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基于二代测序基因组数据的西米棕榈SSR鉴定与标记开发

SSR identification and marker development for sago palm based on NGS genome data.

作者信息

Purwoko Devit, Cartealy Imam Civi, Tajuddin Teuku, Dinarti Diny, Sudarsono Sudarsono

机构信息

Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology, Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten, Indonesia.

Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Bogor Agricultural University, Darmaga, Bogor 16680, West Java, Indonesia.

出版信息

Breed Sci. 2019 Mar;69(1):1-10. doi: 10.1270/jsbbs.18061. Epub 2019 Mar 16.

DOI:10.1270/jsbbs.18061
PMID:31086478
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC6507712/
Abstract

Sago palm ( Rottb.) is one of the most productive carbohydrate-producing crops. Unfortunately, only limited information regarding sago palm genetics is available. This study aimed to develop simple sequence repeat (SSR) markers using sago palm NGS genomic data and use these markers to evaluate the genetic diversity of sago palm from Indonesia. assembly of partial sago palm genomic data and subsequent SSR mining identified 29,953 contigs containing 31,659 perfect SSR loci and 31,578 contigs with 33,576 imperfect SSR loci. The perfect SSR loci density was 132.57/Mb, and AG, AAG and AAAT were the most frequent SSR motifs. Five hundred perfect SSR loci were randomly selected and used for designing SSR primers; 93 SSR primer pairs were identified. After synteny analysis using rice genome sequences, 20 primer pairs were validated using 11 sago palm accessions, and seven primers generated polymorphic alleles. Genetic diversity analysis of 41 sago palm accessions from across Indonesia using polymorphic SSR loci indicated the presence of three clusters. These results demonstrated the success of SSR identification and marker development for sago palm based on NGS genome data, which can be further used for assisting sago palm breeding in the future.

摘要

西米棕榈（Rottb.）是产量最高的碳水化合物生产作物之一。不幸的是，关于西米棕榈遗传学的信息有限。本研究旨在利用西米棕榈的二代测序（NGS）基因组数据开发简单序列重复（SSR）标记，并使用这些标记评估来自印度尼西亚的西米棕榈的遗传多样性。部分西米棕榈基因组数据的组装及随后的SSR挖掘鉴定出29,953个重叠群，包含31,659个完美SSR位点和31,578个重叠群，带有33,576个不完美SSR位点。完美SSR位点密度为132.57/Mb，AG、AAG和AAAT是最常见的SSR基序。随机选择500个完美SSR位点用于设计SSR引物；鉴定出93对SSR引物对。利用水稻基因组序列进行共线性分析后，使用11份西米棕榈种质对20对引物进行了验证，7对引物产生了多态性等位基因。利用多态性SSR位点对来自印度尼西亚各地的41份西米棕榈种质进行遗传多样性分析，结果表明存在三个聚类。这些结果证明了基于NGS基因组数据对西米棕榈进行SSR鉴定和标记开发的成功，这可在未来进一步用于协助西米棕榈育种。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/b68e641f35e5/69_18061_4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/5c2233981a26/69_18061_1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/c67c21f743bb/69_18061_2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/6fb40ad7a9b0/69_18061_3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/b68e641f35e5/69_18061_4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/5c2233981a26/69_18061_1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/c67c21f743bb/69_18061_2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/6fb40ad7a9b0/69_18061_3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/0995/6507712/b68e641f35e5/69_18061_4.jpg

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