Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines
Post-domestication selection refers to the artificial selection on the loci controlling important agronomic traits during the process of genetic improvement in a population. The maize genes Zfl1 and Zfl2 , duplicate orthologs of Arabidopsis LEAFY , are key regulators in plant branching, inflorescenc...
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| Veröffentlicht in: | Molecular biology reports 2014-02, Vol.41 (2), p.1117-1125 |
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| creator | Yang, Zefeng Zhang, Enying Li, Jing Jiang, Ying Wang, Yifan Hu, Yunyun Xu, Chenwu |
| description | Post-domestication selection refers to the artificial selection on the loci controlling important agronomic traits during the process of genetic improvement in a population. The maize genes
Zfl1
and
Zfl2
, duplicate orthologs of
Arabidopsis LEAFY
, are key regulators in plant branching, inflorescence and flower development, and reproduction. In this study, the full gene sequences of
Zfl1
and
Zfl2
from 62 Chinese elite inbred lines were amplified to evaluate their nucleotide polymorphisms and haplotype diversities. A total of 254 and 192 variants that included SNPs and indels were identified from the full sequences of
Zfl1
and
Zfl2
, respectively. Although most of the variants were found to be located in the non-coding regions, the polymorphisms of CDS sequences classified
Zfl1
into 16 haplotypes encoding 16 different proteins and
Zfl2
into 18 haplotypes encoding eight different proteins. The population of Huangzaosi and its derived lines showed statistically significant signals of post-domestication selection on the
Zfl1
CDS sequences, as well as lower nucleotide polymorphism and haplotype diversity than the whole set. However, the
Zfl2
locus was only selected for in the heterotic group Reid. Further evidence revealed that at least 17 recombination events contributed to the genetic and haplotype diversities at the
Zfl1
locus and 16 recombination events at the
Zfl2
locus. |
| doi_str_mv | 10.1007/s11033-013-2958-8 |
| format | Article |
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Zfl1
and
Zfl2
, duplicate orthologs of
Arabidopsis LEAFY
, are key regulators in plant branching, inflorescence and flower development, and reproduction. In this study, the full gene sequences of
Zfl1
and
Zfl2
from 62 Chinese elite inbred lines were amplified to evaluate their nucleotide polymorphisms and haplotype diversities. A total of 254 and 192 variants that included SNPs and indels were identified from the full sequences of
Zfl1
and
Zfl2
, respectively. Although most of the variants were found to be located in the non-coding regions, the polymorphisms of CDS sequences classified
Zfl1
into 16 haplotypes encoding 16 different proteins and
Zfl2
into 18 haplotypes encoding eight different proteins. The population of Huangzaosi and its derived lines showed statistically significant signals of post-domestication selection on the
Zfl1
CDS sequences, as well as lower nucleotide polymorphism and haplotype diversity than the whole set. However, the
Zfl2
locus was only selected for in the heterotic group Reid. Further evidence revealed that at least 17 recombination events contributed to the genetic and haplotype diversities at the
Zfl1
locus and 16 recombination events at the
Zfl2
locus.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-013-2958-8</identifier><identifier>PMID: 24381105</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Animal Anatomy ; Animal Biochemistry ; Arabidopsis ; Asian Continental Ancestry Group ; Biodiversity ; Biomedical and Life Sciences ; Corn ; Genes ; Genetic Variation ; Genome, Plant ; Genotype & phenotype ; Haplotypes ; Histology ; Humans ; Life Sciences ; Linkage Disequilibrium ; Morphology ; Phenotype ; Plant Proteins - genetics ; Polymorphism ; Polymorphism, Genetic ; Polymorphism, Single Nucleotide ; Zea mays ; Zea mays - genetics</subject><ispartof>Molecular biology reports, 2014-02, Vol.41 (2), p.1117-1125</ispartof><rights>Springer Science+Business Media Dordrecht 2013</rights><rights>Springer Science+Business Media Dordrecht 2014</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c405t-53a8d6d288077d8cc161ca788b919268134377eca75dcab09bafc76bffc1601c3</citedby><cites>FETCH-LOGICAL-c405t-53a8d6d288077d8cc161ca788b919268134377eca75dcab09bafc76bffc1601c3</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/s11033-013-2958-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-013-2958-8$$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/24381105$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Yang, Zefeng</creatorcontrib><creatorcontrib>Zhang, Enying</creatorcontrib><creatorcontrib>Li, Jing</creatorcontrib><creatorcontrib>Jiang, Ying</creatorcontrib><creatorcontrib>Wang, Yifan</creatorcontrib><creatorcontrib>Hu, Yunyun</creatorcontrib><creatorcontrib>Xu, Chenwu</creatorcontrib><title>Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Post-domestication selection refers to the artificial selection on the loci controlling important agronomic traits during the process of genetic improvement in a population. The maize genes
Zfl1
and
Zfl2
, duplicate orthologs of
Arabidopsis LEAFY
, are key regulators in plant branching, inflorescence and flower development, and reproduction. In this study, the full gene sequences of
Zfl1
and
Zfl2
from 62 Chinese elite inbred lines were amplified to evaluate their nucleotide polymorphisms and haplotype diversities. A total of 254 and 192 variants that included SNPs and indels were identified from the full sequences of
Zfl1
and
Zfl2
, respectively. Although most of the variants were found to be located in the non-coding regions, the polymorphisms of CDS sequences classified
Zfl1
into 16 haplotypes encoding 16 different proteins and
Zfl2
into 18 haplotypes encoding eight different proteins. The population of Huangzaosi and its derived lines showed statistically significant signals of post-domestication selection on the
Zfl1
CDS sequences, as well as lower nucleotide polymorphism and haplotype diversity than the whole set. However, the
Zfl2
locus was only selected for in the heterotic group Reid. Further evidence revealed that at least 17 recombination events contributed to the genetic and haplotype diversities at the
Zfl1
locus and 16 recombination events at the
Zfl2
locus.</description><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Arabidopsis</subject><subject>Asian Continental Ancestry Group</subject><subject>Biodiversity</subject><subject>Biomedical and Life Sciences</subject><subject>Corn</subject><subject>Genes</subject><subject>Genetic Variation</subject><subject>Genome, Plant</subject><subject>Genotype & phenotype</subject><subject>Haplotypes</subject><subject>Histology</subject><subject>Humans</subject><subject>Life Sciences</subject><subject>Linkage Disequilibrium</subject><subject>Morphology</subject><subject>Phenotype</subject><subject>Plant Proteins - genetics</subject><subject>Polymorphism</subject><subject>Polymorphism, Genetic</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Zea mays</subject><subject>Zea mays - genetics</subject><issn>0301-4851</issn><issn>1573-4978</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>eNqFkUFvFCEYhonR2LX1B3gxJF68jOWDYWGOm02rJpt4qYeeJgzzTZeGGUZgm4w_xN8r263GmBhPEL7neQm8hLwB9gEYU5cJgAlRMRAVb6Su9DOyAqlEVTdKPycrJhhUtZZwRl6ldM8Yq0HJl-SM10IXV67Ij81k_JIw0TDQhN8OOFmkc_DLGOK8d2mkZurp3sw-5GVG2rsHjMnl5SjsrjbXt_QOp-JHfEDjsS9yylUfRkzZWZNdmEqwR_u4cxPNe6TbvSsOUvQuIx2N-45l1MWi--PkgrwYjE_4-mk9J1-vr262n6rdl4-ft5tdZWsmcyWF0f2651ozpXptLazBGqV110DD1xpELZTCciR7azrWdGawat0NQyEZWHFO3p9y5xjK21NuR5csem8mDIfUggQuOMhG_h-tG66Y5JwV9N1f6H04xPLRjxRwXoPghYITZWNIKeLQztGNJi4tsPbYb3vqty39tsd-W12ct0_Jh27E_rfxq9AC8BOQymi6w_jH1f9M_QlnnbHo</recordid><startdate>20140201</startdate><enddate>20140201</enddate><creator>Yang, Zefeng</creator><creator>Zhang, Enying</creator><creator>Li, Jing</creator><creator>Jiang, Ying</creator><creator>Wang, Yifan</creator><creator>Hu, Yunyun</creator><creator>Xu, Chenwu</creator><general>Springer Netherlands</general><general>Springer Nature B.V</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>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</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>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope></search><sort><creationdate>20140201</creationdate><title>Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines</title><author>Yang, Zefeng ; Zhang, Enying ; Li, Jing ; Jiang, Ying ; Wang, Yifan ; Hu, Yunyun ; Xu, Chenwu</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c405t-53a8d6d288077d8cc161ca788b919268134377eca75dcab09bafc76bffc1601c3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Arabidopsis</topic><topic>Asian Continental Ancestry Group</topic><topic>Biodiversity</topic><topic>Biomedical and Life Sciences</topic><topic>Corn</topic><topic>Genes</topic><topic>Genetic Variation</topic><topic>Genome, Plant</topic><topic>Genotype & phenotype</topic><topic>Haplotypes</topic><topic>Histology</topic><topic>Humans</topic><topic>Life Sciences</topic><topic>Linkage Disequilibrium</topic><topic>Morphology</topic><topic>Phenotype</topic><topic>Plant Proteins - genetics</topic><topic>Polymorphism</topic><topic>Polymorphism, Genetic</topic><topic>Polymorphism, Single Nucleotide</topic><topic>Zea mays</topic><topic>Zea mays - genetics</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Yang, Zefeng</creatorcontrib><creatorcontrib>Zhang, Enying</creatorcontrib><creatorcontrib>Li, Jing</creatorcontrib><creatorcontrib>Jiang, Ying</creatorcontrib><creatorcontrib>Wang, Yifan</creatorcontrib><creatorcontrib>Hu, Yunyun</creatorcontrib><creatorcontrib>Xu, Chenwu</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids 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>Science 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>Science 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>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Yang, Zefeng</au><au>Zhang, Enying</au><au>Li, Jing</au><au>Jiang, Ying</au><au>Wang, Yifan</au><au>Hu, Yunyun</au><au>Xu, Chenwu</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2014-02-01</date><risdate>2014</risdate><volume>41</volume><issue>2</issue><spage>1117</spage><epage>1125</epage><pages>1117-1125</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Post-domestication selection refers to the artificial selection on the loci controlling important agronomic traits during the process of genetic improvement in a population. The maize genes
Zfl1
and
Zfl2
, duplicate orthologs of
Arabidopsis LEAFY
, are key regulators in plant branching, inflorescence and flower development, and reproduction. In this study, the full gene sequences of
Zfl1
and
Zfl2
from 62 Chinese elite inbred lines were amplified to evaluate their nucleotide polymorphisms and haplotype diversities. A total of 254 and 192 variants that included SNPs and indels were identified from the full sequences of
Zfl1
and
Zfl2
, respectively. Although most of the variants were found to be located in the non-coding regions, the polymorphisms of CDS sequences classified
Zfl1
into 16 haplotypes encoding 16 different proteins and
Zfl2
into 18 haplotypes encoding eight different proteins. The population of Huangzaosi and its derived lines showed statistically significant signals of post-domestication selection on the
Zfl1
CDS sequences, as well as lower nucleotide polymorphism and haplotype diversity than the whole set. However, the
Zfl2
locus was only selected for in the heterotic group Reid. Further evidence revealed that at least 17 recombination events contributed to the genetic and haplotype diversities at the
Zfl1
locus and 16 recombination events at the
Zfl2
locus.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>24381105</pmid><doi>10.1007/s11033-013-2958-8</doi><tpages>9</tpages></addata></record> |
| fulltext | fulltext |
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| ispartof | Molecular biology reports, 2014-02, Vol.41 (2), p.1117-1125 |
| issn | 0301-4851 1573-4978 |
| language | eng |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Animal Anatomy Animal Biochemistry Arabidopsis Asian Continental Ancestry Group Biodiversity Biomedical and Life Sciences Corn Genes Genetic Variation Genome, Plant Genotype & phenotype Haplotypes Histology Humans Life Sciences Linkage Disequilibrium Morphology Phenotype Plant Proteins - genetics Polymorphism Polymorphism, Genetic Polymorphism, Single Nucleotide Zea mays Zea mays - genetics |
| title | Analyses of sequence polymorphism and haplotype diversity of LEAFY genes revealed post-domestication selection in the Chinese elite maize inbred lines |
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