Folate profile diversity and associated SNPs using genome wide association study in pea
Folates are important metabolic cofactors essential for human growth and development. Eighty-five accessions from a pea genome wide association study (GWAS) panel were evaluated for folate profile using ultra-performance liquid chromatography coupled with mass spectrometry. A GWAS was conducted to i...
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| Veröffentlicht in: | Euphytica 2020-02, Vol.216 (2), Article 18 |
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| description | Folates are important metabolic cofactors essential for human growth and development. Eighty-five accessions from a pea genome wide association study (GWAS) panel were evaluated for folate profile using ultra-performance liquid chromatography coupled with mass spectrometry. A GWAS was conducted to identify SNP markers associated with the folate profile of pea. Five folates were quantified and the sum of folates ranged from 14 to 55 µg/100 g dry weight. Significant differences (
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| doi_str_mv | 10.1007/s10681-020-2553-8 |
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| fullrecord | <record><control><sourceid>gale_cross</sourceid><recordid>TN_cdi_gale_infotracacademiconefile_A714072561</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><galeid>A714072561</galeid><sourcerecordid>A714072561</sourcerecordid><originalsourceid>FETCH-LOGICAL-c383t-18c70bc0a53de5089e797909e389eba41df2689ea08641aaeeed384a7668e7563</originalsourceid><addsrcrecordid>eNqNkV9rFDEUxYMouFY_gG8BH2Xam2TyZx7LYqtQqqDiY8gmd5aU3WRNZiz77c060iIoSB5y4J5f7s09hLxmcM4A9EVloAzrgEPHpRSdeUJWTGrRSVDwlKwAWN9xIdRz8qLWOwAYtIQV-XaVd25Ceih5jDukIf7AUuN0pC4F6mrNPrZ6oJ9vP1U615i2dIsp75Hex4APjpgTrdMcjjQmekD3kjwb3a7iq9_3Gfl69e7L-n138_H6w_rypvPCiKljxmvYeHBSBJRgBtSDHmBA0eTG9SyMXDXpwKieOYeIQZjeaaUMaqnEGXmzvNs-8H3GOtm7PJfUWlouei4Zg6F_dG3dDm1MY56K8_tYvb3UrAfNpWLNdf4XVzsB99HnhKcN_QmwBfAl11pwtIcS964cLQN7isUusdgWiz3FYk1j3i7MPW7yWH3E5PGBa7m0kSUMvCk4dTD_717H6VcQ6zynqaF8QWuzpy2Wx838e7qf3kqucA</addsrcrecordid><sourcetype>Aggregation Database</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2342511094</pqid></control><display><type>article</type><title>Folate profile diversity and associated SNPs using genome wide association study in pea</title><source>SpringerNature Journals</source><source>Web of Science - Science Citation Index Expanded - 2020<img src="https://exlibris-pub.s3.amazonaws.com/fromwos-v2.jpg" /></source><creator>Jha, Ambuj B. ; Gali, Krishna K. ; Zhang, Haixia ; Purves, Randy W. ; Tar’an, Bunyamin ; Vandenberg, Albert ; Warkentin, Thomas D.</creator><creatorcontrib>Jha, Ambuj B. ; Gali, Krishna K. ; Zhang, Haixia ; Purves, Randy W. ; Tar’an, Bunyamin ; Vandenberg, Albert ; Warkentin, Thomas D.</creatorcontrib><description>Folates are important metabolic cofactors essential for human growth and development. Eighty-five accessions from a pea genome wide association study (GWAS) panel were evaluated for folate profile using ultra-performance liquid chromatography coupled with mass spectrometry. A GWAS was conducted to identify SNP markers associated with the folate profile of pea. Five folates were quantified and the sum of folates ranged from 14 to 55 µg/100 g dry weight. Significant differences (
P
< 0.001) were observed among the accessions for all folates. The pea accessions were genotyped using genotyping-by-sequencing. After filtering for a read depth of five and minor allele frequency of 0.05, 14,391 SNPs were used for marker-trait association. Five SNP markers were significantly (
P
< 0.01) associated with the sum of folates. Fifteen, eight, and three SNP markers were associated with 5-methyltetrahydrofolate (5-MTHF), 5-formyltetrahydrofolate, and tetrahydrofolate, respectively. Based on associated SNP markers, an additional 24 accessions were evaluated for folate profile, and those predicted to have a relatively high folate concentration had a significantly greater concentration of 5-MTHF and the sum of folates than those predicted to have a lower concentration. In these accessions, Sc_6992_86348 and Sc_3060_11265 were significantly associated with 5-MTHF and the sum of folates in Saskatoon 2016. Six SNP markers were converted into KASP markers, and these can be used for marker-assisted selection in pea breeding.</description><identifier>ISSN: 0014-2336</identifier><identifier>EISSN: 1573-5060</identifier><identifier>DOI: 10.1007/s10681-020-2553-8</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agriculture ; Agronomy ; Biomedical and Life Sciences ; Biotechnology ; Cofactors ; Folic acid ; Gene frequency ; Genetic research ; Genome-wide association studies ; Genomes ; Genomics ; Genotyping ; Horticulture ; Life Sciences ; Life Sciences & Biomedicine ; Liquid chromatography ; Marker-assisted selection ; Markers ; Mass spectrometry ; Mass spectroscopy ; Peas ; Plant Genetics and Genomics ; Plant Pathology ; Plant Physiology ; Plant Sciences ; Science & Technology ; Single nucleotide polymorphisms ; Tetrahydrofolic acid ; Vitamin B</subject><ispartof>Euphytica, 2020-02, Vol.216 (2), Article 18</ispartof><rights>Springer Nature B.V. 2020</rights><rights>COPYRIGHT 2020 Springer</rights><rights>Euphytica is a copyright of Springer, (2020). All Rights Reserved.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>true</woscitedreferencessubscribed><woscitedreferencescount>12</woscitedreferencescount><woscitedreferencesoriginalsourcerecordid>wos000511509200001</woscitedreferencesoriginalsourcerecordid><citedby>FETCH-LOGICAL-c383t-18c70bc0a53de5089e797909e389eba41df2689ea08641aaeeed384a7668e7563</citedby><cites>FETCH-LOGICAL-c383t-18c70bc0a53de5089e797909e389eba41df2689ea08641aaeeed384a7668e7563</cites><orcidid>0000-0003-3059-0606 ; 0000-0001-6177-1392</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/s10681-020-2553-8$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s10681-020-2553-8$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>315,781,785,27929,27930,28253,41493,42562,51324</link.rule.ids></links><search><creatorcontrib>Jha, Ambuj B.</creatorcontrib><creatorcontrib>Gali, Krishna K.</creatorcontrib><creatorcontrib>Zhang, Haixia</creatorcontrib><creatorcontrib>Purves, Randy W.</creatorcontrib><creatorcontrib>Tar’an, Bunyamin</creatorcontrib><creatorcontrib>Vandenberg, Albert</creatorcontrib><creatorcontrib>Warkentin, Thomas D.</creatorcontrib><title>Folate profile diversity and associated SNPs using genome wide association study in pea</title><title>Euphytica</title><addtitle>Euphytica</addtitle><addtitle>EUPHYTICA</addtitle><description>Folates are important metabolic cofactors essential for human growth and development. Eighty-five accessions from a pea genome wide association study (GWAS) panel were evaluated for folate profile using ultra-performance liquid chromatography coupled with mass spectrometry. A GWAS was conducted to identify SNP markers associated with the folate profile of pea. Five folates were quantified and the sum of folates ranged from 14 to 55 µg/100 g dry weight. Significant differences (
P
< 0.001) were observed among the accessions for all folates. The pea accessions were genotyped using genotyping-by-sequencing. After filtering for a read depth of five and minor allele frequency of 0.05, 14,391 SNPs were used for marker-trait association. Five SNP markers were significantly (
P
< 0.01) associated with the sum of folates. Fifteen, eight, and three SNP markers were associated with 5-methyltetrahydrofolate (5-MTHF), 5-formyltetrahydrofolate, and tetrahydrofolate, respectively. Based on associated SNP markers, an additional 24 accessions were evaluated for folate profile, and those predicted to have a relatively high folate concentration had a significantly greater concentration of 5-MTHF and the sum of folates than those predicted to have a lower concentration. In these accessions, Sc_6992_86348 and Sc_3060_11265 were significantly associated with 5-MTHF and the sum of folates in Saskatoon 2016. Six SNP markers were converted into KASP markers, and these can be used for marker-assisted selection in pea breeding.</description><subject>Agriculture</subject><subject>Agronomy</subject><subject>Biomedical and Life Sciences</subject><subject>Biotechnology</subject><subject>Cofactors</subject><subject>Folic acid</subject><subject>Gene frequency</subject><subject>Genetic research</subject><subject>Genome-wide association studies</subject><subject>Genomes</subject><subject>Genomics</subject><subject>Genotyping</subject><subject>Horticulture</subject><subject>Life Sciences</subject><subject>Life Sciences & Biomedicine</subject><subject>Liquid chromatography</subject><subject>Marker-assisted selection</subject><subject>Markers</subject><subject>Mass spectrometry</subject><subject>Mass spectroscopy</subject><subject>Peas</subject><subject>Plant Genetics and Genomics</subject><subject>Plant Pathology</subject><subject>Plant Physiology</subject><subject>Plant Sciences</subject><subject>Science & Technology</subject><subject>Single nucleotide polymorphisms</subject><subject>Tetrahydrofolic acid</subject><subject>Vitamin B</subject><issn>0014-2336</issn><issn>1573-5060</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>AOWDO</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNqNkV9rFDEUxYMouFY_gG8BH2Xam2TyZx7LYqtQqqDiY8gmd5aU3WRNZiz77c060iIoSB5y4J5f7s09hLxmcM4A9EVloAzrgEPHpRSdeUJWTGrRSVDwlKwAWN9xIdRz8qLWOwAYtIQV-XaVd25Ceih5jDukIf7AUuN0pC4F6mrNPrZ6oJ9vP1U615i2dIsp75Hex4APjpgTrdMcjjQmekD3kjwb3a7iq9_3Gfl69e7L-n138_H6w_rypvPCiKljxmvYeHBSBJRgBtSDHmBA0eTG9SyMXDXpwKieOYeIQZjeaaUMaqnEGXmzvNs-8H3GOtm7PJfUWlouei4Zg6F_dG3dDm1MY56K8_tYvb3UrAfNpWLNdf4XVzsB99HnhKcN_QmwBfAl11pwtIcS964cLQN7isUusdgWiz3FYk1j3i7MPW7yWH3E5PGBa7m0kSUMvCk4dTD_717H6VcQ6zynqaF8QWuzpy2Wx838e7qf3kqucA</recordid><startdate>20200201</startdate><enddate>20200201</enddate><creator>Jha, Ambuj B.</creator><creator>Gali, Krishna K.</creator><creator>Zhang, Haixia</creator><creator>Purves, Randy W.</creator><creator>Tar’an, Bunyamin</creator><creator>Vandenberg, Albert</creator><creator>Warkentin, Thomas D.</creator><general>Springer Netherlands</general><general>Springer Nature</general><general>Springer</general><general>Springer Nature B.V</general><scope>AOWDO</scope><scope>BLEPL</scope><scope>DTL</scope><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>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/0000-0003-3059-0606</orcidid><orcidid>https://orcid.org/0000-0001-6177-1392</orcidid></search><sort><creationdate>20200201</creationdate><title>Folate profile diversity and associated SNPs using genome wide association study in pea</title><author>Jha, Ambuj B. ; 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Eighty-five accessions from a pea genome wide association study (GWAS) panel were evaluated for folate profile using ultra-performance liquid chromatography coupled with mass spectrometry. A GWAS was conducted to identify SNP markers associated with the folate profile of pea. Five folates were quantified and the sum of folates ranged from 14 to 55 µg/100 g dry weight. Significant differences (
P
< 0.001) were observed among the accessions for all folates. The pea accessions were genotyped using genotyping-by-sequencing. After filtering for a read depth of five and minor allele frequency of 0.05, 14,391 SNPs were used for marker-trait association. Five SNP markers were significantly (
P
< 0.01) associated with the sum of folates. Fifteen, eight, and three SNP markers were associated with 5-methyltetrahydrofolate (5-MTHF), 5-formyltetrahydrofolate, and tetrahydrofolate, respectively. Based on associated SNP markers, an additional 24 accessions were evaluated for folate profile, and those predicted to have a relatively high folate concentration had a significantly greater concentration of 5-MTHF and the sum of folates than those predicted to have a lower concentration. In these accessions, Sc_6992_86348 and Sc_3060_11265 were significantly associated with 5-MTHF and the sum of folates in Saskatoon 2016. Six SNP markers were converted into KASP markers, and these can be used for marker-assisted selection in pea breeding.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><doi>10.1007/s10681-020-2553-8</doi><tpages>16</tpages><orcidid>https://orcid.org/0000-0003-3059-0606</orcidid><orcidid>https://orcid.org/0000-0001-6177-1392</orcidid></addata></record> |
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| subjects | Agriculture Agronomy Biomedical and Life Sciences Biotechnology Cofactors Folic acid Gene frequency Genetic research Genome-wide association studies Genomes Genomics Genotyping Horticulture Life Sciences Life Sciences & Biomedicine Liquid chromatography Marker-assisted selection Markers Mass spectrometry Mass spectroscopy Peas Plant Genetics and Genomics Plant Pathology Plant Physiology Plant Sciences Science & Technology Single nucleotide polymorphisms Tetrahydrofolic acid Vitamin B |
| title | Folate profile diversity and associated SNPs using genome wide association study in pea |
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