Providing energy-rich protein to the world while reducing the environmental impact is one of the largest challenges facing the animal industry today.
New technologies that will help to identify which animals will perform optimally in their environment is needed to help farming into the future.
One important aspect of selecting the right breeding animals is understanding structural variations (SV) - these regions of DNA play a major role in genetic diversity and physical variations within species.
But while they’re important, SVs remain largely unexplored in most domesticated animals.
AgResearch is conducting one of the first studies in New Zealand sheep to investigate how to capture and cost-effectively use SV information in New Zealand sheep.
The Genomics Aotearoa-funded project is looking at two technology approaches - SNP-Chip and Oxford Nanopore Technologies (ONT).
Genomics Aotearoa Post Doctoral researcher Dr Rebecca Clarke explained the research focus is on adapting technology to more quickly gather and process valuable genetic information from sheep trials, and from that look at how to cost-effectively integrate these tools into the animal industry to improve selection.
Oxford Nanopore Technologies
A major hurdle in utilising useful genetic data has been the lack of cost-effective and high-throughput methods for data capture.
The software-controlled enrichment that is unique to the nanopore sequencing platform enables targeted sequencing of specific regions of a genome or species of interest at higher coverage.
Adaptive sampling enables many applications to be processed with very basic sample preparation, and it allows simultaneous capture of multiple sources of information (such as methylation, mutations, and structural variances).
Genome-wide association studies (GWAS) help scientists identify genes associated with a particular disease (or another trait). This method studies the entire set of DNA (the genome) of a large group of animals, searching for small variations, called single nucleotide polymorphisms (SNPs).
Dr Clarke has been using adaptive sampling techniques to investigate regions of interest surrounding GWAS peaks and known copy number variation regions in sheep.
Sample multiplexing has also been trialled to evaluate the possible use of adaptive sampling as a cost-effective tool for the animal industry.
Utilising existing SNP-Chip data to identify SV in NZ sheep.
SNP arrays can be used to determine SV by utilising the intensity values derived from each sample.
Commercial SNP arrays are low cost and high density providing an excellent resource in SV detection and functional studies.
The International Sheep Genomics Consortium Ovine High-density chip (HD-SNP) contains 606,006 SNPs and has genotyped thousands of animals in New Zealand’s sheep industry over the last few years. Genotyping is the process of determining differences in the genetic make-up (genotype) of an individual by examining the individual's DNA sequence.
This genotyped population also contains physical data associated with breeding traits, which together can provide an excellent opportunity for investigating structural variations in New Zealand sheep.
Adaptive sampling techniques, SNP array data and assembles, will be used to identify and validate the number of copies of a particular gene present in the genome of an individual (known as CNV), this will feedback into selection of animals for improved genetic gains.
About Rebecca
Rebecca completed a Bachelor of Science (Hons) majoring in Genetics, followed by a PhD at the University of Otago. Her doctoral thesis was titled “Investigating the early stages of regeneration and wound healing in Botrylloides diegensis”.
Her post-graduate work was focused on whole body regeneration in a specific species of sea squirts which have the ability to regenerate their entire bodies from as little as 100 cells in about eight days. Her research focused on the genes and molecular pathways that were utilised to undertake this process and how this differs from the events undertaken for wound healing.
Rebecca’s post-doctoral research on agricultural genetics and genomics has come full circle, from working in GenomNZ (a commercial agricultural genetics lab) in high school and through a summer studentship at AgResearch during her University studies.
Area of expertise:
- Transcriptomics and genomics
- Oxford Nanopore Sequencing Technologies
- Structural Variation Identification