Synchronized Expansion and Contraction of Olfactory, Vomeronasal, and Taste Receptor Gene Families in Hystricomorph Rodents.

Chemical senses, including olfaction, pheromones, and taste, are crucial for the survival of most animals. There has long been a debate about whether different types of senses might influence each other. For instance, primates with a strong sense of vision are thought to have weakened olfactory abilities, although the oversimplified trade-off theory is now being questioned. It is uncertain whether such interactions between different chemical senses occur during evolution. To address this question, we examined four receptor gene families related to olfaction, pheromones, and taste: olfactory receptor (OR), vomeronasal receptor type 1 and type 2 (V1R and V2R), and bitter taste receptor (T2R) genes in Hystricomorpha, which is morphologically and ecologically the most diverse group of rodents. We also sequenced and assembled the genome of the grasscutter, Thryonomys swinderianus. By examining 16 available genome assemblies alongside the grasscutter genome, we identified orthologous gene groups among hystricomorph rodents for these gene families to separate the gene gain and loss events in each phylogenetic branch of the Hystricomorpha evolutionary tree. Our analysis revealed that the expansion or contraction of the four gene families occurred synchronously, indicating that when one chemical sense develops or deteriorates, the others follow suit. The results also showed that V1R/V2R genes underwent the fastest evolution, followed by OR genes, and T2R genes were the most evolutionarily stable. This variation likely reflects the difference in ligands of V1R/V2Rs, ORs, and T2Rs: species-specific pheromones, environment-based scents, and toxic substances common to many animals, respectively.

Genetic architecture of body weight, carcass, and internal organs traits of Ghanaian local chickens.

Information on the genetic architecture of the production traits of indigenous African chicken is limited. We performed a genome-wide association study using imputed Affymetrix Axiom® 600K SNP-chip genotypes on 1,113 chickens from three agroecological zones of Ghana. After quality control, a total of 382,240 SNPs remained. Variance components and heritabilities for some growth, carcass and internal organ traits were estimated. The genetic and phenotypic correlations among these traits were also estimated. The estimated heritabilities of body weight at week 22 (BW22), average daily gain (ADG), dressed weight, breast weight, thigh weight, wing weight, drumstick weight, and neck weight were high and ranged from 0.50 to 0.69. Estimates of heritabilities for head weight, shank weight, and gizzard weight were moderate (0.31-0.35) while those of liver weight, back weight, dressing percentage, and heart weight were low (0.13-0.21). The estimated heritabilities of dressed weight, breast weight, wing weight, drumstick weight, neck weight, shank weight, and gizzard weight, corrected for BW22, were moderate (0.29-0.38), while the remaining traits had low heritability estimates (0.13-0.21). A total of 58 1-Mb SNP windows on chromosomes 1, 2, 4, 5, 6, 7, 8, 9, 13, 18, and 33 each explained more than 1% of the genetic variance for at least one of these traits. These genomic regions contained many genes previously reported to have effects on growth, carcass, and internal organ traits of chickens, including EMX2, CALCUL1, ACVR1B, CACNB1, RB1, MLNR, FOXO1, NCARPG, LCORL, LAP3, LDB2, KPNA3, and CAB39L. The moderate to high heritability estimates and high positive genetic correlations suggest that BW22, ADG, dressed weight, breast weight, thigh weight, wing weight, drumstick weight, and neck weight could be improved through selective breeding.

Whole genome analyses reveal novel genes associated with chicken adaptation to tropical and frigid environments.

INTRODUCTION: Investigating the genetic footprints of historical temperature selection can get insights to the local adaptation and feasible influences of climate change on long-term population dynamics. OBJECT: Chicken is a significative species to study genetic adaptation on account of its similar domestication track related to human activity with the most diversified varieties. Yet, few studies have demonstrated the genetic signatures of its adaptation to naturally tropical and frigid environments. METHOD: Here, we generated whole genome resequencing of 119 domesticated chickens in China including the following breeds which are in order of breeding environmental temperature from more tropical to more frigid: Wenchang chicken (WCC), green-shell chicken (GSC), Tibetan chicken (TBC), and Lindian chicken (LDC). RESULTS: Our results showed WCC branched off earlier than LDC with an evident genetic admixture between WCC and LDC, suggesting their closer genetic relationship. Further comparative genomic analyses solute carrier family 33 member 1 (SLC33A1) and thyroid stimulating hormone receptor (TSHR) genes exhibited stronger signatures for positive selection in the genome of the more tropical WCC. Furthermore, genotype data from about 3,000 African local ecotypes confirmed that allele frequencies of single nucleotide polymorphisms (SNPs) in these 2 genes appeared strongly associated with tropical environment adaptation. In addition, the NADH:ubiquinone oxidoreductase subunit S4 (NDUFS4) gene exhibited a strong signature for positive selection in the LDC genome, and SNPs with marked allele frequency differences indicated a significant relationship with frigid environment adaptation. CONCLUSION: Our findings partially clarify how selection footprints from environmental temperature stress can lead to advantageous genomic adaptions to tropical and frigid environments in poultry and provide a valuable resource for selective breeding of chickens.

Genetic Analyses of Response of Local Ghanaian Tanzanian Chicken Ecotypes to a Natural Challenge with Velogenic Newcastle Disease Virus.

Newcastle disease is a devastating poultry disease that often causes significant economic losses in poultry in the developing countries of Africa, Asia, as well as South and Central America. Velogenic Newcastle disease virus (NDV) outbreaks are associated with high mortalities, which can threaten household livelihoods, especially in the rural areas, and lead to loss of high-quality proteins in the form of meat and eggs, as well as household purchasing power. In this study, we exposed unvaccinated Ghanaian and Tanzanian chickens of six local ecotypes to velogenic NDV strains, measured NDV response traits, sequenced their DNA on a genotyping-by-sequencing platform, and performed variance component analyses. The collected phenotypes included: growth rates (pre- and post-exposure); lesion scores (gross lesion severity) in the trachea, proventriculus, intestine, and cecal tonsils; natural antibody levels; anti-NDV antibody levels at 7 days post exposure (dpe); tear and cloacal viral load at 2, 4, and 6 dpe; and survival time. Heritability estimates were low to moderate, ranging from 0.11 for average lesion scores to 0.36 for pre-exposure growth rate. Heritability estimates for survival time were 0.23 and 0.27 for the Tanzanian and Ghanaian ecotypes, respectively. Similar heritability estimates were observed when data were analyzed either separately or combined for the two countries. Survival time was genetically negatively correlated with lesion scores and with viral load. Results suggested that response to mesogenic or velogenic NDV of these local chicken ecotypes could be improved by selective breeding. Chickens that are more resilient to velogenic NDV can improve household livelihoods in developing countries.

Response of three local chicken ecotypes of Ghana to lentogenic and velogenic Newcastle disease virus challenge.

This study was carried out to assess the response of three Ghanaian local chicken ecotypes to LaSota (lentogenic) and virulent field strains of Newcastle disease virus (NDV). Local chickens sampled from the Interior Savannah (IS), Forest (FO) and Coastal Savannah (CS) agro-ecological zones were bred and their offspring were challenged with LaSota NDV at 4 weeks of age. The LaSota challenge was replicated four times with different chicken groups. A total of 1438 chicks comprising 509 Coastal Savannah, 518 Forest and 411 Interior Savannah ecotypes were used. Pre- and post-challenge anti-NDV antibody titre levels were determined via ELISA assays. A second trial was conducted by introducing sick birds infected with virulent NDV to a flock of immunologically naïve chickens at 4 weeks old. Body weights were measured pre- and post-infection. Sex of the chickens was determined using a molecular method. In both trials, there was no significant difference among ecotypes in body weight and growth rate. In the LaSota trial, anti-NDV antibody titre did not differ by ecotype or sex. However, there was a positive linear relationship between body weight and antibody titre. In the velogenic NDV trial, survivability and lesion scores were similar among the three ecotypes. This study confirms that a relatively high dose of LaSota (NDV) challenge has no undesirable effect on Ghanaian local chicken ecotypes. All three Ghanaian local chicken ecotypes were susceptible to velogenic NDV challenge. Resistance to NDV by Ghanaian local chickens appears to be determined more by the individual's genetic makeup than by their ecotype.

Genetic Basis of Response of Ghanaian Local Chickens to Infection With a Lentogenic Newcastle Disease Virus.

Newcastle disease (ND) is a global threat to domestic poultry, especially in rural areas of Africa and Asia, where the loss of entire backyard local chicken flocks often threatens household food security and income. To investigate the genetics of Ghanaian local chicken ecotypes to Newcastle disease virus (NDV), in this study, three popular Ghanaian chicken ecotypes (regional populations) were challenged with a lentogenic NDV strain at 28 days of age. This study was conducted in parallel with a similar study that used three popular Tanzanian local chicken ecotypes and after two companion studies in the United States, using Hy-line Brown commercial laying birds. In addition to growth rate, NDV response traits were measured following infection, including anti-NDV antibody levels [pre-infection and 10 days post-infection (dpi)], and viral load (2 and 6 dpi). Genetic parameters were estimated, and two genome-wide association study analysis methods were used on data from 1,440 Ghanaian chickens that were genotyped on a chicken 600K Single Nucleotide Polymorphism (SNP) chip. Both Ghana and Tanzania NDV challenge studies revealed moderate to high (0.18 - 0.55) estimates of heritability for all traits, except viral clearance where the heritability estimate was not different from zero for the Tanzanian ecotypes. For the Ghana study, 12 quantitative trait loci (QTL) for growth and/or response to NDV from single-SNP analyses and 20 genomic regions that explained more than 1% of genetic variance using the Bayes B method were identified. Seven of these windows were also identified as having at least one significant SNP in the single SNP analyses for growth rate, anti-NDV antibody levels, and viral load at 2 and 6 dpi. An important gene for growth during stress, CHORDC1 associated with post-infection growth rate was identified as a positional candidate gene, as well as other immune related genes, including VAV2, IL12B, DUSP1, and IL17B. The QTL identified in the Ghana study did not overlap with those identified in the Tanzania study. However, both studies revealed QTL with genes vital for growth and immune response during NDV challenge. The Tanzania parallel study revealed an overlapping QTL on chromosome 24 for viral load at 6 dpi with the US NDV study in which birds were challenged with NDV under heat stress. This QTL region includes genes related to immune response, including TIRAP, ETS1, and KIRREL3. The moderate to high estimates of heritability and the identified QTL suggest that host response to NDV of local African chicken ecotypes can be improved through selective breeding to enhance increased NDV resistance and vaccine efficacy.

Molecular Characterization of Newcastle Disease Viruses Isolated from Chickens in Tanzania and Ghana.

Newcastle disease (ND) is one of the most challenging infectious diseases affecting poultry production in Africa, causing major economic losses. To date, Newcastle disease virus isolates from several African countries have been grouped into class II NDV genotypes I, IV, V, VI, VII, XI, XIII, XIV, XVII, XVIII and XXI. Although ND is endemic in many African countries, information on circulating genotypes is still scarce. In Tanzania, outbreaks with genotypes V and XIII have been reported. In West and Central Africa, genotypes XIV, XVII, and XVIII are the most predominant. To investigate other genotypes circulating in Tanzania and Ghana, we performed molecular genotyping on isolates from Tanzania and Ghana using the MinION, a third-generation portable sequencing device from Oxford Nanopore Technologies. Using the MinION, we successfully sequenced the NDV F gene hypervariable region of 24 isolates from Tanzania and four samples from Ghana. In Tanzania, genotypes V, VII and XIII were detected. All isolates from Ghana belonged to genotype XVIII. The data obtained in this study reflect the genetic diversity of NDV in Africa and highlight the importance of surveillance for monitoring the distribution of NDV genotypes and viral evolution.

Thermophilic Degradation of Hemicellulose, a Critical Feedstock in the Production of Bioenergy and Other Value-Added Products.

Renewable fuels have gained importance as the world moves toward diversifying its energy portfolio. A critical step in the biomass-to-bioenergy initiative is deconstruction of plant cell wall polysaccharides to their unit sugars for subsequent fermentation to fuels. To acquire carbon and energy for their metabolic processes, diverse microorganisms have evolved genes encoding enzymes that depolymerize polysaccharides to their carbon/energy-rich building blocks. The microbial enzymes mostly target the energy present in cellulose, hemicellulose, and pectin, three major forms of energy storage in plants. In the effort to develop bioenergy as an alternative to fossil fuel, a common strategy is to harness microbial enzymes to hydrolyze cellulose to glucose for fermentation to fuels. However, the conversion of plant biomass to renewable fuels will require both cellulose and hemicellulose, the two largest components of the plant cell wall, as feedstock to improve economic feasibility. Here, we explore the enzymes and strategies evolved by two well-studied bacteria to depolymerize the hemicelluloses xylan/arabinoxylan and mannan. The sets of enzymes, in addition to their applications in biofuels and value-added chemical production, have utility in animal feed enzymes, a rapidly developing industry with potential to minimize adverse impacts of animal agriculture on the environment.

Sequence and immunologic conservation of Anaplasma marginale OmpA within strains from Ghana as compared to the predominant OmpA variant.

A primary challenge in developing effective vaccines against obligate, intracellular, bacterial tick-borne pathogens that establish persistent infection is the identification of antigens that cross protect against multiple strains. In the case of Anaplasma marginale, the most prevalent tick-borne pathogen of cattle found worldwide, OmpA is an adhesin and thus a promising vaccine candidate. We sequenced ompA from cattle throughout Ghana naturally infected with A. marginale in order to determine the degree of variation in this gene in an area of suspected high genetic diversity. We compared the Ghanaian sequences with those available from N. America, Mexico, Australia and Puerto Rico. When considering only amino acid changes, three unique Ghanaian OmpA variants were identified. In comparison, strains from all other geographic regions, except one, shared a single OmpA variant, Variant 1, which differed from the Ghanaian variants. Next, using recombinant OmpA based on Variant 1, we determined that amino acid differences in OmpA in Ghanaian cattle as compared to OmpA Variant 1 did not alter the binding capacity of antibody directed against OmpA Variant 1, supporting the value of OmpA as a highly conserved vaccine candidate.

Diversity and evolution of the highly polymorphic tandem repeat LEI0258 in the chicken MHC-B region.

The chicken major histocompatibility complex (MHC) is located on the microchromosome 16 and is described as the most variable region in the genome. The genes of the MHC play a central role in the immune system. Particularly, genes encoding proteins involved in the antigen presentation to T cells. Therefore, describing the genetic polymorphism of this region is crucial in understanding host-pathogen interactions. The tandem repeat LEI0258 is located within the core area of the B region of the chicken MHC (MHC-B region) and its genotypes correlate with serology. This marker was used to provide a picture of the worldwide diversity of the chicken MHC-B region and to categorize chicken MHC haplotypes. More than 1,600 animals from 80 different populations or lines of chickens from Africa, Asia, and Europe, including wild fowl species, were genotyped at the LEI0258 locus. Fifty novel alleles were described after sequencing. The resulting 79 alleles were classified into 12 clusters, based on the SNPs and indels found within the sequences flanking the repeats. Furthermore, hypotheses were formulated on the evolutionary dynamics of the region. This study constitutes the largest variability report for the chicken MHC and establishes a framework for future diversity or association studies.

Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa.

BACKGROUND: Chickens represent an important animal genetic resource for improving farmers' income in Africa. The present study provides a comparative analysis of the genetic diversity of village chickens across a subset of African countries. Four hundred seventy-two chickens were sampled in 23 administrative provinces across Cameroon, Benin, Ghana, Côte d'Ivoire, and Morocco. Geographical coordinates were recorded to analyze the relationships between geographic distribution and genetic diversity. Molecular characterization was performed with a set of 22 microsatellite markers. Five commercial lines, broilers and layers, were also genotyped to investigate potential gene flow. A genetic diversity analysis was conducted both within and between populations. RESULTS: High heterozygosity levels, ranging from 0.51 to 0.67, were reported for all local populations, corresponding to the values usually found in scavenging populations worldwide. Allelic richness varied from 2.04 for a commercial line to 4.84 for one population from Côte d'Ivoire. Evidence of gene flow between commercial and local populations was observed in Morocco and in Cameroon, which could be related to long-term improvement programs with the distribution of crossbred chicks. The impact of such introgressions seemed rather limited, probably because of poor adaptation of exotic birds to village conditions, and because of the consumers' preference for local chickens. No such gene flow was observed in Benin, Ghana, and Côte d'Ivoire, where improvement programs are also less developed. The clustering approach revealed an interesting similarity between local populations found in regions sharing high levels of precipitation, from Cameroon to Côte d'Ivoire. Restricting the study to Benin, Ghana, and Côte d'Ivoire, did not result in a typical breed structure but a south-west to north-east gradient was observed. Three genetically differentiated areas (P<0.01) were identified, matching with Major Farming Systems (namely Tree Crop, Cereal-Root Crop, and Root Crop) described by the FAO. CONCLUSIONS: Local chickens form a highly variable gene pool constituting a valuable resource for human populations. Climatic conditions, farming systems, and cultural practices may influence the genetic diversity of village chickens in Africa. A higher density of markers would be needed to identify more precisely the relative importance of these factors.

Age, genotype and sex effects on growth performance of local chickens kept under improved management in Ghana.

Characterisation of animal genetic resources has been recognised globally as an important step towards their sustainable use. Body weight data of local chickens (213 forest and 160 savannah chickens) and 183 French free-ranging SASSO T44 chickens kept under improved management were collected from hatch to 40 weeks of age and analysed to determine the effects of age, genotype and sex on their growth performance. At all ages, SASSO T44 chickens had significantly (P<0.05) higher weights (2.6-3.2 kg at 28 weeks) than the local chickens (1.2-1.7 kg at 28 weeks). The rate of growth at the earlier ages in the local genotypes (5.57-7.80 g/day) was lower than the range of 13.81-15.42 in SASSO T44 chickens. Except at hatch, savannah chickens were significantly heavier (P<0.05) than the forest chickens at all ages. Male chickens had significantly (P<0.05) superior growth rates than females across all genotypes except from the 20th to the 28th week. Growth trends in both sexes depicted linear increase in body weights; however, the rate of increase in body weights was higher in males as compared to females, thus showing clear sexual dimorphism. There were no significant (P>0.05) differences in the growth rates of SASSO T44 chickens and local genotypes at the later ages (20-28 weeks). Local chickens from the savannah zone had better growth rate than forest chickens. The significant effect of ecozone on the growth potential of local chickens is an indication that their productive potential could be improved through interventions in the environment such as provision of feed and some veterinary care.

Characterisation of local Ghanaian chickens: growth performance evaluation based on Richards growth model and genetic size scaling.

The Richards growth model was fitted to body weight-age data of local and SASSO T44 chickens to describe their growth performance. Males had higher (P < 0.05) asymptotic mature weights than females. Within the local chicken population, birds from the savannah zone had higher (P < 0.05) asymptotic mature weights compared to forest chicken which ironically had higher body weights at hatch. Male local chicken had lower maturing rates compared to the females. Female local chicken were superior to SASSO T44 females in terms of maturing rate. On the average, local chickens took relatively longer time (78.4-83.3 days) to reach the point of inflection than the SASSO T44 population (74.2-79.8 days). However, there were no significant differences (P > 0.05) in the age at inflection among local chicken populations. The shape parameter for SASSO T44 chicken (0.053-0.370) and maturation rate for local chicken (0.177-0.198) were the most critical parameters. Scaling the body weights into degree of maturity highlighted the degree to which genotypes matured over time. Female chickens had the highest (P < 0.05) degree of maturity at all ages. The local chicken populations were also metabolically older than SASSO T44 chickens. Results of this study provide an opportunity to develop breeding strategies for local chicken by modifying either management practices or their genetic makeup to positively affect their growth and productivity.

Genetic diversity of Forest and Savannah chicken populations of Ghana as estimated by microsatellite markers.

The characterization of indigenous animal genetic resources is a requisite step in providing needed information for the conservation of useful genotypes against future needs. Thus, in this study, 22 microsatellite markers were used to genotype 114 local chickens from the Forest (n = 59) and Savannah (n = 55) eco-zones of Ghana and the results compared to those of the ancestral red junglefowl (n = 15) and two European commercial chicken populations--a broiler (n = 25) and white leghorn (n = 25). A total of 171 alleles were observed, with an average of 7.8 alleles per locus. The local Ghanaian chickens showed higher diversity in terms of the observed number of alleles per locus (6.6) and observed heterozygosity (0.568) compared with the combined control populations (6.0 and 0.458, respectively). However, Wright's F-statistics revealed negligible genetic differentiation (F(ST)) in local Ghanaian chicken populations. In addition, 65% of the Savannah chickens were inferred to be more likely from the Forest, suggesting a south-north dispersal of chickens from their probable original location in the Forest zone to the Savannah areas. It is concluded that the Forest and Savannah chickens of Ghana are a single, randomly mating unselected population, characterized by high genetic diversity and constitute a valuable resource for conservation and improvement.

Internalisation of microbes in vegetables: microbial load of Ghanaian vegetables and the relationship with different water sources of irrigation.

The occurrence of pathogens in the internal parts of vegetables is usually associated with irrigation water or contaminated soil and could pose risk to consumers as the internalised pathogens are unaffected by external washing. This study was carried out to assess the rate of internalisation of microbes in common Ghanaian vegetables. Standard microbiological methods were employed in microbial enumeration of vegetables collected at the market and farm levels, as well as irrigation water and soil samples. The overall mean counts of vegetables were 4.0 x 10(3) cfu g(-1); 8.1 x 10(2) cfu g(-1); 2.0 x 10(2) cfu g(-1); 3.5 x 10(2) cfu g(-1) for total bacteria, coliform counts, faecal coliform counts and yeast counts, respectively. The rate of internalisation of coliforms in vegetables irrigated with stream/well water was 2.7 times higher than those irrigated with pipe water. The mean coliform counts (4.7 x 10(7) cfu g(-1)) and faecal coliform counts (1.8 x 10(6) cfu g(-1)) of soil samples were similar to those of stream water suggesting both sources exerted similar contamination rates on the vegetables. Generally, there were no significant variations between the rates of internalisation of microbes at the market and farm levels at p < 05, indicating that internalisation of microbes in the vegetables mainly occurred at the farm level. The study has shown that microbial contamination of vegetables in Ghana is not limited to the external surface, but internal vegetable parts could harbour high microbial loads and pose risk to consumers. Safety practices associated with the commodity should therefore not be limited to external washing only. There is the additional need of heating vegetables to eliminate microbes both externally and internally before consumption.

Application of the WHO keys of safer food to improve food handling practices of food vendors in a poor resource community in Ghana.

Data was collected from food vendors in a poor resource community in Ghana, which showed that the vendors constituted an important source of oro-faecal transmission. Following this, the WHO five keys of safer food were utilized in an evidence based training programme for the vendors to improve their food handling practices. Impact assessment of the food safety training showed that 67.6% of the vendors had acquired some knowledge from the workshop and were putting it into practice. Lack of food safety equipment was a major hinderance to behavioral change among the vendors as far food handling practices are concerned.

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 F2 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 F2. 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.

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.

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.