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通过黑麦EST序列进行EST-SSR鉴定与开发用于遗传多样性分析

EST-SSR Identification and Development through EST Sequences from Rottb. for Genetic Diversity Analysis.

作者信息

Purwoko Devit, Zulaeha Siti, Tajuddin Teuku, Mira Farida Rosana, Solikhah Maharani Dewi, Rahmadara Gemilang, Hanifah Nurul Fitri

机构信息

Research Centre for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency, Science and Technology Park of Soekarno, Cibinong, Bogor West Java 16911, Indonesia.

Directorate of Laboratory Management, Building 630, Science and Technology Park of B. J. Habibie, Serpong, South Tangerang 15314, Indonesia.

出版信息

Trop Life Sci Res. 2024 Mar;35(1):13-32. doi: 10.21315/tlsr2024.35.1.2. Epub 2024 Mar 30.

DOI:10.21315/tlsr2024.35.1.2
PMID:39262857
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11383630/
Abstract

Sago plant ( Rottb.) is one of the most carbohydrate-producing plants in the world. Microsatellites or simple sequence repeats (SSRs) play an important role in the genome and are used extensively compared to other molecular markers. For the first time, we are exploiting data expressed sequence tags (EST) of sago plants to identify and characterise markers in this species. EST data about sago plants are obtained through the EST database on the National Center for Biotechnology Information (NCBI) website. We obtained data of 458 Kb (412 contig) with a maximum and minimum length of 1,138 and 124 nucleotides, respectively. We successfully identified 820 perfectly patterned SSR using Phobos 3.3.12 software. The type characterisation of EST-SSR was dominated by tri-nucleotides 36% (294), followed by hexa-nucleotides 24% (202), tetra-nucleotides 15% (120), penta-nucleotides 13% (108) and di-nucleotides 12% (96). The most frequency of SSR motifs in each type is AG, AAG and AAAG. Analysis of synteny on the EST sequence with the online application Phytozome found that sequences were distributed on 12 chromosomes with a likeness percentage between 63% to 100% and e-value between 0 to 0.094. We developed the primer and generated 19 primers. Furthermore, we validated 7 primers that all generated polymorphic alleles. To our knowledge, this report is the first identification and characterisation of EST-SSR for sago species and these markers can be used for genetic diversity analysis, marker assisted selection (MAS), cultivar identification, kinship analysis and genetic mapping analysis.

摘要

西米植物（Rottb.）是世界上碳水化合物产量最高的植物之一。微卫星或简单序列重复（SSR）在基因组中发挥着重要作用，与其他分子标记相比，其应用更为广泛。我们首次利用西米植物的表达序列标签（EST）数据来鉴定和表征该物种的标记。西米植物的EST数据是通过美国国立生物技术信息中心（NCBI）网站上的EST数据库获得的。我们获得了458 Kb（412个重叠群）的数据，其最大长度和最小长度分别为1138和124个核苷酸。我们使用Phobos 3.3.12软件成功鉴定出820个完美模式的SSR。EST-SSR的类型表征以三核苷酸为主，占36%（294个），其次是六核苷酸，占24%（202个），四核苷酸占15%（120个），五核苷酸占13%（108个），二核苷酸占12%（96个）。每种类型中SSR基序最常见的是AG、AAG和AAAG。利用在线应用程序Phytozome对EST序列进行共线性分析发现，序列分布在12条染色体上，相似性百分比在63%至100%之间，e值在0至0.094之间。我们设计了引物并生成了19个引物。此外，我们验证了7个引物，所有这些引物都产生了多态性等位基因。据我们所知，本报告是首次对西米物种的EST-SSR进行鉴定和表征，这些标记可用于遗传多样性分析、标记辅助选择（MAS）、品种鉴定、亲缘关系分析和遗传图谱分析。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/b9a43527e0c4/TLSR_35-1-13-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/75c31a26e36f/TLSR_35-1-13-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/fb95e5578aa0/TLSR_35-1-13-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/b9359396dd26/TLSR_35-1-13-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/b75b7f87e29d/TLSR_35-1-13-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/08f11c1f518d/TLSR_35-1-13-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/516945e64e13/TLSR_35-1-13-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/fd583eac086c/TLSR_35-1-13-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/749c484c1d3e/TLSR_35-1-13-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/b9a43527e0c4/TLSR_35-1-13-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/75c31a26e36f/TLSR_35-1-13-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/fb95e5578aa0/TLSR_35-1-13-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/b9359396dd26/TLSR_35-1-13-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/b75b7f87e29d/TLSR_35-1-13-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/08f11c1f518d/TLSR_35-1-13-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/516945e64e13/TLSR_35-1-13-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/fd583eac086c/TLSR_35-1-13-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/749c484c1d3e/TLSR_35-1-13-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/28cc/11383630/b9a43527e0c4/TLSR_35-1-13-g009.jpg

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