江永普通野生稻遗传多样性和籼粳基因频率监测分析
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摘要
以栽培稻的8个籼-粳测验种为对照,采用39对SSR引物检测了江永野生稻居群在1982年、2008年、2017年的遗传多样性,采用38对In Del引物检测了江永野生稻居群在1982年、2008年、2017年的籼-粳基因频率。结果表明:在1982年取样保存在异位圃的40份样本的遗传多样性稍高于2008年、2017年原位保护区样本的遗传多样性;2008年取的样本数虽然比2017年多,但两次取的样本之间遗传多样性几乎没差异。不同年份取的样本之间的遗传分化系数Fst都很小,基因流Nm都较大,分化不明显。通过聚类分析和主坐标分析(PCo A),发现野生稻居群与4份栽培粳稻聚为一类,4份栽培籼稻单独聚成一类,显示江永野生稻与粳稻的血缘近于籼稻;籼-粳基因频率的分析表明,野生稻样本多属粳稻型,少数属偏粳稻型,原位保护区的偏粳稻类型单株数占取样单株总数的比例,2008年比1982年的增加了10.0%,2017年比2008年的增加了1.6%,显示江永野生稻原位保护区生境条件有利野生稻从粳稻型向偏粳稻型变异,随着野生稻产生环境适应性变异,籼型基因频率在提高。
This study analyzed the genetic diversity and indica-japonica gene frequencies of Jiangyong wild rice(Oryza rufipogon Griff.)populations,which were sampled in 1982,2008 and 2017,using 39 SSR markers and 38 Indel markers respectively.The results showed that the genetic diversity of 40 accessions sampled and conserved in ex-situ in 1982 was higher than that in-situ conservation sampled in 2008 and 2017.No signi?cant difference was observed in genetic diversity between the samples in 2008 and 2017.In addition,samples collected in different years displayed unobvious differentiation,with low genetic differentiation coefficient(Fst)and high gene ?ow(Nm).According to cluster analysis and principal coordinate analysis,we found that the genetic relationship between wild rice and japonica rice is closer than that between wild rice and indica rice.Most of the wild rice plants were grouped to japonica class,and a few belong to japonicaclinous class.In 2008,the percentage of japonicaclinous individuals increased by 10.0% compared with 1982,and in 2017,the percentage increased by 1.6% compared with 2008.These results implied that the indica gene frequency of wild rice increased with the environmental changes of in-situ conservation.
This study analyzed the genetic diversity and indica-japonica gene frequencies of Jiangyong wild rice(Oryza rufipogon Griff.)populations,which were sampled in 1982,2008 and 2017,using 39 SSR markers and 38 Indel markers respectively.The results showed that the genetic diversity of 40 accessions sampled and conserved in ex-situ in 1982 was higher than that in-situ conservation sampled in 2008 and 2017.No signi?cant difference was observed in genetic diversity between the samples in 2008 and 2017.In addition,samples collected in different years displayed unobvious differentiation,with low genetic differentiation coefficient(Fst)and high gene ?ow(Nm).According to cluster analysis and principal coordinate analysis,we found that the genetic relationship between wild rice and japonica rice is closer than that between wild rice and indica rice.Most of the wild rice plants were grouped to japonica class,and a few belong to japonicaclinous class.In 2008,the percentage of japonicaclinous individuals increased by 10.0% compared with 1982,and in 2017,the percentage increased by 1.6% compared with 2008.These results implied that the indica gene frequency of wild rice increased with the environmental changes of in-situ conservation.
引文
[1]张晓丽,郭辉,王海岗,吕建珍,袁筱萍,彭锁堂,魏兴华·中国普通野生稻与栽培稻种SSR多样性的比较分析·作物学报,2008,34(4):591-597Zhang X L, Guo H, Wang H G, LU J Z, Yuan X P, Peng S T, Wei X H-Comparative assessment of SSR allelic diversity in wild and cultivated rice in China-Acta Agronomica Sinica,2008,34(4):591-597
[2]王黎明,李战胜,高旭华,沈雪峰,方越,陈勇·杂草稻、栽培稻及野生稻的遗传多样性比较·华中农业大学学报,2012, 31(3):275-280Wang L M, Li Z S, Gao X H, Shen X F, Fang Y, Chen Y.Genetic diversities among weedy rice, cultivated rice and wild rice.Journal of Huazhong Agricultural University, 2012, 31(3):275-280
[3]王荣升,魏鑫,曹立荣,乔卫华,张万霞,杨庆文.基于叶绿体基因多样性的中国水稻起源进化研究·植物遗传资源学报,2011,12(5):686-693Wang R S, Wei X, Cao L R, Qiao W H, Zhang W X, Yang Q W.Origin and evolution of cultivated rice(O.sativa L-)in China based on gene diversity of chloroplast genome-Journal of Plant Genetic Resources,2011,12(5):686-693
[4]杨庆文,张万霞,贺丹霞,陈大洲,戴陆元,陈成斌,黄坤德·中国野生稻原生境保护方法研究·植物遗传资源学报,2003,4(1):63-67Yang Q W,Zhang W X,He D X,Chen D Z,Dai L Y,Chen C B,Huang K D.Studies on in-situ conservation methods of wild rice in China.Journal of Plant Genetic Resources, 2003,4(1):63-67
[5]王琳,戴陆园,吴丽华,杨庆文,徐福荣,余腾琼,汤翠凤·云南三种野生稻原生境植物种群的调查及比较分析·中国水稻科学,2006, 20(1):47-52Wang L, Dai L Y, Wu L H, Yang Q W, Xu F R, Yu T Q, Tang C F.Comparative analysis and investigation on plants growing in in-situ environments of three wild rice species in Yunnan Province, Chinese-Chinese Journal of Rice Science, 2006, 20(1):47-52
[6]王家祥,陈友桃,黄娟,乔卫华,张万霞,杨庆文·中国普通野生稻((Oryza rufipogon Griff)原生境保护与未保护居群的遗传多样性比较·作物学报,2009, 35(8):1474-1482Wang J X, Chen Y T, Huang J, Qiao W H, Zhang W X, Yang Q W.Comparison of genetic diversity between in-situ conserved and non-conserved Oryza rufipogon populations in China-Acta Agronomica Sinica,2009, 35(8):1474-1482
[7]陈雨,杨庆文,潘大建,曲延英,范芝兰,陈建酉,李晨·用SSR标记初步分析高州普通野生稻的籼粳分化·分子植物育种,2008,6(2):263-267Chen Y, Yang Q W, Pan D J, Qu Y Y, Fan Z L,Chen J Y,Li C.Preliminary analysis of the indica.japonica differentiation among natural wild rice populations in Gaozhou by SSR markers.Molecular Plant Breeding,2008,6(2):263-267
[8]崔莹莹,郭安平,王晓玲,郭运玲,孔华,贺立卡·海南普通野生稻籼粳分化的SSR分析·江苏农业科学,2009(4):56-58Cui Y Y, Guo A P, Wang X L, Guo Y L, Kong H, He L K SSR analysis of indica-japonica differentiation of Oryza rufipogon Griff. in Hainan Province, China.Jiangsu Agricultural Sciences,2009(4):56-58
[9] Xu X,Liu X,Ge S,Jensen J D,Hu F Y,Li X, Dong Y,Gutenkunst R N, Fang L, Huang L, Li J X, He W M, Zhang G J, Zheng X M, Zhang F M, Li Y R, Yu C, Kristiansen K,Zhang X Q,Wang J,Wright M,McCouch S,Nielsen R,Wang J,Wang W Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.Nature Biotechnology, 2012,30(1):105-111
[10] Huang X H,Kurata N, Wei X H, Wang Z X, Wang A H, Zhao Q,Zhao Y,Liu K Y,LuH Y,Li WJ,Guo Y L,Lu YQ,Zhou C C,Fan D L,Weng Q J,Zhu C R,Huang T,Zhang L,Wang Y C,Feng L,Furuumi H,Kubo T,Miyabayashi T,Yuan X P,Xu Q,Dong G J,Zhan Q L,Li C Y,Fujiyama A,Toyoda A,Lu T T,Feng Q,Qian Q,Li J Y,Han B A map of rice genome variation reveals the origin of cultivated rice-Nature, 2012,490(7421):497-501
[11]蔡星星,刘晶,仇吟秋,赵伟,宋志平,卢宝荣·籼稻93-11和粳稻日本晴DNA插入缺失差异片段揭示的水稻籼-粳分化·复旦学报:自然科学版,2006,45(3):309-315Cai X X,Liu J,Qiu Y Q,Zhao W,Song Z P,Lu B R-Differentiation of indica-japonica rice revealed by insertion/deletion fragments obtained from comparative genomic study of DNA sequences between 93-11(indica)and Nipponbare(japonica).Journal of Fudan University:Natural Science Edition, 2006,45(3):309-315
[12]李小湘,王淑红,段永红,余丽琴,黄海明,李卫红,孙桂华,刘勇·普通野生稻保护和未保护居群遗传多样性的比较·植物遗传资源学报,2007, 8(4):379-386Li X X,Wang S H,Duan Y H,Yu L Q,Huang H M,Li W H,Sun G H, Liu Y.Comparative studies on the genetic diversity between conserved and non-conserved Oryza rufipogon populations-Journal of Plant Genetic Resources, 2007, 8(4):379-386
[13]卢扬江,郑康乐·提取水稻DNA的一种简易方法·中国水稻科学,1992, 6(1):47-48Lu Y J, Zheng K L-A simple method for isolation of rice DNA.Chinese Journal of Rice Science, 1992, 6(1):47-48
[14]卢宝荣,蔡星星,金鑫援·籼稻和粳稻的高效分子鉴定方法及其在水稻育种和进化研究中的意义·自然科学进展,2009,19(6):628-638Lu B R, Cai X X, Jin X Y.An efficient molecular method for the identification of indica and japonica rice and its significance inrice breeding and evolution.Progress in Natural Science,2009,19(6):628-638
[15] Boaretto E, Wu X H, Yuan J R, Bar-Yosef O, Chu V, Pan Y,Liu K X, Cohen D, Jiao T L, Li S C, Gu H B, Goldberg P,Weiner S-Radiocarbon dating of charcoal and bone collagen associated with early pottery at Yuchanyan Cave, Hunan Province, China-Proceedings of the National Academy of Sciences of the United States of America,2009, 106(24):9595-9600
[16]李小湘,詹庆才,魏兴华,段永红,陈祖武,刘勇·湖南江永普通野生稻原位和异位保存种质的SSR多样性差异·中国水稻科学,2006, 20(4):361-366Li X X, Zhan Q C, Wei X H, Duan Y H, Chen Z W, Liu Y.SSR diversity of in-situ and ex-situ conserved Oryza rufipogon populations in Jiangyong County of Hunan Province-Chinese Journal of Rice Science, 2006, 20(4):361-366
[2]王黎明,李战胜,高旭华,沈雪峰,方越,陈勇·杂草稻、栽培稻及野生稻的遗传多样性比较·华中农业大学学报,2012, 31(3):275-280Wang L M, Li Z S, Gao X H, Shen X F, Fang Y, Chen Y.Genetic diversities among weedy rice, cultivated rice and wild rice.Journal of Huazhong Agricultural University, 2012, 31(3):275-280
[3]王荣升,魏鑫,曹立荣,乔卫华,张万霞,杨庆文.基于叶绿体基因多样性的中国水稻起源进化研究·植物遗传资源学报,2011,12(5):686-693Wang R S, Wei X, Cao L R, Qiao W H, Zhang W X, Yang Q W.Origin and evolution of cultivated rice(O.sativa L-)in China based on gene diversity of chloroplast genome-Journal of Plant Genetic Resources,2011,12(5):686-693
[4]杨庆文,张万霞,贺丹霞,陈大洲,戴陆元,陈成斌,黄坤德·中国野生稻原生境保护方法研究·植物遗传资源学报,2003,4(1):63-67Yang Q W,Zhang W X,He D X,Chen D Z,Dai L Y,Chen C B,Huang K D.Studies on in-situ conservation methods of wild rice in China.Journal of Plant Genetic Resources, 2003,4(1):63-67
[5]王琳,戴陆园,吴丽华,杨庆文,徐福荣,余腾琼,汤翠凤·云南三种野生稻原生境植物种群的调查及比较分析·中国水稻科学,2006, 20(1):47-52Wang L, Dai L Y, Wu L H, Yang Q W, Xu F R, Yu T Q, Tang C F.Comparative analysis and investigation on plants growing in in-situ environments of three wild rice species in Yunnan Province, Chinese-Chinese Journal of Rice Science, 2006, 20(1):47-52
[6]王家祥,陈友桃,黄娟,乔卫华,张万霞,杨庆文·中国普通野生稻((Oryza rufipogon Griff)原生境保护与未保护居群的遗传多样性比较·作物学报,2009, 35(8):1474-1482Wang J X, Chen Y T, Huang J, Qiao W H, Zhang W X, Yang Q W.Comparison of genetic diversity between in-situ conserved and non-conserved Oryza rufipogon populations in China-Acta Agronomica Sinica,2009, 35(8):1474-1482
[7]陈雨,杨庆文,潘大建,曲延英,范芝兰,陈建酉,李晨·用SSR标记初步分析高州普通野生稻的籼粳分化·分子植物育种,2008,6(2):263-267Chen Y, Yang Q W, Pan D J, Qu Y Y, Fan Z L,Chen J Y,Li C.Preliminary analysis of the indica.japonica differentiation among natural wild rice populations in Gaozhou by SSR markers.Molecular Plant Breeding,2008,6(2):263-267
[8]崔莹莹,郭安平,王晓玲,郭运玲,孔华,贺立卡·海南普通野生稻籼粳分化的SSR分析·江苏农业科学,2009(4):56-58Cui Y Y, Guo A P, Wang X L, Guo Y L, Kong H, He L K SSR analysis of indica-japonica differentiation of Oryza rufipogon Griff. in Hainan Province, China.Jiangsu Agricultural Sciences,2009(4):56-58
[9] Xu X,Liu X,Ge S,Jensen J D,Hu F Y,Li X, Dong Y,Gutenkunst R N, Fang L, Huang L, Li J X, He W M, Zhang G J, Zheng X M, Zhang F M, Li Y R, Yu C, Kristiansen K,Zhang X Q,Wang J,Wright M,McCouch S,Nielsen R,Wang J,Wang W Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes.Nature Biotechnology, 2012,30(1):105-111
[10] Huang X H,Kurata N, Wei X H, Wang Z X, Wang A H, Zhao Q,Zhao Y,Liu K Y,LuH Y,Li WJ,Guo Y L,Lu YQ,Zhou C C,Fan D L,Weng Q J,Zhu C R,Huang T,Zhang L,Wang Y C,Feng L,Furuumi H,Kubo T,Miyabayashi T,Yuan X P,Xu Q,Dong G J,Zhan Q L,Li C Y,Fujiyama A,Toyoda A,Lu T T,Feng Q,Qian Q,Li J Y,Han B A map of rice genome variation reveals the origin of cultivated rice-Nature, 2012,490(7421):497-501
[11]蔡星星,刘晶,仇吟秋,赵伟,宋志平,卢宝荣·籼稻93-11和粳稻日本晴DNA插入缺失差异片段揭示的水稻籼-粳分化·复旦学报:自然科学版,2006,45(3):309-315Cai X X,Liu J,Qiu Y Q,Zhao W,Song Z P,Lu B R-Differentiation of indica-japonica rice revealed by insertion/deletion fragments obtained from comparative genomic study of DNA sequences between 93-11(indica)and Nipponbare(japonica).Journal of Fudan University:Natural Science Edition, 2006,45(3):309-315
[12]李小湘,王淑红,段永红,余丽琴,黄海明,李卫红,孙桂华,刘勇·普通野生稻保护和未保护居群遗传多样性的比较·植物遗传资源学报,2007, 8(4):379-386Li X X,Wang S H,Duan Y H,Yu L Q,Huang H M,Li W H,Sun G H, Liu Y.Comparative studies on the genetic diversity between conserved and non-conserved Oryza rufipogon populations-Journal of Plant Genetic Resources, 2007, 8(4):379-386
[13]卢扬江,郑康乐·提取水稻DNA的一种简易方法·中国水稻科学,1992, 6(1):47-48Lu Y J, Zheng K L-A simple method for isolation of rice DNA.Chinese Journal of Rice Science, 1992, 6(1):47-48
[14]卢宝荣,蔡星星,金鑫援·籼稻和粳稻的高效分子鉴定方法及其在水稻育种和进化研究中的意义·自然科学进展,2009,19(6):628-638Lu B R, Cai X X, Jin X Y.An efficient molecular method for the identification of indica and japonica rice and its significance inrice breeding and evolution.Progress in Natural Science,2009,19(6):628-638
[15] Boaretto E, Wu X H, Yuan J R, Bar-Yosef O, Chu V, Pan Y,Liu K X, Cohen D, Jiao T L, Li S C, Gu H B, Goldberg P,Weiner S-Radiocarbon dating of charcoal and bone collagen associated with early pottery at Yuchanyan Cave, Hunan Province, China-Proceedings of the National Academy of Sciences of the United States of America,2009, 106(24):9595-9600
[16]李小湘,詹庆才,魏兴华,段永红,陈祖武,刘勇·湖南江永普通野生稻原位和异位保存种质的SSR多样性差异·中国水稻科学,2006, 20(4):361-366Li X X, Zhan Q C, Wei X H, Duan Y H, Chen Z W, Liu Y.SSR diversity of in-situ and ex-situ conserved Oryza rufipogon populations in Jiangyong County of Hunan Province-Chinese Journal of Rice Science, 2006, 20(4):361-366