Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop lesquerella and related species
The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the...
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| description | The advantages of using molecular markers in modern genebanks are well documented. They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa. |
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Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0064062</identifier><identifier>PMID: 23724020</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agriculture ; Arid zones ; Biodiversity ; Biology ; Brassicaceae ; Brassicaceae - genetics ; Breeding ; Breeding status ; Cluster Analysis ; Collection ; Crops ; Crops, Agricultural ; Crops, Agricultural - genetics ; Deoxyribonucleic acid ; DNA ; Ecotype ; Enzymes ; Genetic diversity ; Genetic markers ; Genetic Markers - genetics ; Genetic testing ; genetic traits ; Genetic Variation ; genetics ; Genomes ; genotype ; Geography ; Germplasm ; germplasm conservation ; interspecific variation ; Lesquerella ; Lesquerella fendleri ; Markers ; metabolism ; microarray technology ; microsatellite repeats ; Microsatellites ; new crops ; oilseed crops ; Oligonucleotide Array Sequence Analysis ; Packera fendleri ; Physaria ; Plant breeding ; Plant Oils ; Plant Oils - metabolism ; Platforms ; Polymorphism, Genetic ; Population Dynamics ; Population genetics ; Registration ; Reproducibility ; Seeds ; Seeds - genetics ; Single-nucleotide polymorphism ; Species ; Species diversity ; Taxa ; United States ; USDA</subject><ispartof>PloS one, 2013-05, Vol.8 (5), p.e64062-e64062</ispartof><rights>2013. This is an open-access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. 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They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa.</description><subject>Agriculture</subject><subject>Arid zones</subject><subject>Biodiversity</subject><subject>Biology</subject><subject>Brassicaceae</subject><subject>Brassicaceae - genetics</subject><subject>Breeding</subject><subject>Breeding status</subject><subject>Cluster Analysis</subject><subject>Collection</subject><subject>Crops</subject><subject>Crops, Agricultural</subject><subject>Crops, Agricultural - genetics</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>Ecotype</subject><subject>Enzymes</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Genetic Markers - genetics</subject><subject>Genetic testing</subject><subject>genetic traits</subject><subject>Genetic Variation</subject><subject>genetics</subject><subject>Genomes</subject><subject>genotype</subject><subject>Geography</subject><subject>Germplasm</subject><subject>germplasm conservation</subject><subject>interspecific variation</subject><subject>Lesquerella</subject><subject>Lesquerella fendleri</subject><subject>Markers</subject><subject>metabolism</subject><subject>microarray technology</subject><subject>microsatellite repeats</subject><subject>Microsatellites</subject><subject>new crops</subject><subject>oilseed crops</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Packera fendleri</subject><subject>Physaria</subject><subject>Plant breeding</subject><subject>Plant Oils</subject><subject>Plant Oils - metabolism</subject><subject>Platforms</subject><subject>Polymorphism, Genetic</subject><subject>Population Dynamics</subject><subject>Population genetics</subject><subject>Registration</subject><subject>Reproducibility</subject><subject>Seeds</subject><subject>Seeds - genetics</subject><subject>Single-nucleotide polymorphism</subject><subject>Species</subject><subject>Species diversity</subject><subject>Taxa</subject><subject>United States</subject><subject>USDA</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2013</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNqNUstuFDEQHCEQCYE_QGCJC5cd_Pb6ghQlPCJF4kBytjyeno0Xz3iwZxflP_hgvNnZKEEcOLnlrqpul6uqXhNcE6bIh3XcpMGGeowD1BhLjiV9Uh0TzehCUsyePqiPqhc5rzEWbCnl8-qIMkU5pvi4-n0OWwhx7GGYUOzQ-Wm6Qr1NPyChMdipi6nPyA4tWsEAk3eo9VtI2U-3yOYMOR-Y0w2g6_p7jVwMAdzk43C4HuAXij5kgBa5FEcUIP_cQIIQ7J12qexUmnkE5yG_rJ51tsBfzedJdf3509XZ18Xlty8XZ6eXCyepmBacOyqtY60Gi3mrGyBlAhXOWsoa2nDGBdbYNhQDpoqJruEcCwW0EUvSUnZSvd3rjiFmMxuaDWFCaKyk1AVxsUe00a7NmHyx5tZE683dRUwrY1NxJYDRBJjWHTgrOq4cLMEJx6lQBDdKqKZofZynbZoeWld8SzY8En3cGfyNWcWtYVKKJdut-34WSLHYlyfT--x2Jg4QN2VvziVdCs3_A8qE4lorwQv03V_QfxvB96jyfzkn6O73Jtjs8nhgmV0ezZzHQnvz8M33pEMA2R_ql-Bk</recordid><startdate>20130528</startdate><enddate>20130528</enddate><creator>Cruz, Von Mark V</creator><creator>Kilian, Andrzej</creator><creator>Dierig, David A</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>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>7S9</scope><scope>L.6</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20130528</creationdate><title>Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop lesquerella and related species</title><author>Cruz, Von Mark V ; Kilian, Andrzej ; Dierig, David A</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c625t-44c26ac3d9ea04d9be1eed25caa23b2b4345090ab20e02735fb44057e2b581d23</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2013</creationdate><topic>Agriculture</topic><topic>Arid zones</topic><topic>Biodiversity</topic><topic>Biology</topic><topic>Brassicaceae</topic><topic>Brassicaceae - 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They are commonly used to understand the distribution of genetic diversity in populations and among species which is crucial for efficient management and effective utilization of germplasm collections. We describe the development of two types of DArT molecular marker platforms for the new oilseed crop lesquerella (Physaria spp.), a member of the Brassicaceae family, to characterize a collection in the National Plant Germplasm System (NPGS) with relatively little known in regards to the genetic diversity and traits. The two types of platforms were developed using a subset of the germplasm conserved ex situ consisting of 87 Physaria and 2 Paysonia accessions. The microarray DArT revealed a total of 2,833 polymorphic markers with an average genotype call rate of 98.4% and a scoring reproducibility of 99.7%. On the other hand, the DArTseq platform developed for SNP and DArT markers from short sequence reads showed a total of 27,748 high quality markers. Cluster analysis and principal coordinate analysis indicated that the different accessions were successfully classified by both systems based on species, by geographical source, and breeding status. In the germplasm set analyzed, which represented more than 80% of the P. fendleri collection, we observed that a substantial amount of variation exists in the species collection. These markers will be valuable in germplasm management studies and lesquerella breeding, and augment the microsatellite markers previously developed on the taxa.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>23724020</pmid><doi>10.1371/journal.pone.0064062</doi><oa>free_for_read</oa></addata></record> |
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| subjects | Agriculture Arid zones Biodiversity Biology Brassicaceae Brassicaceae - genetics Breeding Breeding status Cluster Analysis Collection Crops Crops, Agricultural Crops, Agricultural - genetics Deoxyribonucleic acid DNA Ecotype Enzymes Genetic diversity Genetic markers Genetic Markers - genetics Genetic testing genetic traits Genetic Variation genetics Genomes genotype Geography Germplasm germplasm conservation interspecific variation Lesquerella Lesquerella fendleri Markers metabolism microarray technology microsatellite repeats Microsatellites new crops oilseed crops Oligonucleotide Array Sequence Analysis Packera fendleri Physaria Plant breeding Plant Oils Plant Oils - metabolism Platforms Polymorphism, Genetic Population Dynamics Population genetics Registration Reproducibility Seeds Seeds - genetics Single-nucleotide polymorphism Species Species diversity Taxa United States USDA |
| title | Development of DArT marker platforms and genetic diversity assessment of the U.S. collection of the new oilseed crop lesquerella and related species |
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