遗传连锁图谱是研究植物基因组结构、进化的有力工具，是基因定位、克隆和分子标记辅助育种的重要基础。但作为被子植物中起源最早的植物之一，且素有“活化石”之称的莲，其基因组学研究却明显滞后。因此，构建莲遗传连锁图谱有助于莲基因组学研究的快速发展，为莲重要经济性状的分离和克隆提供依据，从而有利于进一步探索和充分利用莲的观赏、食用和药用价值。
中科院武汉植物园水生植物资源学科组首先扫描了中国古代莲基因组序列，发现了86,089个SSR位点，其中73,246个SSR位点可用于开发SSR引物。然后以亚洲莲品种“中国古代莲”和美洲黄莲品种“AL1”杂交F1群体为材料，根据中国古代莲基因组序列信息开发的部分SSR分子标记（500对）分别构建了“中国古代莲”和“AL1”的遗传连锁图谱。由于“中国古代莲”的基因组杂合度比较低，此图谱仅包含7个连锁群，有47个标记，图谱长度为365.67 cM。“AL1”图谱包含11个连锁群，有177个分子标记，图谱长度为524.51 cM。这是首次报道莲的遗传连锁图谱，为莲基因组学研究奠定了良好基础，加快了莲重要基因定位、克隆和分子标记辅助育种的进程。（生物谷Bioon.com）
doi:10.1186/1471-2164-13-653
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Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar
Mei Yang, Yanni Han, Robert VanBuren, Ray Ming, Liming Xu, Yuepeng Han and Yanling Liu
Background The genus Nelumbo Adans. comprises two living species, N. nucifera Gaertan. (Asian lotus) and N. lutea Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for Nelumbo. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for Nelumbo to assist genome assembly and integration of a genetic map with the genome sequence. Results A total of 86,089 SSR motifs were identified from the genome sequences. Di- and tri-nucleotide repeat motifs were the most abundant, and accounted for 60.73% and 31.66% of all SSRs, respectively. AG/GA repeats constituted 51.17% of dinucleotide repeat motifs, followed by AT/TA (44.29%). Of 500 SSR primers tested, 386 (77.20%) produced scorable alleles with an average of 2.59 per primer, and 185 (37.00%) showed polymorphism among two parental genotypes, N. nucifera 'Chinese Antique' and N. lutea 'AL1', and six progenies of their F1 population. The normally segregating markers, which comprised 268 newly developed SSRs, 37 previously published SSRs and 53 sequence-related amplified polymorphism markers, were used for genetic map construction. The map for Asian lotus was 365.67 cM with 47 markers distributed in seven linkage groups. The map for American lotus was 524.51 cM, and contained 177 markers distributed in 11 genetic linkage groups. The number of markers per linkage group ranged from three to 34 with an average genetic distance of 3.97 cM between adjacent markers. Moreover, 171 SSR markers contained in linkage groups were anchored to 97 genomic DNA sequence contigs of 'Chinese Antique'. The 97 contigs were merged into 60 scaffolds. Conclusion Genetic mapping of SSR markers derived from sequenced contigs in Nelumbo enabled the associated contigs to be anchored in the linkage map and facilitated assembly of the genome sequences of 'Chinese Antique'. The present study reports the first construction of genetic linkage maps for Nelumbo, which can serve as reference linkage maps to accelerate characterization germplasm, genetic mapping for traits of economic interest, and molecular breeding with marker-assisted selection.
