Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping
Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the gene...
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| Veröffentlicht in: | Molecular genetics and genomics : MGG 2014-08, Vol.289 (4), p.513-521 |
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| creator | Nimmakayala, Padma Abburi, Venkata L Abburi, Lavanya Alaparthi, Suresh Babu Cantrell, Robert Park, Minkyu Choi, Doil Hankins, Gerald Malkaram, Sridhar Reddy, Umesh K |
| description | Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer five clusters, which was further confirmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R ² of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum. |
| doi_str_mv | 10.1007/s00438-014-0827-3 |
| format | Article |
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The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer five clusters, which was further confirmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R ² of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum.</description><identifier>ISSN: 1617-4615</identifier><identifier>EISSN: 1617-4623</identifier><identifier>DOI: 10.1007/s00438-014-0827-3</identifier><identifier>PMID: 24585251</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer-Verlag</publisher><subject>Alleles ; Animal Genetics and Genomics ; Biochemistry ; Biomedical and Life Sciences ; capsaicin ; Capsicum - genetics ; Capsicum annuum ; Chromosome Mapping ; Chromosomes ; Chromosomes, Plant - genetics ; Cluster Analysis ; Corn ; Cultivars ; DNA, Plant - genetics ; Fruits ; Genetic diversity ; Genetic Markers - genetics ; Genetic Variation ; Genome, Plant - genetics ; Genomes ; Genomics ; Genotype ; Germplasm ; heterozygosity ; Human Genetics ; Life Sciences ; Linkage Disequilibrium ; loci ; marker-assisted selection ; Microbial Genetics and Genomics ; microsatellite repeats ; Microsatellite Repeats - genetics ; Original Paper ; pepper ; peppers ; Phylogeny ; Plant Genetics and Genomics ; population structure ; quantitative trait loci ; Quantitative Trait Loci - genetics ; Software</subject><ispartof>Molecular genetics and genomics : MGG, 2014-08, Vol.289 (4), p.513-521</ispartof><rights>Springer-Verlag Berlin Heidelberg 2014</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c525t-a7f196c0adee1048a03ee9aa7d8cc34c0d731656503f21d20078fafc8bc173f3</citedby><cites>FETCH-LOGICAL-c525t-a7f196c0adee1048a03ee9aa7d8cc34c0d731656503f21d20078fafc8bc173f3</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00438-014-0827-3$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00438-014-0827-3$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/24585251$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Nimmakayala, Padma</creatorcontrib><creatorcontrib>Abburi, Venkata L</creatorcontrib><creatorcontrib>Abburi, Lavanya</creatorcontrib><creatorcontrib>Alaparthi, Suresh Babu</creatorcontrib><creatorcontrib>Cantrell, Robert</creatorcontrib><creatorcontrib>Park, Minkyu</creatorcontrib><creatorcontrib>Choi, Doil</creatorcontrib><creatorcontrib>Hankins, Gerald</creatorcontrib><creatorcontrib>Malkaram, Sridhar</creatorcontrib><creatorcontrib>Reddy, Umesh K</creatorcontrib><title>Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping</title><title>Molecular genetics and genomics : MGG</title><addtitle>Mol Genet Genomics</addtitle><addtitle>Mol Genet Genomics</addtitle><description>Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer five clusters, which was further confirmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R ² of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum.</description><subject>Alleles</subject><subject>Animal Genetics and Genomics</subject><subject>Biochemistry</subject><subject>Biomedical and Life Sciences</subject><subject>capsaicin</subject><subject>Capsicum - genetics</subject><subject>Capsicum annuum</subject><subject>Chromosome Mapping</subject><subject>Chromosomes</subject><subject>Chromosomes, Plant - genetics</subject><subject>Cluster Analysis</subject><subject>Corn</subject><subject>Cultivars</subject><subject>DNA, Plant - genetics</subject><subject>Fruits</subject><subject>Genetic diversity</subject><subject>Genetic Markers - genetics</subject><subject>Genetic Variation</subject><subject>Genome, Plant - genetics</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Germplasm</subject><subject>heterozygosity</subject><subject>Human Genetics</subject><subject>Life Sciences</subject><subject>Linkage Disequilibrium</subject><subject>loci</subject><subject>marker-assisted selection</subject><subject>Microbial Genetics and Genomics</subject><subject>microsatellite repeats</subject><subject>Microsatellite Repeats - genetics</subject><subject>Original Paper</subject><subject>pepper</subject><subject>peppers</subject><subject>Phylogeny</subject><subject>Plant Genetics and Genomics</subject><subject>population structure</subject><subject>quantitative trait loci</subject><subject>Quantitative Trait Loci - genetics</subject><subject>Software</subject><issn>1617-4615</issn><issn>1617-4623</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>eNqNkktv1TAQhSNERUvhB7ABS2zYpPUzdpboipd0JRZt19Zcx4lckjj1xJXKr8dtSoVYIFZjab5zPJozVfWG0TNGqT5HSqUwNWWypobrWjyrTljDdC0bLp4_vZk6rl4iXlPKdMP1i-qYS2UUV-yk-rkP8w8YPOkC-pscxnBIIU8E5o4scckjrCHONa4puzUnXxow3mFAAlOcB7KDBYN7EMy5lP0ZcXlcwy0kJH1MJKMnYSaAGF14MCMTLEuYh1fVUQ8j-teP9bS6_Pzpcve13n__8m33cV-7MuJag-5Z2zgKnfeMSgNUeN8C6M44J6SjnRasUY2ioues42UxpofemYNjWvTitPqw2S4p3mSPq50COj-OMPuY0TKlZCtbrfR_oNI0gsmWFfT9X-h1zKnsZqOEkY3hhWIb5VJETL63SwoTpDvLqL2P0G4R2hKhvY_QiqJ5--icD5PvnhS_MysA3wAsrXnw6Y-v_-H6bhP1EC0MKaC9uuAFKEchVFtm_QUY8rEv</recordid><startdate>20140801</startdate><enddate>20140801</enddate><creator>Nimmakayala, Padma</creator><creator>Abburi, Venkata L</creator><creator>Abburi, Lavanya</creator><creator>Alaparthi, Suresh Babu</creator><creator>Cantrell, Robert</creator><creator>Park, Minkyu</creator><creator>Choi, Doil</creator><creator>Hankins, Gerald</creator><creator>Malkaram, Sridhar</creator><creator>Reddy, Umesh K</creator><general>Springer-Verlag</general><general>Springer Berlin Heidelberg</general><general>Springer Nature B.V</general><scope>FBQ</scope><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>3V.</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</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>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>M7N</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20140801</creationdate><title>Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping</title><author>Nimmakayala, Padma ; Abburi, Venkata L ; Abburi, Lavanya ; Alaparthi, Suresh Babu ; Cantrell, Robert ; Park, Minkyu ; Choi, Doil ; Hankins, Gerald ; Malkaram, Sridhar ; Reddy, Umesh K</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c525t-a7f196c0adee1048a03ee9aa7d8cc34c0d731656503f21d20078fafc8bc173f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Alleles</topic><topic>Animal Genetics and Genomics</topic><topic>Biochemistry</topic><topic>Biomedical and Life Sciences</topic><topic>capsaicin</topic><topic>Capsicum - genetics</topic><topic>Capsicum annuum</topic><topic>Chromosome Mapping</topic><topic>Chromosomes</topic><topic>Chromosomes, Plant - genetics</topic><topic>Cluster Analysis</topic><topic>Corn</topic><topic>Cultivars</topic><topic>DNA, Plant - genetics</topic><topic>Fruits</topic><topic>Genetic diversity</topic><topic>Genetic Markers - genetics</topic><topic>Genetic Variation</topic><topic>Genome, Plant - genetics</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Genotype</topic><topic>Germplasm</topic><topic>heterozygosity</topic><topic>Human Genetics</topic><topic>Life Sciences</topic><topic>Linkage Disequilibrium</topic><topic>loci</topic><topic>marker-assisted selection</topic><topic>Microbial Genetics and Genomics</topic><topic>microsatellite repeats</topic><topic>Microsatellite Repeats - genetics</topic><topic>Original Paper</topic><topic>pepper</topic><topic>peppers</topic><topic>Phylogeny</topic><topic>Plant Genetics and Genomics</topic><topic>population structure</topic><topic>quantitative trait loci</topic><topic>Quantitative Trait Loci - 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Academic</collection><jtitle>Molecular genetics and genomics : MGG</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nimmakayala, Padma</au><au>Abburi, Venkata L</au><au>Abburi, Lavanya</au><au>Alaparthi, Suresh Babu</au><au>Cantrell, Robert</au><au>Park, Minkyu</au><au>Choi, Doil</au><au>Hankins, Gerald</au><au>Malkaram, Sridhar</au><au>Reddy, Umesh K</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping</atitle><jtitle>Molecular genetics and genomics : MGG</jtitle><stitle>Mol Genet Genomics</stitle><addtitle>Mol Genet Genomics</addtitle><date>2014-08-01</date><risdate>2014</risdate><volume>289</volume><issue>4</issue><spage>513</spage><epage>521</epage><pages>513-521</pages><issn>1617-4615</issn><eissn>1617-4623</eissn><abstract>Knowledge of population structure and linkage disequilibrium among the worldwide collections of peppers currently classified as hot, mild, sweet and ornamental types is indispensable for applying association mapping and genomic selection to improve pepper. The current study aimed to resolve the genetic diversity and relatedness of Capsicum annuum germplasm by use of simple sequence repeat (SSR) loci across all chromosomes in samples collected in 2011 and 2012. The physical distance covered by the entire set of SSRs used was 2,265.9 Mb from the 3.48-Gb hot-pepper genome size. The model-based program STRUCTURE was used to infer five clusters, which was further confirmed by classical molecular-genetic diversity analysis. Mean heterozygosity of various loci was estimated to be 0.15. Linkage disequilibrium (LD) was used to identify 17 LD blocks across various chromosomes with sizes from 0.154 Kb to 126.28 Mb. CAMS-142 of chromosome 1 was significantly associated with both capsaicin (CA) and dihydrocapsaicin (DCA) levels. Further, CAMS-142 was located in an LD block of 98.18 Mb. CAMS-142 amplified bands of 244, 268, 283 and 326 bp. Alleles 268 and 283 bp had positive effects on both CA and DCA levels, with an average R ² of 12.15 % (CA) and 12.3 % (DCA). Eight markers from seven different chromosomes were significantly associated with fruit weight, contributing an average effect of 15 %. CAMS-199, HpmsE082 and CAMS-190 are the three major quantitative trait loci located on chromosomes 8, 9, and 10, respectively, and were associated with fruit weight in samples from both years of the study. This research demonstrates the effectiveness of using genome-wide SSR-based markers to assess features of LD and genetic diversity within C. annuum.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer-Verlag</pub><pmid>24585251</pmid><doi>10.1007/s00438-014-0827-3</doi><tpages>9</tpages></addata></record> |
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| subjects | Alleles Animal Genetics and Genomics Biochemistry Biomedical and Life Sciences capsaicin Capsicum - genetics Capsicum annuum Chromosome Mapping Chromosomes Chromosomes, Plant - genetics Cluster Analysis Corn Cultivars DNA, Plant - genetics Fruits Genetic diversity Genetic Markers - genetics Genetic Variation Genome, Plant - genetics Genomes Genomics Genotype Germplasm heterozygosity Human Genetics Life Sciences Linkage Disequilibrium loci marker-assisted selection Microbial Genetics and Genomics microsatellite repeats Microsatellite Repeats - genetics Original Paper pepper peppers Phylogeny Plant Genetics and Genomics population structure quantitative trait loci Quantitative Trait Loci - genetics Software |
| title | Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping |
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