Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.)
The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segrega...
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| creator | Wei, Chunhua Chen, Xiner Wang, Zhongyuan Liu, Qiyan Li, Hao Zhang, Yong Ma, Jianxiang Yang, Jianqiang Zhang, Xian |
| description | The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies. |
| doi_str_mv | 10.1371/journal.pone.0180741 |
| format | Article |
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Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0180741</identifier><identifier>PMID: 28704497</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural production ; Bioinformatics ; Biology and Life Sciences ; Chromosome Mapping - methods ; Chromosomes, Plant - genetics ; Citrullus - anatomy & histology ; Citrullus - genetics ; Cloning ; Gene expression ; Gene Expression Regulation, Plant ; Gene mapping ; Gene sequencing ; Genetic analysis ; Genetic factors ; Genetic Linkage ; Genomes ; Genomics ; Homeobox ; Horticulture ; Leaves ; Leucine ; Leucine zipper proteins ; Markers ; Phenotype ; Plant Leaves - anatomy & histology ; Plant Leaves - genetics ; Plant Proteins - genetics ; Plants ; Polymerase chain reaction ; Polymorphism, Single Nucleotide ; Population ; Quantitative Trait Loci ; Research and Analysis Methods ; Ribonucleic acid ; RNA ; Seeds ; Sequence Analysis, RNA ; Single-nucleotide polymorphism ; Transcription factors</subject><ispartof>PloS one, 2017-07, Vol.12 (7), p.e0180741-e0180741</ispartof><rights>2017 Wei et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies.</description><subject>Agricultural production</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Chromosome Mapping - methods</subject><subject>Chromosomes, Plant - genetics</subject><subject>Citrullus - anatomy & histology</subject><subject>Citrullus - genetics</subject><subject>Cloning</subject><subject>Gene expression</subject><subject>Gene Expression Regulation, Plant</subject><subject>Gene mapping</subject><subject>Gene sequencing</subject><subject>Genetic analysis</subject><subject>Genetic factors</subject><subject>Genetic Linkage</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Homeobox</subject><subject>Horticulture</subject><subject>Leaves</subject><subject>Leucine</subject><subject>Leucine zipper proteins</subject><subject>Markers</subject><subject>Phenotype</subject><subject>Plant Leaves - anatomy & histology</subject><subject>Plant Leaves - genetics</subject><subject>Plant Proteins - genetics</subject><subject>Plants</subject><subject>Polymerase chain reaction</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Population</subject><subject>Quantitative Trait Loci</subject><subject>Research and Analysis Methods</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>Seeds</subject><subject>Sequence Analysis, RNA</subject><subject>Single-nucleotide polymorphism</subject><subject>Transcription factors</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</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><sourceid>DOA</sourceid><recordid>eNptUsFu1DAQjRCIlsIfILDEZXtIGDtxHF8qlWVbKkXqBc6W40zSLE4cnATE3-Nl06pFnMYzfvNm5ulF0VsKCU0F_bh3ix-0TUY3YAK0AJHRZ9EplSmLcwbp80fvk-jVNO0BeFrk-cvohBUCskyK02h_jQPOnSG9HsduaIlryHyHpLz9tPtMyt3lFaFks7VlSc9JG7BkdkQTykSSx98r4rHt3EC6gfzSM_oebcg22272i7XLRKwe9BximZy_jl402k74Zo1n0ber3dftl7i8vb7ZXpax4SyfY65BV1QbiaIROS-kRMzqWnNRcA6GQZNJUxgEYGhSBlLnRQ6GYhNyzpv0LHp_5B2tm9Qq06SopJLTrKAQEDdHRO30Xo2-67X_rZzu1N-C863SPohiUSEgl2ESygYyAFM0VdiuPigpRG6qwHWxTluqHmuDw-y1fUL69Gfo7lTrfqpwjKQ5DwSblcC7HwtOs-q7yaANyqFbDnszkQIrWBqgH_6B_v-67Igy3k2Tx-ZhGQrqYJ37LnWwjlqtE9rePT7koeneK-kfE3u-bA</recordid><startdate>20170713</startdate><enddate>20170713</enddate><creator>Wei, Chunhua</creator><creator>Chen, Xiner</creator><creator>Wang, Zhongyuan</creator><creator>Liu, Qiyan</creator><creator>Li, Hao</creator><creator>Zhang, Yong</creator><creator>Ma, Jianxiang</creator><creator>Yang, Jianqiang</creator><creator>Zhang, Xian</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</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>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0001-9254-0730</orcidid></search><sort><creationdate>20170713</creationdate><title>Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.)</title><author>Wei, Chunhua ; Chen, Xiner ; Wang, Zhongyuan ; Liu, Qiyan ; Li, Hao ; Zhang, Yong ; Ma, Jianxiang ; Yang, Jianqiang ; Zhang, Xian</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-5a0ab1ac9e7f765899ee4dda578550c20f49c8ce002ec3209a6860c1ef2ec55f3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>Agricultural production</topic><topic>Bioinformatics</topic><topic>Biology and Life Sciences</topic><topic>Chromosome Mapping - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>DOAJ Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Wei, Chunhua</au><au>Chen, Xiner</au><au>Wang, Zhongyuan</au><au>Liu, Qiyan</au><au>Li, Hao</au><au>Zhang, Yong</au><au>Ma, Jianxiang</au><au>Yang, Jianqiang</au><au>Zhang, Xian</au><au>Candela, Hector</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.)</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2017-07-13</date><risdate>2017</risdate><volume>12</volume><issue>7</issue><spage>e0180741</spage><epage>e0180741</epage><pages>e0180741-e0180741</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The lobed leaf character is a unique morphologic trait in crops, featuring many potential advantages for agricultural productivity. Although the majority of watermelon varieties feature lobed leaves, the genetic factors responsible for lobed leaf formation remain elusive. The F2:3 leaf shape segregating population offers the opportunity to study the underlying mechanism of lobed leaf formation in watermelon. Genetic analysis revealed that a single dominant allele (designated ClLL1) controlled the lobed leaf trait. A large-sized F3:4 population derived from F2:3 individuals was used to map ClLL1. A total of 5,966 reliable SNPs and indels were identified genome-wide via a combination of BSA and RNA-seq. Using the validated SNP and indel markers, the location of ClLL1 was narrowed down to a 127.6-kb region between markers W08314 and W07061, containing 23 putative ORFs. Expression analysis via qRT-PCR revealed differential expression patterns (fold-changes above 2-fold or below 0.5-fold) of three ORFs (ORF3, ORF11, and ORF18) between lobed and non-lobed leaf plants. Based on gene annotation and expression analysis, ORF18 (encoding an uncharacterized protein) and ORF22 (encoding a homeobox-leucine zipper-like protein) were considered as most likely candidate genes. Furthermore, sequence analysis revealed no polymorphisms in cDNA sequences of ORF18; however, two notable deletions were identified in ORF22. This study is the first report to map a leaf shape gene in watermelon and will facilitate cloning and functional characterization of ClLL1 in future studies.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>28704497</pmid><doi>10.1371/journal.pone.0180741</doi><orcidid>https://orcid.org/0000-0001-9254-0730</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Agricultural production Bioinformatics Biology and Life Sciences Chromosome Mapping - methods Chromosomes, Plant - genetics Citrullus - anatomy & histology Citrullus - genetics Cloning Gene expression Gene Expression Regulation, Plant Gene mapping Gene sequencing Genetic analysis Genetic factors Genetic Linkage Genomes Genomics Homeobox Horticulture Leaves Leucine Leucine zipper proteins Markers Phenotype Plant Leaves - anatomy & histology Plant Leaves - genetics Plant Proteins - genetics Plants Polymerase chain reaction Polymorphism, Single Nucleotide Population Quantitative Trait Loci Research and Analysis Methods Ribonucleic acid RNA Seeds Sequence Analysis, RNA Single-nucleotide polymorphism Transcription factors |
| title | Genetic mapping of the LOBED LEAF 1 (ClLL1) gene to a 127.6-kb region in watermelon (Citrullus lanatus L.) |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2024-12-19T12%3A02%3A36IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genetic%20mapping%20of%20the%20LOBED%20LEAF%201%20(ClLL1)%20gene%20to%20a%20127.6-kb%20region%20in%20watermelon%20(Citrullus%20lanatus%20L.)&rft.jtitle=PloS%20one&rft.au=Wei,%20Chunhua&rft.date=2017-07-13&rft.volume=12&rft.issue=7&rft.spage=e0180741&rft.epage=e0180741&rft.pages=e0180741-e0180741&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0180741&rft_dat=%3Cproquest_plos_%3E1919514810%3C/proquest_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1919514810&rft_id=info:pmid/28704497&rft_doaj_id=oai_doaj_org_article_e0e5902ee9f0400c8fbab1d0538776cb&rfr_iscdi=true |