Association mapping reveals genomic regions associated with bienniality and resistance to biotic stresses in arabica coffee
The bienniality of production and the incidence of pests and diseases, such as coffee leaf miner and coffee leaf rust, stands out among the factors that limit coffee crop yield. Obtaining cultivars with greater stability in production and resistance to these biotic agents are among the main objectiv...
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| Veröffentlicht in: | Euphytica 2021-10, Vol.217 (10), Article 190 |
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| creator | Nonato, Juliana Vieira Almeida Carvalho, Humberto Fanelli Borges, Karina Lima Reis Padilha, Lilian Maluf, Mirian Perez Fritsche-Neto, Roberto Guerreiro Filho, Oliveiro |
| description | The bienniality of production and the incidence of pests and diseases, such as coffee leaf miner and coffee leaf rust, stands out among the factors that limit coffee crop yield. Obtaining cultivars with greater stability in production and resistance to these biotic agents are among the main objectives of coffee breeding programs. In this way, biotechnological tools such as Genomic Wide Association Studies (GWAS) can increase these programs' efficacy since they allow the identification of molecular markers significantly associated with phenotypes of interest. In this context, the aim here is to identify genomic regions associated with yield, bienniality, and resistance to coffee leaf miner and coffee leaf rust in arabica coffee progenies
.
Thus, a population (n = 597) was evaluated for resistance to biotic stresses and for the eight designed scenarios to study yield and bienniality. A matrix of 4,666 SNPs (Single Nucleotide Polymorphism) was built through Genotyping by Sequencing (GBS). After the genomic association analyses, we identified 12 potential SNPs markers associated with resistance to coffee leaf miner and coffee leaf rust, 32 associated with the eight designed scenarios to study yield and bienniality. Of the 44 SNPs significantly associated with this study's traits, 36 were noted in genomic regions responsible for biological processes related to plant response to biotic and abiotic stresses. In addition, four markers were coincident with yield and traits related to coffee leaf rust resistance. The genomic regions identified in this study can be incorporated into the coffee breeding program, through assisted selection, leading to more efficient breeding strategies in coffee. |
| doi_str_mv | 10.1007/s10681-021-02922-9 |
| format | Article |
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.
Thus, a population (n = 597) was evaluated for resistance to biotic stresses and for the eight designed scenarios to study yield and bienniality. A matrix of 4,666 SNPs (Single Nucleotide Polymorphism) was built through Genotyping by Sequencing (GBS). After the genomic association analyses, we identified 12 potential SNPs markers associated with resistance to coffee leaf miner and coffee leaf rust, 32 associated with the eight designed scenarios to study yield and bienniality. Of the 44 SNPs significantly associated with this study's traits, 36 were noted in genomic regions responsible for biological processes related to plant response to biotic and abiotic stresses. In addition, four markers were coincident with yield and traits related to coffee leaf rust resistance. The genomic regions identified in this study can be incorporated into the coffee breeding program, through assisted selection, leading to more efficient breeding strategies in coffee.</description><identifier>ISSN: 0014-2336</identifier><identifier>EISSN: 1573-5060</identifier><identifier>DOI: 10.1007/s10681-021-02922-9</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Analysis ; Biological activity ; Biomedical and Life Sciences ; Biotechnology ; Coffee ; Crop yield ; Cultivars ; Gene mapping ; Genomics ; Genotyping ; Leaf rust ; Leaves ; Life Sciences ; Markers ; Nucleotides ; Pest resistance ; Pests ; Phenotypes ; Plant breeding ; Plant Genetics and Genomics ; Plant Pathology ; Plant Physiology ; Plant Sciences ; Polymorphism ; Single nucleotide polymorphisms ; Single-nucleotide polymorphism ; Stresses</subject><ispartof>Euphytica, 2021-10, Vol.217 (10), Article 190</ispartof><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021</rights><rights>COPYRIGHT 2021 Springer</rights><rights>The Author(s), under exclusive licence to Springer Nature B.V. 2021.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c358t-2fcad937273db50b365a5d46db6b3561c5b96a5e87e0d28babfe4a6d75cbf5313</citedby><cites>FETCH-LOGICAL-c358t-2fcad937273db50b365a5d46db6b3561c5b96a5e87e0d28babfe4a6d75cbf5313</cites><orcidid>0000-0002-9596-9388 ; 0000-0003-4310-0047 ; 0000-0002-2204-6793 ; 0000-0003-3358-2468 ; 0000-0003-4448-4652 ; 0000-0003-0745-7583 ; 0000-0002-8228-2886</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/s10681-021-02922-9$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10681-021-02922-9$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,776,780,27901,27902,41464,42533,51294</link.rule.ids></links><search><creatorcontrib>Nonato, Juliana Vieira Almeida</creatorcontrib><creatorcontrib>Carvalho, Humberto Fanelli</creatorcontrib><creatorcontrib>Borges, Karina Lima Reis</creatorcontrib><creatorcontrib>Padilha, Lilian</creatorcontrib><creatorcontrib>Maluf, Mirian Perez</creatorcontrib><creatorcontrib>Fritsche-Neto, Roberto</creatorcontrib><creatorcontrib>Guerreiro Filho, Oliveiro</creatorcontrib><title>Association mapping reveals genomic regions associated with bienniality and resistance to biotic stresses in arabica coffee</title><title>Euphytica</title><addtitle>Euphytica</addtitle><description>The bienniality of production and the incidence of pests and diseases, such as coffee leaf miner and coffee leaf rust, stands out among the factors that limit coffee crop yield. Obtaining cultivars with greater stability in production and resistance to these biotic agents are among the main objectives of coffee breeding programs. In this way, biotechnological tools such as Genomic Wide Association Studies (GWAS) can increase these programs' efficacy since they allow the identification of molecular markers significantly associated with phenotypes of interest. In this context, the aim here is to identify genomic regions associated with yield, bienniality, and resistance to coffee leaf miner and coffee leaf rust in arabica coffee progenies
.
Thus, a population (n = 597) was evaluated for resistance to biotic stresses and for the eight designed scenarios to study yield and bienniality. A matrix of 4,666 SNPs (Single Nucleotide Polymorphism) was built through Genotyping by Sequencing (GBS). After the genomic association analyses, we identified 12 potential SNPs markers associated with resistance to coffee leaf miner and coffee leaf rust, 32 associated with the eight designed scenarios to study yield and bienniality. Of the 44 SNPs significantly associated with this study's traits, 36 were noted in genomic regions responsible for biological processes related to plant response to biotic and abiotic stresses. In addition, four markers were coincident with yield and traits related to coffee leaf rust resistance. The genomic regions identified in this study can be incorporated into the coffee breeding program, through assisted selection, leading to more efficient breeding strategies in coffee.</description><subject>Analysis</subject><subject>Biological activity</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Coffee</subject><subject>Crop yield</subject><subject>Cultivars</subject><subject>Gene mapping</subject><subject>Genomics</subject><subject>Genotyping</subject><subject>Leaf rust</subject><subject>Leaves</subject><subject>Life Sciences</subject><subject>Markers</subject><subject>Nucleotides</subject><subject>Pest resistance</subject><subject>Pests</subject><subject>Phenotypes</subject><subject>Plant breeding</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Pathology</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Polymorphism</subject><subject>Single nucleotide polymorphisms</subject><subject>Single-nucleotide polymorphism</subject><subject>Stresses</subject><issn>0014-2336</issn><issn>1573-5060</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>BENPR</sourceid><recordid>eNp9kU1rVTEQhoMoeK3-AVcB16fm4yS5Z3kpaoVCN3UdJsnkmHJvck1SpfjnTT0FdxKGkJn3mQnzEvKes0vOmPnYONN7PjHxFIsQ0_KC7LgyclJMs5dkxxifJyGlfk3etHbPGFuMYjvy-9Ba8Ql6Kpme4HxOeaUVfyIcG10xl1Py472OcqPwrMVAf6X-nbqEOSc4pv5IIYeha6l1yB5pL6Na-oBbH-mGjaZMoYJLHqgvMSK-Ja_iGIPvnu8L8u3zp7ur6-nm9svXq8PN5KXa90lED2GRRhgZnGJOagUqzDo47aTS3Cu3aFC4N8iC2DtwEWfQwSjvopJcXpAPW99zLT8esHV7Xx5qHiOtUEZpPTM5D9XlplrhiDblWHoFP07AsYOSMaaRPxg-MyOkEgMQG-Braa1itOeaTlAfLWf2yRW7uWKHK_avK3YZkNygNsR5xfrvL_-h_gDq_JJT</recordid><startdate>20211001</startdate><enddate>20211001</enddate><creator>Nonato, Juliana Vieira Almeida</creator><creator>Carvalho, Humberto Fanelli</creator><creator>Borges, Karina Lima Reis</creator><creator>Padilha, Lilian</creator><creator>Maluf, Mirian Perez</creator><creator>Fritsche-Neto, Roberto</creator><creator>Guerreiro Filho, Oliveiro</creator><general>Springer Netherlands</general><general>Springer</general><general>Springer Nature B.V</general><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7SN</scope><scope>7SS</scope><scope>7T7</scope><scope>7TM</scope><scope>7X2</scope><scope>7XB</scope><scope>88I</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>M0K</scope><scope>M2P</scope><scope>M7N</scope><scope>P64</scope><scope>PATMY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PYCSY</scope><scope>Q9U</scope><scope>RC3</scope><orcidid>https://orcid.org/0000-0002-9596-9388</orcidid><orcidid>https://orcid.org/0000-0003-4310-0047</orcidid><orcidid>https://orcid.org/0000-0002-2204-6793</orcidid><orcidid>https://orcid.org/0000-0003-3358-2468</orcidid><orcidid>https://orcid.org/0000-0003-4448-4652</orcidid><orcidid>https://orcid.org/0000-0003-0745-7583</orcidid><orcidid>https://orcid.org/0000-0002-8228-2886</orcidid></search><sort><creationdate>20211001</creationdate><title>Association mapping reveals genomic regions associated with bienniality and resistance to biotic stresses in arabica coffee</title><author>Nonato, Juliana Vieira Almeida ; Carvalho, Humberto Fanelli ; Borges, Karina Lima Reis ; Padilha, Lilian ; Maluf, Mirian Perez ; Fritsche-Neto, Roberto ; Guerreiro Filho, Oliveiro</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c358t-2fcad937273db50b365a5d46db6b3561c5b96a5e87e0d28babfe4a6d75cbf5313</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Analysis</topic><topic>Biological activity</topic><topic>Biomedical and Life Sciences</topic><topic>Biotechnology</topic><topic>Coffee</topic><topic>Crop yield</topic><topic>Cultivars</topic><topic>Gene mapping</topic><topic>Genomics</topic><topic>Genotyping</topic><topic>Leaf rust</topic><topic>Leaves</topic><topic>Life Sciences</topic><topic>Markers</topic><topic>Nucleotides</topic><topic>Pest resistance</topic><topic>Pests</topic><topic>Phenotypes</topic><topic>Plant breeding</topic><topic>Plant Genetics and Genomics</topic><topic>Plant Pathology</topic><topic>Plant Physiology</topic><topic>Plant Sciences</topic><topic>Polymorphism</topic><topic>Single nucleotide polymorphisms</topic><topic>Single-nucleotide polymorphism</topic><topic>Stresses</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Nonato, Juliana Vieira Almeida</creatorcontrib><creatorcontrib>Carvalho, Humberto Fanelli</creatorcontrib><creatorcontrib>Borges, Karina Lima Reis</creatorcontrib><creatorcontrib>Padilha, Lilian</creatorcontrib><creatorcontrib>Maluf, Mirian Perez</creatorcontrib><creatorcontrib>Fritsche-Neto, Roberto</creatorcontrib><creatorcontrib>Guerreiro Filho, Oliveiro</creatorcontrib><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Ecology Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Industrial and Applied Microbiology Abstracts (Microbiology A)</collection><collection>Nucleic Acids Abstracts</collection><collection>Agricultural Science Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Science Database (Alumni Edition)</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</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>Agricultural & Environmental Science Collection</collection><collection>ProQuest Central Essentials</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>Environmental Sciences and Pollution Management</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>Agricultural Science Database</collection><collection>Science Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Environmental Science 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>Environmental Science Collection</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><jtitle>Euphytica</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nonato, Juliana Vieira Almeida</au><au>Carvalho, Humberto Fanelli</au><au>Borges, Karina Lima Reis</au><au>Padilha, Lilian</au><au>Maluf, Mirian Perez</au><au>Fritsche-Neto, Roberto</au><au>Guerreiro Filho, Oliveiro</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Association mapping reveals genomic regions associated with bienniality and resistance to biotic stresses in arabica coffee</atitle><jtitle>Euphytica</jtitle><stitle>Euphytica</stitle><date>2021-10-01</date><risdate>2021</risdate><volume>217</volume><issue>10</issue><artnum>190</artnum><issn>0014-2336</issn><eissn>1573-5060</eissn><abstract>The bienniality of production and the incidence of pests and diseases, such as coffee leaf miner and coffee leaf rust, stands out among the factors that limit coffee crop yield. Obtaining cultivars with greater stability in production and resistance to these biotic agents are among the main objectives of coffee breeding programs. In this way, biotechnological tools such as Genomic Wide Association Studies (GWAS) can increase these programs' efficacy since they allow the identification of molecular markers significantly associated with phenotypes of interest. In this context, the aim here is to identify genomic regions associated with yield, bienniality, and resistance to coffee leaf miner and coffee leaf rust in arabica coffee progenies
.
Thus, a population (n = 597) was evaluated for resistance to biotic stresses and for the eight designed scenarios to study yield and bienniality. A matrix of 4,666 SNPs (Single Nucleotide Polymorphism) was built through Genotyping by Sequencing (GBS). After the genomic association analyses, we identified 12 potential SNPs markers associated with resistance to coffee leaf miner and coffee leaf rust, 32 associated with the eight designed scenarios to study yield and bienniality. Of the 44 SNPs significantly associated with this study's traits, 36 were noted in genomic regions responsible for biological processes related to plant response to biotic and abiotic stresses. In addition, four markers were coincident with yield and traits related to coffee leaf rust resistance. The genomic regions identified in this study can be incorporated into the coffee breeding program, through assisted selection, leading to more efficient breeding strategies in coffee.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10681-021-02922-9</doi><orcidid>https://orcid.org/0000-0002-9596-9388</orcidid><orcidid>https://orcid.org/0000-0003-4310-0047</orcidid><orcidid>https://orcid.org/0000-0002-2204-6793</orcidid><orcidid>https://orcid.org/0000-0003-3358-2468</orcidid><orcidid>https://orcid.org/0000-0003-4448-4652</orcidid><orcidid>https://orcid.org/0000-0003-0745-7583</orcidid><orcidid>https://orcid.org/0000-0002-8228-2886</orcidid></addata></record> |
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| subjects | Analysis Biological activity Biomedical and Life Sciences Biotechnology Coffee Crop yield Cultivars Gene mapping Genomics Genotyping Leaf rust Leaves Life Sciences Markers Nucleotides Pest resistance Pests Phenotypes Plant breeding Plant Genetics and Genomics Plant Pathology Plant Physiology Plant Sciences Polymorphism Single nucleotide polymorphisms Single-nucleotide polymorphism Stresses |
| title | Association mapping reveals genomic regions associated with bienniality and resistance to biotic stresses in arabica coffee |
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