遺傳連鎖圖譜是研究植物基因組結(jié)構(gòu),、進(jìn)化的有力工具，是基因定位,、克隆和分子標(biāo)記輔助育種的重要基礎(chǔ),。但作為被子植物中起源最早的植物之一，且素有“活化石”之稱的蓮,，其基因組學(xué)研究卻明顯滯后,。因此，構(gòu)建蓮遺傳連鎖圖譜有助于蓮基因組學(xué)研究的快速發(fā)展,，為蓮重要經(jīng)濟(jì)性狀的分離和克隆提供依據(jù)，從而有利于進(jìn)一步探索和充分利用蓮的觀賞,、食用和藥用價值,。
中科院武漢植物園水生植物資源學(xué)科組首先掃描了中國古代蓮基因組序列,，發(fā)現(xiàn)了86,089個SSR位點(diǎn)，其中73,246個SSR位點(diǎn)可用于開發(fā)SSR引物,。然后以亞洲蓮品種“中國古代蓮”和美洲黃蓮品種“AL1”雜交F1群體為材料,，根據(jù)中國古代蓮基因組序列信息開發(fā)的部分SSR分子標(biāo)記（500對）分別構(gòu)建了“中國古代蓮”和“AL1”的遺傳連鎖圖譜。由于“中國古代蓮”的基因組雜合度比較低,，此圖譜僅包含7個連鎖群,，有47個標(biāo)記，圖譜長度為365.67 cM,。“AL1”圖譜包含11個連鎖群,，有177個分子標(biāo)記，圖譜長度為524.51 cM,。這是首次報道蓮的遺傳連鎖圖譜,，為蓮基因組學(xué)研究奠定了良好基礎(chǔ)，加快了蓮重要基因定位,、克隆和分子標(biāo)記輔助育種的進(jìn)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.
