Abstract
BackgroundGene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses.We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (Bos taurus) to capture (enrich for), and subsequently sequence, thousands of exons of B. taurus, B. indicus, and Bison bison (wild bison). Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits.ResultsWe successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the B. taurus genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes.ConclusionsThis study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.
Highlights
Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation
Our understanding of the molecular, genetic basis of adaptations and phenotypic differentiation among individuals will advance quickly thanks to new molecular techniques. This understanding is crucial given that accelerating environmental change and human population growth are increasingly threatening natural populations of fish and wildlife as well as increasing demands for agricultural production in domesticated species. This makes it urgent in many wild and domestic species to investigate the genetic basis of fitness, adaptation, and
The entire exon sets were targeted for capture
Summary
Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Our understanding of the molecular, genetic basis of adaptations and phenotypic differentiation among individuals will advance quickly thanks to new molecular techniques This understanding is crucial given that accelerating environmental change and human population growth are increasingly threatening natural populations of fish and wildlife as well as increasing demands for agricultural production in domesticated species. This makes it urgent in many wild and domestic species to investigate the genetic basis of fitness, adaptation, and Understanding the genetic basis of phenotypes generally requires genotyping thousands of gene-targeted loci, genome-wide. Because exon sequences are relatively conserved we hypothesized that most exons from one species (e.g. with a sequenced genome) could be used to capture exons from another species for use in generation sequencing for SNP discovery
Sign-in/Register to view highlights & summary Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
