A comparison of polymorphism information content and mean of transformed kinships as criteria for selecting informative subsets of barley (Hordeum vulgare L. s. l.) from the USDA Barley Core Collection

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• 作者：Ryan C. Graebner ; Patrick M. Hayes…
• 关键词：Barley ; Germplasm ; GWAS ; Hordeum vulgare ; MTK ; PIC ; Rare phenotypes ; Subset
• 刊名：Genetic Resources and Crop Evolution
• 出版年：2016
• 出版时间：March 2016
• 年：2016
• 卷：63
• 期：3
• 页码：477-482
• 全文大小：596 KB
• 参考文献：Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4:250–255CrossRef
  Holbrook CC, Anderson WF, Pittman RN (1993) Selection of a core collection from the U.S. germplasm collection of peanut. Crop Sci 33:859–861CrossRef
  Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129CrossRef PubMed
  Mahajan RK, Bisht IS, Agrawal RC, Rana RS (1996) Studies on South Asian okra collection: methodology for establishing a representative core set using characterization data. Genet Resour Crop Evol 43:249–255CrossRef
  Muñoz-Amatraín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM (2014) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 9:e94688CrossRef
  Smith JSC, Chin ECL, Shu H, Smith OS, Wall SJ et al (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree. Theor Appl Genet 95:163–173CrossRef
  Upadhyaya HD, Bramel PJ, Singh S (2001) Development of a chickpea core subset using geographic distribution and quantitative traits. Crop Sci 41:206–210CrossRef
  Upadhyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL, Reddy VG, Singh S (2009) Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci 49:1769–1780CrossRef
  Zewdie Y, Tong N, Bosland P (2004) Establishing a core collection of Capsicum using a cluster analysis with enlightened selection of accessions. Genet Resour Crop Evol 51:147–151CrossRef
  
• 作者单位：Ryan C. Graebner (1)
  Patrick M. Hayes (1)
  Christina H. Hagerty (2)
  Alfonso Cuesta-Marcos (1)
  
  1. Department of Crop and Soil Science, Oregon State University, Crop Science Building, Corvallis, OR, USA
  2. Department of Botany and Plant Pathology, Oregon State University, Cordley Hall, Corvallis, OR, USA
  
• 刊物类别：Biomedical and Life Sciences
• 刊物主题：Life Sciences
  Plant Sciences
  Plant Physiology
  Plant Pathology
  
• 出版者：Springer Netherlands
• ISSN：1573-5109

文摘

Recent advances in genetic technologies have given researchers the ability to characterize genetic marker data for large germplasm collections. While some studies are able to capitalize on entire germplasm collections, others, especially those that focus on traits that are difficult to phenotype, instead focus on a subset of the collection. Typically, subsets are selected using phenotypic or geographic data. One major hurdle in identifying favorable subsets is selecting a criterion that can be used to quantify the value of a subset. This study compares two such criteria, polymorphism information content, and a new criterion based on kinship matrices, which will be called the mean of transformed kinships. These criteria were explored in terms of their ability to select subsets that are favorable for genome wide association studies, and in their ability to select subsets that contain a high number of rare phenotypes. Using phenotypic and genotypic data that has been amassed from the USDA Barley Core Collection, evidence was found to support the hypotheses that subsets based on the mean of transformed kinships were well-suited to select subsets intended for genome-wide association studies, but the same was not found for polymorphism information content. Inversely, evidence was found to support the hypothesis that subsets based on polymorphism information content were well-suited to select subsets intended for rare-phenotype discovery, but the same was not found for subsets selected using the mean of transformed kinships criterion. Tools to select subsets using these two criteria have been released in the R package “GeneticSubsetter.”

Keywords Barley Germplasm GWAS Hordeum vulgare MTK PIC Rare phenotypes Subset Page %P Close Plain text Look Inside Reference tools Export citation EndNote (.ENW) JabRef (.BIB) Mendeley (.BIB) Papers (.RIS) Zotero (.RIS) BibTeX (.BIB) Add to Papers Other actions Register for Journal Updates About This Journal Reprints and Permissions Share Share this content on Facebook Share this content on Twitter Share this content on LinkedIn Related Content Supplementary Material (0) References (9) ReferencesEndelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome 4:250–255CrossRefHolbrook CC, Anderson WF, Pittman RN (1993) Selection of a core collection from the U.S. germplasm collection of peanut. Crop Sci 33:859–861CrossRefLiu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129CrossRefPubMedMahajan RK, Bisht IS, Agrawal RC, Rana RS (1996) Studies on South Asian okra collection: methodology for establishing a representative core set using characterization data. Genet Resour Crop Evol 43:249–255CrossRefMuñoz-Amatraín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM (2014) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 9:e94688CrossRefSmith JSC, Chin ECL, Shu H, Smith OS, Wall SJ et al (1997) An evaluation of the utility of SSR loci as molecular markers in maize (Zea mays L.): comparisons with data from RFLPS and pedigree. Theor Appl Genet 95:163–173CrossRefUpadhyaya HD, Bramel PJ, Singh S (2001) Development of a chickpea core subset using geographic distribution and quantitative traits. Crop Sci 41:206–210CrossRefUpadhyaya HD, Pundir RPS, Dwivedi SL, Gowda CLL, Reddy VG, Singh S (2009) Developing a mini core collection of sorghum for diversified utilization of germplasm. Crop Sci 49:1769–1780CrossRefZewdie Y, Tong N, Bosland P (2004) Establishing a core collection of Capsicum using a cluster analysis with enlightened selection of accessions. Genet Resour Crop Evol 51:147–151CrossRef About this Article Title A comparison of polymorphism information content and mean of transformed kinships as criteria for selecting informative subsets of barley (Hordeum vulgare L. s. l.) from the USDA Barley Core Collection Journal Genetic Resources and Crop Evolution Volume 63, Issue 3 , pp 477-482 Cover Date2016-03 DOI 10.1007/s10722-015-0265-z Print ISSN 0925-9864 Online ISSN 1573-5109 Publisher Springer Netherlands Additional Links Register for Journal Updates Editorial Board About This Journal Manuscript Submission Topics Plant Sciences Plant Systematics/Taxonomy/Biogeography Plant Genetics & Genomics Plant Physiology Agriculture Keywords Barley Germplasm GWAS Hordeum vulgare MTK PIC Rare phenotypes Subset Industry Sectors Chemical Manufacturing Consumer Packaged Goods Authors Ryan C. Graebner (1) Patrick M. Hayes (1) Christina H. Hagerty (2) Alfonso Cuesta-Marcos (1) Author Affiliations 1. Department of Crop and Soil Science, Oregon State University, Crop Science Building, Corvallis, OR, USA 2. Department of Botany and Plant Pathology, Oregon State University, Cordley Hall, Corvallis, OR, USA Continue reading... To view the rest of this content please follow the download PDF link above.