Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing
Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequenc...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2016-03-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00334/full |
| _version_ | 1818179397769756672 |
|---|---|
| author | Zhao eZhenqing Gu eHonghui Sheng eXiaoguang Yu eHuifang Wang eJiansheng Huang eLong Wang eDan |
| author_facet | Zhao eZhenqing Gu eHonghui Sheng eXiaoguang Yu eHuifang Wang eJiansheng Huang eLong Wang eDan |
| author_sort | Zhao eZhenqing |
| collection | DOAJ |
| description | Molecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6,815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1,776 high-quality SLAF markers, including 2,741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower. |
| first_indexed | 2024-12-11T21:03:14Z |
| format | Article |
| id | doaj.art-8decf344eec14439a3f90b182ed99ba2 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-11T21:03:14Z |
| publishDate | 2016-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-8decf344eec14439a3f90b182ed99ba22022-12-22T00:50:56ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2016-03-01710.3389/fpls.2016.00334172921Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencingZhao eZhenqing0Gu eHonghui1Sheng eXiaoguang2Yu eHuifang3Wang eJiansheng4Huang eLong5Wang eDan6Zhejiang academy of agricultural sciencesZhejiang academy of agricultural sciencesZhejiang academy of agricultural sciencesZhejiang academy of agricultural sciencesZhejiang academy of agricultural sciencesBiomarker Technologies CorporationBiomarker Technologies CorporationMolecular markers and genetic maps play an important role in plant genomics and breeding studies. Cauliflower is an important and distinctive vegetable; however, very few molecular resources have been reported for this species. In this study, a novel, specific-locus amplified fragment (SLAF) sequencing strategy was employed for large-scale single nucleotide polymorphism (SNP) discovery and high-density genetic map construction in a double-haploid, segregating population of cauliflower. A total of 12.47 Gb raw data containing 77.92 M pair-end reads were obtained after processing and 6,815 polymorphic SLAFs between the two parents were detected. The average sequencing depths reached 52.66-fold for the female parent and 49.35-fold for the male parent. Subsequently, these polymorphic SLAFs were used to genotype the population and further filtered based on several criteria to construct a genetic linkage map of cauliflower. Finally, 1,776 high-quality SLAF markers, including 2,741 SNPs, constituted the linkage map with average data integrity of 95.68%. The final map spanned a total genetic length of 890.01 cM with an average marker interval of 0.50 cM, and covered 364.9 Mb of the reference genome. The markers and genetic map developed in this study could provide an important foundation not only for comparative genomics studies within Brassica oleracea species but also for quantitative trait loci identification and molecular breeding of cauliflower.http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00334/fullSequencingSNPGenetic mapCauliflowerSLAF |
| spellingShingle | Zhao eZhenqing Gu eHonghui Sheng eXiaoguang Yu eHuifang Wang eJiansheng Huang eLong Wang eDan Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing Frontiers in Plant Science Sequencing SNP Genetic map Cauliflower SLAF |
| title | Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing |
| title_full | Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing |
| title_fullStr | Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing |
| title_full_unstemmed | Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing |
| title_short | Genome-wide single-nucleotide polymorphisms discovery and high-density genetic map construction in cauliflower using specific-locus amplified fragment sequencing |
| title_sort | genome wide single nucleotide polymorphisms discovery and high density genetic map construction in cauliflower using specific locus amplified fragment sequencing |
| topic | Sequencing SNP Genetic map Cauliflower SLAF |
| url | http://journal.frontiersin.org/Journal/10.3389/fpls.2016.00334/full |
| work_keys_str_mv | AT zhaoezhenqing genomewidesinglenucleotidepolymorphismsdiscoveryandhighdensitygeneticmapconstructionincauliflowerusingspecificlocusamplifiedfragmentsequencing AT guehonghui genomewidesinglenucleotidepolymorphismsdiscoveryandhighdensitygeneticmapconstructionincauliflowerusingspecificlocusamplifiedfragmentsequencing AT shengexiaoguang genomewidesinglenucleotidepolymorphismsdiscoveryandhighdensitygeneticmapconstructionincauliflowerusingspecificlocusamplifiedfragmentsequencing AT yuehuifang genomewidesinglenucleotidepolymorphismsdiscoveryandhighdensitygeneticmapconstructionincauliflowerusingspecificlocusamplifiedfragmentsequencing AT wangejiansheng genomewidesinglenucleotidepolymorphismsdiscoveryandhighdensitygeneticmapconstructionincauliflowerusingspecificlocusamplifiedfragmentsequencing AT huangelong genomewidesinglenucleotidepolymorphismsdiscoveryandhighdensitygeneticmapconstructionincauliflowerusingspecificlocusamplifiedfragmentsequencing AT wangedan genomewidesinglenucleotidepolymorphismsdiscoveryandhighdensitygeneticmapconstructionincauliflowerusingspecificlocusamplifiedfragmentsequencing |