二穗短柄草全基因组标记和直系同源标记的评估

Evaluation of Genome-Wide Markers and Orthologous Markers in Brachypodium distachyon.

作者信息

Sablok Gaurav, Mudunuri Suresh B, Gudys Korneliya, Chennamsetti Kranthi, Varma G P Saradhi, Kwasniewski Miroslaw

机构信息

Department of Biodiversity and Molecular Ecology, Fondazione Edmund Mach, IASMA, 380010, Italy.

Plant Functional Biology and Climate Change Cluster (C3), University of Technology Sydney, Sydney, NSW, Australia.

出版信息

Methods Mol Biol. 2018;1667:195-201. doi: 10.1007/978-1-4939-7278-4_15.

DOI:10.1007/978-1-4939-7278-4_15

PMID:29039013

Abstract

Molecular markers play an important role in identifying the species variation, characterizing the genic diversity, and also linking the identified markers to trait of interest. Genome- and transcriptome-derived molecular markers have been widely used to understand the geographical diversity and have also played a major role in the development of high-density linkage maps. In the present protocol, we present a detailed protocol on bioinformatics approaches towards the whole-genome and transcriptome-assisted simple sequence repeats (SSRs) marker mining in Brachypodium distachyon and identification of orthologus SSRs and their validation in Brachypodium ecotypes. We also present a protocol for the validation of the identified markers.

摘要

分子标记在识别物种变异、表征基因多样性以及将已识别的标记与感兴趣的性状联系起来方面发挥着重要作用。基于基因组和转录组的分子标记已被广泛用于了解地理多样性，并且在高密度连锁图谱的构建中也发挥了重要作用。在本方案中，我们提供了一个详细的生物信息学方法方案，用于在二穗短柄草中进行全基因组和转录组辅助的简单序列重复（SSR）标记挖掘，以及在二穗短柄草生态型中鉴定直系同源SSR及其验证。我们还提供了一个已识别标记的验证方案。