Population Genomics Related to Adaptation in Elite Oat Germplasm

An oat association‐mapping panel contributed by active breeding programs worldwide. Characterized population structure and found subdivisions related to adaptation Characterized genome‐wide and chromosome‐specific linkage disequilibrium Performed association‐mapping and post hoc modeling of heading date Found several consistently associated QTL

[1]  Gary J. Muehlbauer,et al.  The USDA Barley Core Collection: Genetic Diversity, Population Structure, and Potential for Genome-Wide Association Studies , 2014, PloS one.

[2]  E. N. Jellen,et al.  Geographical distribution of a chromosome 7C and 17 intergenomic translocation in cultivated oat , 2000 .

[3]  Haiyang Wang,et al.  Days to heading 7, a major quantitative locus determining photoperiod sensitivity and regional adaptation in rice , 2014, Proceedings of the National Academy of Sciences.

[4]  H. Buerstmayr,et al.  Genetic diversity among oat varieties of worldwide origin and associations of AFLP markers with quantitative traits , 2008, Theoretical and Applied Genetics.

[5]  Nicholas A. Tinker,et al.  Using Genotyping-By-Sequencing (GBS) for Genomic Discovery in Cultivated Oat , 2014, PloS one.

[6]  B S Weir,et al.  Variances and covariances of squared linkage disequilibria in finite populations. , 1988, Theoretical population biology.

[7]  M. Lee,et al.  Genomic regions controlling vernalization and photoperiod responses in oat , 2002, Theoretical and Applied Genetics.

[8]  N. Tinker,et al.  A molecular linkage map with associated QTLs from a hulless × covered spring oat population , 2004, Theoretical and Applied Genetics.

[9]  S. Tanksley,et al.  Development of a chromosomal arm map for wheat based on RFLP markers , 1992, Theoretical and Applied Genetics.

[10]  D. Reich,et al.  Principal components analysis corrects for stratification in genome-wide association studies , 2006, Nature Genetics.

[11]  P. Smouse,et al.  genalex 6: genetic analysis in Excel. Population genetic software for teaching and research , 2006 .

[12]  N. Tinker,et al.  Tagging and mapping candidate loci for vernalization and flower initiation in hexaploid oat , 2012, Molecular Breeding.

[13]  Peter Wenzl,et al.  New DArT markers for oat provide enhanced map coverage and global germplasm characterization , 2009, BMC Genomics.

[14]  Pat Baird,et al.  Health benefits of dietary fiber. , 2009, Nutrition reviews.

[15]  M. Sorrells,et al.  Association Mapping of Kernel Size and Milling Quality in Wheat (Triticum aestivum L.) Cultivars , 2006, Genetics.

[16]  Rod Peakall,et al.  GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update , 2012, Bioinform..

[17]  Zhongwei Lin,et al.  Parallel Domestication of the Heading Date 1 Gene in Cereals. , 2015, Molecular biology and evolution.

[18]  J. Poland,et al.  A SNP Genotyping Array for Hexaploid Oat , 2014 .

[19]  W. Beavis,et al.  Genomic, Marker-Assisted, and Pedigree-BLUP Selection Methods for β-Glucan Concentration in Elite Oat , 2013 .

[20]  W. Powell,et al.  Control of flowering time in temperate cereals: genes, domestication, and sustainable productivity. , 2007, Journal of experimental botany.

[21]  P. Jones,et al.  Cholesterol-lowering effects of oat β-glucan. , 2011, Nutrition reviews.

[22]  Edward S. Buckler,et al.  TASSEL: software for association mapping of complex traits in diverse samples , 2007, Bioinform..

[23]  M. Sorrells,et al.  Relationships among 70 North Amerian Oat Germplasms: II. Cluster Analysis Using Qualitative Characters , 1991 .

[24]  W. Beavis,et al.  Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin , 2012, Theoretical and Applied Genetics.

[25]  Michael Lee,et al.  QTLs and epistasis associated with vernalization responses in oat , 1997 .

[26]  M. Ganal,et al.  Genetic architecture of main effect QTL for heading date in European winter wheat , 2014, Front. Plant Sci..

[27]  Steven G. Blanchard,et al.  A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement , 2016, The plant genome.

[28]  Weikai Yan,et al.  SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species , 2013, PloS one.

[29]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[30]  Amanda B. Hepler,et al.  Genetic relatedness analysis: modern data and new challenges , 2006, Nature Reviews Genetics.

[31]  Robert J. Elshire,et al.  Switchgrass Genomic Diversity, Ploidy, and Evolution: Novel Insights from a Network-Based SNP Discovery Protocol , 2013, PLoS genetics.

[32]  Alkes L. Price,et al.  New approaches to population stratification in genome-wide association studies , 2010, Nature Reviews Genetics.

[33]  David H. Alexander,et al.  Fast model-based estimation of ancestry in unrelated individuals. , 2009, Genome research.

[34]  M. Sorrells,et al.  Chromosomal regions associated with quantitative traits in oat , 1996 .

[35]  J. Goudet.  HIERFSTAT , a package for R to compute and test hierarchical F -statistics , 2005 .

[36]  D. Cook,et al.  Population structure and linkage disequilibrium in oat (Avena sativa L.): implications for genome-wide association studies , 2011, Theoretical and Applied Genetics.

[37]  E S Buckler,et al.  Structure of linkage disequilibrium and phenotypic associations in the maize genome , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[38]  N. Tinker,et al.  Loci affecting flowering time in oat under short-day conditions. , 2006, Genome.

[39]  L. Hoffman,et al.  The Origin, History, and Production of Oat , 2015 .

[40]  V. Allard,et al.  Predictions of heading date in bread wheat (Triticum aestivum L.) using QTL-based parameters of an ecophysiological model , 2014, Journal of experimental botany.

[41]  E. Buckler,et al.  Structure of linkage disequilibrium in plants. , 2003, Annual review of plant biology.

[42]  P. This,et al.  Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness , 2011, Heredity.

[43]  T. Stanton.  Oat Identification and Classification , 1955 .

[44]  M. Morgante,et al.  Long-range patterns of diversity and linkage disequilibrium surrounding the maize Y1 gene are indicative of an asymmetric selective sweep. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[45]  G. Scoles,et al.  An updated doubled haploid oat linkage map and QTL mapping of agronomic and grain quality traits from Canadian field trials. , 2012, Genome.

[46]  Justin O Borevitz,et al.  Genome-wide association studies in plants: the missing heritability is in the field , 2011, Genome Biology.