Genotyping-by-Sequencing Facilitates a High-Density Consensus Linkage Map for Aegilops umbellulata, a Wild Relative of Cultivated Wheat

High-density genetic maps are useful to precisely localize QTL or genes that might be used to improve traits of nutritional and/or economical importance in crops. However, high-density genetic maps are lacking for most wild relatives of crop species, including wheat. Aegilops umbellulata is a wild relative of wheat known for its potential as a source of biotic and abiotic stress resistance genes. In this work, we have developed a framework consensus genetic map using two biparental populations derived from accessions PI 298905, PI 542369, PI 5422375, and PI 554395. The framework map comprised 3009 genotype-by-sequence SNPs with a total map size of 948.72 cM. On average, there were three SNPs per centimorgan for each chromosome. Chromosome 1U was the shortest (66.5 cM), with only 81 SNPs, whereas the remaining chromosomes had between 391 and 591 SNP markers. A total of 2395 unmapped SNPs were added to the linkage maps through a recombination frequency approach, and increased the number of SNPs placed on the consensus map to a total of 5404 markers. Segregation distortion was disproportionally high for chromosome 1U for both populations used to construct component linkage maps, and thus segregation distortion could be one of the probable reasons for the exceptionally reduced linkage size for chromosome 1U. From comparative analysis, Ae. umbellulata chromosomes except 4U showed moderate to strong collinearity with corresponding homeologous chromosomes of hexaploid wheat and barley. The present consensus map may serve as a reference map in QTL mapping and validation projects, and also in genome assembly to develop a reference genome sequence for Ae. umbellulata.

[1]  C. B. Cardoso-Silva,et al.  GBS-based single dosage markers for linkage and QTL mapping allow gene mining for yield-related traits in sugarcane , 2017, BMC Genomics.

[2]  J. Poland,et al.  Genotype-by-sequencing facilitates genetic mapping of a stem rust resistance locus in Aegilops umbellulata, a wild relative of cultivated wheat , 2016, BMC Genomics.

[3]  J. Doležel,et al.  Dissecting the U, M, S and C genomes of wild relatives of bread wheat (Aegilops spp.) into chromosomes and exploring their synteny with wheat. , 2016, The Plant journal : for cell and molecular biology.

[4]  H. Upadhyaya,et al.  Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea , 2016, Scientific Reports.

[5]  F. Belzile,et al.  Extent and overlap of segregation distortion regions in 12 barley crosses determined via a Pool-GBS approach , 2016, Theoretical and Applied Genetics.

[6]  C. Plomion,et al.  High-density linkage mapping and distribution of segregation distortion regions in the oak genome , 2016, DNA research : an international journal for rapid publication of reports on genes and genomes.

[7]  Kenneth L. McNally,et al.  Open access resources for genome-wide association mapping in rice , 2016, Nature Communications.

[8]  G. Bai,et al.  A High-Density SNP and SSR Consensus Map Reveals Segregation Distortion Regions in Wheat , 2015, BioMed research international.

[9]  Vikram E. Chhatre,et al.  A Consensus Genetic Map for Pinus taeda and Pinus elliottii and Extent of Linkage Disequilibrium in Two Genotype-Phenotype Discovery Populations of Pinus taeda , 2015, G3: Genes, Genomes, Genetics.

[10]  R. Casadio,et al.  A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. , 2015, Plant biotechnology journal.

[11]  S. Tangphatsornruang,et al.  Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). , 2015, Genomics.

[12]  Peter J. Bradbury,et al.  High-resolution genetic mapping of maize pan-genome sequence anchors , 2015, Nature Communications.

[13]  M. Moscou,et al.  Strategies for transferring resistance into wheat: from wide crosses to GM cassettes , 2014, Front. Plant Sci..

[14]  Genying Li,et al.  Cytogenetic and molecular markers for detecting Aegilops uniaristata chromosomes in a wheat background. , 2014, Genome.

[15]  J. Cornelis,et al.  Impact of rice cultivar and organ on elemental composition of phytoliths and the release of bio-available silicon , 2014, Front. Plant Sci..

[16]  J. Clarke,et al.  A consensus framework map of durum wheat (Triticum durum Desf.) suitable for linkage disequilibrium analysis and genome-wide association mapping , 2014, BMC Genomics.

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

[18]  J. Batley,et al.  A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome , 2014, Science.

[19]  Christophe Plomion,et al.  LPmerge: an R package for merging genetic maps by linear programming , 2014, Bioinform..

[20]  Morten Lillemo,et al.  Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array , 2014, Plant biotechnology journal.

[21]  J. Poland,et al.  SNPMeta: SNP annotation and SNP metadata collection without a reference genome , 2014, Molecular ecology resources.

[22]  J. Chapman,et al.  Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ) , 2013, The Plant journal : for cell and molecular biology.

[23]  Wenjun Zhang,et al.  Identification of Wheat Gene Sr35 That Confers Resistance to Ug99 Stem Rust Race Group , 2013, Science.

[24]  J. Doležel,et al.  Syntenic Relationships between the U and M Genomes of Aegilops, Wheat and the Model Species Brachypodium and Rice as Revealed by COS Markers , 2013, PloS one.

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

[26]  Schuyler S. Korban,et al.  A Multi-Population Consensus Genetic Map Reveals Inconsistent Marker Order among Maps Likely Attributed to Structural Variations in the Apple Genome , 2012, PloS one.

[27]  Mihaela M. Martis,et al.  A physical, genetic and functional sequence assembly of the barley genome. , 2022 .

[28]  J. Poland,et al.  Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach , 2012, PloS one.

[29]  A. Kilian,et al.  A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers , 2011, PloS one.

[30]  J. Reif,et al.  Detection of segregation distortion loci in triticale (x Triticosecale Wittmack) based on a high-density DArT marker consensus genetic linkage map , 2011, BMC Genomics.

[31]  Robert J. Elshire,et al.  A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species , 2011, PloS one.

[32]  A. Kilian,et al.  Construction of a high-density composite map and comparative mapping of segregation distortion regions in barley , 2010, Molecular Genetics and Genomics.

[33]  Xuehui Huang,et al.  High-throughput genotyping by whole-genome resequencing. , 2009, Genome research.

[34]  A. Kilian,et al.  A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers , 2009, BMC Plant Biology.

[35]  Stefano Lonardi,et al.  Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph , 2008, PLoS genetics.

[36]  A. Schneider,et al.  Utilisation of Aegilops (goatgrass) species to widen the genetic diversity of cultivated wheat , 2008, Euphytica.

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

[38]  Sunil Kumar,et al.  Identification and characterization of segregation distortion loci along chromosome 5B in tetraploid wheat , 2007, Molecular Genetics and Genomics.

[39]  R. Hajjar,et al.  The use of wild relatives in crop improvement: a survey of developments over the last 20 years , 2007, Euphytica.

[40]  Seishi Ninomiya,et al.  AntMap: Constructing Genetic Linkage Maps Using an Ant Colony Optimization Algorithm , 2006 .

[41]  R. Visser,et al.  Construction of a 10,000-Marker Ultradense Genetic Recombination Map of Potato: Providing a Framework for Accelerated Gene Isolation and a Genomewide Physical Map , 2006, Genetics.

[42]  M. Zaharieva,et al.  Spontaneous hybridization between bread wheat (Triticum aestivum L.) and its wild relatives in Europe , 2006 .

[43]  M. Özgen,et al.  Association of gliadin protein pattern and rust resistance derived from Aegilops umbellulata Zhuk. in winter Triticum durum Desf. , 2004 .

[44]  K. Edwards,et al.  A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.) , 2004, Theoretical and Applied Genetics.

[45]  V. Korzun,et al.  Genetic and physical mapping of homoeologous recombination points involving wheat chromosome 2B and rye chromosome 2R. , 2004, Genome.

[46]  B. Gill,et al.  Map-based cloning of leaf rust resistance gene Lr21 from the large and polyploid genome of bread wheat. , 2003, Genetics.

[47]  Steven G. Schroeder,et al.  Development and mapping of SSR markers for maize , 2002, Plant Molecular Biology.

[48]  V. Korzun,et al.  A genetic map of rye (Secale cereale L.) combining RFLP, isozyme, protein, microsatellite and gene loci , 2001, Theoretical and Applied Genetics.

[49]  K. Devos,et al.  Genome Relationships: The Grass Model in Current Research , 2000, Plant Cell.

[50]  B. Gill,et al.  Molecular mapping of segregation distortion loci in Aegilops tauschii. , 1998, Genetics.

[51]  K. Devos,et al.  Relationships between the chromosomes of Aegilops umbellulata and wheat , 1998, Theoretical and Applied Genetics.

[52]  S. Tanksley,et al.  Seed banks and molecular maps: unlocking genetic potential from the wild. , 1997, Science.

[53]  G. Wricke,et al.  An extended genetic map of rye (Secale cereale L.) , 1996 .

[54]  Katrien M. Devos,et al.  Chromosomal rearrangements in the rye genome relative to that of wheat , 1993, Theoretical and Applied Genetics.

[55]  R. Koebner,et al.  Allosyndetic recombination between a chromosome of Aegilops umbellulata and wheat chromosomes , 1987, Heredity.

[56]  G. Kimber.  The addition of the chromosomes of Aegilops umbellulata to Triticum aestivum (var. Chinese Spring) , 1967 .

[57]  Douglas R. Taylor,et al.  Common Features of Segregation Distortion in Plants and Animals , 2004, Genetica.

[58]  Jiming Jiang,et al.  Recent advances in alien gene transfer in wheat , 2004, Euphytica.

[59]  Jiming Jiang,et al.  Characterization of wheat-alien translocations conferring resistance to diseases and pests: current status , 2004, Euphytica.

[60]  R. Doerge.  Multifactorial genetics: Mapping and analysis of quantitative trait loci in experimental populations , 2002, Nature Reviews Genetics.

[61]  E. Lander,et al.  Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. , 1989, Genetics.

[62]  R. Prescott-Allen,et al.  Genes from the Wild: Using Wild Genetic Resources for Food and Raw Materials , 1988 .

[63]  S. Reader,et al.  The simultaneous substitution of two pairs of chromosomes from two alien species into Triticum aestivum cv. Chinese Spring. , 1987 .

[64]  B. Gill,et al.  Evaluation of Aegilops species for resistance to wheat powdery mildew, wheat leaf rust, hessian fly, and greenbug , 1985 .

[65]  E. R. Sears.  The transfer of leaf-rust resistance from Aegilops umbellulata to wheat. , 1956 .