Agrigenomics: Tools for plant and animal breeding, fish and fowl

By Enrique Neumann

The term genomics might at first lead you to think of the human genome and the new micro-industry subsectors it has spawned, from prenatal genetic screening for heritable diseases (and one day perhaps to select for "desirable" traits) to companion diagnostics for personalized medicine, and nutraceuticals targeted to correct imbalances in the gut microbiome.Those same types of genomic applications and many, many more can translate directly to the plant and animal world, in which agrigenomic technology is transforming traditional approaches to breeding of commercial species and monitoring and protection of wild populations.

Agrigenomic research and development produces hardy rice variants that grow in adverse conditions.

The methods and tools for agrigenomic analysis – including microarrays for genotyping and single nucleotide polymorphism (SNP) analysis, next-generation sequencing (NGS), and polymerase chain reaction (PCR) – are familiar ones. The demands are for ever-faster, more powerful technology, with ongoing needs for higher sample throughput and multiplexing capabilities and increased automation and reliability. These challenges are compounded by the greater complexity of working with the polyploid genomes of many plant species.

Improving crop yields and animal breeding to feed the world

Illumina recently announced the Donald Danforth Plant Science Center as the 2016 recipient of its Greater Good Initiative Grant. The grant is intended "to help identify measures that can increase crop yields and improve livestock welfare and productivity to alleviate poverty and hunger in the developing world."¹ The Danforth Center's project, in collaboration with researchers at HudsonAlpha Institute for Biotechnology, is to study the genetic diversity of grain sorghum (Sorghum bicolor) -- a main source of nutrition for people in sub-Saharan Africa -- and use the information to guide breeding programs aimed at improving the yield and stress-tolerance of the crop plant.

This type of agrigenomic research is on the rise as global population growth, decreasing acreage of arable land, and climate change are applying mounting pressure on the environment, ecosystems, and farmers' ability to produce enough food. This pressure is driving efforts to develop higher-producing crops, livestock for both dairy and meat, chickens for eggs, etc., using less land, water, and other resources, fewer pesticides and antibiotics, and more sustainable farming practices that have a less harmful impact on the environment. Companies such as Bayer CropSciences, Monsanto, Dow Agro Sciences and Syngenta are focused on increasing crop yields, protecting agricultural ecosystems from the effects of climate change, and developing new plant varieties that require less water and chemicals to grow and thrive. They are relying on genomic strategies to guide and accelerate their efforts.

Using NGS and microarrays to probe plant and animal genomes

"Recent advances in high-throughput sequencing and phenotyping platforms have transformed molecular breeding to genomics-assisted breeding," according to Kole et al.³ "Genomics possesses the potential to increase the diversity of alleles available to breeders through mining the gene pools of crop wild relatives," they add. Furthermore, the gene editing technology CRISPR-Cas9 "has emerged as an alternative to classical plant breeding and transgenic methods to improve crop plants."

Using the information gleaned from genomics research, including genome, exome, transcriptome sequencing, genotyping, and genome-wide association studies (GWAS), researchers are able to select for and introduce genes, for example, to promote disease or drought resistance, help plants adapt to high salinity soil, and enhance the taste, texture, or appearance of fruit, vegetables, and meat. These same strategies are being applied to fish populations to increase commercial availability, overcome problems with modern fish farming, and protect endangered species. In November 2015, the U.S. FDA approved the first genetically modified animal intended for use as food, AquaBounty's genetically modified AquAdvantage® Salmon, and Health Canada followed suit this past May.^4,5

"Next-generation sequencing (NGS) can be useful to agricultural researchers who want to understand the complex genomes of crops or livestock, and can be used to develop a reference genome sequence from which to develop future tools for analysis of genetic traits in these plants and animals," according to Mike Thompson, Ph.D., Director of Market Development for Agrigenomics at Illumina.⁶

 "Seed companies and academic institutions alike can use genomic information to accelerate breeding programs by selecting for combinations of genomic markers associated with desirable traits such as drought tolerance, disease resistance, or crop yield," adds Dr. Thompson. In livestock breeding, "Genome-wide arrays are utilized at the birth of an animal to predict the future performance of that animal," he explains. Genetic sequencing has a range of applications, such as characterizing the animals, as well as the viruses that infect them and the bacteria that live on or in them, to help prevent and treat disease outbreaks. "Similarly, the bacteria colonizing the gut of livestock animals can be sequenced and analyzed to enable wide-ranging research into optimizing animal feed and diagnosing infections, among other applications," Dr. Thompson says.⁶      

Whether your technique of choice is de novo sequencing using NGS, genotyping with microarrays, SNP analysis to identify variation among species, RNAseq to study gene expression, or targeted resequencing to probe the exome, increasingly sophisticated instruments and methods are available. To improve the efficiency and accuracy of genomic workflows, automated solutions such as the Tecan Freedom EVO® and Fluent™ workstations standardize sample preparation for increased reproducibility.

Download the case study to discover an efficient and reliable cloning workflow.

 FURTHER READING

1. Illumina (press release). Illumina announces Donald Danforth Plant Science Center to receive Agricultural Greater Good Initiative Grant to improve food security in Sub-Saharan Africa.
   Available at: www.illumina.com (Last accessed June 2016). 
2. Kole C, Muthamilarasan M, Henry R, et al. Application of genomics-assisted breeding for generation of climate resilient crops: Progress and prospects. Front Plant Sci 2015;6:563.
3. AquaBounty (press release). FDA approves AquAdvantage® Salmon.
   Available at: www.aquabounty.com (Last accessed June 2016).
4. AquaBounty (press release). AquaBounty’s AquAdvantage® Salmon approved by Health Canada.
   Available at: www.aquabounty.com (Last accessed June 2016).
5. The Agrigenomics Market. Technology Networks. May 7, 2015.
   Available at: www.technologynetworks.com (Last accessed July 2016).