Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm
Development of apple ( Malus domestica ) cultivars resistant to fire blight, a devastating bacterial disease caused by Erwinia amylovora, is a priority for apple breeding programs. Towards this goal, the inactivation of members of the HIPM and DIPM gene families with a role in fire blight susceptibi...
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| Veröffentlicht in: | Scientific reports 2020-10, Vol.10 (1), p.16317-16317, Article 16317 |
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| creator | Tegtmeier, Richard Pompili, Valerio Singh, Jugpreet Micheletti, Diego Silva, Katchen Julliany Pereira Malnoy, Mickael Khan, Awais |
| description | Development of apple (
Malus domestica
) cultivars resistant to fire blight, a devastating bacterial disease caused by
Erwinia amylovora,
is a priority for apple breeding programs. Towards this goal, the inactivation of members of the
HIPM
and
DIPM
gene families with a role in fire blight susceptibility (
S
genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of
HIPM
and
DIPM
genes in
Malus
germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in
HIPM
and
DIPM
genes across 93
Malus
accessions. Thirty SNPs showed significant associations (
p
|
| doi_str_mv | 10.1038/s41598-020-73284-w |
| format | Article |
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Malus domestica
) cultivars resistant to fire blight, a devastating bacterial disease caused by
Erwinia amylovora,
is a priority for apple breeding programs. Towards this goal, the inactivation of members of the
HIPM
and
DIPM
gene families with a role in fire blight susceptibility (
S
genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of
HIPM
and
DIPM
genes in
Malus
germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in
HIPM
and
DIPM
genes across 93
Malus
accessions. Thirty SNPs showed significant associations (
p
< 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (
p
< 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight
S
genes in diverse apple accessions and identified candidate
HIPM
and
DIPM
alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.</description><identifier>ISSN: 2045-2322</identifier><identifier>EISSN: 2045-2322</identifier><identifier>DOI: 10.1038/s41598-020-73284-w</identifier><identifier>PMID: 33004843</identifier><language>eng</language><publisher>London: Nature Publishing Group UK</publisher><subject>631/208 ; 631/208/207 ; 631/208/2491 ; 631/208/480 ; 631/208/711 ; 631/208/721 ; 631/208/727 ; 631/208/8 ; 631/449/711 ; Apples ; Bacterial diseases ; Biotechnology ; Blight ; Chromosome Mapping - methods ; Cultivars ; Disease resistance ; Disease Resistance - genetics ; Erwinia amylovora ; Fruits ; Gene families ; Gene mapping ; Genes ; Genes, Plant - genetics ; Genetic diversity ; Genetic Predisposition to Disease - genetics ; Genetic Variation - genetics ; Genotyping Techniques ; Germplasm ; Humanities and Social Sciences ; Inactivation ; Malus - genetics ; Malus - immunology ; Malus - microbiology ; Malus domestica ; multidisciplinary ; Plant Breeding ; Plant Diseases - immunology ; Plant Diseases - microbiology ; Polymorphism, Single Nucleotide - genetics ; Science ; Science (multidisciplinary) ; Seed Bank ; Sequence Analysis, DNA ; Single-nucleotide polymorphism ; Susceptibility</subject><ispartof>Scientific reports, 2020-10, Vol.10 (1), p.16317-16317, Article 16317</ispartof><rights>The Author(s) 2020</rights><rights>The Author(s) 2020. This work is published under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c539t-f84599075dfd82813abb7e5f4fa1954bc62717de8526478659c90b7e8e3362ea3</citedby><cites>FETCH-LOGICAL-c539t-f84599075dfd82813abb7e5f4fa1954bc62717de8526478659c90b7e8e3362ea3</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/PMC7529791/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7529791/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,725,778,782,862,883,27911,27912,41107,42176,51563,53778,53780</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33004843$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Tegtmeier, Richard</creatorcontrib><creatorcontrib>Pompili, Valerio</creatorcontrib><creatorcontrib>Singh, Jugpreet</creatorcontrib><creatorcontrib>Micheletti, Diego</creatorcontrib><creatorcontrib>Silva, Katchen Julliany Pereira</creatorcontrib><creatorcontrib>Malnoy, Mickael</creatorcontrib><creatorcontrib>Khan, Awais</creatorcontrib><title>Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm</title><title>Scientific reports</title><addtitle>Sci Rep</addtitle><addtitle>Sci Rep</addtitle><description>Development of apple (
Malus domestica
) cultivars resistant to fire blight, a devastating bacterial disease caused by
Erwinia amylovora,
is a priority for apple breeding programs. Towards this goal, the inactivation of members of the
HIPM
and
DIPM
gene families with a role in fire blight susceptibility (
S
genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of
HIPM
and
DIPM
genes in
Malus
germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in
HIPM
and
DIPM
genes across 93
Malus
accessions. Thirty SNPs showed significant associations (
p
< 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (
p
< 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight
S
genes in diverse apple accessions and identified candidate
HIPM
and
DIPM
alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.</description><subject>631/208</subject><subject>631/208/207</subject><subject>631/208/2491</subject><subject>631/208/480</subject><subject>631/208/711</subject><subject>631/208/721</subject><subject>631/208/727</subject><subject>631/208/8</subject><subject>631/449/711</subject><subject>Apples</subject><subject>Bacterial diseases</subject><subject>Biotechnology</subject><subject>Blight</subject><subject>Chromosome Mapping - methods</subject><subject>Cultivars</subject><subject>Disease resistance</subject><subject>Disease Resistance - genetics</subject><subject>Erwinia amylovora</subject><subject>Fruits</subject><subject>Gene families</subject><subject>Gene mapping</subject><subject>Genes</subject><subject>Genes, Plant - genetics</subject><subject>Genetic diversity</subject><subject>Genetic Predisposition to Disease - genetics</subject><subject>Genetic Variation - genetics</subject><subject>Genotyping Techniques</subject><subject>Germplasm</subject><subject>Humanities and Social Sciences</subject><subject>Inactivation</subject><subject>Malus - genetics</subject><subject>Malus - immunology</subject><subject>Malus - microbiology</subject><subject>Malus domestica</subject><subject>multidisciplinary</subject><subject>Plant Breeding</subject><subject>Plant Diseases - immunology</subject><subject>Plant Diseases - microbiology</subject><subject>Polymorphism, Single Nucleotide - genetics</subject><subject>Science</subject><subject>Science (multidisciplinary)</subject><subject>Seed Bank</subject><subject>Sequence Analysis, DNA</subject><subject>Single-nucleotide polymorphism</subject><subject>Susceptibility</subject><issn>2045-2322</issn><issn>2045-2322</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>C6C</sourceid><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>eNp9Ustu1TAQtRCIVm1_gAWyxIZNwM_E3iChy6OVWsEC1paTOPdOlTjBdlr1A_rfdXJLaVnUG1ueM2fmzByE3lDygRKuPkZBpVYFYaSoOFOiuH6BDhkRsmCcsZeP3gfoJMZLko9kWlD9Gh1wTohQgh-i2431LbQ2Obx13uHBThP4LYbW-QQduLj8jwM0-MoGsAlGHzF4nHYOdxAcrnvY7hKOc2zclKCGHtLNShbx6dnPC5wL4C_rowljjGvmhe3nhTkMU2_jcIxedbaP7uT-PkK_v339tTktzn98P9t8Pi8ayXUqOiWk1qSSbdcqpii3dV052YnOUi1F3ZSsolXrlGSlqFQpdaNJRijHecmc5Ufo0553muvBtU3WGGxvpgCDDTdmtGCeRjzszHa8MlUeXaVpJnh_TxDGP7OLyQyQdfe99W6co2EijzWPtlyg7_6DXo5z8FleRimic3uKP48SWkhG6cLF9qh1gsF1Dy1TYhY7mL0dTLaDWe1grnPS28diH1L-Lj8D-B4Qc8jnZfyr_QztHWYIwXI</recordid><startdate>20201001</startdate><enddate>20201001</enddate><creator>Tegtmeier, Richard</creator><creator>Pompili, Valerio</creator><creator>Singh, Jugpreet</creator><creator>Micheletti, Diego</creator><creator>Silva, Katchen Julliany Pereira</creator><creator>Malnoy, Mickael</creator><creator>Khan, Awais</creator><general>Nature Publishing Group UK</general><general>Nature Publishing Group</general><scope>C6C</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>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</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>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>Q9U</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20201001</creationdate><title>Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm</title><author>Tegtmeier, Richard ; Pompili, Valerio ; Singh, Jugpreet ; Micheletti, Diego ; Silva, Katchen Julliany Pereira ; Malnoy, Mickael ; Khan, Awais</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c539t-f84599075dfd82813abb7e5f4fa1954bc62717de8526478659c90b7e8e3362ea3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>631/208</topic><topic>631/208/207</topic><topic>631/208/2491</topic><topic>631/208/480</topic><topic>631/208/711</topic><topic>631/208/721</topic><topic>631/208/727</topic><topic>631/208/8</topic><topic>631/449/711</topic><topic>Apples</topic><topic>Bacterial diseases</topic><topic>Biotechnology</topic><topic>Blight</topic><topic>Chromosome Mapping - methods</topic><topic>Cultivars</topic><topic>Disease resistance</topic><topic>Disease Resistance - genetics</topic><topic>Erwinia amylovora</topic><topic>Fruits</topic><topic>Gene families</topic><topic>Gene mapping</topic><topic>Genes</topic><topic>Genes, Plant - genetics</topic><topic>Genetic diversity</topic><topic>Genetic Predisposition to Disease - genetics</topic><topic>Genetic Variation - genetics</topic><topic>Genotyping Techniques</topic><topic>Germplasm</topic><topic>Humanities and Social Sciences</topic><topic>Inactivation</topic><topic>Malus - genetics</topic><topic>Malus - immunology</topic><topic>Malus - microbiology</topic><topic>Malus domestica</topic><topic>multidisciplinary</topic><topic>Plant Breeding</topic><topic>Plant Diseases - immunology</topic><topic>Plant Diseases - microbiology</topic><topic>Polymorphism, Single Nucleotide - genetics</topic><topic>Science</topic><topic>Science (multidisciplinary)</topic><topic>Seed Bank</topic><topic>Sequence Analysis, DNA</topic><topic>Single-nucleotide polymorphism</topic><topic>Susceptibility</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Tegtmeier, Richard</creatorcontrib><creatorcontrib>Pompili, Valerio</creatorcontrib><creatorcontrib>Singh, Jugpreet</creatorcontrib><creatorcontrib>Micheletti, Diego</creatorcontrib><creatorcontrib>Silva, Katchen Julliany Pereira</creatorcontrib><creatorcontrib>Malnoy, Mickael</creatorcontrib><creatorcontrib>Khan, Awais</creatorcontrib><collection>Springer Nature OA Free Journals</collection><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>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 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 One Sustainability</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 (ProQuest)</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</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>Publicly Available Content Database</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 Basic</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Scientific reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Tegtmeier, Richard</au><au>Pompili, Valerio</au><au>Singh, Jugpreet</au><au>Micheletti, Diego</au><au>Silva, Katchen Julliany Pereira</au><au>Malnoy, Mickael</au><au>Khan, Awais</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm</atitle><jtitle>Scientific reports</jtitle><stitle>Sci Rep</stitle><addtitle>Sci Rep</addtitle><date>2020-10-01</date><risdate>2020</risdate><volume>10</volume><issue>1</issue><spage>16317</spage><epage>16317</epage><pages>16317-16317</pages><artnum>16317</artnum><issn>2045-2322</issn><eissn>2045-2322</eissn><abstract>Development of apple (
Malus domestica
) cultivars resistant to fire blight, a devastating bacterial disease caused by
Erwinia amylovora,
is a priority for apple breeding programs. Towards this goal, the inactivation of members of the
HIPM
and
DIPM
gene families with a role in fire blight susceptibility (
S
genes) can help achieve sustainable tolerance. We have investigated the genomic diversity of
HIPM
and
DIPM
genes in
Malus
germplasm collections and used a candidate gene-based association mapping approach to identify SNPs (single nucleotide polymorphisms) with significant associations to fire blight susceptibility. A total of 87 unique SNP variants were identified in
HIPM
and
DIPM
genes across 93
Malus
accessions. Thirty SNPs showed significant associations (
p
< 0.05) with fire blight susceptibility traits, while two of these SNPs showed highly significant (
p
< 0.001) associations across two different years. This research has provided knowledge about genetic diversity in fire blight
S
genes in diverse apple accessions and identified candidate
HIPM
and
DIPM
alleles that could be used to develop apple cultivars with decreased fire blight susceptibility via marker-assisted breeding or biotechnological approaches.</abstract><cop>London</cop><pub>Nature Publishing Group UK</pub><pmid>33004843</pmid><doi>10.1038/s41598-020-73284-w</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record> |
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| issn | 2045-2322 2045-2322 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_7529791 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Springer Nature OA Free Journals; Nature Free; PubMed Central; Alma/SFX Local Collection; Free Full-Text Journals in Chemistry |
| subjects | 631/208 631/208/207 631/208/2491 631/208/480 631/208/711 631/208/721 631/208/727 631/208/8 631/449/711 Apples Bacterial diseases Biotechnology Blight Chromosome Mapping - methods Cultivars Disease resistance Disease Resistance - genetics Erwinia amylovora Fruits Gene families Gene mapping Genes Genes, Plant - genetics Genetic diversity Genetic Predisposition to Disease - genetics Genetic Variation - genetics Genotyping Techniques Germplasm Humanities and Social Sciences Inactivation Malus - genetics Malus - immunology Malus - microbiology Malus domestica multidisciplinary Plant Breeding Plant Diseases - immunology Plant Diseases - microbiology Polymorphism, Single Nucleotide - genetics Science Science (multidisciplinary) Seed Bank Sequence Analysis, DNA Single-nucleotide polymorphism Susceptibility |
| title | Candidate gene mapping identifies genomic variations in the fire blight susceptibility genes HIPM and DIPM across the Malus germplasm |
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