基于SRAP标记的哈尼梯田红米遗传多样性及群体结构分析
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摘要
著名的哈尼梯田核心区位于云南省元阳县,至今仍以种植水稻地方品种为主,梯田红米是其中的主要类型。本研究利用筛选的20对SRAP标记分析60份哈尼梯田红米品种的遗传多样性和群体结构。20对SRAP标记共扩增出182个条带,其中165个具有多态性,多态性比率达90.66%,平均每对引物可扩增9.10个条带;观测等位基因数(Na)、有效等位基因数(Ne)、Nei's基因多样度(H)和Shannon信息指数(I)分别为1.907、1.404、0.239和0.366,表明云南哈尼梯田水稻红米品种具有较丰富的遗传多样性。聚类分析和主成分分析均将60份红米品种分为两大类,即57个籼稻品种聚为第一类,3个粳稻品种聚为第二类,表明哈尼梯田红米以籼稻为主,在籼稻亚群中有部分品种存在遗传分化现象,这一结果与STRUCTURE软件分析的群体结构类型一致。本研究为哈尼梯田红米资源的保护和利用提供了科学依据。
The core area of the famous Hani terraces fields is located in Yuanyang County, Yunnan Province. So far, rice landraces are still the main varieties, especially red rice resources. The genetic diversity and population structure of 60 red rice landraces were analyzed using 20 screened sequence-related amplified polymorphism(SRAP) markers in this study. A total of 182 bands were amplified by 20 pairs of SRAP markers, of which 165 were polymorphic and the polymorphism rate was 90.66%, averaging 9.10 alleles per primer pair. Observed number of alleles(Na), Nei's gene diversity(H) and Shannon's Information index(I) were 1.907, 1.404, 0.239, and0.366, respectively, indicating that the red rice in Hani terraces fields had rich genetic diversity. According to the cluster analysis and principal component analysis, 60 red rice landraces were divided into two major clusters. 57 Indica rice landraces clustered into the first category, and 3 Japonica rice landraces clustered into the second category, suggesting that Indica rice was the main variety in red rice of Hani terraces fields. Genetic differentiation existed in some rice landraces of Indica rice, which was consistent with population structure analyzed by STRUCTURE software. These results could provide scientific reference for protection and application of red rice from Hani terraced fields.
The core area of the famous Hani terraces fields is located in Yuanyang County, Yunnan Province. So far, rice landraces are still the main varieties, especially red rice resources. The genetic diversity and population structure of 60 red rice landraces were analyzed using 20 screened sequence-related amplified polymorphism(SRAP) markers in this study. A total of 182 bands were amplified by 20 pairs of SRAP markers, of which 165 were polymorphic and the polymorphism rate was 90.66%, averaging 9.10 alleles per primer pair. Observed number of alleles(Na), Nei's gene diversity(H) and Shannon's Information index(I) were 1.907, 1.404, 0.239, and0.366, respectively, indicating that the red rice in Hani terraces fields had rich genetic diversity. According to the cluster analysis and principal component analysis, 60 red rice landraces were divided into two major clusters. 57 Indica rice landraces clustered into the first category, and 3 Japonica rice landraces clustered into the second category, suggesting that Indica rice was the main variety in red rice of Hani terraces fields. Genetic differentiation existed in some rice landraces of Indica rice, which was consistent with population structure analyzed by STRUCTURE software. These results could provide scientific reference for protection and application of red rice from Hani terraced fields.
引文
Bai X.H.,Gao D.,Yu L.,and Su Y.,2012,Genetic diversity of rice landraces from Yuanyang Hani's terraced wetland in Yunnan,Fengzi Zhiwu Yuzhong(Molecular Plant Breeding),10(1):1017-1024(白秀红,高东,余磊,苏源,2012,云南元阳梯田湿地水稻地方品种遗传多样性分析,分子植物育种,10(1):1017-1024)
Gao D.,Li R.,Yang M.Q.,and He X.H.,2011a,Rice landraces'genetic diversity of Hani terrace wetland in Qingkou village of Yuanyang county,Fengzi Zhiwu Yuzhong(Molecular Plant Breeding),9(1):1857-1863(高东,李锐,杨木青,何霞红,2011a,元阳箐口村哈尼梯田水稻品种SSR遗传多样性分析,分子植物育种,9(1):1857-1863)
Gao D.,He X.H.,and Zhu Y.Y.,2011b,Changes of rice landrace diversity and rules of seed exchange in Yuanyang,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),12(2):311-313(高东,何霞红,朱有勇,2011b,元阳水稻地方品种多样性变化及换种规律研究,植物遗传资源学报,12(2):311-313)
Gunaratne A.,Wu K.,Li D.,Bentota A.,Corke H.,and Cai Y.Z.,2013,Antioxidant activity and nutritional quality of traditional red-grained rice varieties containing proanthocyanidins,Food Chem.,138(2):1153-1161
Li G.,and Quiros C.F.,2001,Sequence-related amplified polymorphism(SRAP),a new marker system based on a simple PCR reaction:its application to mapping and gene tagging in Brassica,Theor.Appl.Genet.,103(3):455-461
Liu C.C.,Zhao F.W.,Wu X.X.,Zhang C.Q.,Zhu K.Z.,Xue D.Y.,Wu J.Y.,Huang S.W.,Xu X.Y.,Jin Y.G.,and Liu Q.Q,2015,Genetic diversity and population structure analysis of currently cultivated rice landraces from Hani's Terraced Fields in Yunnan Province moleal,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),29(1):28-34(刘承晨,赵富伟,吴晓霞,张昌泉,朱孔志,薛达元,武建勇,黄绍文,徐小颖,金银根,刘巧泉,2015,云南哈尼梯田当前栽培水稻遗传多样性及群体结构分析,中国水稻科学,29(1):28-34)
Liu D.,Sun J.,Ma D.R.,Wang J.Y.,Tang L.,Miao W.,and Chen W.F.,2012,Genetic diversity of 47 weedy rice with SRAPmarkers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),26(1):70-76(刘丹,孙健,马殿荣,王嘉宇,唐亮,苗微,陈温福,2012,利用SRAP分子标记分析47份杂草稻样品遗传多样性,中国水稻科学,26(1):70-76)
Pritchard J.K.,Stephens M.,and Donnelly P.,2000,Inference of population structure using multilocus genotype data,Genetics,155(6):945-959
Qi L.,Wang X.N.,Zhang J.Z.,Tang Q.J.,Meng W.D.,and Yan X.W.,2013,Study on genetic diversity and differentiation of three wild rice species in Hainan using SRAP markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(3):402-406(齐兰,王效宁,张吉贞,唐清杰,孟卫东,严小微,2013,利用SRAP标记研究海南野生稻的遗传多样性与遗传分化,植物遗传资源学报,14(3):402-406)
Sumczynski D.,KotáskováE.,Dru觩bíkováH.,and Mlcek J.,2016,Determination of contents and antioxidant activity of free and bound phenolics compounds and in vitro digestibility of commercial black and red rice(Oryza sativa L.)varieties,Food Chem.,211:339-346
Xu F.R.,Dong C.,Yang W.Y.,Tang C.F.,A X.X.,Zhang E.L.,Yang Y.Y.,Zhang F.F.,Dai L.Y.,and Zhang H.S.,2011,Comparison of genetic diversity of rice landraces planted in two periods in Hani's terraced fields in Yuanyang county,Yunnan Province,China using microsatellite markers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),25(4):381-386(徐福荣,董超,杨文毅,汤翠凤,阿新祥,张恩来,杨雅云,张斐斐,戴陆园,张红生,2011,利用微卫星标记比较云南元阳哈尼梯田两个不同时期种植的水稻地方品种的遗传多样性,中国水稻科学,25(4):381-386)
Xu F.R.,Tang C.F.,Yu T.Q.,Dai L.Y.,and Zhang H.S.,2010,Diversity of paddy rice varieties from Yuanyang Hani's terraced fields in Yunnan,Shengtai Xuebao(Acta Ecologica Sinica),30(12):3346-3357(徐福荣,汤翠凤,余腾琼,戴陆园,张红生,2010,中国云南元阳哈尼梯田种植的稻作品种多样性,生态学报,30(12):3346-3357)
Yao Y.F.,Wang Y.,Zhuang N.S.,and Gao H.Q.,2014,Analysis on genetic diversity of Hainan upland rice local varietiesand establishment of molecular ID with SRAP markers,Shengwu Jishu Tongbao(Biotechnology Bulletin),(11):97-106(姚宇飞,王英,庄南生,高和琼,2014,利用SRAP标记分析海南旱稻地方品种的遗传多样性及其分子身份证的构建,生物技术通报,(11):97-106)
Zeng Y.W.,Zhang H.L.,Li Z.C.,Shen S.Q.,Sun J.L.,Wang M.X.,Liao D.Q.,Liu X.,Wang X.K.,Xiao F.H.,and Wen G.S.,2007,Evaluation of genetic diversity of rice landraces(O-ryza sativa L.)in Yunnan,China,Breed.Sci.,57(2):91-99
Zhang A.S.,Xu J.W.,Xin C.Y.,Zhang L.M.,Xing Z.F.,and Wei H.Y.,2010,Analysis of genetic diversity of new middle-late lines of Japonica rice in Henan Province by SRAP,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),26(2):50-54(张安世,徐九文,辛长永,张利民,邢智峰,韦慧彦,2010,河南省水稻中晚粳新品系遗传多样性的SRAP分析,中国农学通报,26(2):50-54)
Zhong L.,Liu G.M.,Cheng C.,and Chen Z.G.,2016,Analysis on genetic differences in rice by SRAP molecular markers,Hunan Nongye Kexue(Hunan Agricultural Sciences),(12):5-9(钟丽,刘冠明,程诚,陈兆贵,2016,不同粒型水稻品种遗传差异的SRAP分子标记分析,湖南农业科学,(12):5-9)
Gao D.,Li R.,Yang M.Q.,and He X.H.,2011a,Rice landraces'genetic diversity of Hani terrace wetland in Qingkou village of Yuanyang county,Fengzi Zhiwu Yuzhong(Molecular Plant Breeding),9(1):1857-1863(高东,李锐,杨木青,何霞红,2011a,元阳箐口村哈尼梯田水稻品种SSR遗传多样性分析,分子植物育种,9(1):1857-1863)
Gao D.,He X.H.,and Zhu Y.Y.,2011b,Changes of rice landrace diversity and rules of seed exchange in Yuanyang,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),12(2):311-313(高东,何霞红,朱有勇,2011b,元阳水稻地方品种多样性变化及换种规律研究,植物遗传资源学报,12(2):311-313)
Gunaratne A.,Wu K.,Li D.,Bentota A.,Corke H.,and Cai Y.Z.,2013,Antioxidant activity and nutritional quality of traditional red-grained rice varieties containing proanthocyanidins,Food Chem.,138(2):1153-1161
Li G.,and Quiros C.F.,2001,Sequence-related amplified polymorphism(SRAP),a new marker system based on a simple PCR reaction:its application to mapping and gene tagging in Brassica,Theor.Appl.Genet.,103(3):455-461
Liu C.C.,Zhao F.W.,Wu X.X.,Zhang C.Q.,Zhu K.Z.,Xue D.Y.,Wu J.Y.,Huang S.W.,Xu X.Y.,Jin Y.G.,and Liu Q.Q,2015,Genetic diversity and population structure analysis of currently cultivated rice landraces from Hani's Terraced Fields in Yunnan Province moleal,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),29(1):28-34(刘承晨,赵富伟,吴晓霞,张昌泉,朱孔志,薛达元,武建勇,黄绍文,徐小颖,金银根,刘巧泉,2015,云南哈尼梯田当前栽培水稻遗传多样性及群体结构分析,中国水稻科学,29(1):28-34)
Liu D.,Sun J.,Ma D.R.,Wang J.Y.,Tang L.,Miao W.,and Chen W.F.,2012,Genetic diversity of 47 weedy rice with SRAPmarkers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),26(1):70-76(刘丹,孙健,马殿荣,王嘉宇,唐亮,苗微,陈温福,2012,利用SRAP分子标记分析47份杂草稻样品遗传多样性,中国水稻科学,26(1):70-76)
Pritchard J.K.,Stephens M.,and Donnelly P.,2000,Inference of population structure using multilocus genotype data,Genetics,155(6):945-959
Qi L.,Wang X.N.,Zhang J.Z.,Tang Q.J.,Meng W.D.,and Yan X.W.,2013,Study on genetic diversity and differentiation of three wild rice species in Hainan using SRAP markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(3):402-406(齐兰,王效宁,张吉贞,唐清杰,孟卫东,严小微,2013,利用SRAP标记研究海南野生稻的遗传多样性与遗传分化,植物遗传资源学报,14(3):402-406)
Sumczynski D.,KotáskováE.,Dru觩bíkováH.,and Mlcek J.,2016,Determination of contents and antioxidant activity of free and bound phenolics compounds and in vitro digestibility of commercial black and red rice(Oryza sativa L.)varieties,Food Chem.,211:339-346
Xu F.R.,Dong C.,Yang W.Y.,Tang C.F.,A X.X.,Zhang E.L.,Yang Y.Y.,Zhang F.F.,Dai L.Y.,and Zhang H.S.,2011,Comparison of genetic diversity of rice landraces planted in two periods in Hani's terraced fields in Yuanyang county,Yunnan Province,China using microsatellite markers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),25(4):381-386(徐福荣,董超,杨文毅,汤翠凤,阿新祥,张恩来,杨雅云,张斐斐,戴陆园,张红生,2011,利用微卫星标记比较云南元阳哈尼梯田两个不同时期种植的水稻地方品种的遗传多样性,中国水稻科学,25(4):381-386)
Xu F.R.,Tang C.F.,Yu T.Q.,Dai L.Y.,and Zhang H.S.,2010,Diversity of paddy rice varieties from Yuanyang Hani's terraced fields in Yunnan,Shengtai Xuebao(Acta Ecologica Sinica),30(12):3346-3357(徐福荣,汤翠凤,余腾琼,戴陆园,张红生,2010,中国云南元阳哈尼梯田种植的稻作品种多样性,生态学报,30(12):3346-3357)
Yao Y.F.,Wang Y.,Zhuang N.S.,and Gao H.Q.,2014,Analysis on genetic diversity of Hainan upland rice local varietiesand establishment of molecular ID with SRAP markers,Shengwu Jishu Tongbao(Biotechnology Bulletin),(11):97-106(姚宇飞,王英,庄南生,高和琼,2014,利用SRAP标记分析海南旱稻地方品种的遗传多样性及其分子身份证的构建,生物技术通报,(11):97-106)
Zeng Y.W.,Zhang H.L.,Li Z.C.,Shen S.Q.,Sun J.L.,Wang M.X.,Liao D.Q.,Liu X.,Wang X.K.,Xiao F.H.,and Wen G.S.,2007,Evaluation of genetic diversity of rice landraces(O-ryza sativa L.)in Yunnan,China,Breed.Sci.,57(2):91-99
Zhang A.S.,Xu J.W.,Xin C.Y.,Zhang L.M.,Xing Z.F.,and Wei H.Y.,2010,Analysis of genetic diversity of new middle-late lines of Japonica rice in Henan Province by SRAP,Zhongguo Nongxue Tongbao(Chinese Agricultural Science Bulletin),26(2):50-54(张安世,徐九文,辛长永,张利民,邢智峰,韦慧彦,2010,河南省水稻中晚粳新品系遗传多样性的SRAP分析,中国农学通报,26(2):50-54)
Zhong L.,Liu G.M.,Cheng C.,and Chen Z.G.,2016,Analysis on genetic differences in rice by SRAP molecular markers,Hunan Nongye Kexue(Hunan Agricultural Sciences),(12):5-9(钟丽,刘冠明,程诚,陈兆贵,2016,不同粒型水稻品种遗传差异的SRAP分子标记分析,湖南农业科学,(12):5-9)