使用GnpIS信息系统挖掘植物基因组和遗传数据。

Mining Plant Genomic and Genetic Data Using the GnpIS Information System.

作者信息

Adam-Blondon A-F, Alaux M, Durand S, Letellier T, Merceron G, Mohellibi N, Pommier C, Steinbach D, Alfama F, Amselem J, Charruaud D, Choisne N, Flores R, Guerche C, Jamilloux V, Kimmel E, Lapalu N, Loaec M, Michotey C, Quesneville H

机构信息

Research Unit in Genomics-Info UR1164, INRA, Université Paris-Saclay, Versailles, Route de Saint-Cyr, 78026, Versailles Cedex, France.

Research Unit GQE-Le Moulon UMR 320, INRA, Université Paris-Sud, Université Paris-Saclay, CNRS, AgroParisTech, Ferme du Moulon, 91190, Gif-sur-Yvette, France.

出版信息

Methods Mol Biol. 2017;1533:103-117. doi: 10.1007/978-1-4939-6658-5_5.

DOI:10.1007/978-1-4939-6658-5_5

PMID:27987166

Abstract

GnpIS is an information system designed to help scientists working on plants and fungi to decipher the molecular and genetic architecture of trait variations by facilitating the navigation through genetic, genomic, and phenotypic information. The purpose of the present chapter is to illustrate how users can (1) explore datasets from phenotyping experiments in order to build new datasets for studying genotype × environment interactions in traits, (2) browse into the results of other genetic analysis data such as GWAS to generate or check working hypothesis about candidate genes or to identify important alleles and germplasms for breeding programs, and (3) explore the polymorphism in specific area of the genome using InterMine, JBrowse tools embedded in the GnpIS information system.

摘要

GnpIS是一个信息系统，旨在帮助从事植物和真菌研究的科学家，通过促进对遗传、基因组和表型信息的浏览，来解读性状变异的分子和遗传结构。本章的目的是说明用户如何：（1）探索表型分析实验的数据集，以便构建用于研究性状中基因型×环境相互作用的新数据集；（2）浏览其他遗传分析数据（如全基因组关联研究（GWAS））的结果，以生成或检验关于候选基因的工作假设，或识别用于育种计划的重要等位基因和种质；（3）使用GnpIS信息系统中嵌入的InterMine、JBrowse工具，探索基因组特定区域的多态性。