Udit Sharma , Manoj K. Rai , N.S. Shekhawat , Vinod Kataria
{"title":"柽柳遗传多样性研究h .岩溶。使用CAAT盒衍生多态性(CBDP)和起始密码子靶向多态性(SCoT)标记","authors":"Udit Sharma , Manoj K. Rai , N.S. Shekhawat , Vinod Kataria","doi":"10.1016/j.egg.2023.100200","DOIUrl":null,"url":null,"abstract":"<div><p><em>Tamarix aphylla</em> (L.) H. Karst. is an evergreen, haloxeric, ecologically and economically important tree species of the Indian Thar desert. Genetic diversity analysis of this tree species is vital as it survives in extreme climatic conditions. In this study, we employed first time two gene-targeted CAAT box-derived polymorphism (CBDP) and start codon-targeted (SCoT) polymorphism markers for the analysis of the genetic diversity in <em>Tamarix aphylla</em>. A total of 47 wild genotypes of <em>T. aphylla</em> from eight populations of the Indian Thar Desert were analyzed using 12 primers, six from each CBDP and SCoT markers. The percent polymorphism was higher for CBDP (94.84%) than for the SCoT (76.57%) markers. The average PIC value for CBDP and SCoT marker was 0.601 and 0.409, respectively. Both CBDP and SCoT markers demonstrated high levels of genetic differentiation, low gene flow, and high fixation index. Using both marker systems, AMOVA revealed the percent molecular variation was higher in the case of within population than among population. The clustering pattern based on UPGMA and PCoA plots clearly showed that the grouping of genotypes is associated with their geographical origin and habitat. However, few genotypes were significantly diverse from their respective population and grouped in separate clusters with the genotypes of other populations. The findings observed in the present study can be further exploited in the breeding and conservation programs of <em>T. aphylla</em>.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":null,"pages":null},"PeriodicalIF":0.0000,"publicationDate":"2023-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genetic diversity in Tamarix aphylla (L.) H. Karst. using CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers\",\"authors\":\"Udit Sharma , Manoj K. Rai , N.S. Shekhawat , Vinod Kataria\",\"doi\":\"10.1016/j.egg.2023.100200\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p><em>Tamarix aphylla</em> (L.) H. Karst. is an evergreen, haloxeric, ecologically and economically important tree species of the Indian Thar desert. Genetic diversity analysis of this tree species is vital as it survives in extreme climatic conditions. In this study, we employed first time two gene-targeted CAAT box-derived polymorphism (CBDP) and start codon-targeted (SCoT) polymorphism markers for the analysis of the genetic diversity in <em>Tamarix aphylla</em>. A total of 47 wild genotypes of <em>T. aphylla</em> from eight populations of the Indian Thar Desert were analyzed using 12 primers, six from each CBDP and SCoT markers. The percent polymorphism was higher for CBDP (94.84%) than for the SCoT (76.57%) markers. The average PIC value for CBDP and SCoT marker was 0.601 and 0.409, respectively. Both CBDP and SCoT markers demonstrated high levels of genetic differentiation, low gene flow, and high fixation index. Using both marker systems, AMOVA revealed the percent molecular variation was higher in the case of within population than among population. The clustering pattern based on UPGMA and PCoA plots clearly showed that the grouping of genotypes is associated with their geographical origin and habitat. However, few genotypes were significantly diverse from their respective population and grouped in separate clusters with the genotypes of other populations. The findings observed in the present study can be further exploited in the breeding and conservation programs of <em>T. aphylla</em>.</p></div>\",\"PeriodicalId\":37938,\"journal\":{\"name\":\"Ecological Genetics and Genomics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2023-09-26\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Ecological Genetics and Genomics\",\"FirstCategoryId\":\"1085\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S2405985423000411\",\"RegionNum\":0,\"RegionCategory\":null,\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q3\",\"JCRName\":\"Agricultural and Biological Sciences\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Ecological Genetics and Genomics","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2405985423000411","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
Genetic diversity in Tamarix aphylla (L.) H. Karst. using CAAT box-derived polymorphism (CBDP) and start codon targeted (SCoT) polymorphism markers
Tamarix aphylla (L.) H. Karst. is an evergreen, haloxeric, ecologically and economically important tree species of the Indian Thar desert. Genetic diversity analysis of this tree species is vital as it survives in extreme climatic conditions. In this study, we employed first time two gene-targeted CAAT box-derived polymorphism (CBDP) and start codon-targeted (SCoT) polymorphism markers for the analysis of the genetic diversity in Tamarix aphylla. A total of 47 wild genotypes of T. aphylla from eight populations of the Indian Thar Desert were analyzed using 12 primers, six from each CBDP and SCoT markers. The percent polymorphism was higher for CBDP (94.84%) than for the SCoT (76.57%) markers. The average PIC value for CBDP and SCoT marker was 0.601 and 0.409, respectively. Both CBDP and SCoT markers demonstrated high levels of genetic differentiation, low gene flow, and high fixation index. Using both marker systems, AMOVA revealed the percent molecular variation was higher in the case of within population than among population. The clustering pattern based on UPGMA and PCoA plots clearly showed that the grouping of genotypes is associated with their geographical origin and habitat. However, few genotypes were significantly diverse from their respective population and grouped in separate clusters with the genotypes of other populations. The findings observed in the present study can be further exploited in the breeding and conservation programs of T. aphylla.
期刊介绍:
Ecological Genetics and Genomics publishes ecological studies of broad interest that provide significant insight into ecological interactions or/ and species diversification. New data in these areas are published as research papers, or methods and resource reports that provide novel information on technologies or tools that will be of interest to a broad readership. Complete data sets are shared where appropriate. The journal also provides Reviews, and Perspectives articles, which present commentary on the latest advances published both here and elsewhere, placing such progress in its broader biological context. Topics include: -metagenomics -population genetics/genomics -evolutionary ecology -conservation and molecular adaptation -speciation genetics -environmental and marine genomics -ecological simulation -genomic divergence of organisms