An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)
Kompetitive allele-specific PCR (KASP) is a cost-effective single-step SNP genotyping technology, With an objective to enhance the marker repertoire and develop high efficient KASP-SNP markers in Chinese cabbage, we re-sequenced four Chinese cabbage doubled haploid (DH) lines, Y177-47, Y635-10, Y510...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531813/?tool=EBI |
| _version_ | 1828803109314363392 |
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| author | Shuangjuan Yang Wentao Yu Xiaochun Wei Zhiyong Wang Yanyan Zhao Xiaobin Zhao Baoming Tian Yuxiang Yuan Xiaowei Zhang Maoteng Li |
| author_facet | Shuangjuan Yang Wentao Yu Xiaochun Wei Zhiyong Wang Yanyan Zhao Xiaobin Zhao Baoming Tian Yuxiang Yuan Xiaowei Zhang Maoteng Li |
| author_sort | Shuangjuan Yang |
| collection | DOAJ |
| description | Kompetitive allele-specific PCR (KASP) is a cost-effective single-step SNP genotyping technology, With an objective to enhance the marker repertoire and develop high efficient KASP-SNP markers in Chinese cabbage, we re-sequenced four Chinese cabbage doubled haploid (DH) lines, Y177-47, Y635-10, Y510-1 and Y510-9, and generated a total of more than 38.5 billion clean base pairs. A total of 827,720 SNP loci were identified with an estimated density of 3,217 SNPs/Mb. Further, a total of 387,354 SNPs with at least 30 bp to the next most adjacent SNPs on either side were selected as resource for KASP markers. From this resource, 258 (96.27%) of 268 SNP loci were successfully transformed into KASP-SNP markers using a Roche LightCycler 480-II instrument. Among these markers, 221 (85.66%) were co-dominant markers, 220 (85.27%) were non-synonymous SNPs, and 257 (99.6%) were newly developed markers. In addition, 53 markers were applied for genotyping of 34 Brassica rapa accessions. Cluster analysis separated these 34 accessions into three clusters based on heading types. The millions of SNP loci, a large set of resource for KASP markers, as well as the newly developed KASP markers in this study may facilitate further genetic and molecular breeding studies in Brassica rapa. |
| first_indexed | 2024-12-12T07:17:17Z |
| format | Article |
| id | doaj.art-81a05167b3494bed97a5f72c58e4a10e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-12T07:17:17Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-81a05167b3494bed97a5f72c58e4a10e2022-12-22T00:33:29ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-011510An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis)Shuangjuan YangWentao YuXiaochun WeiZhiyong WangYanyan ZhaoXiaobin ZhaoBaoming TianYuxiang YuanXiaowei ZhangMaoteng LiKompetitive allele-specific PCR (KASP) is a cost-effective single-step SNP genotyping technology, With an objective to enhance the marker repertoire and develop high efficient KASP-SNP markers in Chinese cabbage, we re-sequenced four Chinese cabbage doubled haploid (DH) lines, Y177-47, Y635-10, Y510-1 and Y510-9, and generated a total of more than 38.5 billion clean base pairs. A total of 827,720 SNP loci were identified with an estimated density of 3,217 SNPs/Mb. Further, a total of 387,354 SNPs with at least 30 bp to the next most adjacent SNPs on either side were selected as resource for KASP markers. From this resource, 258 (96.27%) of 268 SNP loci were successfully transformed into KASP-SNP markers using a Roche LightCycler 480-II instrument. Among these markers, 221 (85.66%) were co-dominant markers, 220 (85.27%) were non-synonymous SNPs, and 257 (99.6%) were newly developed markers. In addition, 53 markers were applied for genotyping of 34 Brassica rapa accessions. Cluster analysis separated these 34 accessions into three clusters based on heading types. The millions of SNP loci, a large set of resource for KASP markers, as well as the newly developed KASP markers in this study may facilitate further genetic and molecular breeding studies in Brassica rapa.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531813/?tool=EBI |
| spellingShingle | Shuangjuan Yang Wentao Yu Xiaochun Wei Zhiyong Wang Yanyan Zhao Xiaobin Zhao Baoming Tian Yuxiang Yuan Xiaowei Zhang Maoteng Li An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis) PLoS ONE |
| title | An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis) |
| title_full | An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis) |
| title_fullStr | An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis) |
| title_full_unstemmed | An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis) |
| title_short | An extended KASP-SNP resource for molecular breeding in Chinese cabbage(Brassica rapa L. ssp. pekinensis) |
| title_sort | extended kasp snp resource for molecular breeding in chinese cabbage brassica rapa l ssp pekinensis |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7531813/?tool=EBI |
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