Application of Genomic Tools in Plant Breeding

Plant breeding has been very successful in developing improved varieties using conventional tools and methodologies. Nowadays, the availability of genomic tools and resources is leading to a new revolution of plant breeding, as they facilitate the study of the genotype and its relationship with the phenotype, in particular for complex traits. Next Generation Sequencing (NGS) technologies are allowing the mass sequencing of genomes and transcriptomes, which is producing a vast array of genomic information. The analysis of NGS data by means of bioinformatics developments allows discovering new genes and regulatory sequences and their positions, and makes available large collections of molecular markers. Genome-wide expression studies provide breeders with an understanding of the molecular basis of complex traits. Genomic approaches include TILLING and EcoTILLING, which make possible to screen mutant and germplasm collections for allelic variants in target genes. Re-sequencing of genomes is very useful for the genome-wide discovery of markers amenable for high-throughput genotyping platforms, like SSRs and SNPs, or the construction of high density genetic maps. All these tools and resources facilitate studying the genetic diversity, which is important for germplasm management, enhancement and use. Also, they allow the identification of markers linked to genes and QTLs, using a diversity of techniques like bulked segregant analysis (BSA), fine genetic mapping, or association mapping. These new markers are used for marker assisted selection, including marker assisted backcross selection, ‘breeding by design’, or new strategies, like genomic selection. In conclusion, advances in genomics are providing breeders with new tools and methodologies that allow a great leap forward in plant breeding, including the ‘superdomestication’ of crops and the genetic dissection and breeding for complex traits.

[1]  Martin Parniske,et al.  A TILLING Reverse Genetics Tool and a Web-Accessible Collection of Mutants of the Legume Lotus japonicus 1 , 2003, Plant Physiology.

[2]  Peter J. Bradbury,et al.  Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population , 2011, Nature Genetics.

[3]  S. Deschamps,et al.  Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery , 2010, Molecular Breeding.

[4]  Haichao Li,et al.  Second-Generation Sequencing Supply an Effective Way to Screen RNAi Targets in Large Scale for Potential Application in Pest Insect Control , 2011, PloS one.

[5]  Bjarni J. Vilhjálmsson,et al.  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines , 2010 .

[6]  G. Malerba,et al.  Characterization of Transcriptional Complexity during Berry Development in Vitis vinifera Using RNA-Seq1[W] , 2010, Plant Physiology.

[7]  Cécile Donnadieu,et al.  Highly-multiplexed SNP genotyping for genetic mapping and germplasm diversity studies in pea , 2010, BMC Genomics.

[8]  Robenzon E. Lorenzana,et al.  Accuracy of genotypic value predictions for marker-based selection in biparental plant populations , 2009, Theoretical and Applied Genetics.

[9]  S. Henikoff,et al.  High-throughput screening for induced point mutations. , 2001, Plant physiology.

[10]  Sergey V Anisimov.  Serial Analysis of Gene Expression (SAGE): 13 years of application in research. , 2008, Current pharmaceutical biotechnology.

[11]  G. Wenzel,et al.  Characterization of phenylpropanoid pathway genes within European maize (Zea mays L.) inbreds , 2008, BMC Plant Biology.

[12]  J. Cañizares,et al.  Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae) , 2011, BMC Genomics.

[13]  P. Langridge,et al.  Breeding Technologies to Increase Crop Production in a Changing World , 2010, Science.

[14]  C. Chevalet,et al.  Using markers in gene introgression breeding programs. , 1992, Genetics.

[15]  R. Mott,et al.  The 1001 Genomes Project for Arabidopsis thaliana , 2009, Genome Biology.

[16]  M. Metzker.  Sequencing technologies — the next generation , 2010, Nature Reviews Genetics.

[17]  Zhonghua Zhang,et al.  Fine genetic mapping localizes cucumber scab resistance gene Ccu into an R gene cluster , 2011, Theoretical and Applied Genetics.

[18]  Jean-Luc Jannink,et al.  Genomic selection in plant breeding: from theory to practice. , 2010, Briefings in functional genomics.

[19]  M. Goddard,et al.  Prediction of total genetic value using genome-wide dense marker maps. , 2001, Genetics.

[20]  Steven Henikoff,et al.  Mismatch cleavage by single-strand specific nucleases. , 2004, Nucleic acids research.

[21]  Stefan R. Henz,et al.  A gene expression map of Arabidopsis thaliana development , 2005, Nature Genetics.

[22]  Evandro Novaes,et al.  High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome , 2008, BMC Genomics.

[23]  Steven B Cannon,et al.  High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence , 2010, BMC Genomics.

[24]  P. Rigault,et al.  Association Genetics of Wood Physical Traits in the Conifer White Spruce and Relationships With Gene Expression , 2011, Genetics.

[25]  李佩芳.  International Rice Genome Sequencing Project. 2005. The map-based sequence of the rice genome. , 2005 .

[26]  Nunzio D'Agostino,et al.  Comparative 454 pyrosequencing of transcripts from two olive genotypes during fruit development , 2009, BMC Genomics.

[27]  Rajeev K. Varshney,et al.  Genomics-Assisted Crop Improvement, Vol 1: Genomics Approaches and Platforms , 2007 .

[28]  Tomas Hruz,et al.  Genevestigator transcriptome meta-analysis and biomarker search using rice and barley gene expression databases. , 2008, Molecular plant.

[29]  Qi Feng,et al.  Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing , 2010, Proceedings of the National Academy of Sciences.

[30]  H. D. Vanguilder,et al.  Twenty-five years of quantitative PCR for gene expression analysis. , 2008, BioTechniques.

[31]  R. Bernardo.  Molecular Markers and Selection for Complex Traits in Plants: Learning from the Last 20 Years , 2008 .

[32]  T. Sharma,et al.  RESEARCH ARTICLE Open Access Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh] , 2022 .

[33]  Richard Shen,et al.  Medium- to high-throughput SNP genotyping using VeraCode microbeads. , 2009, Methods in molecular biology.

[34]  Peter Kokol,et al.  Gene set enrichment meta-learning analysis: next- generation sequencing versus microarrays , 2009, BMC Bioinformatics.

[35]  Thomas Lübberstedt,et al.  Functional markers in plants. , 2003, Trends in plant science.

[36]  M. Gelfand,et al.  De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum) , 2011, BMC Genomics.

[37]  J. Prioul,et al.  Epistatic Interactions between Opaque2 Transcriptional Activator and Its Target Gene CyPPDK1 Control Kernel Trait Variation in Maize1[C][W][OA] , 2009, Plant Physiology.

[38]  C. Weil,et al.  Getting the Point—Mutations in Maize , 2007 .

[39]  J. Cañizares,et al.  EcoTILLING in Capsicum species: searching for new virus resistances , 2010, BMC Genomics.

[40]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[41]  E. Balázs,et al.  From Crop Domestication to Super-domestication , 2007, Annals of botany.

[42]  J. Poulain,et al.  The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla , 2007, Nature.

[43]  Steven Henikoff,et al.  Large-scale discovery of induced point mutations with high-throughput TILLING. , 2003, Genome research.

[44]  D. Mackill,et al.  Marker-assisted selection: an approach for precision plant breeding in the twenty-first century , 2008, Philosophical Transactions of the Royal Society B: Biological Sciences.

[45]  Jianbing Yan,et al.  Natural Genetic Variation in Lycopene Epsilon Cyclase Tapped for Maize Biofortification , 2008, Science.

[46]  Yan Long,et al.  Single nucleotide polymorphism (SNP) discovery in the polyploid Brassica napus using Solexa transcriptome sequencing. , 2009, Plant biotechnology journal.

[47]  S. Rasmussen,et al.  EcoTILLING for the identification of allelic variation in the powdery mildew resistance genes mlo and Mla of barley , 2006 .

[48]  Gustavo A. Slafer,et al.  Breeding for Yield Potential and Stress Adaptation in Cereals , 2008 .

[49]  D. Neale,et al.  Patterns of Population Structure and Environmental Associations to Aridity Across the Range of Loblolly Pine (Pinus taeda L., Pinaceae) , 2010, Genetics.

[50]  M. Gribskov,et al.  The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray) , 2006, Science.

[51]  S. Ranade,et al.  Stem cell transcriptome profiling via massive-scale mRNA sequencing , 2008, Nature Methods.

[52]  M. Caboche,et al.  Mutation detection using ENDO1: Application to disease diagnostics in humans and TILLING and Eco-TILLING in plants , 2008, BMC Molecular Biology.

[53]  Heng Li,et al.  A survey of sequence alignment algorithms for next-generation sequencing , 2010, Briefings Bioinform..

[54]  Chenwu Xu,et al.  Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.) , 2010, BMC Genomics.

[55]  S. Salzberg,et al.  Bioinformatics challenges of new sequencing technology. , 2008, Trends in genetics : TIG.

[56]  D. Grattapaglia,et al.  A high-density transcript linkage map with 1,845 expressed genes positioned by microarray-based Single Feature Polymorphisms (SFP) in Eucalyptus , 2011, BMC Genomics.

[57]  Sydney Brenner,et al.  Massively parallel signature sequencing (MPSS) as a tool for in-depth quantitative gene expression profiling in all organisms. , 2002, Briefings in functional genomics & proteomics.

[58]  Carlos H. Galeano,et al.  CEL I Nuclease Digestion for SNP Discovery and Marker Development in Common Bean ( Phaseolus vulgaris L.) , 2009 .

[59]  D. Fairbanks,et al.  Development, Characterization, and Linkage Mapping of Single Nucleotide Polymorphisms in the Grain Amaranths (Amaranthus sp.) , 2011 .

[60]  J. Peleman,et al.  Breeding by design. , 2003, Trends in plant science.

[61]  Stefano Lonardi,et al.  Development and implementation of high-throughput SNP genotyping in barley , 2009, BMC Genomics.

[62]  M. Stephens,et al.  RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. , 2008, Genome research.

[63]  D. Pot,et al.  A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica1[W] , 2010, Plant Physiology.

[64]  S. Henikoff,et al.  Efficient discovery of DNA polymorphisms in natural populations by Ecotilling. , 2004, The Plant journal : for cell and molecular biology.

[65]  Akhilesh K. Tyagi,et al.  De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification , 2011, DNA research : an international journal for rapid publication of reports on genes and genomes.

[66]  T. Joshi,et al.  SNP discovery by high-throughput sequencing in soybean , 2010, BMC Genomics.

[67]  R. Van der Hoeven,et al.  Visualization of differential gene expression using a novel method of RNA fingerprinting based on AFLP: analysis of gene expression during potato tuber development. , 1996, The Plant journal : for cell and molecular biology.

[68]  J. Oard,et al.  Alternative ecotilling protocol for rapid, cost-effective single-nucleotide polymorphism discovery and genotyping in rice (Oryza sativa L.) , 2006, Plant Molecular Biology Reporter.

[69]  Muhammad Ali Amer,et al.  Genome-wide association study of 107 phenotypes in a common set of Arabidopsis thaliana inbred lines , 2010, Nature.

[70]  J. Batley,et al.  New technologies for ultra-high throughput genotyping in plants. , 2009, Methods in molecular biology.

[71]  S. Aubourg,et al.  Characterization of Arabidopsis thaliana mismatch specific endonucleases: application to mutation discovery by TILLING in pea. , 2007, The Plant journal : for cell and molecular biology.

[72]  M. Rakszegi,et al.  Mutation discovery for crop improvement. , 2009, Journal of experimental botany.

[73]  S. Tingey,et al.  Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize , 2007, Molecular Genetics and Genomics.

[74]  D. Zamir,et al.  An Induced Mutation in Tomato eIF4E Leads to Immunity to Two Potyviruses , 2010, PloS one.

[75]  Dawn H. Nagel,et al.  The B73 Maize Genome: Complexity, Diversity, and Dynamics , 2009, Science.

[76]  P. Cregan,et al.  Bulked Segregant Analysis Using the GoldenGate Assay to Locate the Rpp3 Locus that Confers Resistance to Soybean Rust in Soybean , 2009 .

[77]  M. S. Grando,et al.  A candidate gene association study on muscat flavor in grapevine (Vitis vinifera L.) , 2010, BMC Plant Biology.

[78]  A. Boualem,et al.  Engineering Melon Plants with Improved Fruit Shelf Life Using the TILLING Approach , 2010, PloS one.

[79]  Roberto Tuberosa,et al.  Genomics-Assisted Crop Improvement, Vol 2: Genomics Applications in Crops , 2007 .

[80]  N. Fedoroff.  The past, present and future of crop genetic modification. , 2010, New biotechnology.

[81]  T. Shah,et al.  High-throughput SNP genotyping with the GoldenGate assay in maize , 2010, Molecular Breeding.

[82]  Dennis B. Troup,et al.  NCBI GEO: archive for functional genomics data sets—10 years on , 2010, Nucleic Acids Res..

[83]  M. Morgante,et al.  From plant genomics to breeding practice. , 2003, Current opinion in biotechnology.

[84]  Mark H. Wright,et al.  High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.) , 2008, Tree Genetics & Genomes.

[85]  K. Takeda,et al.  A high-density transcript linkage map of barley derived from a single population , 2009, Heredity.

[86]  Yasukazu Nakamura,et al.  SNP Discovery and Linkage Map Construction in Cultivated Tomato , 2010, DNA research : an international journal for rapid publication of reports on genes and genomes.

[87]  Sanzhen Liu,et al.  High-Throughput Genetic Mapping of Mutants via Quantitative Single Nucleotide Polymorphism Typing , 2010, Genetics.

[88]  C. Bustamante,et al.  Development of genome-wide SNP assays for rice , 2010 .

[89]  G. Khush,et al.  Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR , 1997, Theoretical and Applied Genetics.

[90]  Chengying Shi,et al.  Deep sequencing of the Camellia sinensis transcriptome revealed candidate genes for major metabolic pathways of tea-specific compounds , 2011, BMC Genomics.

[91]  Patrick M Hayes,et al.  Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley , 2011, BMC Genomics.

[92]  M. Rubenfield,et al.  Model SNP development for complex genomes based on hexaploid oat using high-throughput 454 sequencing technology , 2011, BMC Genomics.

[93]  Liuda Ziaugra,et al.  SNP Genotyping Using the Sequenom MassARRAY iPLEX Platform , 2009, Current protocols in human genetics.

[94]  E. Finkel.  Imaging. With 'phenomics,' plant scientists hope to shift breeding into overdrive. , 2009, Science.

[95]  T. Ishii,et al.  Optimization of the marker-based procedures for pyramiding genes from multiple donor lines: II. strategies for selecting the objective homozygous plant , 2007 .

[96]  Y. Long,et al.  Analysis of QTLs for erucic acid and oil content in seeds on A8 chromosome and the linkage drag between the alleles for the two traits in Brassica napus. , 2010, Journal of genetics and genomics = Yi chuan xue bao.

[97]  Qifa Zhang,et al.  Genome-wide association studies of 14 agronomic traits in rice landraces , 2010, Nature Genetics.

[98]  Mihaela M. Martis,et al.  The Sorghum bicolor genome and the diversification of grasses , 2009, Nature.

[99]  Mark H. Wright,et al.  Large‐Scale Discovery of Gene‐Enriched SNPs , 2009 .

[100]  N. Barkley,et al.  Application of TILLING and EcoTILLING as Reverse Genetic Approaches to Elucidate the Function of Genes in Plants and Animals , 2008, Current genomics.

[101]  Stephen M. Mount,et al.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus) , 2008, Nature.

[102]  Yuan-Ming Zhang,et al.  Epistatic Association Mapping in Homozygous Crop Cultivars , 2011, PloS one.

[103]  H. Leung,et al.  More genomic resources for less-studied crops. , 2010, Trends in biotechnology.

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

[105]  Shirong Zhang,et al.  A phenylalanine in DGAT is a key determinant of oil content and composition in maize , 2008, Nature Genetics.

[106]  R. Bernardo,et al.  Prospects for genomewide selection for quantitative traits in maize , 2007 .

[107]  Thomas Altmann,et al.  SNP identification in crop plants. , 2009, Current opinion in plant biology.

[108]  R. Schafleitner,et al.  A sweetpotato gene index established by de novo assembly of pyrosequencing and Sanger sequences and mining for gene-based microsatellite markers , 2010, BMC Genomics.

[109]  B. Bainbridge,et al.  Genetics , 1981, Experientia.

[110]  Ibrahim Emam,et al.  ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments , 2010, Nucleic Acids Res..

[111]  A I Saeed,et al.  TM4: a free, open-source system for microarray data management and analysis. , 2003, BioTechniques.

[112]  S. S. Yang,et al.  Using RNA-Seq for gene identification, polymorphism detection and transcript profiling in two alfalfa genotypes with divergent cell wall composition in stems , 2011, BMC Genomics.

[113]  J. Dvorak,et al.  Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence , 2011, BMC Genomics.

[114]  G. Weinstock,et al.  A SNP discovery method to assess variant allele probability from next-generation resequencing data. , 2010, Genome research.

[115]  Ronald W. Davis,et al.  Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.

[116]  Robert J. Elshire,et al.  A First-Generation Haplotype Map of Maize , 2009, Science.

[117]  R. Varshney,et al.  Genome-wide association mapping: a case study in bread wheat (Triticum aestivum L.) , 2010, Molecular Breeding.

[118]  J. Cañizares,et al.  Analysis of gene expression during the fruit set of tomato: A comparative approach , 2007 .

[119]  Kenneth L. McNally,et al.  Genomewide SNP variation reveals relationships among landraces and modern varieties of rice , 2009, Proceedings of the National Academy of Sciences.

[120]  H. Zhai,et al.  Breeding strategies for optimum heading date using genotypic information in rice , 2010, Molecular Breeding.

[121]  Jinghua Xiao,et al.  Correction: Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP/SSR Markers , 2011, PLoS ONE.

[122]  S. Deschamps,et al.  Rapid Genome‐wide Single Nucleotide Polymorphism Discovery in Soybean and Rice via Deep Resequencing of Reduced Representation Libraries with the Illumina Genome Analyzer , 2010 .

[123]  M. Yano,et al.  Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms , 2010, BMC Genomics.

[124]  M. L. Ramos,et al.  Identification and characterization of a hypoallergenic ortholog of Ara h 2.01 , 2009, Plant Molecular Biology.

[125]  R. Bernardo.  Genomewide selection for rapid introgression of exotic germplasm in maize. , 2009 .

[126]  Xinliang Chen,et al.  De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas) , 2010, BMC Genomics.

[127]  T. Sakurai,et al.  Genome sequence of the palaeopolyploid soybean , 2010, Nature.

[128]  A. Christoffels,et al.  Genome-wide SNP identification by high-throughput sequencing and selective mapping allows sequence assembly positioning using a framework genetic linkage map , 2010, BMC Biology.

[129]  Paul D. Shaw,et al.  A structured mutant population for forward and reverse genetics in Barley (Hordeum vulgare L.). , 2004, The Plant journal : for cell and molecular biology.

[130]  S. Myles,et al.  Rapid Genomic Characterization of the Genus Vitis , 2010, PloS one.

[131]  Aaron J. Lorenz,et al.  Genomic Selection in Plant Breeding. Knowledge and Prospects. , 2011 .

[132]  Dov A. Pechenick,et al.  Association mapping and marker-assisted selection of the lettuce dieback resistance gene Tvr1 , 2009, BMC Plant Biology.

[133]  B. Sobral,et al.  Open Access Research Article Transcriptome Sequencing and Comparative Analysis of Cucumber Flowers with Different Sex Types , 2022 .

[134]  T. Brutnell,et al.  Exploring plant transcriptomes using ultra high-throughput sequencing. , 2010, Briefings in functional genomics.

[135]  Peter J. Bradbury,et al.  The Genetic Architecture of Maize Flowering Time , 2009, Science.

[136]  P. Wincker,et al.  Bioinformatic analysis of ESTs collected by Sanger and pyrosequencing methods for a keystone forest tree species: oak , 2010, BMC Genomics.

[137]  Ed Ready,et al.  Soybean Genomics Research Program Strategic Plan , 2011 .

[138]  J. Dvorak,et al.  Population- and genome-specific patterns of linkage disequilibrium and SNP variation in spring and winter wheat (Triticum aestivum L.) , 2010, BMC Genomics.

[139]  Paul Gepts,et al.  Plant Genetic Resources Conservation and Utilization: The Accomplishments and Future of a Societal Insurance Policy , 2006 .

[140]  Ernesto Picardi,et al.  Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing , 2010, Briefings Bioinform..

[141]  R. Henry,et al.  Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. , 2009, Plant biotechnology journal.

[142]  T. Mohapatra,et al.  Integrating marker assisted background analysis with foreground selection for identification of superior bacterial blight resistant recombinants in Basmati rice , 2008 .

[143]  Kevin P. Smith,et al.  Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm , 2011, Molecular Breeding.

[144]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[145]  Ramesh Buyyarapu,et al.  Generation and analysis of expressed sequence tags (ESTs) for marker development in yam (Dioscorea alata L.) , 2011, BMC Genomics.

[146]  Daowen Wang,et al.  Analysis of Pina and Pinb alleles in the micro-core collections of Chinese wheat germplasm by Ecotilling and identification of a novel Pinb allele , 2008 .

[147]  Joaquín Dopazo,et al.  BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments , 2005, Nucleic Acids Res..