微卫星分子标记揭示的杂草稻遗传多样性及群体分化
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摘要
为了明确不同地理位置杂草稻群体的遗传多样性现状、遗传分化水平以及杂草稻群体之间的基因流。本研究利用24对SSR引物对来自黑龙江、吉林、辽宁、江苏和广东共17个杂草稻群体的469份杂草稻样本进行的遗传多样性及遗传分化分析。结果表明杂草稻群体的总体遗传多样性较为丰富(I=0.36, He=0.23),不同杂草稻群体间的遗传多样性指数差异较大,He在0.07～0.35之间。AMOVA分析结果表明,杂草稻群体70%的变异来源于群体间,30%的变异来源于群体内。聚类分析显示,相邻地区的种群间相似性较高,江苏省杂草稻的不同种群间存在较高遗传分化;遗传分化与基因流结果表明,17个杂草稻种群间总的Nm值为0.117,总Fst值为0.694。地理位置较近的种群间Nm普遍较高,Fst较低;而地理位置较远的种群间Nm普遍较低,Fst较高。总之,本实验中的杂草稻群体总体的遗传多样性水平较高,群体之间的遗传多样性指数差异较大;杂草稻群体间的遗传分化显著大于群体内的分化,符合遗传距离的空间隔离模型;杂草稻群体间和地区间有一定水平的基因流,本研究对理解杂草稻在农田生态系统中的适应性进化及制定杂草稻控制策略具有重要意义。
To identify the status of genetic diversity, genetic differentiation, and gene flow among weedy rice populations in weedy rice populations in different geographic locations, the genetic diversity and genetic differentiation of 469 weedy rice samples from 17 weedy rice populations in Heilongjiang, Jilin, Liaoning, Jiangsu,and Guangdong province were analyzed by using 24 pairs of SSR primers. The results showed that the overall genetic diversity of weedy rice population indicated relatively high(I=0.36, He=0.23), and the genetic diversity index among different weedy rice populations was quite different, He was between 0.07～0.35. The results of AMOVA analysis showed that 70% of the variation in the weedy rice population originated from inter-population and 30% of the variation originated from within the population. AMOVA analyze showed 70% of genetic variation among weedy rice populations and 30% of genetic variation within weedy rice populations. Cluster analysis showed that there was a high similarity between populations in adjacent regions, and there was a high genetic differentiation among different populations of weedy rice in Jiangsu province. Genetic differentiation and gene flow results showed that the total Nm value of the 17 weedy rice populations was 0.117 and the total Fst value was0.694. The Nm was generally higher and the Fst was lower among the populations with relatively close geographical locations, while the Nm is generally lower and the Fst is higher between the geographically distant populations. Overall, the overall genetic diversity of the weedy rice population in this experiment was high, and the genetic diversity index of the populations was quite different. The genetic differentiation among the weedy rice populations was significantly greater than that within the populations, fitting with the genetic isolation-by-distance model, and there was a certain level of gene flow between the weedy rice populations and the regions. This study might be of great significance in understanding the adaptive evolution of weedy rice in farmland ecosystem and in formulating the control strategy of weedy rice.
To identify the status of genetic diversity, genetic differentiation, and gene flow among weedy rice populations in weedy rice populations in different geographic locations, the genetic diversity and genetic differentiation of 469 weedy rice samples from 17 weedy rice populations in Heilongjiang, Jilin, Liaoning, Jiangsu,and Guangdong province were analyzed by using 24 pairs of SSR primers. The results showed that the overall genetic diversity of weedy rice population indicated relatively high(I=0.36, He=0.23), and the genetic diversity index among different weedy rice populations was quite different, He was between 0.07～0.35. The results of AMOVA analysis showed that 70% of the variation in the weedy rice population originated from inter-population and 30% of the variation originated from within the population. AMOVA analyze showed 70% of genetic variation among weedy rice populations and 30% of genetic variation within weedy rice populations. Cluster analysis showed that there was a high similarity between populations in adjacent regions, and there was a high genetic differentiation among different populations of weedy rice in Jiangsu province. Genetic differentiation and gene flow results showed that the total Nm value of the 17 weedy rice populations was 0.117 and the total Fst value was0.694. The Nm was generally higher and the Fst was lower among the populations with relatively close geographical locations, while the Nm is generally lower and the Fst is higher between the geographically distant populations. Overall, the overall genetic diversity of the weedy rice population in this experiment was high, and the genetic diversity index of the populations was quite different. The genetic differentiation among the weedy rice populations was significantly greater than that within the populations, fitting with the genetic isolation-by-distance model, and there was a certain level of gene flow between the weedy rice populations and the regions. This study might be of great significance in understanding the adaptive evolution of weedy rice in farmland ecosystem and in formulating the control strategy of weedy rice.
引文
Chen H.H.,a nd Sato Y.,2005,The map-based sequence of the rice genome international rice genome sequencing project Nature,436(7052):793-800
Chen X.F.,Qiang S.,Yang J.L.,Zhang B.H.,Zhang Z.,Song XL.,and Dai W.M.,2015,Hierarchical clustering and indica-japonica classification:uncover mutual spread and indicajaponica differentiation for weedy rice in Jiangsu Province Zhongguo Suidao Kexue(Chinese Journal of Rice Science)29(1):82-90(陈晓锋,强胜,杨金玲,张帮华,张峥,宋小玲,戴伟民,2015,江苏省杂草稻的传播与籼粳分化研究中国水稻科学,29(1):82-90)
Dauer J.,Hulting A.,Carlson D.,Mankin L.,Harden J.,and Mallory-Smith C.,2018,Gene flow from single and stacked herbicide-resistant rice(Oryza sativa):modeling occurrence of multiple herbicide-resistant weedy rice,Pest Manag Sci.,74(2):348-355
Jr S.C.,and Via L.E.,1993,A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications,Biotechniques,14(5):748-50
Li X.J.,Fan W.Z.,Wang S.L.,Hu Y.S.,Liu Y.L.,Zhao W.R.,and Yang X.B.,2018,Research on the genetic diversity of weedy rice in Jilin province by using SSR marker,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(3):1020-1026(李新江,范文忠,王淑玲,胡延生,刘玉兰,赵文若,杨祥波,2018,利用SSR标记对吉林省杂草稻遗传多样性的研究,分子植物育种,16(3):1020-1026)
Li Y.H.,Ma J.,Wu B.,Sun J.C.,Wang X.S.,and Han L.Z.,2016,Analysis of genetic diversity and genetic relationship for the weedy rice in Ningxia province,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),17(1):32-38(李亚卉,马静,吴斌,孙建昌,王兴盛,韩龙植,2016,宁夏杂草稻的遗传多样性及其亲缘关系分析,植物遗传资源学报,17(1):32-38)
Mccouch S.R.,Chen X.,Panaud O.,Temnykh S.,Xu Y.,Yong G.C.,Huang N.,Ishii T.,and Blair M.,1997,Microsatellite marker development,mapping and applications in rice genetics and breedingedition,Plant Mol.Biol.,35(1-2):89-99
Nei M.,1978,Estimation of average heterozygosity and genetic distance from a small number of individuals,Genetics,89(3):583-590
Niruntrayakul S.,Rerkasem B.,and Jamjod S.,2009,Crossability between cultivated rice(Oryza sativa)and common wild rice(O.rufipogon)and characterization of F1and F2populations,Scienceasia,35(2):161-169
Peakall R.,and Smouse P.E.,2012,GenAlEx 6.5:Genetic analysis in Excel.Population genetic software for teaching and research--an update,Bioinformatics,28(28):2537-2539
Qiu J.,Zhu J.,Fu F.,Ye C.Y.,Wang W.,Mao L.,Lin Z.,Chen L.,Zhang H.,and Guo L.,2014,Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization:a case study from southern China,Planta,240(6):1353-1363
Shao J.,Dai W.M.,Zhang L.J.,Song X.L.,and Qiang S.,2011,Genetic diversity and origin of weedy rice in central region of Jiangsu Province,China,Zuowu Xuebao(Acta Agronomica Sinica),37(8):1324-1332(邵菁,戴伟民,张连举,宋小玲,强胜,2011,江苏省中部地区杂草稻遗传多样性及其起源分析,作物学报,37(8):1324-1332)
Zhang L.,Dai W.,Wu C.,Song X.,and Sheng Q.,2012,Genetic diversity and origin of Japonica-and Indica-like rice biotypes of weedy rice in the Guangdong and Liaoning provinces of China,Genet.Resour.Crop Ev.,59(3):399-410
Chen X.F.,Qiang S.,Yang J.L.,Zhang B.H.,Zhang Z.,Song XL.,and Dai W.M.,2015,Hierarchical clustering and indica-japonica classification:uncover mutual spread and indicajaponica differentiation for weedy rice in Jiangsu Province Zhongguo Suidao Kexue(Chinese Journal of Rice Science)29(1):82-90(陈晓锋,强胜,杨金玲,张帮华,张峥,宋小玲,戴伟民,2015,江苏省杂草稻的传播与籼粳分化研究中国水稻科学,29(1):82-90)
Dauer J.,Hulting A.,Carlson D.,Mankin L.,Harden J.,and Mallory-Smith C.,2018,Gene flow from single and stacked herbicide-resistant rice(Oryza sativa):modeling occurrence of multiple herbicide-resistant weedy rice,Pest Manag Sci.,74(2):348-355
Jr S.C.,and Via L.E.,1993,A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications,Biotechniques,14(5):748-50
Li X.J.,Fan W.Z.,Wang S.L.,Hu Y.S.,Liu Y.L.,Zhao W.R.,and Yang X.B.,2018,Research on the genetic diversity of weedy rice in Jilin province by using SSR marker,Fenzi Zhiwu Yuzhong(Molecular Plant Breeding),16(3):1020-1026(李新江,范文忠,王淑玲,胡延生,刘玉兰,赵文若,杨祥波,2018,利用SSR标记对吉林省杂草稻遗传多样性的研究,分子植物育种,16(3):1020-1026)
Li Y.H.,Ma J.,Wu B.,Sun J.C.,Wang X.S.,and Han L.Z.,2016,Analysis of genetic diversity and genetic relationship for the weedy rice in Ningxia province,Zhiwu Yichuan Ziyuan Xuebao(Journal of Plant Genetic Resources),17(1):32-38(李亚卉,马静,吴斌,孙建昌,王兴盛,韩龙植,2016,宁夏杂草稻的遗传多样性及其亲缘关系分析,植物遗传资源学报,17(1):32-38)
Mccouch S.R.,Chen X.,Panaud O.,Temnykh S.,Xu Y.,Yong G.C.,Huang N.,Ishii T.,and Blair M.,1997,Microsatellite marker development,mapping and applications in rice genetics and breedingedition,Plant Mol.Biol.,35(1-2):89-99
Nei M.,1978,Estimation of average heterozygosity and genetic distance from a small number of individuals,Genetics,89(3):583-590
Niruntrayakul S.,Rerkasem B.,and Jamjod S.,2009,Crossability between cultivated rice(Oryza sativa)and common wild rice(O.rufipogon)and characterization of F1and F2populations,Scienceasia,35(2):161-169
Peakall R.,and Smouse P.E.,2012,GenAlEx 6.5:Genetic analysis in Excel.Population genetic software for teaching and research--an update,Bioinformatics,28(28):2537-2539
Qiu J.,Zhu J.,Fu F.,Ye C.Y.,Wang W.,Mao L.,Lin Z.,Chen L.,Zhang H.,and Guo L.,2014,Genome re-sequencing suggested a weedy rice origin from domesticated indica-japonica hybridization:a case study from southern China,Planta,240(6):1353-1363
Shao J.,Dai W.M.,Zhang L.J.,Song X.L.,and Qiang S.,2011,Genetic diversity and origin of weedy rice in central region of Jiangsu Province,China,Zuowu Xuebao(Acta Agronomica Sinica),37(8):1324-1332(邵菁,戴伟民,张连举,宋小玲,强胜,2011,江苏省中部地区杂草稻遗传多样性及其起源分析,作物学报,37(8):1324-1332)
Zhang L.,Dai W.,Wu C.,Song X.,and Sheng Q.,2012,Genetic diversity and origin of Japonica-and Indica-like rice biotypes of weedy rice in the Guangdong and Liaoning provinces of China,Genet.Resour.Crop Ev.,59(3):399-410