Breeding Grasscutter: Sequencing Its Genome To Combat Its Aggressiveness

By Marian Yaa Baby Attakumah
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By Marian Yaa Baby Attakumah

6/27/2013 12:16:33 AM -

The genome of an organism is the totality or the entirety of its genetic make-up. Sequencing this genome, however, means determining the number of genes in that organism, the order in which the genes occur and how these same genes are expressed. A researcher would sequence a genome for a number of reasons. For example, the human genome was sequenced to better understand human diseases which are genetically related, to understand human evolution and to advance forensic applied sciences1. These are but a few of the reasons for which the human genome was sequenced. Advancement in genomics has opened new avenues for the improvement of breeding goals in farm animals, especially in the developed countries. Developing countries like Ghana are however limited by the absence of programmes that record phenotypes on pedigreed animals and the lack of evaluation or national testing programmes to assess the genetic value of germplasms. Genomic approaches should therefore help in identifying critical populations for conservation.

1Page Title: Human Genome Project - Wikipedia, the free encyclopaedia;URL: http://en.m.wikipedia.org/wiki/Human_Genome_Project#section_2; Year: (2013)

2Page Title: Greater cane rat - Wikipedia, the free encyclopaedia; URL: http://en.wikipedia.org/wiki/Greater_cane_rat#section_1; Year: (2012)

3Page Title: Cane Rat - Wikipedia, the free encyclopaedia; URL: http://en.wikipedia.org/wiki/Cane_Rat#section_1; Year: (2007)

4Author: Samuel Hinneh; Page Title: Ghana Scores Low In Protein Quality | General News 2012-09-28; URL: http://www.ghanaweb.com/GhanaHomePage/NewsArchive/artikel.php?ID=251673; Year: (2012)

5 Author: MOFA; Page Title: GHANA'S MEDIUM TERM AGRICULTURE SECTOR INVESTMENT PLAN (METASIP) - Ministry of Food & Agriculture; URL: http://mofa.gov.gh/site/?page_id=2754; Year: (2010)

The greater cane rat, (Thryonomys swinderianus), popularly known as the grasscutter in Ghana and many other African countries, is a rodent found in the Western and Southern Regions of Africa. They live in small groups along river banks and marshy areas and are often led by an adult male. Their nests are often made out of grass and they feed normally on grass and other agricultural produce such as cassava, maize, plantain, etc.2 They can grow up to between 35-60cm in length and weigh about 8.5kg. They are sexually mature and able to reproduce 6 months after birth3. They serve as a potential source of food and protein in many Sub-Saharan African countries. It is however difficult to capture them all year round and its supply as a source of food and protein is also restricted to certain seasons of the year. As a result of the increase in demand for their meat and the extremely dangerous methods of capturing them from the wild, which includes starting bush fires, rearing them has become an area of interest in some of these countries, especially in Ghana and Nigeria.

With regard to the quality of protein in food consumption, Ghana ranks low according to the new Global Food Security Index 20124. Ghana is yet to attain food protein sufficiency and therefore imports the bulk of its protein or meat requirements5.

Grasscutter meat production could help in breaching this gap on account of its high fecundity. Additionally, many people in Ghana, particularly the youth, are interested in rearing this animal to improve their lives financially. The meat of the grasscutter is tender, highly nutritious and low in cholesterol and fat. It is also highly relished by both Ghanaians and foreigners as a delicacy. The grasscutter however lives in the wild and efforts to domesticate it have faced many challenges. Instinctively, the animal attempts to escape when in captivity. This often leads to the banging of its head against the walls of its enclosure and may result in death from internal bleeding, increasing mortality rates while trying to rear them for an income and causing heart-breaking losses to the farmer. Secondly, because of fear or fright, instead of secreting hormones for reproduction and growth, it secretes adrenaline which causes a reduction in conception rates. How sad. Therefore, given the chance to sequence a novel genome, it would be the genome of the grasscutter for the following reasons.

Sequencing and re-sequencing of economically important livestock species has resulted in the discovery of millions of Single Nucleotide Polymorphisms (SNPs). These SNPs are being deployed in a massively parallel fashion on DNA microarrays, enabling genome-wide association studies to identify genotype-phenotype correlations for simple and more important complex traits6. My motivation for sequencing the genome of the grasscutter stems from the fact that animal behavioural traits are quantitative and are determined by a set of genes acting together, coupled with the environment. These include aggressiveness, temperaments and docility. These quantitative traits vary continuously on the chromosome and are expressed externally as the phenotype or behaviour of the organism7. This indicates that artificially altering or changing the genetic sequence that influences docility in the grasscutter is feasible. If successful in sequencing the genome of the grasscutter, the appropriate Quantitative Trait Loci (QTL) controlling its temperaments could be identified and manipulated to make the animal calmer or more docile. If positive results are obtained from this study, the grasscutter can be bred to be more docile in captivity leading to its successful domestication and rearing.

6 Author: André Eggen; Page Title: The development and the application of genomic selection as a new breeding paradigm; URL: http://animalfrontiers.org/content/2/1/10.full; Year: (2012)

7Author: Michael D. Breed. Page Title: QTL's. URL: http://www.animalbehavioronline.com/qtl.html; Year: (2003)

8Author: Ismail AbdulAzeez; Page Title: ECONOMIC IMPORTANCE OF GRASSCUTTER FARMING; URL: http://m.articlesbase.com/business-ideas-articles/economic-importance-of-grasscutter-farming-870286.html; Year: (2009)

Other people might not be interested in rearing the grasscutter but may be interested in keeping them as pets8, just like the guinea pig or the rabbit. However, this animal is not calm enough to serve that purpose. With my proposal in mind, this animal could be made calm enough to be kept as a pet. Other benefits from this work could include increased litter size, reduced mortality and higher growth rates. The government of

Ghana would also be able to deal with annual bush fires that result from hunting the grasscutter in the wild, because more people would be able to rear this animal at home and its meat would be readily available on the market all year round rather than seasonally.

Another potential advantage of sequencing the genome of the grasscutter is the ability to identify and manipulate QTLs responsible for growth, reproduction and carcass quality. Together with my team, I would be able to lead other scientists to delve deeper into the genomics of grasscutter breeding since its biology is not fully known. For instance, in the case of carcass quality, we could manipulate the grasscutter meat to be juicier and tenderer. Growth rate could also be manipulated to enable the animal reach the market weight at relatively younger ages which has the potential of improving the tenderness of the meat. I am optimistic about this because, the Melanocortin 4 Receptor (MC4R) gene responsible for growth in pigs has been identified and manipulated to enhance faster growth of pigs and to increase the carcass quality9.

9 Author: Bijal P. Trivedi; Page Title: Appetite gene suspected in pigs; URL: http://www.genomenewsnetwork.org/articles/05_00/fat_gene.shtml; Year: (2000)

10Page Title: Goat meat - Wikipedia, the free encyclopaedia; URL: http://en.wikipedia.org/wiki/Goat_meat#section_2; Year: (2013)

There are many livestock that are bred for their meat. Some of the meat they produce are tough and sometimes very difficult to chew. One of such meat is the chevon (goat meat). This does not imply that chevon is the only tough meat on the market. Though this meat contains lesser amounts of cholesterol and fats as compared to lamb and beef10, its toughness turns some consumers away. From a personal survey I conducted on both local and foreign students on my campus in view of this, 7 out of 10 said they liked goat meat. However the only thing they didn't like was the fact that it was tough. I further asked if they would purchase it more if it were made tender and the response was positive. Since grasscutter meat is tender, it possibly has an amino acid sequence or QTL which is responsible for this trait. If this QTL is identified, it can be introduced into the embryo of a goat and then this breed of goat can also have tender meat. This method is not limited only to goat meat, other meat producing livestock can benefit. This is the beauty of genomics!

Finally, sequencing the grasscutter genome would help identify some of the diseases this animal is prone to. After the animal has been made docile and reproduction and growth rates have both increased and mortality rates have decreased, they could be attacked by diseases which may not be known by the farmer or the veterinary doctor. However, if its genome is sequenced, the possibility of identifying such diseases and obtaining or finding cures for them is very high. Therefore in case an animal falls sick or is attacked by a disease while in captivity, the veterinary doctor can conduct diagnostic

tests to know exactly what is wrong with it hence would be able to administer the appropriate drugs.

Economically, Ghana stands to benefit greatly from this endeavour. Not only would there be a better, more productive breed of grasscutter which is docile and has tenderer meat, but as consumption and market demands grow, a great potential for income generation and employment creation would be enhanced in the country for many unemployed youth. This would go a long way to contribute to an increase in the Gross Domestic Income (GDI) of the country, reduce the high level of youth unemployment and enhance the small scale financial market in Ghana.

My research into the grasscutter's world, its genome, could add some knowledge to existing research conducted by other scientists. It would also make it possible to know the precautions to take before subjecting it to any experimental tests. Also the experience I acquire from conducting this research would enable me develop a bigger research platform, contribute to genomic selection in Ghana and also help me lay a better foundation for my career as an animal research scientist in future.

I also hope to share my findings with the university faculty and my other colleagues, females especially, so that they could also be inspired to take the step or initiative to venture into the study area of genomics instead of avoiding it. Currently there are only two female professors in the department of animal science at the University of Ghana, Legon where I school, and they are both on post-pension contracts. This is very heart-breaking and shows that just few females are involved in this area of study. This may be due to discouragement from well-meaning people, mostly family and friends, lack of incentives or role-models. I could use this opportunity to be a role-model to them and give them the inspiration needed to take up genomic studies. Given the right urge or encouragement, other females may get motivated to involve themselves with this area of study, which currently is male dominated.

My country Ghana, though at the formative stage, is currently promoting genomic research and is working hard at promoting grasscutter rearing as well. Hence, my study would fit well into the national agenda of sustainable animal genetic resource management, and my findings would contribute to successful grasscutter rearing.

As an individual, I am very adventurous and always want to try new things. Ever since I read about Genomic Selection, I have been amazed at its potential for animal breeding and conservation. In preparation of this essay, I have gained more understanding and knowledge about the subject and I am firmly convinced that this is the right area of study for me. Winning the Wellcome Trust Sanger Institute Prize Competition would thus afford me the opportunity to realise my potentials to the full. I am very passionate about this project and if given the opportunity to prove my worth, I would leave no stone unturned, acquit myself creditably and successfully achieve my goal.

There's nothing that is IMPOSSIBLE the word itself says I'M POSSIBLE
By: akoaso -H-H

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