Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)
Key message Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton. Six hundred fifty-seven accessions that included elite cotton...
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| Veröffentlicht in: | Theoretical and applied genetics 2023-11, Vol.136 (11), p.230-230, Article 230 |
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| creator | Gowda, S. Anjan Bourland, Fred M. Kaur, Baljinder Jones, Don C. Kuraparthy, Vasu |
| description | Key message
Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton.
Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of
Gossypium hirsutum
L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (
F
ST
) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest
F
ST
values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including
Transcription factor Vascular Plant One-Zinc Finger 1
(
VOZ1
) and
Protein Photoperiod-Independent Early Flowering 1
(
PIE1
) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton. |
| doi_str_mv | 10.1007/s00122-023-04477-w |
| format | Article |
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Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton.
Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of
Gossypium hirsutum
L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (
F
ST
) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest
F
ST
values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including
Transcription factor Vascular Plant One-Zinc Finger 1
(
VOZ1
) and
Protein Photoperiod-Independent Early Flowering 1
(
PIE1
) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.</description><identifier>ISSN: 0040-5752</identifier><identifier>EISSN: 1432-2242</identifier><identifier>DOI: 10.1007/s00122-023-04477-w</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Agriculture ; Analysis ; Biochemistry ; Biological diversity ; Biomedical and Life Sciences ; Biotechnology ; Chromosomes ; Cotton ; Cultivars ; DNA binding proteins ; Epistasis ; Flowering ; Genetic analysis ; Genetic aspects ; Genetic diversity ; Genome-wide association studies ; Genomes ; Genomic analysis ; Germplasm ; Gossypium hirsutum ; Life Sciences ; Original Article ; Photoperiodism ; Photoperiods ; Plant Biochemistry ; Plant breeding ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Plants ; Population genetics ; Population structure ; Single-nucleotide polymorphism ; Subpopulations ; Zinc finger proteins</subject><ispartof>Theoretical and applied genetics, 2023-11, Vol.136 (11), p.230-230, Article 230</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><rights>COPYRIGHT 2023 Springer</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c453t-f6cfa99aba0e5dbb3ca51ee2ab098127b485f4993e12733298b1c876ec4225a93</citedby><cites>FETCH-LOGICAL-c453t-f6cfa99aba0e5dbb3ca51ee2ab098127b485f4993e12733298b1c876ec4225a93</cites><orcidid>0000-0002-5913-0403</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00122-023-04477-w$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00122-023-04477-w$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>315,781,785,27929,27930,41493,42562,51324</link.rule.ids></links><search><creatorcontrib>Gowda, S. Anjan</creatorcontrib><creatorcontrib>Bourland, Fred M.</creatorcontrib><creatorcontrib>Kaur, Baljinder</creatorcontrib><creatorcontrib>Jones, Don C.</creatorcontrib><creatorcontrib>Kuraparthy, Vasu</creatorcontrib><title>Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)</title><title>Theoretical and applied genetics</title><addtitle>Theor Appl Genet</addtitle><description>Key message
Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton.
Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of
Gossypium hirsutum
L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (
F
ST
) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest
F
ST
values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including
Transcription factor Vascular Plant One-Zinc Finger 1
(
VOZ1
) and
Protein Photoperiod-Independent Early Flowering 1
(
PIE1
) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.</description><subject>Agriculture</subject><subject>Analysis</subject><subject>Biochemistry</subject><subject>Biological diversity</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Chromosomes</subject><subject>Cotton</subject><subject>Cultivars</subject><subject>DNA binding proteins</subject><subject>Epistasis</subject><subject>Flowering</subject><subject>Genetic analysis</subject><subject>Genetic aspects</subject><subject>Genetic diversity</subject><subject>Genome-wide association studies</subject><subject>Genomes</subject><subject>Genomic analysis</subject><subject>Germplasm</subject><subject>Gossypium hirsutum</subject><subject>Life Sciences</subject><subject>Original Article</subject><subject>Photoperiodism</subject><subject>Photoperiods</subject><subject>Plant Biochemistry</subject><subject>Plant breeding</subject><subject>Plant Breeding/Biotechnology</subject><subject>Plant Genetics and Genomics</subject><subject>Plants</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Single-nucleotide polymorphism</subject><subject>Subpopulations</subject><subject>Zinc finger proteins</subject><issn>0040-5752</issn><issn>1432-2242</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2023</creationdate><recordtype>article</recordtype><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9ksuO0zAUhiMEEmXgBVhFYjOzSDm-pE6WoxGUkSohcVlbjnPS8Si1gy_T6XvwwLgNCIoQ8sI-Pt__Wz76i-I1gSUBEG8DAKG0Asoq4FyIav-kWBDOaEUpp0-LBQCHqhY1fV68COEeAGgNbFF8X6PFaHTZmwf0wcRDqWxfTm5Ko4rG2TJEn3RMHnNDjYeA4URs0bodVnvT50YITptfeOpNZtxQTncuugm9cX0Z0GZz83B8wNhSuxgzfLl2IRwmk3blnfEhxXzYLK9eFs8GNQZ89XO_KL6-f_fl5kO1-bi-vbneVJrXLFbDSg-qbVWnAOu-65hWNUGkqoO2IVR0vKkH3rYMc8EYbZuO6EasUHNKa9Wyi-Jy9p28-5YwRLkzQeM4KosuBUmbhghCQdCMvvkLvXfJ54HMFNR0xf6gtmpEaezgolf6aCqvhcgj53Cilv-g8upxZ7SzOJh8fya4OhNkJuJj3KoUgrz9_OmcpTOrfZ6tx0FO3uyUP0gC8pgVOWdF5qzIU1bkPovYLAoZtlv0v3_3H9UPb6_DDA</recordid><startdate>20231101</startdate><enddate>20231101</enddate><creator>Gowda, S. Anjan</creator><creator>Bourland, Fred M.</creator><creator>Kaur, Baljinder</creator><creator>Jones, Don C.</creator><creator>Kuraparthy, Vasu</creator><general>Springer Berlin Heidelberg</general><general>Springer</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>ISR</scope><scope>3V.</scope><scope>7SS</scope><scope>7TK</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>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-5913-0403</orcidid></search><sort><creationdate>20231101</creationdate><title>Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)</title><author>Gowda, S. Anjan ; Bourland, Fred M. ; Kaur, Baljinder ; Jones, Don C. ; Kuraparthy, Vasu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c453t-f6cfa99aba0e5dbb3ca51ee2ab098127b485f4993e12733298b1c876ec4225a93</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2023</creationdate><topic>Agriculture</topic><topic>Analysis</topic><topic>Biochemistry</topic><topic>Biological diversity</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Chromosomes</topic><topic>Cotton</topic><topic>Cultivars</topic><topic>DNA binding proteins</topic><topic>Epistasis</topic><topic>Flowering</topic><topic>Genetic analysis</topic><topic>Genetic aspects</topic><topic>Genetic diversity</topic><topic>Genome-wide association studies</topic><topic>Genomes</topic><topic>Genomic analysis</topic><topic>Germplasm</topic><topic>Gossypium hirsutum</topic><topic>Life Sciences</topic><topic>Original Article</topic><topic>Photoperiodism</topic><topic>Photoperiods</topic><topic>Plant Biochemistry</topic><topic>Plant breeding</topic><topic>Plant Breeding/Biotechnology</topic><topic>Plant Genetics and Genomics</topic><topic>Plants</topic><topic>Population genetics</topic><topic>Population structure</topic><topic>Single-nucleotide polymorphism</topic><topic>Subpopulations</topic><topic>Zinc finger proteins</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Gowda, S. Anjan</creatorcontrib><creatorcontrib>Bourland, Fred M.</creatorcontrib><creatorcontrib>Kaur, Baljinder</creatorcontrib><creatorcontrib>Jones, Don C.</creatorcontrib><creatorcontrib>Kuraparthy, Vasu</creatorcontrib><collection>CrossRef</collection><collection>Gale In Context: Science</collection><collection>ProQuest Central (Corporate)</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</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>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>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Theoretical and applied genetics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Gowda, S. Anjan</au><au>Bourland, Fred M.</au><au>Kaur, Baljinder</au><au>Jones, Don C.</au><au>Kuraparthy, Vasu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.)</atitle><jtitle>Theoretical and applied genetics</jtitle><stitle>Theor Appl Genet</stitle><date>2023-11-01</date><risdate>2023</risdate><volume>136</volume><issue>11</issue><spage>230</spage><epage>230</epage><pages>230-230</pages><artnum>230</artnum><issn>0040-5752</issn><eissn>1432-2242</eissn><abstract>Key message
Genetic diversity and population structure analyses showed progressively narrowed diversity in US Upland cotton compared to land races. GWAS identified genomic regions and candidate genes for photoperiod sensitivity in cotton.
Six hundred fifty-seven accessions that included elite cotton germplasm (DIV panel), lines of a public cotton breeding program (FB panel), and tropical landrace accessions (TLA panel) of
Gossypium hirsutum
L. were genotyped with cottonSNP63K array and phenotyped for photoperiod sensitivity under long day-length conditions. The genetic diversity analysis using 26,952 polymorphic SNPs indicated a progressively narrowed diversity from the landraces (0.230) to the DIV panel accessions (0.195) and FB panel (0.116). Structure analysis in the US germplasm identified seven subpopulations representing all four major regions of the US cotton belt. Three subpopulations were identified within the landrace accessions. The highest fixation index (
F
ST
) of 0.65 was found between landrace accessions of Guatemala and the Plains-type cultivars from Southwest cotton region while the lowest
F
ST
values were between the germplasms of Mid-South and Southeastern regions. Genome wide association studies (GWAS) of photoperiod response using 600 phenotyped accessions identified 14 marker trait associations spread across eight Upland cotton chromosomes. Six of these marker trait associations, on four chromosomes (A10, D04, D05, and D06), showed significant epistatic interactions. Targeted genomic analysis identified regions with 19 candidate genes including
Transcription factor Vascular Plant One-Zinc Finger 1
(
VOZ1
) and
Protein Photoperiod-Independent Early Flowering 1
(
PIE1
) genes. Genetic diversity and genome wide analyses of photoperiod sensitivity in diverse cotton germplasms will enable the use of genomic tools to systematically utilize the tropical germplasm and its beneficial alleles for broadening the genetic base in Upland cotton.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s00122-023-04477-w</doi><tpages>1</tpages><orcidid>https://orcid.org/0000-0002-5913-0403</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0040-5752 |
| ispartof | Theoretical and applied genetics, 2023-11, Vol.136 (11), p.230-230, Article 230 |
| issn | 0040-5752 1432-2242 |
| language | eng |
| recordid | cdi_proquest_miscellaneous_2881712072 |
| source | SpringerNature Journals |
| subjects | Agriculture Analysis Biochemistry Biological diversity Biomedical and Life Sciences Biotechnology Chromosomes Cotton Cultivars DNA binding proteins Epistasis Flowering Genetic analysis Genetic aspects Genetic diversity Genome-wide association studies Genomes Genomic analysis Germplasm Gossypium hirsutum Life Sciences Original Article Photoperiodism Photoperiods Plant Biochemistry Plant breeding Plant Breeding/Biotechnology Plant Genetics and Genomics Plants Population genetics Population structure Single-nucleotide polymorphism Subpopulations Zinc finger proteins |
| title | Genetic diversity and population structure analyses and genome-wide association studies of photoperiod sensitivity in cotton (Gossypium hirsutum L.) |
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