title: Genic microsatellite markers in Brassica rapa: development, characterization, mapping, and their utility in other cultivated and wild Brassica relatives.
abstract: Genic microsatellite markers, also known as functional markers, are preferred over anonymous markers as they reveal the variation in transcribed genes among individuals. In this study, we developed a total of 707 expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) and used for development of a high-density integrated map using four individual mapping populations of B. rapa. This map contains a total of 1426 markers, consisting of 306 EST-SSRs, 153 intron polymorphic markers, 395 bacterial artificial chromosome-derived SSRs (BAC-SSRs), and 572 public SSRs and other markers covering a total distance of 1245.9 cM of the B. rapa genome. Analysis of allelic diversity in 24 B. rapa germplasm using 234 mapped EST-SSR markers showed amplification of 2 alleles by majority of EST-SSRs, although amplification of alleles ranging from 2 to 8 was found. Transferability analysis of 167 EST-SSRs in 35 species belonging to cultivated and wild brassica relatives showed 42.51% (Sysimprium leteum) to 100% (B. carinata, B. juncea, and B. napus) amplification. Our newly developed EST-SSRs and high-density linkage map based on highly transferable genic markers would facilitate the molecular mapping of quantitative trait loci and the positional cloning of specific genes, in addition to marker-assisted selection and comparative genomic studies of B. rapa with other related species.
authors.affiliation: Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea.
authors.forename: Nirala
authors.initials: N
authors.lastname: Ramchiary
authors.forename: Van Dan
authors.initials: VD
authors.lastname: Nguyen
authors.forename: Xiaonan
authors.initials: X
authors.lastname: Li
authors.forename: Chang Pyo
authors.initials: CP
authors.lastname: Hong
authors.forename: Vignesh
authors.initials: V
authors.lastname: Dhandapani
authors.forename: Su Ryun
authors.initials: SR
authors.lastname: Choi
authors.forename: Ge
authors.initials: G
authors.lastname: Yu
authors.forename: Zhong Yun
authors.initials: ZY
authors.lastname: Piao
authors.forename: Yong Pyo
authors.initials: YP
authors.lastname: Lim
mesh_terms: D000483:Alleles; D001937:Brassica / Q000145:classification / Q000235:genetics*; D029741:Brassica rapa / Q000235:genetics*; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D018744:DNA, Plant / Q000235:genetics; D020224:Expressed Sequence Tags; D005819:Genetic Markers; D018745:Genome, Plant; D018895:Microsatellite Repeats / Q000235:genetics*; D011110:Polymorphism, Genetic
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers