Genome-wide DNA markers to support genetic management for domestication and commercial production in a large rodent, the Ghanaian grasscutter (<i>Thryonomys swinderianus</i>)

Adenyo, Christopher; Ogden, Rob; Kayang, Boniface B.; Onuma, Manabu; Nakajima, Nobuyoshi; Inoue‐Murayama, Miho

doi:10.1111/age.12478

Cited by 11 publications

(7 citation statements)

References 9 publications

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“…Other works reported in the literature include: characterization of the estrus cycle, determination of the ovulatory mechanisms, detection of mating and pregnancy, efficacy of vaginal mucous plug formation in pregnancy detection, and efficacy of sex determination using ano‐genital distance, amongst others. More recently, advanced techniques such as the use of mitochondrial D‐loop and double‐digest restriction‐site associated DNA (RAD) sequencing markers (single nucleotide polymorphisms, SNPs) have been deployed to improve understanding of genetic diversity in the GCR and for genetic management of production …”

Section: Resultsmentioning

confidence: 99%

A study of scientific publications on the greater cane rat (Thryonomys swinderianus, Temminck 1827)

Mustapha

Teriba

Ezekiel

et al. 2020

Anim Models and Exp Med

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Background: The greater cane rat (GCR), reputed to be African's second largest rodent, is a precocial hystricomorph with an uncommon phenotype and life history. Scientific and socio-economic interests in the GCR have led to heightened research efforts targeted towards a better understanding of its biology and exploration of its economic and translational usefulness.Methods: Records of all online scientific publications on the GCR from Google, Google Scholar, PubMed, science.gov, Ebscohost and Worldwide science, with the exception of research theses, proceedings, unpublished projects and abstracts, were collated and analyzed using descriptive statistics. Results:A total of 146 published scholarly articles spanning about six decades were retrieved, with 98% of the GCR publications originating from African countries. Nigeria boasts the highest number of publications (58.22%) followed by Ghana (21.23%) and South Africa (5.48%) while Senegal contributed the least (0.69%).Publications were sorted into ten field categories. The field with the highest number of articles (41.78%) was animal breeding and management recording, closely followed by anatomy (37.67%). Lesser contributions were made by parasitology (5.48%), biochemistry/hematology (4.8%), pharmacology/toxicology (4.11%), pathology (2.06%), and surgery/anesthesia and physiology (1.37% apiece). The fields with fewest contributions were microbiology and developmental biology (0.69% each). Conclusion:This study chronicles the spectrum of knowledge available on the GCR, highlighting the knowledge gap that still exists in various fields in order to provide advocacy for new frontiers in research efforts on this rodent. We suggest the need for a clearly defined and well integrated national/regional policy aimed at establishing Africa's foremost micro-livestock rodent, the greater cane rat, on the world's scientific radar. K E Y W O R D SAfrican rodent, grasscutter, greater cane rat, micro-livestock, review, wildlife | 41 MUSTAPHA eT Al.

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Section: Resultsmentioning

confidence: 99%

A study of scientific publications on the greater cane rat (Thryonomys swinderianus, Temminck 1827)

Mustapha

Teriba

Ezekiel

et al. 2020

Anim Models and Exp Med

View full text Add to dashboard Cite

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“…Around 9% of the SNPs were found to depart from HWE ( p < 0.01), but it has to be noted that the population genotyped for the validation is the commercial strain that has undergone up to 25 generations of selection. Hence, these departures might be important as they could represent regions under selection, domestication and the outcome of assortative mating ( Gutierrez et al, 2016 ; Adenyo et al, 2017 ). Whereas the extreme departures might suggest lethal recessive mutations and/or recent mutations or copy number variants ( Lee et al, 2008 ; Graffelman et al, 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia (O. niloticus)

et al. 2018

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Despite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper, we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia (Oreochromis niloticus). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and were selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O_niloticus_UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups (LGs). Around one-third of the LGs showed a different recombination rate between sexes, with the female being greater than the male map by a factor of 1.2 (1632.9 to 1359.6 cM, respectively), with most LGs displaying a sigmoid recombination profile. Finally, the sex-determining locus was mapped to position 40.53 cM on LG23, in the vicinity of the anti-Müllerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasively measured traits in Nile tilapia.

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“…Currently, there is an on-going project in northwestern Ghana aiming to enhance the domestication of a large rodent native to West Africa called grasscutter (Thryonomys swinderianus, also known as the greater cane rat), whose meat is a delicacy for people in West Africa [6]. As part of this project, we developed DNA markers to support the genetic management of the grasscutter in Ghana [7]. Still, there is limited information on grasscutter physiology.…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana

et al. 2020

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The grasscutter (also known as the greater cane rat; Thryonomys swinderianus) is a large rodent native to West Africa that is currently under domestication process for meat production. However, little is known about the physiology of this species. In the present study, aiming to provide information about gut microbiota of the grasscutter and better understand its physiology, we investigated the intestinal microbiota of grasscutters and compared it with that of other livestock (cattle, goat, rabbit, and sheep) using 16S rRNA metagenomics analysis. Similar to the other herbivorous animals, bacteria classified as Bacteroidales, Clostridiales, Ruminococcaceae, and Lachnospiraceae were abundant in the microbiome of grasscutters. However, Prevotella and Treponema bacteria, which have fiber fermentation ability, were especially abundant in grasscutters, where the relative abundance of these genera was higher than that in the other animals. The presence of these genera might confer grasscutters the ability to easily breakdown dietary fibers. Diets for grasscutters should be made from ingredients not consumed by humans to avoid competition for resources and the ability to digest fibers may allow the use of fiber-rich feed materials not used by humans. Our findings serve as reference and support future studies on changes in the gut microbiota of the grasscutter as domestication progresses in order to establish appropriate feeding methods and captivity conditions.

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Genome-wide DNA markers to support genetic management for domestication and commercial production in a large rodent, the Ghanaian grasscutter (Thryonomys swinderianus)

Cited by 11 publications

References 9 publications

A study of scientific publications on the greater cane rat (Thryonomys swinderianus, Temminck 1827)

A study of scientific publications on the greater cane rat (Thryonomys swinderianus, Temminck 1827)

Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia (O. niloticus)

Comparative Analysis of Fecal Microbiota in Grasscutter (Thryonomys swinderianus) and Other Herbivorous Livestock in Ghana

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