Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar
<p>Abstract</p> <p>Background</p> <p>The genus <it>Nelumbo</it> Adans. comprises two living species, <it>N. nucifera</it> Gaertan. (Asian lotus) and <it>N. lutea</it> Pers. (American lotus). A genetic linkage map is an essential resou...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2012-11-01
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| Series: | BMC Genomics |
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| Online Access: | http://www.biomedcentral.com/1471-2164/13/653 |
| _version_ | 1818163032125079552 |
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| author | Yang Mei Han Yanni VanBuren Robert Ming Ray Xu Liming Han Yuepeng Liu Yanling |
| author_facet | Yang Mei Han Yanni VanBuren Robert Ming Ray Xu Liming Han Yuepeng Liu Yanling |
| author_sort | Yang Mei |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>The genus <it>Nelumbo</it> Adans. comprises two living species, <it>N. nucifera</it> Gaertan. (Asian lotus) and <it>N. lutea</it> Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for <it>Nelumbo</it>. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for <it>Nelumbo</it> to assist genome assembly and integration of a genetic map with the genome sequence.</p> <p>Results</p> <p>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, <it>N. nucifera</it> ‘Chinese Antique’ and <it>N. lutea</it> ‘AL1’, and six progenies of their F<sub>1</sub> 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.</p> <p>Conclusion</p> <p>Genetic mapping of SSR markers derived from sequenced contigs in <it>Nelumbo</it> 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 <it>Nelumbo</it>, 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.</p> |
| first_indexed | 2024-12-11T16:43:06Z |
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| id | doaj.art-dd1d3d3f71ed4667b1af53226b033b5f |
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| language | English |
| last_indexed | 2024-12-11T16:43:06Z |
| publishDate | 2012-11-01 |
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| spelling | doaj.art-dd1d3d3f71ed4667b1af53226b033b5f2022-12-22T00:58:17ZengBMCBMC Genomics1471-21642012-11-0113165310.1186/1471-2164-13-653Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivarYang MeiHan YanniVanBuren RobertMing RayXu LimingHan YuepengLiu Yanling<p>Abstract</p> <p>Background</p> <p>The genus <it>Nelumbo</it> Adans. comprises two living species, <it>N. nucifera</it> Gaertan. (Asian lotus) and <it>N. lutea</it> Pers. (American lotus). A genetic linkage map is an essential resource for plant genetic studies and crop improvement but has not been generated for <it>Nelumbo</it>. We aimed to develop genomic simple sequence repeat (SSR) markers from the genome sequence and construct two genetic maps for <it>Nelumbo</it> to assist genome assembly and integration of a genetic map with the genome sequence.</p> <p>Results</p> <p>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, <it>N. nucifera</it> ‘Chinese Antique’ and <it>N. lutea</it> ‘AL1’, and six progenies of their F<sub>1</sub> 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.</p> <p>Conclusion</p> <p>Genetic mapping of SSR markers derived from sequenced contigs in <it>Nelumbo</it> 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 <it>Nelumbo</it>, 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.</p>http://www.biomedcentral.com/1471-2164/13/653Genetic linkage mapGenome sequence<it>Nelumbo</it>SRAPSSR |
| spellingShingle | Yang Mei Han Yanni VanBuren Robert Ming Ray Xu Liming Han Yuepeng Liu Yanling Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar BMC Genomics Genetic linkage map Genome sequence <it>Nelumbo</it> SRAP SSR |
| title | Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar |
| title_full | Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar |
| title_fullStr | Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar |
| title_full_unstemmed | Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar |
| title_short | Genetic linkage maps for Asian and American lotus constructed using novel SSR markers derived from the genome of sequenced cultivar |
| title_sort | genetic linkage maps for asian and american lotus constructed using novel ssr markers derived from the genome of sequenced cultivar |
| topic | Genetic linkage map Genome sequence <it>Nelumbo</it> SRAP SSR |
| url | http://www.biomedcentral.com/1471-2164/13/653 |
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