Plant and animal genomics articles

In this blog we will demonstrate how to use Gencove Explorer to perform genomic prediction in maize. Specifically, we will be building a genomic prediction model for maize grain yield. Genomic prediction is a technique from statistical genetics that uses genome-wide genetic markers to estimate the breeding value (sometimes referred to as genetic merit) of plants or animals in modern breeding programs. This estimated breeding value (EBV) can be used to identify and selectively breed the best individuals in the population in order to improve agronomically relevant traits.

In recent years, the scientific community has made remarkable strides in genomics, transforming our understanding of the genetic makeup of various organisms. Among these, honey bees (Apis mellifera) hold a special place due to their crucial role in agriculture. Despite this progress, decoding the genomic variation in honey bees presents unique challenges, with high recombination rates and large genomic variation.

Dog research is at a crossroads. Like in humans, genetic tools could revolutionize veterinary care and improve the health and welfare of all dogs, but widely used genetic testing services don’t provide the information needed by researchers to achieve this vision. A collaboration between Gencove, genomic scientists, and dog breeders has developed a new solution that combines high-accuracy genetic testing with comprehensive whole genome genotyping. This dual-purpose product supports breed ancestry analysis, Mendelian disease testing, and large-scale genomics.

At Gencove, we’ve long talked about Moo-res law, the trend of increasing genotype adoption in the cattle breeding world, with global genotyping in the cattle industry likely to hit 5 million samples annually by mid-decade. The successes of genomic selection are well known, led by the US dairy evaluation’s pioneering efforts over 15 years ago, with adoption following in many cattle breeding programs globally.

Gencove and Twist Biosciences have partnered to pressure test the utility of lp-WGS plus target capture and imputation for a major crop species, soybeans, demonstrating that lp-WGS with target capture works well in plants and covers a large panel.

Over the past decade, the cost of genome sequencing has significantly decreased, leading to a rise in popularity of alternative sequencing methods such as low-pass whole genome sequencing instead of genotyping arrays. To meet this demand, at Gencove, we offer a cost-effective solution for generating genome-wide information by providing low-pass whole genome sequencing plus imputation as a high-throughput alternative to genotyping arrays. Our previous research has already established that low-pass whole genome sequencing outperforms traditional genotyping arrays in terms of imputation in humans (Li et al., 2021). In this blog post, we describe the results of a recent experiment where we demonstrate that imputation using low-pass whole genome sequencing is also superior to genotyping arrays in cattle.

New pipeline available: salmon

Invest in a genotyping solution that changes with your breeding program. The Gencove platform ensures backward compatibility, adaptability to new markers and reference genomes, additional analyses, and continual innovation.

Improve molecular breeding efficiency with a modern genotyping approach that can be set up in a few weeks plus turns your samples around quickly!

Gencove’s low-pass sequencing platform is at cost-per-sample price parity with many microarray assays across a wide range of species in both plants and animals. That makes Gencove the best choice for getting the utility of sequencing data at microarray prices.

There’s no question that sequencing is a powerhouse of utility for genetics in breeding. However, does it meet the requirements to become a routine tool for genomic selection in breeding programs?

The Simplot and Gencove genomic EPD provides a benchmark from which bulls can be evaluated for cardiac morphology significantly reducing their calves’ morbidity and mortality and increasing their overall economic performance.