Genome-wide association study of cassava starch paste properties
An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was pe...
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| description | An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 |
| doi_str_mv | 10.1371/journal.pone.0262888 |
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This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0262888</identifier><identifier>PMID: 35061844</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agricultural research ; Biology and Life Sciences ; Cassava ; Chemical properties ; Chromosome 17 ; Chromosome 18 ; Chromosomes ; Chromosomes, Plant - genetics ; Chromosomes, Plant - metabolism ; Cloning ; Cold ; Dolichol ; Food ; Food science ; Gene regulation ; Genetic aspects ; Genetic control ; Genetic diversity ; Genome-wide association studies ; Genome-Wide Association Study ; Genomes ; Genomics ; Genotype ; Germplasm ; Glycosidases ; Glycosyl hydrolase ; Heritability ; Hydrolase ; Identification and classification ; Linkage Disequilibrium ; Manihot - genetics ; Manihot - metabolism ; Mannose ; Nucleotides ; Physical Sciences ; Physiological aspects ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; Single-nucleotide polymorphism ; Starch ; Starch - biosynthesis ; Starch - genetics ; Starches ; Transcription ; Viscosity</subject><ispartof>PloS one, 2022-01, Vol.17 (1), p.e0262888-e0262888</ispartof><rights>COPYRIGHT 2022 Public Library of Science</rights><rights>2022 Santos 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. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2022 Santos et al 2022 Santos et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c758t-d73aad75e58b70f37eff80d22792da13bca4bd545c3e01ee634478336cff58433</citedby><cites>FETCH-LOGICAL-c758t-d73aad75e58b70f37eff80d22792da13bca4bd545c3e01ee634478336cff58433</cites><orcidid>0000-0001-8992-7459 ; 0000-0003-0491-8380</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782291/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8782291/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79342,79343</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/35061844$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Santos, Cristiano Silva Dos</creatorcontrib><creatorcontrib>Sousa, Massaine Bandeira</creatorcontrib><creatorcontrib>Brito, Ana Carla</creatorcontrib><creatorcontrib>de Oliveira, Luciana Alves</creatorcontrib><creatorcontrib>Carvalho, Carlos Wanderlei Piler</creatorcontrib><creatorcontrib>de Oliveira, Eder Jorge</creatorcontrib><title>Genome-wide association study of cassava starch paste properties</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>An understanding of cassava starch paste properties (CSPP) can contribute to the selection of clones with differentiated starches. This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.</description><subject>Agricultural research</subject><subject>Biology and Life Sciences</subject><subject>Cassava</subject><subject>Chemical properties</subject><subject>Chromosome 17</subject><subject>Chromosome 18</subject><subject>Chromosomes</subject><subject>Chromosomes, Plant - genetics</subject><subject>Chromosomes, Plant - metabolism</subject><subject>Cloning</subject><subject>Cold</subject><subject>Dolichol</subject><subject>Food</subject><subject>Food science</subject><subject>Gene regulation</subject><subject>Genetic aspects</subject><subject>Genetic control</subject><subject>Genetic diversity</subject><subject>Genome-wide association studies</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotype</subject><subject>Germplasm</subject><subject>Glycosidases</subject><subject>Glycosyl hydrolase</subject><subject>Heritability</subject><subject>Hydrolase</subject><subject>Identification and classification</subject><subject>Linkage Disequilibrium</subject><subject>Manihot - genetics</subject><subject>Manihot - metabolism</subject><subject>Mannose</subject><subject>Nucleotides</subject><subject>Physical Sciences</subject><subject>Physiological aspects</subject><subject>Polymorphism, Single Nucleotide</subject><subject>Quantitative Trait Loci</subject><subject>Single-nucleotide polymorphism</subject><subject>Starch</subject><subject>Starch - biosynthesis</subject><subject>Starch - genetics</subject><subject>Starches</subject><subject>Transcription</subject><subject>Viscosity</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNkl1r1EAUhoMotq7-A9GAIHqx62S-MrkRS9G6UCj4dTucnTmzOyWbSTNJtf_e2W5aNtILmcCEk-e85yNvlr0syKJgZfHhMgxdA_WiDQ0uCJVUKfUoOy4qRueSEvb44P0oexbjJSGCKSmfZkdMEFkozo-zT2fYhC3Of3uLOcQYjIfehyaP_WBv8uByk6JwDSkAndnkLcQe87YLLXa9x_g8e-KgjvhivGfZzy-ff5x-nZ9fnC1PT87nphSqn9uSAdhSoFCrkjhWonOKWErLiloo2MoAX1nBhWFICkTJOC8VY9I4JxRnbJa93uu2dYh6HD7qNHdRpYfzRCz3hA1wqdvOb6G70QG8vg2Ebq0htWxq1JJbJ1GY0laOlwhpdVIwkJQyBc6IpPVxrDastmgNNn0H9UR0-qXxG70O11qVitKqSALvRoEuXA0Ye7310WBdQ4NhuO2bUlWRVHGWvfkHfXi6kVpDGsA3LqS6ZieqT2RFSCWU3FGLB6h0LG69SU5xPsUnCe8nCYnp8U-_hiFGvfz-7f_Zi19T9u0Bu0Go-00M9bDzVpyCfA-aLsTYobtfckH0zuh329A7o-vR6Cnt1eEPuk-6czb7C1j_9_A</recordid><startdate>20220121</startdate><enddate>20220121</enddate><creator>Santos, Cristiano Silva Dos</creator><creator>Sousa, Massaine Bandeira</creator><creator>Brito, Ana Carla</creator><creator>de Oliveira, Luciana Alves</creator><creator>Carvalho, Carlos Wanderlei Piler</creator><creator>de Oliveira, Eder Jorge</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>IOV</scope><scope>ISR</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>AEUYN</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/0000-0001-8992-7459</orcidid><orcidid>https://orcid.org/0000-0003-0491-8380</orcidid></search><sort><creationdate>20220121</creationdate><title>Genome-wide association study of cassava starch paste properties</title><author>Santos, Cristiano Silva Dos ; Sousa, Massaine Bandeira ; Brito, Ana Carla ; de Oliveira, Luciana Alves ; Carvalho, Carlos Wanderlei Piler ; de Oliveira, Eder Jorge</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c758t-d73aad75e58b70f37eff80d22792da13bca4bd545c3e01ee634478336cff58433</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Agricultural research</topic><topic>Biology and Life Sciences</topic><topic>Cassava</topic><topic>Chemical properties</topic><topic>Chromosome 17</topic><topic>Chromosome 18</topic><topic>Chromosomes</topic><topic>Chromosomes, Plant - 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This study aimed to identify genomic regions associated with CSPP using different genome-wide association study (GWAS) methods (MLM, MLMM, and Farm-CPU). The GWAS was performed using 23,078 single-nucleotide polymorphisms (SNPs). The rapid viscoanalyzer (RVA) parameters were pasting temperature (PastTemp), peak viscosity (PeakVisc), hot-paste viscosity (Hot-PVisc), cool-paste viscosity (Cold-PVisc), final viscosity (FinalVis), breakdown (BreDow), and setback (Setback). Broad phenotypic and molecular diversity was identified based on the genomic kinship matrix. The broad-sense heritability estimates (h2) ranged from moderate to high magnitudes (0.66 to 0.76). The linkage disequilibrium (LD) declined to between 0.3 and 2.0 Mb (r2 <0.1) for most chromosomes, except chromosome 17, which exhibited an extensive LD. Thirteen SNPs were found to be significantly associated with CSPP, on chromosomes 3, 8, 17, and 18. Only the BreDow trait had no associated SNPs. The regional marker-trait associations on chromosome 18 indicate a LD block between 2907312 and 3567816 bp and that SNP S18_3081635 was associated with SetBack, FinalVis, and Cold-PVisc (all three GWAS methods) and with Hot-PVisc (MLM), indicating that this SNP can track these four traits simultaneously. The variance explained by the SNPs ranged from 0.13 to 0.18 for SetBack, FinalVis, and Cold-PVisc and from 0.06 to 0.09 for PeakVisc and Hot-PVisc. The results indicated additive effects of the genetic control of Cold-PVisc, FinalVis, Hot-PVisc, and SetBack, especially on the large LD block on chromosome 18. One transcript encoding the glycosyl hydrolase family 35 enzymes on chromosome 17 and one encoding the mannose-p-dolichol utilization defect 1 protein on chromosome 18 were the most likely candidate genes for the regulation of CSPP. These results underline the potential for the assisted selection of high-value starches to improve cassava root quality through breeding programs.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>35061844</pmid><doi>10.1371/journal.pone.0262888</doi><tpages>e0262888</tpages><orcidid>https://orcid.org/0000-0001-8992-7459</orcidid><orcidid>https://orcid.org/0000-0003-0491-8380</orcidid><oa>free_for_read</oa></addata></record> |
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| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2022-01, Vol.17 (1), p.e0262888-e0262888 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2621921944 |
| source | MEDLINE; DOAJ Directory of Open Access Journals; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; PubMed Central; Free Full-Text Journals in Chemistry; Public Library of Science (PLoS) |
| subjects | Agricultural research Biology and Life Sciences Cassava Chemical properties Chromosome 17 Chromosome 18 Chromosomes Chromosomes, Plant - genetics Chromosomes, Plant - metabolism Cloning Cold Dolichol Food Food science Gene regulation Genetic aspects Genetic control Genetic diversity Genome-wide association studies Genome-Wide Association Study Genomes Genomics Genotype Germplasm Glycosidases Glycosyl hydrolase Heritability Hydrolase Identification and classification Linkage Disequilibrium Manihot - genetics Manihot - metabolism Mannose Nucleotides Physical Sciences Physiological aspects Polymorphism, Single Nucleotide Quantitative Trait Loci Single-nucleotide polymorphism Starch Starch - biosynthesis Starch - genetics Starches Transcription Viscosity |
| title | Genome-wide association study of cassava starch paste properties |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-09T02%3A43%3A49IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Genome-wide%20association%20study%20of%20cassava%20starch%20paste%20properties&rft.jtitle=PloS%20one&rft.au=Santos,%20Cristiano%20Silva%20Dos&rft.date=2022-01-21&rft.volume=17&rft.issue=1&rft.spage=e0262888&rft.epage=e0262888&rft.pages=e0262888-e0262888&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0262888&rft_dat=%3Cgale_plos_%3EA690095864%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2621921944&rft_id=info:pmid/35061844&rft_galeid=A690095864&rft_doaj_id=oai_doaj_org_article_64df6e5c7d9f47ea888653a62238afc5&rfr_iscdi=true |