abstract)
[21]Xian J Q,Kai C,Wen K L,Xiao X O,Ya J Z,Dan Y X,Long W Y,Fang J F,Jie Y,Jian L X,Tian Q Z,Zhi K L.Examining two sets of introgression lines reveals background independent and stably expressed QTL that improve grain appearance quality in rice(Oryza sativa L.).Theor Appl Genet,2017,130:951–967
[22]Zhou L,Chen L,Jiang L,Zhang W,Liu L,Liu X,Zhao Z,Liu S,Zhang L,Wang J,Wan J.Fine mapping of the grain chalkiness QTL q PGWC-7 in rice(Oryza sativa L.).Theor Appl Genet,2009,118:581–590
[23]Guo T,Liu X,Wan X,Weng J,Liu S,Liu X,Chen M,Li J,Su N,Wu F,Cheng Z,Guo X,Lei C,Wang J,Jiang L,Wan J.Identification of a stable quantitative trait locus for percentage grains with white chalkiness in rice(Oryza sativa).J Integr Plant Biol,2011,53:598–607
[24]Gao Y,Liu C,Li Y,Zhang A,Dong G,Xie L,Zhang B,Ruan B,Hong K,Xue D,Zeng D,Guo L,Qian Q,Gao Z.QTL analysis for chalkiness of rice and fine mapping of a candidate gene for q ACE9.Rice(N Y),2016,9:41
[25]Li Y,Fan C,Xing Y,Yun P,Luo L,Yan B,Peng B,Xie W,Wang G,Li X,Xiao J,Xu C,He Y.Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase influencing grain chalkiness in rice.Nat Genet,2014,46:398–404
[26]胡苗,孙志忠,孙学武,谭炎宁,余东,刘瑞芬,袁贵龙,丁佳,袁定阳,段美娟.利用高密度SNP标记定位水稻粒形相关QTL.杂交水稻,2015,30(5):54–58Hu M,Sun Z Z,Sun X W,Tan Y N,Yu D,Liu R F,Yuan G L,Ding J,Yuan D Y,Duan M J.Mapping of rice grain shape relevant QTLs using high-density SNP markers.Hybrid Rice,2015,30(5):54–58(in Chinese with English abstract)
[27]Sun X,Liu D,Zhang X,Li W,Liu H,Hong W,Jiang C,Guan N,Ma C,Zeng H,Xu C,Song J,Huang L,Wang C,Shi J,Wang R,Zheng X,Lu C,Wang X,Zheng H.SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing.PLo S One,2013,8(3):e58700
[28]Wei Q,Wang Y,Qin X,Zhang Y,Zhang Z,Wang J,Li J,Lou Q,Chen J.An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment(SLAF)sequencing.BMC Genomics,2014,15:1158
[29]Zhang Y,Wang L,Xin H,Li D,Ma C,Ding X,Hong W,Zhang X.Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment(SLAF)sequencing.BMC Plant Biol,2013,13:141
[30]Kozich J J,Westcott S L,Baxter N T,Highlander S K,Schloss P D.Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the Mi Seq Illumina sequencing platform.Appl Environ Microb,2013,79:5112–5120
[31]Liu D,Ma C,Hong W,Huang L,Liu M,Liu H,Zeng H,Deng D,Xin H,Song J,Xu C,Sun X,Hou X,Wang X,Zheng H.Construction and analysis of high-density linkage map using high-throughput sequencing data.PLo S One,2014,9(6):e98855
[2]李一博,赵雷.水稻品质性状的遗传改良及其关键科学问题.生命科学,2016,28:1168–1179Li Y B,Zhao L.Genetic improvement and key scientific questions of grain quality traits in rice.Chin Bull Life Sci,2016,28:1168–1179(in Chinese with English abstract)
[3]江良荣,李义珍,王侯聪,黄育民.稻米外观品质的研究进展与分子改良策略.分子植物育种,2003,1:243–255Jiang L R,Li Y Z,Wang H C,Huang Y M.Research progresses on appearance quality of rice grain and strategies for its molecular improvement.Mol Plant Breed,2003,1:243–255(in Chinese with English abstract)
[4]王忠华,方振华,干建彗.稻米外观品质性状遗传与分子定位研究进展.生命科学,2009,21:444–351Wang Z H,Fang Z H,Gan J H.Advances in genetic research and molecular mapping of the rice grain appearance quality.Chin Bull Life Sci,2009,21:444–351(in Chinese with English abstract)
[5]Qiu X,Chen K,Lv W,Ou X,Zhu Y,Xing D,Yang L,Fan F,Yang J,Xu J,Zheng T,Li Z.Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice(Oryza sativa L.).Theor Appl Genet,2017,130:951–967
[6]Wan X Y,Wan J M,Weng J F,Jiang L,Bi J C,Wang C M,Zhai H Q.Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments.Theor Appl Genet,2005,110:1334–1346
[7]杨亚春,倪大虎,宋丰顺,李泽福,易成新,杨剑波.不同生态地点下稻米外观品质性状的QTL定位分析.中国水稻科学,2011,25:43–51Yang Y C,Ni D H,Song F S,Li Z F,Yi C X,Yang J B.Identification of QTLs for rice appearance quality traits across different ecological sites.Chin J Rice Sci,2011,25:43–51(in Chinese with English abstract)
[8]Fan C C,Xing Y Z,Mao H L,Lu T T,Han B,Xu C G,Li X H,Zhang Q F.GS3,a major QTL for grain length and weight and minor QTL for grain width and thickness in rice,encodes a putative transmembrane protein.Theor Appl Genet,2006,112:1164–1171
[9]Mao H,Sun S,Yao J,Wang C,Yu S,Xu C,Li X,Zhang Q.Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.Proc Natl Acad Sci USA,2010,107:19579–19584
[10]Shomura A,Izawa T,Ebana K,Ebitani T,Kanegae H,Konishi S,Yano M.Deletion in a gene associated with grain size increased yields during rice domestication.Nat Genet,2008,40:1023–1028
[11]Weng J F,Gu S H,Wan X Y,Gao H,Guo T,Su N,Lei C L,Zhang X,Cheng Z J,Guo X P,Wang J L,Jiang L,Zhai H Q,Wan J M.Isolation and initial characterization of GW5,a major QTL associated with rice grain width and weight.Cell Res,2008,18:1199–1209
[12]Che R,Tong H,Shi B,Liu Y,Fang S,Liu D,Xiao Y,Hu B,Liu L,Wang H,Zhao M,Chu C.Control of grain size and rice yield by GL2-mediated brassinosteroid responses.Nat Plants,2015,2:15195
[13]Hu J,Wang Y,Fang Y,Zeng L,Xu J,Yu H,Shi Z,Pan J,Zhang D,Kang S,Zhu L,Dong G,Guo L,Zeng D,Zhang G,Xie L,Xiong G,Li J,Qian Q.A rare allele of GS2 enhances grain size and grain yield in rice.Mol Plant,2015,8:1455–1465
[14]Song X J,Huang W,Shi M,Zhu M Z,Lin H X.A QTL for rice grain width and weight encodes a previously unknown RING type E3 ubiquitin ligase.Nat Genet,2007,39:623–630
[15]Wang S K,Li S,Liu Q,Wu K,Zhang J Q,Wang S S,Wang Y,Chen X B,Zhang Y,Gao C X,Wang F,Huang H X,Fu X D.The Os SPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality.Nat Genet,2015,47:949–954
[16]Wang Y X,Xiong G S,Hu J,Jiang L,Yu H,Xu J,Fang Y X,Zeng L J,Xu E B,Xu J,Ye W J,Meng X B,Liu R F,Chen H Q,Jing Y H,Wang Y H,Zhu X D,Li J Y,Qian Q.Copy number variation at the GL7 locus contributes to grain size diversity in rice.Nat Genet,2015,47:944–948
[17]Wang S K,Wu K,Yuan Q B,Liu X Y,Liu Z B,Lin X Y,Zeng R Z,Zhu H T,Dong G J,Qian Q,Zhang G Q,Fu X D.Control of grain size,shape and quality by Os SPL16 in rice.Nat Genet,2012,44:950–954
[18]Peng B,Wang L,Fan C,Jiang G,Luo L,Li Y,He Y.Comparative mapping of chalkiness components in rice using five populations across two environments.BMC Genet,2014,15:49
[19]Zhao X,Daygon V D,Mc Nally K L,Hamilton R S,Xie F,Reinke R F,Fitzgerald M A.Identification of stable QTLs causing chalk in rice grains in nine environments.Theor Appl Genet,2016,129:141–153
[20]邱先进,袁志华,陈凯,杜斌,何文静,杨隆维,徐建龙,邢丹英,吕文恺.用全基因组关联分析解析籼稻垩白的遗传基础.作物学报,2015,41:1007–1016Qiu X J,Yuan Z H,Chen K,Du B,He W J,Yang L W,Xu J L,Xing D Y,Lyu W K.Genetic dissection of grain chalkiness in indica mini-core germplasm using genome-wide association method.Acta Agron Sin,2015,41:1007–1016(in Chinese with English abstract)
[21]Xian J Q,Kai C,Wen K L,Xiao X O,Ya J Z,Dan Y X,Long W Y,Fang J F,Jie Y,Jian L X,Tian Q Z,Zhi K L.Examining two sets of introgression lines reveals background independent and stably expressed QTL that improve grain appearance quality in rice(Oryza sativa L.).Theor Appl Genet,2017,130:951–967
[22]Zhou L,Chen L,Jiang L,Zhang W,Liu L,Liu X,Zhao Z,Liu S,Zhang L,Wang J,Wan J.Fine mapping of the grain chalkiness QTL q PGWC-7 in rice(Oryza sativa L.).Theor Appl Genet,2009,118:581–590
[23]Guo T,Liu X,Wan X,Weng J,Liu S,Liu X,Chen M,Li J,Su N,Wu F,Cheng Z,Guo X,Lei C,Wang J,Jiang L,Wan J.Identification of a stable quantitative trait locus for percentage grains with white chalkiness in rice(Oryza sativa).J Integr Plant Biol,2011,53:598–607
[24]Gao Y,Liu C,Li Y,Zhang A,Dong G,Xie L,Zhang B,Ruan B,Hong K,Xue D,Zeng D,Guo L,Qian Q,Gao Z.QTL analysis for chalkiness of rice and fine mapping of a candidate gene for q ACE9.Rice(N Y),2016,9:41
[25]Li Y,Fan C,Xing Y,Yun P,Luo L,Yan B,Peng B,Xie W,Wang G,Li X,Xiao J,Xu C,He Y.Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase influencing grain chalkiness in rice.Nat Genet,2014,46:398–404
[26]胡苗,孙志忠,孙学武,谭炎宁,余东,刘瑞芬,袁贵龙,丁佳,袁定阳,段美娟.利用高密度SNP标记定位水稻粒形相关QTL.杂交水稻,2015,30(5):54–58Hu M,Sun Z Z,Sun X W,Tan Y N,Yu D,Liu R F,Yuan G L,Ding J,Yuan D Y,Duan M J.Mapping of rice grain shape relevant QTLs using high-density SNP markers.Hybrid Rice,2015,30(5):54–58(in Chinese with English abstract)
[27]Sun X,Liu D,Zhang X,Li W,Liu H,Hong W,Jiang C,Guan N,Ma C,Zeng H,Xu C,Song J,Huang L,Wang C,Shi J,Wang R,Zheng X,Lu C,Wang X,Zheng H.SLAF-seq:an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing.PLo S One,2013,8(3):e58700
[28]Wei Q,Wang Y,Qin X,Zhang Y,Zhang Z,Wang J,Li J,Lou Q,Chen J.An SNP-based saturated genetic map and QTL analysis of fruit-related traits in cucumber using specific-length amplified fragment(SLAF)sequencing.BMC Genomics,2014,15:1158
[29]Zhang Y,Wang L,Xin H,Li D,Ma C,Ding X,Hong W,Zhang X.Construction of a high-density genetic map for sesame based on large scale marker development by specific length amplified fragment(SLAF)sequencing.BMC Plant Biol,2013,13:141
[30]Kozich J J,Westcott S L,Baxter N T,Highlander S K,Schloss P D.Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the Mi Seq Illumina sequencing platform.Appl Environ Microb,2013,79:5112–5120
[31]Liu D,Ma C,Hong W,Huang L,Liu M,Liu H,Zeng H,Deng D,Xin H,Song J,Xu C,Sun X,Hou X,Wang X,Zheng H.Construction and analysis of high-density linkage map using high-throughput sequencing data.PLo S One,2014,9(6):e98855