title: A platform of high-density INDEL/CAPS markers for map-based cloning in Arabidopsis.
abstract: Map-based cloning has been widely used to identify genes responsible for mutant phenotypes in Arabidopsis, especially those mutants generated by EMS or fast neutron mutagenesis. The success of map-based cloning relies on the availability of molecular markers that distinguish the polymorphisms between two Arabidopsis ecotypes. So far, most molecular markers in Arabidopsis have been generated by individual laboratories or the Arabidopsis Information Resource (TAIR). However, the TAIR markers, which are distributed unevenly on the five Arabidopsis chromosomes, only cover approximately 25% of the Arabidopsis BACs. Designing and testing molecular markers is still a time-consuming endeavor. Here we report the construction of a high-resolution BAC-based Arabidopsis mapping platform (AMP), using Col-0 and Ler as model ecotypes. The AMP comprises 1346 markers (1073 INDEL and 273 CAPS/dCAPS markers), of which 971 were newly designed and experimentally confirmed, 179 were from published papers and 196 were TAIR markers. These AMP markers cover 1186 BACs, 1121 of which are in non-centromere regions, representing approximately 75% of the Arabidopsis BACs in non-centromere regions. All the marker information is included on the AMP website (http://amp.genomics.org.cn/) for easy access and download, and sets of standard markers for initial chromosomal localization of a particular gene are recommended. The feasibility of using the AMP to map mutated genes is also discussed.
authors.affiliation: National Laboratory for Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China.
authors.forename: Xianhui
authors.initials: X
authors.lastname: Hou
authors.forename: Linchuan
authors.initials: L
authors.lastname: Li
authors.forename: Zhiyu
authors.initials: Z
authors.lastname: Peng
authors.forename: Baoye
authors.initials: B
authors.lastname: Wei
authors.forename: Saijun
authors.initials: S
authors.lastname: Tang
authors.forename: Maoyu
authors.initials: M
authors.lastname: Ding
authors.forename: Jingjing
authors.initials: J
authors.lastname: Liu
authors.forename: Fangxian
authors.initials: F
authors.lastname: Zhang
authors.forename: Yunde
authors.initials: Y
authors.lastname: Zhao
authors.forename: Hongya
authors.initials: H
authors.lastname: Gu
authors.forename: Li-Jia
authors.initials: LJ
authors.lastname: Qu
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics*; D003001:Cloning, Molecular / Q000379:methods; D004351:Drug Resistance / Q000235:genetics; D054643:INDEL Mutation / Q000235:genetics; D007210:Indoleacetic Acids / Q000494:pharmacology; D020407:Internet; D015335:Molecular Probes / Q000235:genetics*; D009154:Mutation
chemical_list: C552594:2-methyl-indole-3-acetic acid; D007210:Indoleacetic Acids; D015335:Molecular Probes