Agric-Bioformatics is a data analytics company that provides user-interface and the intelligence to end-users to aggregate and visually analyze data.

Our first product launch, AgBoost, is designed as a data driven tool specifically to aid livestock producers to optimally manage and selectively breed genetically superior animals. We aim to provide livestock producers an affordable, easy-to-use tool that allows for better access to , and understanding of , genomic information. Agric-Bioformatics overall goal is to help all livestock producers and Farmers to be more sustainable and improve productivity.

AgBoost^® Frequently Asked Questions

• What are the benefits of using livestock genomics on my herd? Use of scientific information about the genetic merit and superiority of individual animals and herds of animals in livestock production can optimize and/or increase the commercial value of the livestock. Genetic information may provide guidance as to how producers feed their livestock (i.e., nutrigenomics), breed their livestock, valuate individual animals, forecast the value of a herd, and maintain high-quality animal lineages through parentage and/or lineage traceability.



• How does AgBoost ^® perform genetic analysis of livestock? The AgBoost ^® technology platform enables producers to input and maintain a personalized genetic database of individual and herds of animals in order to assess and/or change genetic profiles of their agricultural and livestock products, suggest and/or select optimal breeding pairs, assess the value and forecast of livestock, estimate the optimal time to keep livestock before sales, and track lineage or crops or animal, and provide nutritional recommendations. AgBoost ^® is a cloud-based technology, so producers have access to their livestock information at all times and available from any computing device.



• Why is Genomic Profiling and Assessments of livestock important? The Genetic Profiling and Assessments feature of AgBoost^®is a simple user interface and profiling process that gives producers the ability to input genetic information about individual and/or herds of animals, and to use that genetic information to rank and/or sort their animals based on specific genetic merit and/or traits of interest.



• How does AgBoost ^® perform Valuation and Forecasting of livestock? The Valuation and Forecasting feature of AgBoost ^® uses a collection of relevant genomic data incorporated with real-time market data about the agriculture products (e.g., feed prices, sale barn data), and enables easy visualization of a genetic profile, performance qualities and marketability. The valuation feature is easy to understand, easy to interpret, and easy for the producers to assess and make decisions regarding the value of livestock and to estimate the optimal time to keep livestock before sale.



• What type of sample is required to get genetic testing on my livestock performed? Since it is generally the easiest type of sample for a producer to retrieve from an animal, the preferred sample to perform DNA genetic testing for livestock genomics is an animal hair sample. However, the hair sample should contain the root (i.e., the white or black bulb at the base of the hair), which comprises DNA upon which genetic analyses will be performed. Other DNA samples, such as animal blood or tissue may also be used.

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The Science of Genomics - Animal Agriculture

1. Why genetics is important?

Genetics is the study of inheritance and in animal breeding, we use what we know about genetics to improve the merit of our cattle. If the genetic merit of a herd is not high, producers will incur a lot of unnecessary costs (e.g. extra feed, replacement costs, and veterinary costs). In other words, genetics creates the potential for what an animal can be, management delivers on that potential. If the potential is not there, either very expensive management or no amount of management can deliver the animal you want. Genetic improvement provides a way for cattle producers to enhance the performance of their herds. The investment in genetic improvement is important and worthwhile due to it being cumulative (improvements made in one generation are added to those made in previous generations) and permanent (the performance of an animal is influenced for life and the superior genetics can remain in the selection population).

2. Tools for genetic improvement

• Data recording
  Simply put you have to measure what you want to improve. Or, in the modern era of genomics, capitalise on those measurements and research and that have gone into the development of tools developed for DNA assisted selection (genomic selection). There are many software available for the capture of phenotypic data and its subsequent analysis. The analysis of this data for genetic merit usually requires a third party.
  
  
• Parentage and pedigree recording
  This also ties into the aforementioned data recording. To know what sire does what and/or to build a pedigree of your herd or population, parentage need to be known on animals of interest. The investment in parentage verification has been shown to have a huge benefit when choosing or culling breeding stock and is a necessity when doing a genetic evaluation.
  
  
• Genetic merit calculations (EBVs and EPDs)
  Choosing animals based on how they look comes with all types of pitfalls. One animal may look better than the other for a whole host of reasons (better management from one farm to the next, different parity of dam, different age at time of selection, mother had more milk etc.) which clouds the judgment of an individual animal's true genetic merit. To this end, expected breeding values (EBVs) or expected progeny differences (EPDs) are genetic merit scores which are derived by pulling apart the environmental and genetic effects. Ranking animals based on their genetic merit is best practice when choosing the best breeding animals.

3. Another new tool for genetic improvement - Genomics

• What is genomics?
  Genomics is a branch of molecular biology that's concerned with the structure, function, evolution and mapping of genomes (a genome being the whole compliment of genes in an organism). We use this new technology to increase the accuracy of our selection which in turn equates to an increase in the rate of genetic gain.
  
  
• How is it used?
  When talking about utilizing genomic technology for breeding and genetics, the term "density" needs further understanding. Cattle's genetic code is ~3bn pairs of letters long but we are only interested in those that show differences among animals. 35m of these are single nucleotide polymorphisms (SNP) which show difference among animals and largely dictate the physical differences we see e.g. live weight, stature, coat color, butterfat, horns, marbling, ADG etc. Different SNP across the genome are associated with different traits (fig 1.). To measure all ~35m of these SNP is very expensive and so we take smaller snapshots of these SNP which makes genotyping affordable for animal breeding and genetics purposes. One could categorise these densities or panels into 5 different categories:
  
  
  • Small panel: Ranging from just a few SNP to ~2k SNP. Used for parentage, condition testing and population specific genomics.
  • Low Density (LD): ~5k to 3k SNP. Used for genomic prediction/selection purposes when there are a lot of higher density genotypes available to refer to.
  • Medium Density (50K): 50k to 100k SNP. This density is able to tell you a lot about your population without having to go any denser. Usually a breed will begin by building a good reference set of 50k to be able to elucidate what less dense genotypes mean for performance traits.
  • High Density (HD): 500k to 1M SNP. Not so popular any more as the cost benefit ratio (benefit being an increase in EPD accuracy) was low.
  • Whole Genome Sequence (WGS): A measure of an animal's entire genome. Presently used for research. Too expensive to be commercially employed.
  
  
  

  Fig 1. Schematic interpretation of a genome with different SNP associated with different traits

  
  
  
• Utilizing genomics
  
  
  • Parentage: Either verification or discovery.
  • Condition Testing: The presence of deleterious recessive alleles in a population can be problematic as they can result in dead, deformed or very sick progeny. The genetics for a condition may be present in a population but may not present hence the importance of testing.
  • Genomic selection (GE-EPDs, MBVs, Profiles): Inferring an animal's genetic merit is one of the more modern uses of a genotype. These predictions are delivered as genomically enhanced EPDs (GE-EPDs) or as molecular breeding values (MBVs) which are based solely on genotype.
  • Nutrition (Breed composition, inbreeding, mate allocation, relationships/inbreeding, nutrition); Management of an animal or group of animals can be differentiated based on their genetics e.g. different nutritional responses. Adoptable tools in this field are currently in the research phase.
  • Breed proportion; Knowledge of the breed proportion is useful in the design of mating programs to maximise heterosis.
  • Inbreeding, mate allocation & relationships; genomic matings or "precision breeding". Avoid potential inbreeding of certain matings or investigate whether a potential mating would indeed result in inbreeding.
    
    
  Once all the information is in front of you, it can be a daunting decision to make sense of it all and many traits are economically relevant at the same time. For this, we use a balanced selection objective which is key to multiple trait selection. Depending on whether you want to create a terminal, maternal or an all-purpose animal, that end goal will dictate how much selection pressure you place on any one trait or group of traits. Again, looking at the genetic merit for different traits on different animals will enable you to rank potential selection candidates. For example, when multiple traits are indexed together for a maternal type animal, most often, fertility will command the greatest relative economic weight (fig 2.). This selection index approach is ideal when making sense of a plethora of data at the same time.
  
  

  Fig 2. Example of a maternal index where different traits are weighted based on their economic relevance

  
  

Conclusions

Utilizing genomics will increase the accuracy of genetic evaluations of cattle. Where genetic evaluation is presently performed using pedigree analysis, genomics will enhance this evaluation. Where genetic evaluation of an animal is absent altogether, it now enables genetic merit scores to be delivered on a cohort of selection candidates. The accuracy from genomic means greater confidence that the estimated breeding values will be reflected in their progenies performance which results in accelerated genetic gain.