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An Improved Brassica rapa Genetic Linkage Map and Locus-specific Variations in a Doubled Haploid Population

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Abstract

In this study, we describe the construction of an improved Chinese cabbage genetic linkage map by integrating simple sequence repeats (SSRs) and insertion/deletion polymorphisms (InDels) into a previously published map of a doubled haploid (DH) population. The population was derived from a cross between the Chinese cabbage line BY (Brassica rapa ssp. pekinensis) and a European turnip line MM (Brassica rapa L. ssp. rapifera). A total of 629 markers were aligned to ten linkage groups, with a total map length of 1,173.8 cM, and an average distance between markers of 1.87 cm. Of the 126 SSRs and 133 InDels mapped, 46 and 34 were novel, respectively. A comparison of the linkage map with the B. rapa genome showed that more than 93 % of the markers, including 112 SSRs and 129 InDels, could be anchored unambiguously to a specific location on one of the ten chromosomes. In most cases, the order of markers on the linkage map and physical map was similar; however, the majority of linkage groups contained a number of markers whose positions were either transposed or had moved slightly forwards or backwards. During microspore culture, it was observed that 11 SSRs and one InDel showed either variation in size, or the appearance of new marker bands in the DH lines. As a first step to addressing this SSR/InDel marker instability, six SSR and one InDel loci were sequenced, which revealed that the size variation was due mainly to changes in repeat-motif number or to the insertion/deletion of new fragments of DNA.

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Acknowledgments

This work was supported in part by grants from the National High Technology Research and Development Program of China (863 Program) (No. 2012AA100104), the Program of Beijing Municipal Science and Technology Committee (D111100001311002), the Beijing Natural Science Foundation, China (No. 6102011) and the National Natural Science Foundation of China (No. C150202).

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  1. Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing Vegetable Research Center (BVRC), Beijing, 100097, China

    Shuancang Yu, Fenglan Zhang, Xiang Zhao, Yangjun Yu, Deshuang Zhang, Xiuyun Zhao & Weihong Wang

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  1. Shuancang Yu
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  2. Fenglan Zhang
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  3. Xiang Zhao
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Correspondence to Fenglan Zhang.

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Yu, S., Zhang, F., Zhao, X. et al. An Improved Brassica rapa Genetic Linkage Map and Locus-specific Variations in a Doubled Haploid Population. Plant Mol Biol Rep 31, 558–568 (2013). https://doi.org/10.1007/s11105-012-0530-7

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