Genic Microsatellite Markers in Brassica rapa: Development, Characterization, Mapping, and Their Utility in Other Cultivated and Wild Brassica Relatives |
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Authors: | Nirala Ramchiary Van Dan Nguyen Xiaonan Li Chang Pyo Hong Vignesh Dhandapani Su Ryun Choi Ge Yu Zhong Yun Piao Yong Pyo Lim |
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Institution: | 1Molecular Genetics and Genomics Lab, Department of Horticulture, Chungnam National University, Gung-Dong, Yuseong-Gu, Daejeon 305-764, Republic of Korea;2Department of Life Science, and BK21 Program of Bio-Molecular Function, Pohang University of Science and Technology, Pohang 790-784, Republic of Korea;3Department of Vegetable Genetics and Breeding, College of Horticulture, Shenyang Agricultural University, Shenyang 110 161, Liaoning, PR China |
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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. |
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Keywords: | Brassica rapa expressed sequence-derived SSRs integrated map polymorphism information content transferability |
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