Application of large-scale sequencing to marker discovery in plants

• Published in: Journal of biosciences Vol. 37; no. 5; pp. 829 - 841
• Main Authors: Henry, Robert J, Edwards, Mark, Waters, Daniel L E, S, Gopala Krishnan, Bundock, Peter, Sexton, Timothy R, Masouleh, Ardashir K, Nock, Catherine J, Pattemore, Julie
• Format: Journal Article
• Language: English
• Published: India Springer-Verlag 01-11-2012; Springer Nature B.V
• Subjects: Biochemistry; Biomedical and Life Sciences; Biomedicine; Breeding; Cell Biology; Contig Mapping; Deoxyribonucleic acid; DNA; DNA fingerprints; Epigenesis, Genetic; Gene Expression; genes; Genetic Markers; Genome, Plant; Genomic Library; genomics; Genotype; Genotypes; germplasm conservation; High-Throughput Nucleotide Sequencing - methods; Hybridization; Hybridization, Genetic; Life Sciences; Microbiology; nucleotide sequences; parents; Phenotype; phenotypic variation; Phenotypic variations; Plant Sciences; Plants, Edible - genetics; polymerase chain reaction; Polymorphism, Single Nucleotide; progeny; Quantitative Trait Loci; Selection, Genetic; sequence analysis; transcriptomics; Zoology; plants; DNA markers; sequencing
• ISSN: 0250-5991; 0973-7138
• DOI: 10.1007/s12038-012-9253-z

Advances in DNA sequencing provide tools for efficient large-scale discovery of markers for use in plants. Discovery options include large-scale amplicon sequencing, transcriptome sequencing, gene-enriched genome sequencing and whole genome sequencing. Examples of each of these approaches and their potential to generate molecular markers for specific applications have been described. Sequencing the whole genome of parents identifies all the polymorphisms available for analysis in their progeny. Sequencing PCR amplicons of sets of candidate genes from DNA bulks can be used to define the available variation in these genes that might be exploited in a population or germplasm collection. Sequencing of the transcriptomes of genotypes varying for the trait of interest may identify genes with patterns of expression that could explain the phenotypic variation. Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Examples of application of the above-mentioned techniques have been described.