Genetic diversity of grasscutter (Thryonomys swinderianus, Rodentia, Hystricomorpha) in Ghana based on microsatellite markers

Grasscutter (Thryonomys swinderianus) is a fairly large rodent that inhabits sub-Saharan Africa. There are very limited ecological studies on the grasscutter despite its importance as a protein resource. The objective of this study was to apply novel microsatellite markers to determine the genetic structure and diversity of grasscutter populations in Ghana. A total of 66 hair samples were collected from grasscutters in three main agro-ecological zones of Ghana, namely Guinea Savanna (n = 19), Forest (n = 16) and Coastal Savanna (n = 16) as well as Volta Region (n = 15). Samples were genotyped at 12 polymorphic loci and the results showed relatively high diversity (MNA = 7.3, HE = 0.745) within populations. Phylogenetic analysis revealed that Forest population is closer to the Coastal Savanna population than the other populations whilst Volta Region population is closer to the Guinea Savanna population than the other populations. Pairwise FST values however indicated that all populations were significantly differentiated (p < 0.01). STRUCTURE clustering analysis showed that Volta population split from the Guinea Savanna population. Grasscutter populations in Ghana are genetically differentiated according to agro-ecological zones and the Volta Lake could be serving as a barrier to gene flow

Comparison of vent sexing and polymerase chain reaction for reliable sex determination in guinea fowls

The guinea fowl is an important poultry species with great economic potential in Africa. It is a monomorphic bird with less conspicuous sexual dimorphism. Inability to sex birds accurately early in their life imposes multiple challenges on breeding, conservation and production of these birds. Several methods have been employed for sexing monomorphic birds each with specific advantages and disadvantages. In the present study, sexes of 215 guinea fowls were determined by Polymerase Chain Reaction (PCR), Vent Sexing and determination of gonads. PCR was used to amplify a sequence homologous to Chicken EcoR1 fragment of 0.6 kb (EE0.6) using Universal Sex Primer (USP) 1 and USP3 and internal control primers. Vent sexing could only diagnose 48.7 % of males accurately while it was able to diagnose females with an accuracy of 81%. Results from PCR was in complete agreement with sex indicated by gonads. Differences in results between PCR and vent sexing were significant (p < 0.05). Vent Sexing alone is not reliable for sexing guinea fowls prior to breeding decisions. Molecular sexing using the method described is recommended for accurate sex determination for breeders and researchers while future research is necessary to develop farmer friendly guidelines for reliable sex determination of guinea fowls

Non-invasive sex determination of guinea fowl keets (numida meleagris) by polymerase chain reaction

Early sex determination of birds is crucial for controlled breeding for both production andconservation. Amidst the potential of the guinea fowl (Numida meleagris) industry for theeconomies of African countries and as a rich genetic resource to be conserved, inability toaccurately sex guinea fowl keets is a major constraint for breeding. In the present study sex of dayold guinea keets (n=132) and keets of 4 - 8 weeks (n=72) was determined by polymerase chain reaction (PCR) by amplifying a sequence homologous to Chicken EcoR1 fragment of 0.6 kb (EE0.6) using Universal Sex Primer 1(USP 1) and Universal Sex Primer 3 (USP 3) together with internal control primers using DNA extracted from feathers. Out of 72 keets, aged 4 - 8 weeks, 38 were identified as males and 34 were identified as females. Out of the 132, day-olds 69 and 63 were identified as female and male keets, respectively, were results from PCR were confirmed by the presence of respective gonads. The methods described can be used for accurate sex determination of guinea fowl keets from day-old with minimal stress and discomfort to the birds. The method can be used by researchers, breeders, conservationists directly or to develop farmer friendly methods in the future

Search for QTL affecting the shape of the egg laying curve of the Japanese quail

BACKGROUND: Egg production is of critical importance in birds not only for their reproduction but also for human consumption as the egg is a highly nutritive and balanced food. Consequently, laying in poultry has been improved through selection to increase the total number of eggs laid per hen. This number is the cumulative result of the oviposition, a cyclic and repeated process which leads to a pattern over time (the egg laying curve) which can be modelled and described individually. Unlike the total egg number which compounds all variations, the shape of the curve gives information on the different phases of egg laying, and its genetic analysis using molecular markers might contribute to understand better the underlying mechanisms. The purpose of this study was to perform the first QTL search for traits involved in shaping the egg laying curve, in an F(2 )experiment with 359 female Japanese quail. RESULTS: Eight QTL were found on five autosomes, and six of them could be directly associated with egg production traits, although none was significant at the genome-wide level. One of them (on CJA13) had an effect on the first part of the laying curve, before the production peak. Another one (on CJA06) was related to the central part of the curve when laying is maintained at a high level, and the four others (on CJA05, CJA10 and CJA14) acted on the last part of the curve where persistency is determinant. The QTL for the central part of the curve was mapped at the same position on CJA06 than a genome-wide significant QTL for total egg number detected previously in the same F(2). CONCLUSION: Despite its limited scope (number of microsatellites, size of the phenotypic data set), this work has shown that it was possible to use the individual egg laying data collected daily to find new QTL which affect the shape of the egg laying curve. Beyond the present results, this new approach could also be applied to longitudinal traits in other species, like growth and lactation in ruminants, for which good marker coverage of the genome and theoretical models with a biological significance are available

Microsatellite mapping of QTL affecting growth, feed consumption, egg production, tonic immobility and body temperature of Japanese quail

BACKGROUND: The Japanese quail (Coturnix japonica) is both an animal model in biology and a commercial bird for egg and meat production. Modern research developments with this bird, however, have been slowed down by the limited information that is available on the genetics of the Japanese quail. Recently, quail genetic maps with microsatellites and AFLP have been produced which open the way to comparative works with the chicken (Gallus gallus), and to QTL detection for a variety of traits. The purpose of this work was to detect for the first time QTL for commercial traits and for more basic characters in an F2 experiment with 434 female quail, and to compare the nature and the position of the detected QTL with those from the first chicken genome scans carried out during the last few years. RESULTS: Genome-wide significant or suggestive QTL were found for clutch length, body weight and feed intake on CJA01, age at first egg and egg number on CJA06, and eggshell weight and residual feed intake on CJA20, with possible pleiotropy for the QTL affecting body weight and feed intake, and egg number and age at first egg. A suggestive QTL was found for tonic immobility on CJA01, and chromosome-wide significant QTL for body temperature were detected on CJA01 and CJA03. Other chromosome-wide significant QTL were found on CJA02, CJA05, CJA09 and CJA14. Parent-of-origin effects were found for QTL for body weight and feed intake on CJA01. CONCLUSION: Despite its limited length, the first quail microsatellite map was useful to detect new QTL for rarely reported traits, like residual feed intake, and to help establish some correspondence between the QTL for feed intake, body weight and tonic immobility detected in the present work and those reported on GGA01 in the chicken. Further comparative work is now possible in order to better estimate and understand the genetic similarities and differences of these two Phasianidae species

Phenotypic characterisation and molecular polymorphism of indigenous poultry populations of the species Gallus gallus of Savannah and Forest ecotypes of Benin

The study of the phenotypic characterisation and molecular polymorphism of local chicken populations was carried out in Benin on 326 chickens of the Forest ecological area and 316 of the Savannah ecological area, all were 7 months old at least. The collection of blood for the molecular typing wasachieved on 121 indigenous chickens of which 60 from the Savannah ecological area and 61 from the Forest ecological area. The genotyping was carried out for 22 microsatellite loci. Weight and body measures of the Savannah chickens were significantly higher (P < 0.001) than those of the Forest chickens. In the Savannah ecological area, the most frequent plumage colours were the black (22.15%), the white (19.62%), the coppery black (7.59%) and the golden partridge (7.59%). In the Forest area, thefawn (15.34%), the black (10.43%), the white (6.8%), the silver white (6.8%) and the golden partridge (6.75%) were the dominant feather colours. Thus, phenotypic characterisation showed significant differences between Savannah and Forest local chickens. The FST calculated between the Savannah and Forest populations revealed a low genetic differentiation and the dendogram showed that Savannah and Forest chickens were quite intermingled. In conclusion, local populations from Savannah andForest area may be considered as ecotypes, but not as two distinct breeds

Integrated maps in quail (Coturnix japonica) confirm the high degree of synteny conservation with chicken (Gallus gallus) despite 35 million years of divergence

BACKGROUND: By comparing the quail genome with that of chicken, chromosome rearrangements that have occurred in these two galliform species over 35 million years of evolution can be detected. From a more practical point of view, the definition of conserved syntenies helps to predict the position of genes in quail, based on information taken from the chicken sequence, thus enhancing the utility of this species in biological studies through a better knowledge of its genome structure. A microsatellite and an Amplified Fragment Length Polymorphism (AFLP) genetic map were previously published for quail, as well as comparative cytogenetic data with chicken for macrochromosomes. Quail genomics will benefit from the extension and the integration of these maps. RESULTS: The integrated linkage map presented here is based on segregation analysis of both anonymous markers and functional gene loci in 1,050 quail from three independent F2 populations. Ninety-two loci are resolved into 14 autosomal linkage groups and a Z chromosome-specific linkage group, aligned with the quail AFLP map. The size of linkage groups ranges from 7.8 cM to 274.8 cM. The total map distance covers 904.3 cM with an average spacing of 9.7 cM between loci. The coverage is not complete, as macrochromosome CJA08, the gonosome CJAW and 23 microchromosomes have no marker assigned yet. Significant sequence identities of quail markers with chicken enabled the alignment of the quail linkage groups on the chicken genome sequence assembly. This, together with interspecific Fluorescence In Situ Hybridization (FISH), revealed very high similarities in marker order between the two species for the eight macrochromosomes and the 14 microchromosomes studied. CONCLUSION: Integrating the two microsatellite and the AFLP quail genetic maps greatly enhances the quality of the resulting information and will thus facilitate the identification of Quantitative Trait Loci (QTL). The alignment with the chicken chromosomes confirms the high conservation of gene order that was expected between the two species for macrochromosomes. By extending the comparative study to the microchromosomes, we suggest that a wealth of information can be mined in chicken, to be used for genome analyses in quail

Performance of three local chicken ecotypes of Ghana naturally exposed to velogenic Newcastle disease virus

This study was to evaluate the performance of three Ghanaian local ecotypes that were exposed to a natural velogenic Newcastle Disease Virus (NDV) challenge. The birds at four weeks of age had been challenged with a lentogenic (vaccine) form of the virus and later exposed to velogenic NDV when their anti-NDV antibody titres had fallen below 1000. All the birds lost weight over the 21 days of exposure to the virus, with the Coastal Savannah ecotype showing the fastest weight loss albeit not significant (p\u3e0.05). Lesion scores for all ecotypes were low and similar across ecotypes suggesting that the challenge was not severe. Heritability was zero for the lesion scores and low (0.01) for post-challenge growth rate across ecotypes. Hence, not much progress can be made in selection to improve post infection growth rate

Genotypic and phenotypic characterisation of three local chicken ecotypes of Ghana based on principal component analysis and body measurements

This study was to characterise three Ghanaian local chicken ecotypes, namely, Interior Savannah, Forest and Coastal Savannah ecotypes, based on morphological data and single nucleotide polymorphism (SNP) genotypes. Morphological data including shank length, body girth, back length, thigh length, beak length, comb length and wattle length were collected. Blood samples were also obtained for SNP genotyping with Affymetrix chicken 600k SNP chip. Principal component analysis showed that Forest and Coastal Savannah birds were closely related. Generally, all three ecotypes seemed very diverse especially birds from the Interior Savannah zone. Morphological characterisation showed ecotype, sex and pen had significant effect on body weights (p0.05). Very few of the phenotypes reported to be associated with heat resistance – frizzle (2%) and naked neck (1.6%) – were found in the current study. It is concluded that the three local ecotypes are genetically diverse but with similar morphological features

Genetic parameters and genomic regions associated with growth rate and response to Newcastle disease in local chicken ecotypes in Ghana and Tanzania

Local chicken breeds play an important role in the livelihoods of people in both rural and urban areas of Africa. One of the main constraints to the poultry sector in many sub-Saharan countries is disease, with Newcastle disease (ND) being the most important. Because vaccination does not adequately control ND, selective breeding offers an effective complement, provided there is genetic variation in resistance, tolerance and/or response to ND. We investigated this topic by challenging 6 local ecotypes from Ghana and Tanzania with a lentogenic (vaccine) strain of Newcastle disease virus (NDV), then measuring growth, anti-NDV antibody levels, and viral load from hatch to 38 days of age. We estimated variance components and performed a genome-wide association study using 2800 birds genotyped with the 600K Affymetrix chicken genotyping array. Heritabilities were moderate to high (0.14 – 0.55) for all the traits studied, which indicates that selection to improve these breeds for resistance to ND can be feasible. GWAS also revealed several genomic regions that explained ≥0.5% of the genetic variance, including a candidate gene region for antibody response on GGA1. We conclude that all traits investigated in this study appear to be highly polygenic in nature. Future studies will characterize differences between the breeds/ecotypes, determine if large breed-specific quantitative trait loci can be identified, and evaluate the response of the same birds to endemic, velogenic NDV strains