Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome
High-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns of population structure and linkage disequilibrium (LD). In this study we used the Brassica 60kSNP Illumina consortium genotyping ar...
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| creator | Qian, Lunwen Qian, Wei Snowdon, Rod J |
| description | High-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns of population structure and linkage disequilibrium (LD). In this study we used the Brassica 60kSNP Illumina consortium genotyping array to assess the influence of selection and breeding for important agronomic traits on LD and haplotype structure in a diverse panel of 203 Chinese semi-winter rapeseed (Brassica napus) breeding lines.
Population structure and principal coordinate analysis, using a subset of the SNPs, revealed diversification into three subpopulations and one mixed population, reflecting targeted introgressions from external gene pools during breeding. Pairwise LD analysis within the A- and C-subgenomes of allopolyploid B. napus revealed that mean LD, at a threshold of r2=0.1, decayed on average around ten times more rapidly in the A-subgenome (0.25-0.30 Mb) than in the C-subgenome (2.00-2.50 Mb). A total of 3,097 conserved haplotype blocks were detected over a total length of 182.49 Mb (15.17% of the genome). The mean size of haplotype blocks was considerably longer in the C-subgenome (102.85 Kb) than in the A-subgenome (33.51 Kb), and extremely large conserved haplotype blocks were found on a number of C-genome chromosomes. Comparative sequence analysis revealed conserved blocks containing homoloeogous quantitative trait loci (QTL) for seed erucic acid and glucosinolate content, two key seed quality traits under strong agronomic selection. Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues.
The data we present in this paper provide evidence for strong selection of large chromosome regions associated with important rapeseed seed quality traits conferred by C-subgenome QTL. This implies that an increase in genetic diversity and recombination within the C-genome is particularly important for breeding. The resolution of genome-wide association studies is also expected to vary greatly across different genome regions. |
| doi_str_mv | 10.1186/1471-2164-15-1170 |
| format | Article |
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Population structure and principal coordinate analysis, using a subset of the SNPs, revealed diversification into three subpopulations and one mixed population, reflecting targeted introgressions from external gene pools during breeding. Pairwise LD analysis within the A- and C-subgenomes of allopolyploid B. napus revealed that mean LD, at a threshold of r2=0.1, decayed on average around ten times more rapidly in the A-subgenome (0.25-0.30 Mb) than in the C-subgenome (2.00-2.50 Mb). A total of 3,097 conserved haplotype blocks were detected over a total length of 182.49 Mb (15.17% of the genome). The mean size of haplotype blocks was considerably longer in the C-subgenome (102.85 Kb) than in the A-subgenome (33.51 Kb), and extremely large conserved haplotype blocks were found on a number of C-genome chromosomes. Comparative sequence analysis revealed conserved blocks containing homoloeogous quantitative trait loci (QTL) for seed erucic acid and glucosinolate content, two key seed quality traits under strong agronomic selection. Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues.
The data we present in this paper provide evidence for strong selection of large chromosome regions associated with important rapeseed seed quality traits conferred by C-subgenome QTL. This implies that an increase in genetic diversity and recombination within the C-genome is particularly important for breeding. The resolution of genome-wide association studies is also expected to vary greatly across different genome regions.</description><identifier>ISSN: 1471-2164</identifier><identifier>EISSN: 1471-2164</identifier><identifier>DOI: 10.1186/1471-2164-15-1170</identifier><identifier>PMID: 25539568</identifier><language>eng</language><publisher>England: BioMed Central Ltd</publisher><subject>Analysis ; Biological diversity ; Brassica napus ; Brassica napus - genetics ; Brassica napus - growth & development ; Breeding ; Chromosomes ; Consortia ; Genes ; Genetic aspects ; Genetic Markers - genetics ; Genetic research ; Genome, Plant - genetics ; Genomics ; Genotype & phenotype ; Haplotypes ; Linkage Disequilibrium ; Phylogeny ; Polymorphism, Single Nucleotide ; Polyploidy ; Quantitative genetics ; Quantitative Trait Loci - genetics ; Seasons ; Seeds - growth & development ; Studies</subject><ispartof>BMC genomics, 2014-12, Vol.15 (1), p.1170-1170, Article 1170</ispartof><rights>COPYRIGHT 2014 BioMed Central Ltd.</rights><rights>2014 Qian et al.; licensee BioMed Central. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.</rights><rights>Qian et al.; licensee BioMed Central. 2014</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-b692t-294d4bb295bdc002a3fd10481d1fcadba3fa9fa90328e300d5d7174f3e6c39b73</citedby><cites>FETCH-LOGICAL-b692t-294d4bb295bdc002a3fd10481d1fcadba3fa9fa90328e300d5d7174f3e6c39b73</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367848/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4367848/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,315,728,781,785,865,886,27928,27929,53795,53797</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/25539568$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Qian, Lunwen</creatorcontrib><creatorcontrib>Qian, Wei</creatorcontrib><creatorcontrib>Snowdon, Rod J</creatorcontrib><title>Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome</title><title>BMC genomics</title><addtitle>BMC Genomics</addtitle><description>High-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns of population structure and linkage disequilibrium (LD). In this study we used the Brassica 60kSNP Illumina consortium genotyping array to assess the influence of selection and breeding for important agronomic traits on LD and haplotype structure in a diverse panel of 203 Chinese semi-winter rapeseed (Brassica napus) breeding lines.
Population structure and principal coordinate analysis, using a subset of the SNPs, revealed diversification into three subpopulations and one mixed population, reflecting targeted introgressions from external gene pools during breeding. Pairwise LD analysis within the A- and C-subgenomes of allopolyploid B. napus revealed that mean LD, at a threshold of r2=0.1, decayed on average around ten times more rapidly in the A-subgenome (0.25-0.30 Mb) than in the C-subgenome (2.00-2.50 Mb). A total of 3,097 conserved haplotype blocks were detected over a total length of 182.49 Mb (15.17% of the genome). The mean size of haplotype blocks was considerably longer in the C-subgenome (102.85 Kb) than in the A-subgenome (33.51 Kb), and extremely large conserved haplotype blocks were found on a number of C-genome chromosomes. Comparative sequence analysis revealed conserved blocks containing homoloeogous quantitative trait loci (QTL) for seed erucic acid and glucosinolate content, two key seed quality traits under strong agronomic selection. Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues.
The data we present in this paper provide evidence for strong selection of large chromosome regions associated with important rapeseed seed quality traits conferred by C-subgenome QTL. This implies that an increase in genetic diversity and recombination within the C-genome is particularly important for breeding. The resolution of genome-wide association studies is also expected to vary greatly across different genome regions.</description><subject>Analysis</subject><subject>Biological diversity</subject><subject>Brassica napus</subject><subject>Brassica napus - genetics</subject><subject>Brassica napus - growth & development</subject><subject>Breeding</subject><subject>Chromosomes</subject><subject>Consortia</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Markers - genetics</subject><subject>Genetic research</subject><subject>Genome, Plant - genetics</subject><subject>Genomics</subject><subject>Genotype & phenotype</subject><subject>Haplotypes</subject><subject>Linkage Disequilibrium</subject><subject>Phylogeny</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Polyploidy</subject><subject>Quantitative genetics</subject><subject>Quantitative Trait Loci - genetics</subject><subject>Seasons</subject><subject>Seeds - growth & development</subject><subject>Studies</subject><issn>1471-2164</issn><issn>1471-2164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkl1r1jAUx4sobk4_gDcS8MZddCZN07Q3wl58GQwEp9chL6ddRp6kJq24b2-6Zz6uMkF6oHn5nT8n_3OK4iXBR4S0zVtSc1JWpKlLwkpCOH5U7O_OHt9b7xXPUrrGmPC2Yk-LvYox2rGm3S_M5azKAXzYWI0SONCTDR6Ncpog-oRkDpTs4OU0R0ChRyoCGOsHZD2argBJ58IY3M3ogjXoJMqUrJbIy3FO6FYZnhdPeukSvLj7HxTfPrz_evqpvPj88fz0-KJUTVdNZdXVplaq6pgyGuNK0t4QXLfEkF5Lo_JedjkwrVqgGBtmOOF1T6HRtFOcHhTvtrrjrDZgNPgpSifGaDcy3oggrVjfeHslhvBD1LThbd1mgbOtgLLhHwLrGx02YnFZLC4LwsTShSzz5q6OGL7PkCaxsUmDc9JDmJPILMdV07L2f1DGOc1Pzujrv9DrMEefDV0omqOl7A81SAfC-j7kQvUiKo5vm855s1R49ACVPwN5EIKH3ubzVcLhKiEzE_ycBjmnJM4vv6xZsmV1DClF6HcGEiyWwX3Qslf3W7fL-D2p9BevRefG</recordid><startdate>20141223</startdate><enddate>20141223</enddate><creator>Qian, Lunwen</creator><creator>Qian, Wei</creator><creator>Snowdon, Rod J</creator><general>BioMed Central Ltd</general><general>BioMed Central</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7QP</scope><scope>7QR</scope><scope>7SS</scope><scope>7TK</scope><scope>7U7</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M7P</scope><scope>P64</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20141223</creationdate><title>Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome</title><author>Qian, Lunwen ; Qian, Wei ; Snowdon, Rod J</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-b692t-294d4bb295bdc002a3fd10481d1fcadba3fa9fa90328e300d5d7174f3e6c39b73</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Analysis</topic><topic>Biological diversity</topic><topic>Brassica napus</topic><topic>Brassica napus - genetics</topic><topic>Brassica napus - growth & development</topic><topic>Breeding</topic><topic>Chromosomes</topic><topic>Consortia</topic><topic>Genes</topic><topic>Genetic aspects</topic><topic>Genetic Markers - genetics</topic><topic>Genetic research</topic><topic>Genome, Plant - genetics</topic><topic>Genomics</topic><topic>Genotype & phenotype</topic><topic>Haplotypes</topic><topic>Linkage Disequilibrium</topic><topic>Phylogeny</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Polyploidy</topic><topic>Quantitative genetics</topic><topic>Quantitative Trait Loci - genetics</topic><topic>Seasons</topic><topic>Seeds - growth & development</topic><topic>Studies</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Qian, Lunwen</creatorcontrib><creatorcontrib>Qian, Wei</creatorcontrib><creatorcontrib>Snowdon, Rod J</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Chemoreception Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Toxicology Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Medical Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Access via ProQuest (Open Access)</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>BMC genomics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Qian, Lunwen</au><au>Qian, Wei</au><au>Snowdon, Rod J</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome</atitle><jtitle>BMC genomics</jtitle><addtitle>BMC Genomics</addtitle><date>2014-12-23</date><risdate>2014</risdate><volume>15</volume><issue>1</issue><spage>1170</spage><epage>1170</epage><pages>1170-1170</pages><artnum>1170</artnum><issn>1471-2164</issn><eissn>1471-2164</eissn><abstract>High-density single-nucleotide polymorphism (SNP) genotyping arrays are a powerful tool for genome-wide association studies and can give valuable insight into patterns of population structure and linkage disequilibrium (LD). In this study we used the Brassica 60kSNP Illumina consortium genotyping array to assess the influence of selection and breeding for important agronomic traits on LD and haplotype structure in a diverse panel of 203 Chinese semi-winter rapeseed (Brassica napus) breeding lines.
Population structure and principal coordinate analysis, using a subset of the SNPs, revealed diversification into three subpopulations and one mixed population, reflecting targeted introgressions from external gene pools during breeding. Pairwise LD analysis within the A- and C-subgenomes of allopolyploid B. napus revealed that mean LD, at a threshold of r2=0.1, decayed on average around ten times more rapidly in the A-subgenome (0.25-0.30 Mb) than in the C-subgenome (2.00-2.50 Mb). A total of 3,097 conserved haplotype blocks were detected over a total length of 182.49 Mb (15.17% of the genome). The mean size of haplotype blocks was considerably longer in the C-subgenome (102.85 Kb) than in the A-subgenome (33.51 Kb), and extremely large conserved haplotype blocks were found on a number of C-genome chromosomes. Comparative sequence analysis revealed conserved blocks containing homoloeogous quantitative trait loci (QTL) for seed erucic acid and glucosinolate content, two key seed quality traits under strong agronomic selection. Interestingly, C-subgenome QTL were associated with considerably greater conservation of LD than their corresponding A-subgenome homoeologues.
The data we present in this paper provide evidence for strong selection of large chromosome regions associated with important rapeseed seed quality traits conferred by C-subgenome QTL. This implies that an increase in genetic diversity and recombination within the C-genome is particularly important for breeding. The resolution of genome-wide association studies is also expected to vary greatly across different genome regions.</abstract><cop>England</cop><pub>BioMed Central Ltd</pub><pmid>25539568</pmid><doi>10.1186/1471-2164-15-1170</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Biological diversity Brassica napus Brassica napus - genetics Brassica napus - growth & development Breeding Chromosomes Consortia Genes Genetic aspects Genetic Markers - genetics Genetic research Genome, Plant - genetics Genomics Genotype & phenotype Haplotypes Linkage Disequilibrium Phylogeny Polymorphism, Single Nucleotide Polyploidy Quantitative genetics Quantitative Trait Loci - genetics Seasons Seeds - growth & development Studies |
| title | Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome |
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