Agrigenomics application notes and case studies

LGC works with Universities& labs on application notes & case studies to showcase how we are accelerating Marker-Assisted Selection (MAS) and Breeding (MAB)

University of Bristol - Wheat genomics application

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.)

Read on to see how researchers led by the University of Bristol used KASP™ genotyping to validate a large number of varietal SNPs mined from UK and European cultivars of wheat.

The team created the first large scale assembly of genotyping and genetic map information for elite UK wheat varieties based on individual SNP markers, and were the first to demonstrate the use of KASP-based technology to genotype wheat cultivars and generate an extensive linkage map.

Wheat is a key food source both for humans and animals, but the modern varieties are reducing in genetic diversification. Identifying and breeding in useful genes from related species could increase its resistance to pests and diseases, and increase crop yields.

The LGC wheat genotyping panel, developed in conjunction with the University of Bristol, School of Biological Sciences UK, contains over 7,000 functionally validated SNP assays that breeders and scientists can use to enable the development of precision breeding in wheat hybrids. The panel offers pre-validated assays thus facilitating cost benefits, guaranteed performance and fast delivery.

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The Jackson Laboratory – Mouse genomics app note

Trans-regulation of mouse meiotic recombination hotspots by Rcr1

Meiotic homologous recombination generates genetic variety amongst offspring, and ensures that the chromosomes are segregated accurately during meiosis. Recombination occurs in hotspots, and the aim of this study was to identify trans-acting factors that control hotspot positioning in mammals, specifically congenic mice, using a combination of analyses including SNP genotyping.

Use of KASP to develop speed congenics

Congenic strains of mice typically require 10 generations of backcrossing to generate, which can be a time-consuming process. The time involved in creating congenic mice can be significantly reduced through the use of marker-assisted selection (MAS), and this is termed ‘speed congenics’. Genetic markers, such as SNPs are used to identify mice from the second generation of backcrossing that contain the highest percentages of the desired genome; these mice are then used as parents for the subsequent generation. This marker-assisted selection procedure is repeated for each subsequent generation, and hence enables congenic mice to be attained after only three or four generations of backcrossing. Read here about our ‘'mouse panel’ which offers a set of pre-validated KASP genotyping assays that can be easily applied to the development of speed congenics.

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Hy-Line - app note

The quality of eggshells is an important trait for commercial egg production. A number of studies have linked polymorphisms in the gene encoding the eggshell protein ovocalyxin-32 (OCX32) with eggshell features including strength and thickness, indicating that variants in the gene may be relevant to the selection of commercial egg-laying poultry lines.

In this study (Fulton et al., 2012), exons 2-6 of the OCX32 gene were sequenced in multiple elite commercial egg-laying lines, and SNP detection and analysis carried out using LGC’s KASP genotyping chemistry to identify multiple polymorphisms. In contrast with other studies, this work identified a large number of SNPs not previously reported, in a far greater number of poultry lines, and thus encompassing a much larger gene pool.

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University of Bristol - Wheat genomics case study

Read more about why Professor Keith Edwards at Bristol University said “We selected LGC’s KASP genotyping chemistry because it was the only platform on the market that could overcome our challenges. We had confidence in the technological ability of KASP to increase our quality of data, ensuring the accuracy and efficiency of our findings, in addition to improving the credibility and validity of our studies. We worked closely with LGC to both validate SNPs as a marker system in wheat and transfer the SNP markers, as working assays, to UK wheat breeders.”

Why wheat?

Wheat is one of the three most important crops for human and livestock feed, and with food supply an increasing global concern, the pressure is on to increase cereal crop production as a solution to feeding the growing world population. It has been estimated that the demand on cereal production will increase by 50% by 2030; scientists and breeders alike must now look to understanding the genetic make-up of wheat to help maximise its growing potential.

Industry challenge: struggling to meet a growing demand

Compared with other crops, the increase in wheat yields has slowed since the ‘green revolution’ of the 20th century due to the domestication of the crop.

This domestication of wheat has resulted in a decline of genetic diversity and it has been suggested that in order to increase it, genes from ‘wild relatives’ of the crop could be introduced. However such strategies often referred to as pre-breeding, can be resource intensive.

Aside from the challenge of meeting a growing global demand for wheat, the crop is also vulnerable to pests and disease. To combat this, researchers need to identify genes within the wheat genome that can provide a strong and durable resistance; access to new screening technology is essential in defending it from this and other threats and to sustainably produce sufficient and safe food.

The LGC wheat genotyping panel, developed in conjunction with the University of Bristol, School of Biological Sciences UK, contains over 7,000 functionally validated SNP assays that breeders and scientists can use to enable the development of precision breeding in wheat hybrids. The panel offers pre-validated assays thus facilitating cost benefits, guaranteed performance and fast delivery.

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The Jackson Laboratory – Mouse genomics case stud

The Jackson Laboratory, in a joint effort with LGC, has developed 1638 working assays for pre-validated mouse SNPs. These assays provide a powerful tool for the mapping of traits within mouse disease models and breeding populations.

In addition, The Jackson Laboratory has used LGC’s KASP genotyping to facilitate a key part of their recent research into meiotic recombination hotspots (Parvanov et al. (2009) PLoS Biol; Parvanov et al. (2010) Science).

“The advancement in genotyping technology has allowed us to design compatible assays to narrow down the genomic region and identify the gene responsible for hotspot regulation. The discovery of Prdm9 will lead to further improvements in our research to gain insight on its functions. KASP has been a valuable tool in reaching those meaningful conclusions and we are confident that it will continue to support us in better understanding of genetic factors underlying human fertility and evolution.” Dr. P. Petkov, The Jackson Laboratory.

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Colorado State University - Wheat Breeding and Genetics Program

The Colorado State University Wheat Breeding and Genetics Program is a long standing initiative run out of Colorado State University (CSU), USA. Lead by Scott Haley, Professor of Plant Breeding at CSU, this ground breaking program is using traditional breeding techniques combined with modern plant genomics to breed the next generation of wheat varieties for the Colorado wheat growing industry and beyond. As well as breeding crops tailored for the Colorado climate, traits for human health are now a focus, including traits related to starch production and antioxidant properties.

In the past year, the Wheat Breeding and Genetics Program has conducted over 16,000 KASP™ assays to enable selection for 15 different trait-associated SNP markers. They have had great success with how easy KASP genotyping is to use in their labs, and found that KASP assays lend themselves very well to exactly the type of work that they are doing. After an initial period trialling KASP genotyping to see whether it would work for their projects, the team has now been using KASP in earnest for full blown production work for over a year. Adoption of KASP genotyping has enabled the team to do more where previously costs and time prohibited them.

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Seed Biotechnology Center - Pepper case study

The group at the Seed Biotechnology Center at University California, Davis are applying the most up to date tools and understanding of genetics, genomics and molecular biology to characterise peppers and their diverse characteristics.

Pepper is a highly valued plant globally with demand increasing 40-fold since the 1980s. One of the biggest problems the pepper industry faces is Phytophthora capsici (Pc), root rot or late blight, from which most commercial pepper varieties suffer yield losses despite good management practices and resistance strategies.

Identifying and selectively breeding for pepper strains resistant to Pc is exactly what Allen Van Deynze and his fellow researchers at the Seed Biotechnology Center have set about achieving with significant progress, as reported in their recent paper “CaDMR1 cosegregates with QTL Pc5.1 for resistance to Phytophthora capsici in Pepper (Capsicum annuum)”1.The study identified a gene that encodes an enzyme which is highly associated with Pc resistance in pepper; this is the first report to relate candidate genes to a known Pc resistance factor in pepper.

“LGC’s high-throughput and fast turnaround times (40 SNP markers each run on 250 different plant lines in 6 weeks) produced high-resolution data that was crucial for validating our research and getting it published ahead of the field.” said Van Deynze.

1Rehrig, W. Z., Ashrafi, H., Hill, T., Prince, J., & Van Deynze, A. (2014). CaDMR1 Cosegregates with QTL Pc5.1 for Resistance to Phytophthora capsici in Pepper (Capsicum annuum). The Plant Genome, 7(2).

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Hy-Line - case study

Hy-Line International strive to create the highest standard of commercial egg-laying hen with good liveability, feed efficiency, nesting behaviour and persistency of lay that also produces a good quality shell and subsequently the best egg to get to market. Hy-Line International uses genetic research and testing to combat these challenges.

The benefit for Hy-Line’s research is KASP’s ability for rapid SNP testing while still producing highly accurate results needed for input into a commercial breeding program.

KASP genotyping perfectly fits the requirements of very large numbers of samples to be tested over a large number of individual SNP assays; recent research by Hy-Line on OCX32, a candidate gene for selection for eggshell traits in commercial poultry populations, is a perfect example of the use of KASP genotyping. Janet Fulton commends KASP’s versatility and accuracy, explaining that,

“You have so much control over what you can do in terms of designing the primers to detect your specific variants. You can detect this variation with different equipment but using the same materials and you’ll get the same results. This makes it easy to adjust assay volumes when moving between low and high numbers of samples and manual to semi-automated systems.”

Hy-Line found that KASP genotyping allowed them to do rapid in-house detection of SNP variations and that the technology permitted them to carry out individual testing of thousands of samples, for hundreds of carefully selected SNPs, at a rate of over 100,000 tests per day.

“The KASP technology provided the best and most rapid identification of genetic variation within our populations." Dr. Fulton

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