Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation
Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources...
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| description | Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance. |
| doi_str_mv | 10.1371/journal.pone.0235089 |
| format | Article |
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The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0235089</identifier><identifier>PMID: 32673346</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural production ; Agronomy ; Analysis ; Animals ; Biology and Life Sciences ; Biomass ; Breeding ; Computer and Information Sciences ; Cultivars ; Disease Resistance - genetics ; Diseases and pests ; Gene polymorphism ; Genes, Plant ; Genetic aspects ; Genetic Markers ; Genetics ; Genome, Plant ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genotypes ; Glycine max - genetics ; Glycine max - parasitology ; Horticulture ; Infestation ; Markers ; Model accuracy ; Nematode plant diseases ; Nematodes ; Nucleotides ; Pathogens ; Pest resistance ; Phenotypes ; Plant breeding ; Plant Diseases - genetics ; Plant hardiness ; Plant introductions ; Polymorphism ; Polymorphism, Single Nucleotide ; Population number ; Proteins ; Reduction ; Secernentea Infections - prevention & control ; Seeds ; Single-nucleotide polymorphism ; Soils ; Soybeans ; Tylenchoidea - pathogenicity ; Virulence</subject><ispartof>PloS one, 2020-07, Vol.15 (7), p.e0235089-e0235089</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Ravelombola 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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This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance.</description><subject>Agricultural production</subject><subject>Agronomy</subject><subject>Analysis</subject><subject>Animals</subject><subject>Biology and Life Sciences</subject><subject>Biomass</subject><subject>Breeding</subject><subject>Computer and Information Sciences</subject><subject>Cultivars</subject><subject>Disease Resistance - genetics</subject><subject>Diseases and pests</subject><subject>Gene polymorphism</subject><subject>Genes, Plant</subject><subject>Genetic aspects</subject><subject>Genetic Markers</subject><subject>Genetics</subject><subject>Genome, Plant</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genotypes</subject><subject>Glycine max - genetics</subject><subject>Glycine max - parasitology</subject><subject>Horticulture</subject><subject>Infestation</subject><subject>Markers</subject><subject>Model accuracy</subject><subject>Nematode plant diseases</subject><subject>Nematodes</subject><subject>Nucleotides</subject><subject>Pathogens</subject><subject>Pest resistance</subject><subject>Phenotypes</subject><subject>Plant breeding</subject><subject>Plant Diseases - 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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>Ravelombola, Waltram Second</au><au>Qin, Jun</au><au>Shi, Ainong</au><au>Nice, Liana</au><au>Bao, Yong</au><au>Lorenz, Aaron</au><au>Orf, James H</au><au>Young, Nevin D</au><au>Chen, Senyu</au><au>Rajcan, Istvan</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-07-16</date><risdate>2020</risdate><volume>15</volume><issue>7</issue><spage>e0235089</spage><epage>e0235089</epage><pages>e0235089-e0235089</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>Soybean cyst nematode (SCN), Heterodera glycines Ichinohe, is one of the most devastating pathogens affecting soybean production in the U.S. and worldwide. The use of SCN-resistant soybean cultivars is one of the most affordable strategies to cope with SCN infestation. Because of the limited sources of SCN resistance and changes in SCN virulence phenotypes, host resistance in current cultivars has increasingly been overcome by the pathogen. Host tolerance has been recognized as an additional tool to manage the SCN. The objectives of this study were to conduct a genome-wide association study (GWAS), to identify single nucleotide polymorphism (SNP) markers, and to perform a genomic selection (GS) study for SCN tolerance in soybean based on reduction in biomass. A total of 234 soybean genotypes (lines) were evaluated for their tolerance to SCN in greenhouse using four replicates. The tolerance index (TI = 100 × Biomass of a line in SCN infested / Biomass of the line without SCN) was used as phenotypic data of SCN tolerance. GWAS was conducted using a total of 3,782 high quality SNPs. GS was performed based upon the whole set of SNPs and the GWAS-derived SNPs, respectively. Results showed that (1) a large variation in soybean TI to SCN infection among the soybean genotypes was identified; (2) a total of 35, 21, and 6 SNPs were found to be associated with SCN tolerance using the models SMR, GLM (PCA), and MLM (PCA+K) with 6 SNPs overlapping between models; (3) GS accuracy was SNP set-, model-, and training population size-dependent; and (4) genes around Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, Glyma.15G107200, and Glyma.19G121200.1 (Table 4). Glyma.06G134900, Glyma.15G097500.1, Glyma.15G100900.3, Glyma.15G105400, and Glyma.19G121200.1 are best candidates. To the best of our knowledge, this is the first report highlighting SNP markers associated with tolerance index based on biomass reduction under SCN infestation in soybean. This research opens a new approach to use SCN tolerance in soybean breeding and the SNP markers will provide a tool for breeders to select for SCN tolerance.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>32673346</pmid><doi>10.1371/journal.pone.0235089</doi><tpages>e0235089</tpages><orcidid>https://orcid.org/0000-0002-1066-7920</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2020-07, Vol.15 (7), p.e0235089-e0235089 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2424386578 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Public Library of Science (PLoS); PubMed Central; Free Full-Text Journals in Chemistry |
| subjects | Agricultural production Agronomy Analysis Animals Biology and Life Sciences Biomass Breeding Computer and Information Sciences Cultivars Disease Resistance - genetics Diseases and pests Gene polymorphism Genes, Plant Genetic aspects Genetic Markers Genetics Genome, Plant Genome-wide association studies Genome-Wide Association Study Genomes Genotypes Glycine max - genetics Glycine max - parasitology Horticulture Infestation Markers Model accuracy Nematode plant diseases Nematodes Nucleotides Pathogens Pest resistance Phenotypes Plant breeding Plant Diseases - genetics Plant hardiness Plant introductions Polymorphism Polymorphism, Single Nucleotide Population number Proteins Reduction Secernentea Infections - prevention & control Seeds Single-nucleotide polymorphism Soils Soybeans Tylenchoidea - pathogenicity Virulence |
| title | Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation |
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