{"title":"手指粟 SSR 标记与小米（Panicum sumatrense Roth. Ex Roem & Schult.）","authors":"Komal G. Lakhani , Kirankumar Suthar , Diwakar Singh , Sumankumar Jha , Harshal Patil , Rehana Niyaria","doi":"10.1016/j.egg.2024.100281","DOIUrl":null,"url":null,"abstract":"<div><p>Little millet is an important cereal known as a “nutra-grain' because of its numerous health benefits. Due to lack of genomic information, the present study analyzed the cross-transferability of finger millet SSR markers to little millet. SSR analysis using genomic DNA with 18 available markers in little millet revealed that 12 SSR markers had unique amplicons with the expected size, indicating 66.66 % cross-transferability. This indicates the conservation of the repetitive motifs AG, CTG, GTT, ACG, CGG, (GA)<sub>26</sub>, (TC)21, (CA)<sub>7</sub>N<sub>12</sub> (GA)<sub>15</sub>, and (GA)<sub>7</sub>AA (GA)<sub>19</sub> in both species. Genetic analysis with these transferable twelve SSR markers in 16 little millet genotypes revealed a total of 39 alleles with an average of 3.25 alleles per primer. The highest number of alleles (8) was found at GB-FM -53, while the lowest number of alleles (2) was found at GB-FM -67, GB-FM -87, GB-FM -98 and UGEP-101. Out of the total twelve amplified primers, four primers GB-FM -53, GB-FM -67, GB-FM -70 and UGEP-93 were found to be highly effective and best based on highest SSR primer index value, observed and effective number of alleles, Nei genetic diversity, Shannon information index and polymorphic information content. Finger millet SSR markers distinguished sixteen genotypes of little into two major clusters, where two genotypes, WV-151 and WV-152, were highly diverse. This study establishes the high cross-transferability of finger millet SSR markers to little millet facilitating genomic research and breeding efforts for genetically neglected little millet.</p></div>","PeriodicalId":37938,"journal":{"name":"Ecological Genetics and Genomics","volume":"32 ","pages":"Article 100281"},"PeriodicalIF":0.0000,"publicationDate":"2024-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Cross transferability of finger millet SSR markers to little millet (Panicum sumatrense Roth. Ex Roem & Schult.)\",\"authors\":\"Komal G. Lakhani , Kirankumar Suthar , Diwakar Singh , Sumankumar Jha , Harshal Patil , Rehana Niyaria\",\"doi\":\"10.1016/j.egg.2024.100281\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><p>Little millet is an important cereal known as a “nutra-grain' because of its numerous health benefits. Due to lack of genomic information, the present study analyzed the cross-transferability of finger millet SSR markers to little millet. SSR analysis using genomic DNA with 18 available markers in little millet revealed that 12 SSR markers had unique amplicons with the expected size, indicating 66.66 % cross-transferability. This indicates the conservation of the repetitive motifs AG, CTG, GTT, ACG, CGG, (GA)<sub>26</sub>, (TC)21, (CA)<sub>7</sub>N<sub>12</sub> (GA)<sub>15</sub>, and (GA)<sub>7</sub>AA (GA)<sub>19</sub> in both species. Genetic analysis with these transferable twelve SSR markers in 16 little millet genotypes revealed a total of 39 alleles with an average of 3.25 alleles per primer. The highest number of alleles (8) was found at GB-FM -53, while the lowest number of alleles (2) was found at GB-FM -67, GB-FM -87, GB-FM -98 and UGEP-101. Out of the total twelve amplified primers, four primers GB-FM -53, GB-FM -67, GB-FM -70 and UGEP-93 were found to be highly effective and best based on highest SSR primer index value, observed and effective number of alleles, Nei genetic diversity, Shannon information index and polymorphic information content. Finger millet SSR markers distinguished sixteen genotypes of little into two major clusters, where two genotypes, WV-151 and WV-152, were highly diverse. This study establishes the high cross-transferability of finger millet SSR markers to little millet facilitating genomic research and breeding efforts for genetically neglected little millet.</p></div>\",\"PeriodicalId\":37938,\"journal\":{\"name\":\"Ecological Genetics and Genomics\",\"volume\":\"32 \",\"pages\":\"Article 100281\"},\"PeriodicalIF\":0.0000,\"publicationDate\":\"2024-07-22\",\"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/S240598542400065X\",\"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/S240598542400065X","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"Agricultural and Biological Sciences","Score":null,"Total":0}
引用次数: 0
摘要
小米是一种重要的谷物，因其对健康有诸多益处而被称为 "营养谷物"。由于缺乏基因组信息，本研究分析了手指粟 SSR 标记对小米的交叉转移性。利用小黍基因组 DNA 和 18 个可用标记进行的 SSR 分析表明，12 个 SSR 标记具有预期大小的独特扩增子，表明其具有 66.66% 的交叉转移性。这表明在这两个物种中保留了重复基序 AG、CTG、GTT、ACG、CGG、(GA)26、(TC)21、(CA)7N12 (GA)15 和 (GA)7AA (GA)19。利用这些可转移的 12 个 SSR 标记对 16 个小米基因型进行遗传分析，共发现 39 个等位基因，平均每个引物有 3.25 个等位基因。等位基因数最多的是 GB-FM -53（8 个），最少的是 GB-FM -67、GB-FM -87、GB-FM -98 和 UGEP-101（2 个）。根据最高的 SSR 引物指数值、观察到的等位基因数和有效等位基因数、Nei 遗传多样性、香农信息指数和多态信息含量，发现在总共 12 个扩增引物中，GB-FM -53、GB-FM -67、GB-FM -70 和 UGEP-93 这 4 个引物是高效和最佳的。小指稷的 SSR 标记将 16 个基因型区分为两大群，其中 WV-151 和 WV-152 这两个基因型的多样性很高。这项研究证实了黍SSR标记对黍的高度交叉转移性，有助于基因组研究和育种工作，以培育在遗传上被忽视的黍。
Cross transferability of finger millet SSR markers to little millet (Panicum sumatrense Roth. Ex Roem & Schult.)
Little millet is an important cereal known as a “nutra-grain' because of its numerous health benefits. Due to lack of genomic information, the present study analyzed the cross-transferability of finger millet SSR markers to little millet. SSR analysis using genomic DNA with 18 available markers in little millet revealed that 12 SSR markers had unique amplicons with the expected size, indicating 66.66 % cross-transferability. This indicates the conservation of the repetitive motifs AG, CTG, GTT, ACG, CGG, (GA)26, (TC)21, (CA)7N12 (GA)15, and (GA)7AA (GA)19 in both species. Genetic analysis with these transferable twelve SSR markers in 16 little millet genotypes revealed a total of 39 alleles with an average of 3.25 alleles per primer. The highest number of alleles (8) was found at GB-FM -53, while the lowest number of alleles (2) was found at GB-FM -67, GB-FM -87, GB-FM -98 and UGEP-101. Out of the total twelve amplified primers, four primers GB-FM -53, GB-FM -67, GB-FM -70 and UGEP-93 were found to be highly effective and best based on highest SSR primer index value, observed and effective number of alleles, Nei genetic diversity, Shannon information index and polymorphic information content. Finger millet SSR markers distinguished sixteen genotypes of little into two major clusters, where two genotypes, WV-151 and WV-152, were highly diverse. This study establishes the high cross-transferability of finger millet SSR markers to little millet facilitating genomic research and breeding efforts for genetically neglected little millet.
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
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