基于SSR标记的高原粳稻品种遗传多样性分析
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摘要
利用中国农业行业标准(NY/T 1433-2014)推荐的48对SSR引物,对81个高原常规粳稻推广品种进行遗传多样性分析。结果表明:37对SSR引物在81个品种间具有多态性,共检测到139个等位基因(分子量变异范围为89～288 bp),每对引物检测到的等位基因数(Na)为2～10个,平均3.76个。Nei基因多样性指数(He)为0.025～0.769,平均为0.438。SSR多态信息量(PIC)分布范围为0.024～0.727,平均为0.416。遗传相似系数变幅为0.42～1.0,平均为0.65。2007-2016年育成的品种遗传多样性低于2007年前育成的品种,两个时期育成的品种有15个SSR位点的等位基因存在差异。聚类分析表明,遗传相似系数为0.62时,81个品种划分为4个类群,其中第Ⅰ类、第Ⅱ类和第Ⅲ类分别包括4个、5个和12个品种,第Ⅳ类包括60个品种,占供试品种数的74.1%。表明大多数品种间遗传距离近,遗传基础较窄。在今后的水稻育种中,应加强有利基因发掘、引进和创新利用,以拓宽高原粳稻的遗传基础。
The genetic diversity analysis of 81 plateau conventional japonica rice varieties was carried out using48 pairs of SSR primers recommended by Chinese agricultural industry standard(NY/T 1433-2014). The results showed that 37 pairs of SSR primers were polymorphic among 81 varieties, and 139 alleles(molecular weight variation ranged from 89 to 288 bp) were detected. The number of alleles(Na) detected by each pair of primers was 2 to10, with an average of 3.76. The Nei's gene diversity index(He) was 0.025 to 0.769, with an average of 0.438. The SSR polymorphic information(PIC) distribution ranged from 0.024 to 0.727, with an average of 0.416. The genetic similarity coefficient ranged from 0.42 to 1.0, with an average of 0.65. The genetic diversity of the varieties bred from 2007 to 2016 was lower than those bred before 2007, and 15 alleles of SSR loci were different between the two periods. The cluster analysis indicated that when the genetic similarity coefficient was 0.62, 81 varieties were divided into 4 groups, of which groupsⅠ, groupsⅡand groupsⅢincluded 4, 5 and 12 varieties, respectively. While the group Ⅳ included 60 cultivars, which accounted for 74.1% of the tested cultivars, indicating that the genetic distance between most varieties was close and the genetic basis was narrow. In the future rice breeding, beneficial gene discovery, introduction and innovative utilization should be strengthened to broaden the genetic basis of plateau japonica rice in Yunnan Province.
The genetic diversity analysis of 81 plateau conventional japonica rice varieties was carried out using48 pairs of SSR primers recommended by Chinese agricultural industry standard(NY/T 1433-2014). The results showed that 37 pairs of SSR primers were polymorphic among 81 varieties, and 139 alleles(molecular weight variation ranged from 89 to 288 bp) were detected. The number of alleles(Na) detected by each pair of primers was 2 to10, with an average of 3.76. The Nei's gene diversity index(He) was 0.025 to 0.769, with an average of 0.438. The SSR polymorphic information(PIC) distribution ranged from 0.024 to 0.727, with an average of 0.416. The genetic similarity coefficient ranged from 0.42 to 1.0, with an average of 0.65. The genetic diversity of the varieties bred from 2007 to 2016 was lower than those bred before 2007, and 15 alleles of SSR loci were different between the two periods. The cluster analysis indicated that when the genetic similarity coefficient was 0.62, 81 varieties were divided into 4 groups, of which groupsⅠ, groupsⅡand groupsⅢincluded 4, 5 and 12 varieties, respectively. While the group Ⅳ included 60 cultivars, which accounted for 74.1% of the tested cultivars, indicating that the genetic distance between most varieties was close and the genetic basis was narrow. In the future rice breeding, beneficial gene discovery, introduction and innovative utilization should be strengthened to broaden the genetic basis of plateau japonica rice in Yunnan Province.
引文
Bao G.L.,Kobayashi A.,Tomita K.,Jin Q.S.,Zhang X.M.,Yan W.C.,and Ye S.H.,2005,Polymorphism analysis of closely related japonica rice varieties by using SSR markers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),19(1):21-24(鲍根良,小林麻子,富田桂,金庆生,张小明,严文潮,叶胜海,2005,粳稻近缘品种的SSR,中国水稻科学,19(1):21-24)
Chen Y.M.,Shan Y.,Shi R.,Su Z.X.,Zou Q.,Liu W.H.,Zhu Z.H.,Kou S.Y.,Yuan P.R.,Dai L.Y.,and Zhao G.Z.,2016,Comparative analysis of the main agronomic characters of plateau Japonica rice backbone of parents and their derivative cultivars,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),17(1):20-26(陈于敏,单艳,世荣,苏振喜,邹茜,刘慰华,朱振华,寇姝燕,袁平荣,戴陆园,赵国珍,2016,高原粳稻骨干亲本及其衍生品种的主要农艺性状比较分析,植物遗传资源学报,17(1):20-26)
Hua L.,Yuan Y.P.,Yu H.Y.,Wang Y.P.,Xu Q.,Tang S.X.,and Wei X.H.,2007,Acomparative study on SSR diversity in Chinese major rice varieties planted in 1950's and during the most recent ten years,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),21(2):150-154(华蕾,袁筱萍,余汉勇,王一平,徐群,汤圣祥,魏兴华,2007,我国水稻主栽品种SSR多样性的比较分析,中国水稻科学,21(2):150-154)
Liu W.,Li Z.C.,Shi Y.L.,Wang J.,Ma H.W.,and Zheng H.L.,2005,Genetic diversity of Japonica rice varieties based on SSR markers,Xinan Nongye Xuebao(Southwest China Journal of Agricultural Sciences),18(5):509-513(刘炜,李自超,史延丽,王坚,马洪文,张洪亮,2005,利用SSR标记进行粳稻品种的遗传多样性研究,西南农业学报,18(5):509-513)
Li H.Y.,Hou Y.M.,Chen Y.H.,Xu Z.J.,Chen W.F.,Zhao M.H.,Ma D.Y.,Xu H.,and Wang J.Y.,2009,Evaluation on genetic diversity of the commercial rice varieties in northeast china by microsatellite markers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),23(4):383-390(李红宇,侯昱铭,陈英华,徐正进,陈温福,赵明辉,马殿荣,徐海,王嘉宇,2009,用SSR标记评估东北三省水稻推广品种的遗传多样性,中国水稻科学,23(4):383-390)
Lv Z.H.,and Guo H.C.,2018,Comparison of genetic diversity analysis by RSAP,SSR and SRAP markers in potato,Jiyin zuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(6):2544-2550(吕志华,郭华春,2018,RSAP,SSR和SRAP分析马铃薯遗传多样性的应用比较,基因组学与应用生物学,37(6):2544-2550)
Ma J.,Sun J.C.,An Y.P.,Wuang X.S.,Zhang Z.H.,and Han L.Z.,2013,Analysis of genetic diversity with population of Japonica rice from Ningxia using microsatellite markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(5):826-832(马静,孙建昌,安永平,王兴盛,张振海,韩龙植,2013,基于SSR标记的宁夏水稻遗传多样性分析,植物遗传资源学报,14(5):826-832)
Shu A.P.,Liu Z.B.,Yu L.Q.,Li M.M.,and Chen D.Z.,2013,Research progress on genetic diversity in rice based on SSRmarker analysis,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(5):778-783(束爱萍,刘增兵,余丽琴,黎毛毛,陈大洲,2013,水稻SSR标记的遗传多样性研究进展,植物遗传资源学报,14(5):778-783)
Wang F.G.,Tian H.L.,Zhao J.R.,Wang L.,Yi H.M.,Song W.,Gao Y.Q.,and Yang G.H.,2014,Genetic diversity analysis of 328 maize varieties(hybridized combinations)using SSRmarkers,Zhongguo Nongye Kexue(Scientia Agricultura S-inica),47(5):856-864(王凤格,田红丽,赵久然,王璐,易红梅,宋伟,高玉倩,杨国航,2014,中国328个玉米品种(组合)SSR标记遗传多样性分析,中国农业科学,47(5):856-864)
Yu H.Y.,Wei X.H.,Wang Y.P.,Yuan Y.P.,and Tang Y.X.,2004,Study on genetic variation of rice varieties derived from aizizhan by using morphological traits,allozymes and simple sequence repeat(SSR)markers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),18(6):477-482(余汉勇,魏兴华,王一平,袁筱萍,汤圣祥,2004,应用形态,等位酶和SSR标记研究水稻矮仔占衍生品种的遗传差异,中国水稻科学,18(6):477-482)
Yang J.,Liu H.Y.,Qian C.R.,and Jin Z.X.,2008,Analysis on genetic diversity of rice varieties in Heilongjiang province by using SSR,Dongbei Nongye Daxue Xuebao(Journal of Northeast Agricultural University),39(6):1-10(杨静,刘海英,钱春荣,金正勋,2008,黑龙江省水稻品种SSR标记遗传多样性分析,东北农业大学学报,39(6):1-10)
Ying J.Z.,Shi Y.F.,Zhuang J.Y.,and Xue Q.Z.,2007,Assessment of uniformity of major rice varieties in China using microsatellite markers,Zhongguo Shuidao Kexue(Scientia Agricultura Sinica),40(4):649-654(应杰政,施勇烽,庄杰云,薛庆中,2007,用微卫星标记评估中国水稻主栽品种的遗传多样性,中国农业科学,40(4):649-654)
Zhu Y.Y.,Chen H.R.,Fan J.H.,Wang Y.Y.,L Y.,Chen J.B.,Fan J.X.,Yang S.S.,Hu L.P.,Leung H.,Mew T.W.,Teng P.S.,Wang Z.H.,and Mundt C.C.,2000,Genetic diversity and disease control in rice,Nature,406(6797):718-722
Zhao T.,Jin L.Y.,Li Y.,An H.J.,Xing Z.H.,Wang R.H.,Liu G.R.,and Wen S.M.,2015,Genetic diversity analysis for bread wheat(Tritscum aestivum L.)cultivars in Hebei province based on genome-wide SSR markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),16(1):45-53(赵檀,金柳艳,李远,安浩军,邢志华,王睿辉,刘桂茹,温树敏,2015,基于全基因组的河北省小麦品种遗传多样性分析,植物遗传资源学报,16(1):45-53)
Zhang K.,Wei H.F.,Zhuo D.L.,Zhang X.J.,Zhang F.,Zhou Y.L.,and Li Z.K.,2016,Genetic diversity analysis of registered rice(Oryza sativa L.)varieties in Heilongjiang province based on SSR markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),17(3):447-454(张科,魏海锋,卓大龙,张晓敬,张帆,周永力,黎志康,2016,黑龙江省近年审定水稻品种基于SSR标记的遗传多样性分析,植物遗传资源学报,17(3):447-454)
Zhan g L.N.,Cao G.L.,and Han L.Z.,2012,Analysis of genetic diversity of japonica rice landrace in china with microsatellite marker,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(3):405-413(张立娜,曹桂兰,韩龙植,2012,利用SSR标记揭示中国粳稻地方品种遗传多样性,中国农业科学,45(3):405-413)
Zeng Y.W.,Li Z.C.,Shen S.Q.,Wang X.K.,Yang Z.Y.,Zhang H.L.,and Chen Y.M.,2007,Diversity and good germplasm of indigenous rice varieties in Yunnan province,2001,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),15(3):169-174(曾亚文,李自超,申时全,王象坤,杨忠义,张洪亮,陈于敏,2001,云南地方稻种的多样性及优异种质研究,中国水稻科学,15(3):169-174)
Zhu M.Y.,Wang Y.Y.,Zhu Y.Y.,and Lu B.R.,Genetic diversity of rice landraces from Yunnan revealed by SSR analysis and its significance for conservation,2004,Huazhong Nongye Daxue Xuebao(Journal of Huazhong Agricultural University),23(2):187-191(朱明雨,王云月,朱有勇,卢宝荣,2004,云南地方水稻品种遗传多样性分析及其保护意义,华中农业大学学报,23(2):187-191)
Zhao G.Z.,Yang S.J.,Cho Y.C.,Li J.H.,Su Z.X.,Zhu Z.H.,Zou Q.,and Dai L.Y.,2008,Analysis of genetic diversity between japonica rice of Yunnan and Korea,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),6(3):451-456(赵国珍,杨世准,曹永灿,李彀镎,苏振喜,朱振华,邹茜,戴陆园,2008,云南粳稻和韩国粳稻的遗传差异分析,分子植物育种,6(3):451-456)
Zheng K.L.,Subudhi P.K.,Domingo J.,Magpantay G.,and Huang N.,1995,Rapid DNA isolation for marker-assisted selection in rice breeding,Rice Genet.News,12:255-257
Chen Y.M.,Shan Y.,Shi R.,Su Z.X.,Zou Q.,Liu W.H.,Zhu Z.H.,Kou S.Y.,Yuan P.R.,Dai L.Y.,and Zhao G.Z.,2016,Comparative analysis of the main agronomic characters of plateau Japonica rice backbone of parents and their derivative cultivars,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),17(1):20-26(陈于敏,单艳,世荣,苏振喜,邹茜,刘慰华,朱振华,寇姝燕,袁平荣,戴陆园,赵国珍,2016,高原粳稻骨干亲本及其衍生品种的主要农艺性状比较分析,植物遗传资源学报,17(1):20-26)
Hua L.,Yuan Y.P.,Yu H.Y.,Wang Y.P.,Xu Q.,Tang S.X.,and Wei X.H.,2007,Acomparative study on SSR diversity in Chinese major rice varieties planted in 1950's and during the most recent ten years,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),21(2):150-154(华蕾,袁筱萍,余汉勇,王一平,徐群,汤圣祥,魏兴华,2007,我国水稻主栽品种SSR多样性的比较分析,中国水稻科学,21(2):150-154)
Liu W.,Li Z.C.,Shi Y.L.,Wang J.,Ma H.W.,and Zheng H.L.,2005,Genetic diversity of Japonica rice varieties based on SSR markers,Xinan Nongye Xuebao(Southwest China Journal of Agricultural Sciences),18(5):509-513(刘炜,李自超,史延丽,王坚,马洪文,张洪亮,2005,利用SSR标记进行粳稻品种的遗传多样性研究,西南农业学报,18(5):509-513)
Li H.Y.,Hou Y.M.,Chen Y.H.,Xu Z.J.,Chen W.F.,Zhao M.H.,Ma D.Y.,Xu H.,and Wang J.Y.,2009,Evaluation on genetic diversity of the commercial rice varieties in northeast china by microsatellite markers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),23(4):383-390(李红宇,侯昱铭,陈英华,徐正进,陈温福,赵明辉,马殿荣,徐海,王嘉宇,2009,用SSR标记评估东北三省水稻推广品种的遗传多样性,中国水稻科学,23(4):383-390)
Lv Z.H.,and Guo H.C.,2018,Comparison of genetic diversity analysis by RSAP,SSR and SRAP markers in potato,Jiyin zuxue Yu Yingyong Shengwuxue(Genomics and Applied Biology),37(6):2544-2550(吕志华,郭华春,2018,RSAP,SSR和SRAP分析马铃薯遗传多样性的应用比较,基因组学与应用生物学,37(6):2544-2550)
Ma J.,Sun J.C.,An Y.P.,Wuang X.S.,Zhang Z.H.,and Han L.Z.,2013,Analysis of genetic diversity with population of Japonica rice from Ningxia using microsatellite markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(5):826-832(马静,孙建昌,安永平,王兴盛,张振海,韩龙植,2013,基于SSR标记的宁夏水稻遗传多样性分析,植物遗传资源学报,14(5):826-832)
Shu A.P.,Liu Z.B.,Yu L.Q.,Li M.M.,and Chen D.Z.,2013,Research progress on genetic diversity in rice based on SSRmarker analysis,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),14(5):778-783(束爱萍,刘增兵,余丽琴,黎毛毛,陈大洲,2013,水稻SSR标记的遗传多样性研究进展,植物遗传资源学报,14(5):778-783)
Wang F.G.,Tian H.L.,Zhao J.R.,Wang L.,Yi H.M.,Song W.,Gao Y.Q.,and Yang G.H.,2014,Genetic diversity analysis of 328 maize varieties(hybridized combinations)using SSRmarkers,Zhongguo Nongye Kexue(Scientia Agricultura S-inica),47(5):856-864(王凤格,田红丽,赵久然,王璐,易红梅,宋伟,高玉倩,杨国航,2014,中国328个玉米品种(组合)SSR标记遗传多样性分析,中国农业科学,47(5):856-864)
Yu H.Y.,Wei X.H.,Wang Y.P.,Yuan Y.P.,and Tang Y.X.,2004,Study on genetic variation of rice varieties derived from aizizhan by using morphological traits,allozymes and simple sequence repeat(SSR)markers,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),18(6):477-482(余汉勇,魏兴华,王一平,袁筱萍,汤圣祥,2004,应用形态,等位酶和SSR标记研究水稻矮仔占衍生品种的遗传差异,中国水稻科学,18(6):477-482)
Yang J.,Liu H.Y.,Qian C.R.,and Jin Z.X.,2008,Analysis on genetic diversity of rice varieties in Heilongjiang province by using SSR,Dongbei Nongye Daxue Xuebao(Journal of Northeast Agricultural University),39(6):1-10(杨静,刘海英,钱春荣,金正勋,2008,黑龙江省水稻品种SSR标记遗传多样性分析,东北农业大学学报,39(6):1-10)
Ying J.Z.,Shi Y.F.,Zhuang J.Y.,and Xue Q.Z.,2007,Assessment of uniformity of major rice varieties in China using microsatellite markers,Zhongguo Shuidao Kexue(Scientia Agricultura Sinica),40(4):649-654(应杰政,施勇烽,庄杰云,薛庆中,2007,用微卫星标记评估中国水稻主栽品种的遗传多样性,中国农业科学,40(4):649-654)
Zhu Y.Y.,Chen H.R.,Fan J.H.,Wang Y.Y.,L Y.,Chen J.B.,Fan J.X.,Yang S.S.,Hu L.P.,Leung H.,Mew T.W.,Teng P.S.,Wang Z.H.,and Mundt C.C.,2000,Genetic diversity and disease control in rice,Nature,406(6797):718-722
Zhao T.,Jin L.Y.,Li Y.,An H.J.,Xing Z.H.,Wang R.H.,Liu G.R.,and Wen S.M.,2015,Genetic diversity analysis for bread wheat(Tritscum aestivum L.)cultivars in Hebei province based on genome-wide SSR markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),16(1):45-53(赵檀,金柳艳,李远,安浩军,邢志华,王睿辉,刘桂茹,温树敏,2015,基于全基因组的河北省小麦品种遗传多样性分析,植物遗传资源学报,16(1):45-53)
Zhang K.,Wei H.F.,Zhuo D.L.,Zhang X.J.,Zhang F.,Zhou Y.L.,and Li Z.K.,2016,Genetic diversity analysis of registered rice(Oryza sativa L.)varieties in Heilongjiang province based on SSR markers,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),17(3):447-454(张科,魏海锋,卓大龙,张晓敬,张帆,周永力,黎志康,2016,黑龙江省近年审定水稻品种基于SSR标记的遗传多样性分析,植物遗传资源学报,17(3):447-454)
Zhan g L.N.,Cao G.L.,and Han L.Z.,2012,Analysis of genetic diversity of japonica rice landrace in china with microsatellite marker,Zhongguo Nongye Kexue(Scientia Agricultura Sinica),45(3):405-413(张立娜,曹桂兰,韩龙植,2012,利用SSR标记揭示中国粳稻地方品种遗传多样性,中国农业科学,45(3):405-413)
Zeng Y.W.,Li Z.C.,Shen S.Q.,Wang X.K.,Yang Z.Y.,Zhang H.L.,and Chen Y.M.,2007,Diversity and good germplasm of indigenous rice varieties in Yunnan province,2001,Zhongguo Shuidao Kexue(Chinese Journal of Rice Science),15(3):169-174(曾亚文,李自超,申时全,王象坤,杨忠义,张洪亮,陈于敏,2001,云南地方稻种的多样性及优异种质研究,中国水稻科学,15(3):169-174)
Zhu M.Y.,Wang Y.Y.,Zhu Y.Y.,and Lu B.R.,Genetic diversity of rice landraces from Yunnan revealed by SSR analysis and its significance for conservation,2004,Huazhong Nongye Daxue Xuebao(Journal of Huazhong Agricultural University),23(2):187-191(朱明雨,王云月,朱有勇,卢宝荣,2004,云南地方水稻品种遗传多样性分析及其保护意义,华中农业大学学报,23(2):187-191)
Zhao G.Z.,Yang S.J.,Cho Y.C.,Li J.H.,Su Z.X.,Zhu Z.H.,Zou Q.,and Dai L.Y.,2008,Analysis of genetic diversity between japonica rice of Yunnan and Korea,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),6(3):451-456(赵国珍,杨世准,曹永灿,李彀镎,苏振喜,朱振华,邹茜,戴陆园,2008,云南粳稻和韩国粳稻的遗传差异分析,分子植物育种,6(3):451-456)
Zheng K.L.,Subudhi P.K.,Domingo J.,Magpantay G.,and Huang N.,1995,Rapid DNA isolation for marker-assisted selection in rice breeding,Rice Genet.News,12:255-257