Genetic distinctness of African, Asian and South American local chickens

Molecular Characterization and Seasonal Variation in Expression of HSP70.1 Gene in Gangatiri Cattle and Its Comparison with Buffalo

Under tropical climate heat stress is a major challenge for livestock production. HSP70.1 is a ubiquitously expressed protein maintaining cellular machinery through proper folding of denatured proteins and prevents cellular apoptosis and protect cell from heat stress. Therefore, present investigation was undertaken to explore genetic variability in HSP70.1 gene in Gangatiri cattle, its comparison with buffalo sequences and differential expression in different season. The allelic variant was identified by sequencing amplified PCR product of HSP70.1 gene by primer walking. Season-wise total RNA samples was prepared for differential expression study. Brilliant SYBR Green QPCR technique was used to study the expression kinetics of this gene. DNA sequencing by primer walking identified four allelic variants in Gangatiri cattle. Sequence alignment study revealed four, six and one substitutions in the 5' untranslated region (5'UTR), coding and 3' untranslated region ((3'UTR) of HSP70.1 gene, respectively. Comparative analysis of HSP70.1 gene revealed that Cattle has shorter 5'UTR and 3' UTR than the buffalo. In Gangatiri cattle, summer season has significantly higher (P ≤ 0.05) expression of HSP70.1 than the spring and winter. The relative expression of HSP70.1 was increased by more than six folds in summer and nearly 1.5 folds higher in winter in comparison to the spring season. Therefore, HSP70.1 may be considered to have a critical role in the development of thermal tolerance in Gangatiri cattle.

Mapping genome-wide diversity and population dynamics in Indian chicken breeds for targeted conservation and breeding

1. Genetic improvement and widespread use of artificial selection may have impacted the genetic make-up of Indian chicken breeds. The genetic architecture of contemporary chicken population of India needs to be assessed for future improvement and conservation programmes. This study utilised whole-genome sequences in 180 chicken samples from 16 indigenous breeds, along with the Red Jungle Fowl and the commercial White Leghorn.2. A panel of 76 978 genome-wide single-nucleotide polymorphisms (SNP) was selected for comparative genome analysis after stringent screening. Breeds originating from the eastern regions of India exhibited higher genomic diversity, indicative of a rich repository of distinct germplasm. Conversely, the Uttara breed, from the northern hilly areas, display considerable genetic differentiation with diminished diversity compared to others, underscoring conservation concerns. The average coefficient (FIS) of 0.084 caution the need to mitigate risks associated with inbreeding.3. The study revealed that the analysis of 76 978 genome-wide SNP will serve as a cornerstone in refining conservation strategies, to design interventions with greater precision.4. The contribution of Red Jungle Fowl to the gene pool of all native breeds was supported by this study. Genetic structuring indicated a relationship among breeds based on geographical proximity, underscored by varying levels of admixture.

Morphometric characteristics and microsatellite markers based diversity and differentiation recognizes the first prospective cattle breed from the Jharkhand state of India

India is bestowed with immense cattle biodiversity with 50 registered breeds. However, the majority (59.3%) is yet not characterized. Identification and characterization are the gateways to the management of prized indigenous resources. Present research described a unique cattle population of Jharkhand state, managed under a traditional low-input, low-output system. It was characterized by morphological traits, performance parameters, and management practices. Animals have the characteristic pre-scapular location of the hump. Genetic variation within this population and its differentiation with the six closely distributed cattle breeds were evaluated using FAO recommended microsatellite markers. Jharkhandi cattle have substantial genetic variation based on gene diversity (>0.6) and the average number of alleles per locus (>8). The population did not suffer from a genetic bottleneck in the recent past. Pairwise Nei's genetic distance, phylogenetic relationship, population differentiation, and the correct assignment of all the animals to self group substantiated its separate genetic identity. Since gene flow (Nm = 2.8-7.32) was identified and admixture was indicated by the Bayesian analysis there is a pressing need for scientific management of this population. Results endow authorities with critical information for registering a new Indian cattle breed (Medini) that contributes to the food security, livelihood, and economic sustainability of rural tribal households.

Conservation priority and run of homozygosity pattern assessment of global chicken genetic resources

The conservation of genetic resources is becoming increasingly important for the sustainable development of the poultry industry. In the present study, we systematically analyzed the population structure, conservation priority, runs of homozygosity (ROH) of chicken breeds globally, and proposed rational conservation strategies. We used a 600K Affymetrix Axiom HD genotyping SNP array dataset of 2,429 chickens from 134 populations. The chickens were divided into 5 groups based on their country of origin and sampling location: Asian chickens (AS-LOC), African chickens (AF), European local chickens (EU-LOC), Asian breeds sampled in Germany (AS-DE), and European breeds sampled in Germany (EU-DE). The results indicated that the population structure was consistent with the actual geographical distribution of the populations. AS-LOC had the highest positive contribution to the total gene (HT, 1.00%,) and allelic diversity (AT, 0.0014%), the lowest inbreeding degree and the fastest linkage disequilibrium (LD) decay rate; the lowest contribution are derived by European ex situ chicken breeds (EU-DE:HT = -0.072%, AT = -0.0014%), which showed the highest inbreeding and slowest LD decay. Breeds farmed in ex situ (AS-DE, EU-DE) conditions exhibited reduced genetic diversity and increased inbreeding due to small population size. Given limited funds, it is a better choice for government to conserve the breeds with the highest contribution to genetic diversity in each group. Therefore, we evaluated the contribution of each breed to genetic and allelic diversity in 5 groups. Among each group, KUR(AF), BANG(AS-LOC), ALxx(EU-LOC), BHwsch(AS-DE), and ARw(EU-DE) had the highest contribution to gene diversity in the order of the above grouping. Similarly, according to the allelic diversity standard (in the same order), ZIMxx, PIxx, ALxx, SHsch, and ARsch had the highest contribution. After analyzing ROH, we found a total of 144,708 fragments and 27 islands. The gene and genome regions identified by the ROH islands and QTLs indicate that chicken breeds have potential for adaptation to different production systems. Based on these findings, it is recommended to prioritize the conservation of breeds with the highest genetic diversity in each group, while paying more attention to the conservation of Asian and African breeds. Furthermore, providing a valuable reference for the conservation and utilization of chicken.

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH hotspots harbored genes related to immune response and adaptation to local hot temperatures. The results on genetic relationship and population structure reported a clear clustering of the populations according to their geographic origin. The COS formed a nonoverlapping genomic cluster and clearly separated from the other populations, but showed evident proximity to the Siciliana breed (SIC). The VPL highlighted intermediate relationships between the COS-SIC group and the rest of the sample, but closer to the other Italian local chickens. Moreover, VPL showed a complex genomic structure, highlighting the presence of 2 subpopulations that match with the different source of the samples. The results obtained from the survey on genetic differentiation underline the hypothesis that Cornuta is a population with a defined genetic structure. The substructure that characterizes the Val Platani chicken is probably the consequence of the combined effects of genetic drift, small population size, reproductive isolation, and inbreeding. These findings contribute to the understanding of genetic diversity and population structure, and represent a starting point for designing programs to monitor and safeguard these local genetic resources, in order to define a possible official recognition program as breeds.

Genetic diversity of indigenous guinea fowl (Numida meleagris) using microsatellite markers in northern Togo

Indigenous guinea fowl is an important animal resource for improving rural household income. In order to provide molecular data for a sustainable management of this poultry resource, an assessment of the genetic diversity and phylogenic relationships was undertaken on seven guinea fowl phenotypes from two agroecological zones (Dry Savannah and Atakora) of Togo. Genotyping was carried out using 18 microsatellite markers on 94 individuals from Dry Savannah (59) and Atakora (35) zones. The results obtained showed a high genetic diversity, with six as an average alleles per locus and an observed heterozygosity of 0.512. However, the F_IS values varied from 0.047 (Lavender) to 0.257 (Albino), reflecting a deficit of heterozygotes, which suggests low to moderate inbreeding levels. The genetic distances between phenotypes are low, ranging from 0.0068 (Bonaparte-Pearl grey) to 0.1559 (Lavender-Albino), unlike the strong genetic identities that reflect a strong genetic similarity between the seven phenotypes of indigenous guinea fowl studied. These results indicate the existence of a single indigenous guinea fowl population, derived from three probable parental populations, with a high within population genetic diversity (phenotypic or agroecological zone). These results could be of use to conservation and improvement programs aiming at the maintenance and sustainable exploitation of this important socio-cultural and economic resource in Togo.

Diversity and Genetic Relationship of Free-Range Chickens from the Northeast Region of Brazil

Simple Summary

Local animal breeds represent a national genetic heritage for every country. Creole free-range chickens have important cultural, historical, genetic, and economic roles in several countries. In Brazil, there is a lack of information regarding the genetic formation of local chicken breeds. These animals were brought to Brazil during colonization in the 16th century. Currently, Brazilian Creole chickens are highly adapted to the edaphoclimatic conditions of the country and are mostly reared by smallholders. In this study, we used microsatellite markers to determine the genetic composition of three chicken breeds from the northeast region of Brazil. Our results confirm the existence of interbreed genetic diversity and high genetic variability within the Brazilian Creole chickens studied. Furthermore, our findings show that the formation of these genetic groups had contributions from different ancestors. Our results will be useful to support the development of conservation programs, as well as the sustainable use and official recognition of these breeds.

Abstract

In this study, we aimed to evaluate the genetic diversity within and among chicken breeds from the northeast region of Brazil (states of Bahia and Piauí) using microsatellite markers. In addition, we assessed the identity and genetic relationships of chickens from Europe, Africa, and South America, as well as their influence on the formation of the Brazilian breeds. A total of 25 microsatellite markers and a panel containing 886 samples from 20 breeds (including the Brazilian chickens) were used in this study. Different statistical parameters were used to estimate the genetic diversity and relationship among the genetic groups studied. Our study indicates that the Brazilian Creole chickens have high genetic variability. The results show that chickens reared in the states of Bahia and Piauí could have originated from different ancestors. The Brazilian breeds studied have an evolutionary relationship with chickens from Portugal, Nigeria, Chile, and Spain. Our results will contribute directly to the conservation and recognition of Brazilian Creole chicken breeds and provide a solid basis for the demonstration of their genetic identity and genetic conservation of American Creole chicken populations.

Identification of a new Indian camel germplasm by microsatellite markers based genetic diversity and population structure of three camel populations

Camel invokes fascinating chapter of Indian desert history and is integral component of its ecosystem. Camel population has reached a crisis point after three decades of decline (75%) causing major concern to the policy makers. >28% of Indian camel is not yet characterized. It is imperative to describe country’s camel germplasm and its existing diversity for designing conservation plan. One such population is Sindhi, distributed along border with Pakistan. Twenty five microsatellite markers being valuable tool for estimating genetic diversity were selected to elucidate genetic variability and relationship of Sindhi with two registered camel breeds of India- Marwari and Kharai. The standard metrics of genomic diversity detected moderate variability in all the three populations. A total of 303 alleles with a mean of 8.116 ± 0.587 alleles per locus were found in total of 143 animals. Sindhi population had intermediate allelic diversity with 8.522 ± 1.063 alleles per locus. Corresponding values in Marwari and Kharai were 8.783 ± 0.962 and 7.043 ± 1.030, respectively. Genetic variability within the breeds was moderate as evidenced by the mean observed heterozygosity of 0.556 ± 0.025. Sindhi camel population harbors higher genetic variability (Ho = 0.594) as compared to the two registered camel breeds (Marwari, 0.543 and Kharai, 0.531). Mean expected heterozygosity under Hardy-Weinberg equilibrium was higher than the observed values across the three camel groups, indicating deviations from assumptions of this model. In fact, average positive F value of 0.084 to 0.206 reflected heterozygote deficiency in these populations. These Indian camel populations have not experienced serious demographic bottlenecks in the recent past. Differences among populations were medium and accounted for 7.3% of total genetic variability. Distinctness of three camel populations was supported by all the approaches utilized to study genetic relationships such as genetic distances, phylogenetic relationship, correspondence analysis, clustering method based on Bayesian approach and individual assignment. Sindhi camel population was clearly separated from two registered breeds of Indian camel. Results conclude Sindhi to be a separate genepool. Moderate genetic diversity provides an optimistic viewpoint for the survival of severely declining indigenous camel populations with appropriate planning strategies for conserving the existing genetic variation and to avoid any escalation of inbreeding.

Investigating genetic variability in Hsp70 gene-5'-fragment and its association with thermotolerance in Murrah buffalo (Bubalus bubalis) under sub-tropical climate of India

The present study was undertaken to investigate genetic variability in a fragment comprising 5'UTR along with partial coding sequence of Hsp70 gene and its association with thermotolerance traits in Murrah buffalo at ICAR-Research Complex for Eastern Region, Patna (India). The allelic variants were identified from genomic DNA samples using SSCP technique. The PCR products were sequenced and analyzed. Data on different thermotolerance traits recorded in three seasons were analyzed by least squares ANOVA taking the SSCP genotypes as fixed effect. Two allelic variants (A and B), each of 503-bp in size, were documented with frequency of 0.59 and 0.41, respectively, and three genotypes (AA, AB and BB) with corresponding frequency of 0.30, 0.58 and 0.12. The allelic variants were due to single nucleotide substitution at 55th base position leading to a change of threonine (A) to methionine (B) in amino acid sequence. Both the allelic variants had 99.8% similarity in nucleotide sequence. In phylogenetic tree, allele A was in a cluster while allele B and Gangatiri cattle sequence formed a different cluster. The SSCP genotypes had significant effect on different thermotolerance traits in summer with thermo-humidity index of ≥ 84. Buffaloes with AA genotype had the highest (P ˂ 0.05) summer evening rectal temperature, respiration rate and pulse rate, inferring that the buffaloes carrying AA genotype had more stress in summer than those with AB and BB genotype. These SSCP genotypes might have differential role in heat shock protein response to induce thermotolerance of Murrah buffaloes in Gangetic plains.

Genetic profiling of Hsp70 gene in Murrah buffalo (Bubalus bubalis) under sub-tropical climate of India

This study was aimed to genetic profiling of heat shock protein 70 (Hsp70) gene in Murrah buffalo investigating 50 unrelated adult animals at ICAR-Research Complex for Eastern Region, Patna (India) in winter, spring, and summer. PCR ready genomic DNA samples and season-wise total RNA samples were prepared. The PCR products of Hsp70 eluted from agarose gel were sequenced and analyzed. The first-strand cDNA was synthesized and concentration was equalized to 25 ng/μl. Expression kinetics of mRNA transcripts in different seasons was studied using Brilliant SYBR Green QPCR technique and the data retrieved was analyzed by least-squares ANOVA. DNA sequencing by primer walking revealed four allelic variants of Hsp70 gene. Alignment study revealed one substitution in 5'UTR, six substitutions in coding region, and one addition in 3'UTR. The highest percent identity and negligible phylogenetic distance were found among the alleles and reference bovine sequences. The relative mRNA expression was significantly higher in summer when THI ≥ 84 than the spring and winter; fold change increased by 4.5 times in summer than the spring whereas found nearly half in winter. These findings can be useful for heat stress management in buffaloes and help in understanding the mechanism of thermo-regulation well.

The SYNBREED chicken diversity panel: a global resource to assess chicken diversity at high genomic resolution

BACKGROUND

Since domestication, chickens did not only disperse into the different parts of the world but they have also undergone significant genomic changes in this process. Many breeds, strains or lines have been formed and those represent the diversity of the species. However, other than the natural evolutionary forces, management practices (including those that threaten the persistence of genetic diversity) following domestication have shaped the genetic make-up of and diversity between today's chicken breeds. As part of the SYNBREED project, samples from a wide variety of chicken populations have been collected across the globe and were genotyped with a high density SNP array. The panel consists of the wild type, commercial layers and broilers, indigenous village/local type and fancy chicken breeds. The SYNBREED chicken diversity panel (SCDP) is made available to serve as a public basis to study the genetic structure of chicken diversity. In the current study we analyzed the genetic diversity between and within the populations in the SCDP, which is important for making informed decisions for effective management of farm animal genetic resources.

RESULTS

Many of the fancy breeds cover a wide spectrum and clustered with other breeds of similar supposed origin as shown by the phylogenetic tree and principal component analysis. However, the fancy breeds as well as the highly selected commercial layer lines have reduced genetic diversity within the population, with the average observed heterozygosity estimates lower than 0.205 across their breeds' categories and the average proportion of polymorphic loci lower than 0.680. We show that there is still a lot of genetic diversity preserved within the wild and less selected African, South American and some local Asian and European breeds with the average observed heterozygosity greater than 0.225 and the average proportion of polymorphic loci larger than 0.720 within their breeds' categories.

CONCLUSIONS

It is important that such highly diverse breeds are maintained for the sustainability and flexibility of future chicken breeding. This diversity panel provides opportunities for exploitation for further chicken molecular genetic studies. With the possibility to further expand, it constitutes a very useful community resource for chicken genetic diversity research.

Genetic diversity of indigenous chickens from selected areas in Kenya using microsatellite markers

In this study, indigenous chickens were collected from eight different regions in Kenya and kept at InCIP-Egerton University. These were studied using eighteen microsatellite markers to determine genetic variation. Statistics related to genetic variation were estimated using GenALEx6. Mean percentage polymorphic loci (PPL) was 96.71% and 4% genetic variance (p ≥ 0.003) was seen between the eight populations. MCW0123 marker had the highest genetic variance of 13% among populations (p ≥ 0.003) at 95% CI. Mean He ranged from 0.351 ± 0.031 (SIB) to 0.434 ± 0.022 (BM) with a grand mean He of 0.399 ± 0.011 across the populations using the microsatellite markers. Nei’s genetic distance ranged from 0.016 (SIB and WP) to 0.126 (NR and SIB). DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. This study found a lot of genetic variation and relatedness within and among populations. Based on the phylogenetic tree result, it is concluded that the clustering of the chicken populations in the present study is not based on geographical proximity. The microsatellite markers used in this study were suitable for the measurement of the genetic biodiversity and relationship of Kenyan chicken populations. These results can therefore serve as an initial step to plan the conservation of indigenous chickens in Kenya.

Genetic variability in egg production-associated microsatellites in Rhode Island Red chicken

Present investigation was carried out in 114 birds belonging to selected strains of Rhode Island Red chicken maintained at institute experimental layer farm with the objective to analyze polymorphism in egg production associated microsatellite loci and to determine various population genetics statistics based on allelic polymorphism. Genomic DNA samples were isolated from all experimental birds and PCR was performed using primers for ten microsatellite loci, reported to be associated with egg production traits in chicken. Alleles were separated on 3.4% MetaPhoreTM agarose and their sizes were determined by Quantity One software. Allelic data were analyzed by POPGENE. Allele numbers varied from 2 to 5 and average number of alleles per locus was 4.00±0.37 (Na). Allele sizes ranged from 99-280 bp. Allele frequency per locus ranged from 0.0225-0.8919. Nei's heterozygosity, Botstein's polymorphic information content (PIC) and Wright's fixation indices at each locus were estimated. All studied microsatellite loci were polymorphic and estimated PIC ranged from 0.19 (ADL0273) to 0.72 (MCW0110). Seven loci were moderate to highly polymorphic (PIC>0.50). Nei's heterozygosity per locus ranged from 0.20 (ADL0273) to 0.77 (MCW0110). Averaged effective number of alleles (Ne), Shannon's Information index (I) and Wright's fixation indices were 2.71±0.26, 1.0654±0.1046 and 0.5126±0.0757, respectively. Average observed (Ho) and expected (He) heterozygosities were 0.3036±0.0625 and 0.5930±0.0505, respectively. Study revealed prevalence of heterozygosity as the Ne was lesser than the Na. It further revealed that the population was under Hardy-Weinberg disequilibrium as (He) was more than (Ho).Chi square and G-square estimates were significant, which suggested that the studied microsatellite loci might have some association with ongoing selection for 40-week part-period egg production in RIR chicken.

Genetic Variation of Nine Chicken Breeds Collected from Different Altitudes Revealed by Microsatellites

Genetic polymorphisms of 19 microsatellites were investigated in nine local chicken breeds collected from low, middle and high altitudes areas in China (total number was 256) and their population genetic diversity and population structure were analyzed. All breeds were assigned into three groups, including the high (Tibetan chicken (T) and Grey chicken (G), their altitudes were above 1000 m); middle (Chengkou mountainous chicken (CK), Jiuyuan chicken (JY) and Pengxian yellow chicken (PY), their altitudes were between 500 and 1000 m), and low groups (Da ninghe chicken (DH), Tassel first chicken (TF), Gushi chicken (GS) and Wenchang chicken (WC), their altitudes were below 500 m). We found 780 genotypes and 324 alleles via the 19 microsatellites primers, and the results showed that the mean number of alleles (N_a) was 17.05; the average polymorphism information content (PIC) was 0.767; the mean expected heterozygosity (He) was 0.662; as for observed heterozygosity (H_o), it was 0.647. The AMOVA results indicated the genetic variation mainly existed within individuals among populations (80%). There was no genetic variation among the three altitude groups (0%). The mean inbreeding coefficient among individuals within population (F_IS) was 0.031 and the mean gene flow (N_m) was 1.790. The mean inbreeding coefficient among populations within a group (F_ST) was 0.157. All loci deviated Hardy-Weinberg equilibrium. The genetic distance ranged from 0.090 to 0.704. Generally, genetic variations were mainly made up of the variations among populations and within individuals. There were rich gene diversities in the populations for the detected loci. Meanwhile, frequent genes exchange existed among the populations. This can lead to extinction of the peripheral species, such as the Tibetan chicken breed.

Assessment of genetic diversity and differentiation of two major camel ecotypes (<i>Camelus dromedarius</i>) in Sudan using microsatellite markers

Abstract. Although Sudan has the second largest camel population in Africa, it has not yet been genetically differentiated. The present study was undertaken to evaluate, for the first time, the genetic diversity and relationship of two major camel ecotypes representing the eastern (Butana) and western (Darfur) regions of Sudan using 12 microsatellite markers. A total of 107 samples of study ecotypes were investigated displaying high mean values of genetic diversity (mean number of alleles: 11.5 ± 1.45; polymorphism information content: 0.67 ± 0.04; observed heterozygosity: 0.69 ± 0.05; expected heterozygosity: 0.72 ± 0.04). The global inbreeding coefficient (FIT = 0.041 ± 0.03, P > 0.05) was attributed to substantial and non-significant within-population inbreeding (FIS = 0.034 ± 0.03) and scarce but highly significant differentiation between ecotypes (FST = 0.008 ± 0.00; P < 0.0001). Multivariate analysis indicated a historical intermixing between different genealogical lineages making up the current admixed gene pool of the geographically divergent ecotypes. Consistent with this, STRUCTURE cluster analysis showed these ecotypes to be one mosaic admixed population. The results showed abundant genetic diversity within Sudanese dromedaries. Our study indicates that the two Sudanese camel ecotypes (Butana and Darfur) appear as an admixture of two geographical branches and do not support the contemporary division of Sudanese dromedaries into their respective socio-ethno-geography.

Genetic diversity and relationships of korean chicken breeds based on 30 microsatellite markers

The effective management of endangered animal genetic resources is one of the most important concerns of modern breeding. Evaluation of genetic diversity and relationship of local breeds is an important factor towards the identification of unique and valuable genetic resources. This study aimed to analyze the genetic diversity and population structure of six Korean native chicken breeds (n = 300), which were compared with three imported breeds in Korea (n = 150). For the analysis of genetic diversity, 30 microsatellite markers from FAO/ISAG recommended diversity panel or previously reported microsatellite markers were used. The number of alleles ranged from 2 to 15 per locus, with a mean of 8.13. The average observed heterozygosity within native breeds varied between 0.46 and 0.59. The overall heterozygote deficiency (F IT) in native chicken was 0.234±0.025. Over 30.7% of F IT was contributed by within-population deficiency (F IS). Bayesian clustering analysis, using the STRUCTURE software suggested 9 clusters. This study may provide the background for future studies to identify the genetic uniqueness of the Korean native chicken breeds.

Population structure of four Thai indigenous chicken breeds

BACKGROUND

In recent years, Thai indigenous chickens have increasingly been bred as an alternative in Thailand poultry market. Due to their popularity, there is a clear need to improve the underlying quality and productivity of these chickens. Studying chicken genetic variation can improve the chicken meat quality as well as conserving rare chicken species. To begin with, a minimal set of molecular markers that can characterize the Thai indigenous chicken breeds is required.

RESULTS

Using AFLP-PCR, 30 single nucleotide polymorphisms (SNPs) from Thai indigenous chickens were obtained by DNA sequencing. From these SNPs, we genotyped 465 chickens from 7 chicken breeds, comprising four Thai indigenous chicken breeds--Pradhuhangdum (PD), Luenghangkhao (LK), Dang (DA) and Chee (CH), one wild chicken--the red jungle fowls (RJF), and two commercial chicken breeds--the brown egg layer (BL) and commercial broiler (CB). The chicken genotypes reveal unique genetic structures of the four Thai indigenous chicken breeds. The average expected heterozygosities of PD=0.341, LK=0.357, DA=0.349 and CH=0.373, while the references RJF= 0.327, CB=0.324 and BL= 0.285. The F(ST) values among Thai indigenous chicken breeds vary from 0.051 to 0.096. The F(ST) values between the pairs of Thai indigenous chickens and RJF vary from 0.083 to 0.105 and the FST values between the Thai indigenous chickens and the two commercial chicken breeds vary from 0.116 to 0.221. A neighbour-joining tree of all individual chickens showed that the Thai indigenous chickens were clustered into four groups which were closely related to the wild RJF but far from the commercial breeds. Such commercial breeds were split into two closely groups. Using genetic admixture analysis, we observed that the Thai indigenous chicken breeds are likely to share common ancestors with the RJF, while both commercial chicken breeds share the same admixture pattern.

CONCLUSION

These results indicated that the Thai indigenous chicken breeds may descend from the same ancestors. These indigenous chicken breeds were more closely related to red jungle fowls than those of the commercial breeds. These findings showed that the proposed SNP panel can effectively be used to characterize the four Thai indigenous chickens.

Reconstructing the origin and dispersal patterns of village chickens across East Africa: insights from autosomal markers

Unravelling the genetic history of any livestock species is central to understanding the origin, development and expansion of agricultural societies and economies. Domestic village chickens are widespread in Africa. Their close association with, and reliance on, humans for long-range dispersal makes the species an important biological marker in tracking cultural and trading contacts between human societies and civilizations across time. Archaezoological and linguistic evidence suggest a complex history of arrival and dispersion of the species on the continent, with mitochondrial DNA (mtDNA) D-loop analysis revealing the presence of five distinct haplogroups in East African village chickens. It supports the importance of the region in understanding the history of the species and indirectly of human interactions. Here, through a detailed analysis of 30 autosomal microsatellite markers genotyped in 657 village chickens from four East African countries (Kenya, Uganda, Ethiopia and Sudan), we identify three distinct autosomal gene pools (I, II and III). Gene pool I is predominantly found in Ethiopia and Sudan, while II and III occur in both Kenya and Uganda. A gradient of admixture for gene pools II and III between the Kenyan coast and Uganda's hinterland (P = 0.001) is observed, while gene pool I is clearly separated from the other two. We propose that these three gene pools represent genetic signatures of separate events in the history of the continent that relate to the arrival and dispersal of village chickens and humans across the region. Our results provide new insights on the history of chicken husbandry which has been shaped by terrestrial and maritime contacts between ancient and modern civilizations in Asia and East Africa.

Analysis of Geographic and Pairwise Distances among Chinese Cashmere Goat Populations

This study investigated the geographic and pairwise distances of nine Chinese local Cashmere goat populations through the analysis of 20 microsatellite DNA markers. Fluorescence PCR was used to identify the markers, which were selected based on their significance as identified by the Food and Agriculture Organization of the United Nations (FAO) and the International Society for Animal Genetics (ISAG). In total, 206 alleles were detected; the average allele number was 10.30; the polymorphism information content of loci ranged from 0.5213 to 0.7582; the number of effective alleles ranged from 4.0484 to 4.6178; the observed heterozygosity was from 0.5023 to 0.5602 for the practical sample; the expected heterozygosity ranged from 0.5783 to 0.6464; and Allelic richness ranged from 4.7551 to 8.0693. These results indicated that Chinese Cashmere goat populations exhibited rich genetic diversity. Further, the Wright’s F-statistics of subpopulation within total (FST) was 0.1184; the genetic differentiation coefficient (GST) was 0.0940; and the average gene flow (Nm) was 2.0415. All pairwise FST values among the populations were highly significant (p<0.01 or p<0.001), suggesting that the populations studied should all be considered to be separate breeds. Finally, the clustering analysis divided the Chinese Cashmere goat populations into at least four clusters, with the Hexi and Yashan goat populations alone in one cluster. These results have provided useful, practical, and important information for the future of Chinese Cashmere goat breeding.

The History of African Village Chickens: an Archaeological and Molecular Perspective

The history of the introduction and dispersal of village chickens across the African continent is a subject of intense debate and speculation among scholars. Here, we synthesize and summarise the current scientific genetic and nongenetic knowledge in relation to the history of the species on the continent. Sociocultural, linguistic, archaeological and historic data all suggest a complex history for the species in Africa, characterized by multiple maritime and/or terrestrial introductions over time and several dispersal routes towards and within Africa. Molecular genetics information supports these observations and in addition suggests possible Asian centers of origin for African domestic chickens, including South Asia and Island Southeast Asia. However, both sets of data were until now too limited in their geographic scope, both within Africa and in comparison with chickens from Asia, to unravel the history of the species in detail. We anticipate that further continent-wide studies combining archaeological, ancient and/or modern genetic information may shed new insights on the history of the species. These will contribute to a deeper understanding of the history of trading networks and human interactions within Africa and between African and Asian societies, at the root of the development and expansion of African civilizations.

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.

Genetic diversity of the major histocompatibility complex region in commercial and noncommercial chicken flocks using the LEI0258 microsatellite marker

Microsatellite marker LEI0258 was used as an indicator to examine the variability of the major histocompatibility complex (MHC) region in 2 commercial layer flocks, 1 experimental layer cross, and 5 noncommercial flocks (used for free-run and free-range meat and egg production). We hypothesized that the populations from noncommercial sources may have more diversity in MHC genes than that in the commercial-source populations. Two related parameters, heterozygosity and the number of alleles harbored by a population, were used to assess the genetic variability. The different combinations of the 22 alleles created 66 genotypes in the 8 chicken populations that were studied. The noncommercial populations, except for the Silkies (SK), harbored more alleles than those in the 2 commercial populations, Lohmann Brown and Lohmann White. The observed heterozygosity of the MHC region was high in all of the populations, except for SK. Considering the 2 parameters we have examined, we can generalize that the intensively selected commercial egg-layer varieties seem to have less genetic variability in their MHC regions compared with that of the noncommercial flocks, which are less intensively selected. The LEI0258 variants can be used as markers to detect most of the MHC haplotypes, but in the different populations the same allele size may not always be associated with the same serologically defined haplotype. The information obtained from this study will be useful for genetic resource conservation and the development of breeding stocks that are suitable for free-range production.

Genetic diversity and population structure of five Ethiopian chicken ecotypes

This study aimed to analyse the genetic diversity and population structure of five Ethiopian chicken ecotypes (N = 155), which were compared with six commercial purebreds (N = 180). For the analysis of genetic diversity, 26 AVIANDIV microsatellite markers were used. The number of alleles in Ethiopian ecotypes ranged from 2 to 19 per locus, with a mean of 6.1. The average observed heterozygosity within ecotype varied between 0.53 and 0.57. The overall heterozygote deficiency (F(IT)) in Ethiopian ecotypes was 0.124 ± 0.037. Over 68% of F(IT) was because of within-ecotype deficiency (F(IS)). In the phylogenetic tree, Ethiopian ecotypes clustered into two groups. The analysis of the relationship between populations using the structure program provided further evidence for the occurrence of at least two subgroups in the Ethiopian ecotypes. Findings of this study may provide the background for future studies to identify the origin of the two gene pools representing the Ethiopian chicken ecotypes and to characterize the gene variants influencing economically important traits.

On-farm investigation of local chicken biodiversity and performance potentials in rural areas of Jordan

On-farm surveys were conducted to investigate the biodiversity of local chickens and their performance potential. The study was carried out in rural areas of northern Jordan. A sample of 846 adult local chickens was phenotypically characterized based on morphology, feather colors, comb shape and performance. Body measurements for cluster analyses were recorded on 460 adult females. The most predominant chicken type was the Jordan Baladi (67.3%) followed by the Pakistani (27.7%) and the Brahma (5%). Cluster analyses showed that the three populations are distinct. The Jordan Baladi and the Pakistani were closer to each other than the Brahma. Plumage colors were observed either as single color or mottled (a mix of many colors). The latter was the most predominant (23.1 %) followed by black (19.5%) and light brownish (19.1%). The single comb type was the most predominant (80.3%). Hens of the local chicken reached sexual maturity at about 22-30 weeks of age. The average clutch number was 1-5 per year, with 18-30 eggs per clutch. Each hen laid on average 68.9±3.3 eggs per year. The body size of adult females and males was about 1 240±10g and 1 890±30g, respectively. Indiscriminate crossbreeding was taking place frequently. Genetic characterization would complement the phenotypic characterization and should be conducted. This would help to initiate a program for the preservation of genetic diversity in local chickens in Jordan.

Toll-like receptor mRNA expression, iNOS gene polymorphism and serum nitric oxide levels in indigenous chickens

Toll-like receptor (TLR) family is one of the important members of innate immune system that recognizes conserved microbial patterns and induces innate immune response. They also act as a link to adaptive immune response. Nitric oxide (NO) is a multi-functional mediator with diverse physiological and immunological roles. In the present study TLR mRNA expression in heterophils, serum nitric oxide level and iNOS (inducible Nitric Oxide Synthase) gene polymorphism were investigated in cockerels of two Indian native chicken breeds, Aseel and Kadaknath. TLR (4 and 5) mRNA expression as quantified by real time RT-PCR revealed Kadaknath males expressed significantly (P < 0.01) higher TLR4 mRNA than Aseel males. iNOS gene polymorphism analyzed by PCR-RFLP method revealed difference in allele frequency. Kadaknath males had higher allele B frequency (0.81) than Aseel males (0.56). However, there were no genotype and breed effect on serum nitric oxide level. Based on the present study we conclude that Kadaknath has comparatively higher innate immunity levels than Aseel, however further investigations are needed.

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.

Haematological studies on frizzled and naked neck genotypes of Nigerian native chickens

Variation in haematological parameters of Nigerian native chickens was studied using 60 clinically normal frizzle-feathered, naked-neck, and normal-feathered native chickens. These included red blood cell count, haemoglobin, packed cell volume, white blood cell count, mean corpuscular volume, mean corpuscular haemoglobin concentration, serum glucose, urea, cholesterol, albumin, globulin and creatinine. Normal-feathered birds had higher (p<0.05) mean values compared to frizzled and native neck genotypes except for albumin, red blood and white blood cells, and mean cell haemoglobin concentration. Males generally had higher mean values than their female counterparts across all genotypes. Correlation coefficients among the parameters were significant (p<0.001) with r values ranging from 0.26 between red blood cell and mean corpuscular haemoglobin to 0.92 between red blood cell and cholesterol. Sufficient genetic variation therefore exists for haematological parameters among Nigerian native chickens that may represent indicator traits for further study. However, the application of molecular tools will provide better understanding and application of these differences.

Assessment of genetic relatedness of crossbred chicken populations using microsatellite markers

To measure genetic relatedness between populations, for breeding purposes, we analyzed 170 birds from six crossbred populations of three pure lines of White Leghorn chickens, using 14 microsatellite markers. All the microsatellites were polymorphic, with 2-6 alleles. The mean number of alleles per locus was 3.21. The effective number of alleles varied from 1.14 to 3.94. The observed heterozygosity varied from 0.133 to 1.00, with a mean of 0.748. The F (IS) values were mostly negative, with an average of -0.345. The mean F (ST) value was 0.056. The Nm values ranged from 1.91 to 42.17. The highest genetic identity was observed between IWI x IWK and IWK x IWI. The relation between any two groups of crosses was more than 85%. The results suggest that the crossbred populations were very closely related.

Genetic diversity in farm animals--a review

Domestication of livestock species and a long history of migrations, selection and adaptation have created an enormous variety of breeds. Conservation of these genetic resources relies on demographic characterization, recording of production environments and effective data management. In addition, molecular genetic studies allow a comparison of genetic diversity within and across breeds and a reconstruction of the history of breeds and ancestral populations. This has been summarized for cattle, yak, water buffalo, sheep, goats, camelids, pigs, horses, and chickens. Further progress is expected to benefit from advances in molecular technology.

Evaluation of diversity between different Spanish chicken breeds, a tester line, and a White Leghorn population based on microsatellite markers

The present study was conducted to evaluate the genetic variability and the genetic divergence of 13 Spanish chicken breeds, a tester line, and a White Leghorn population, using 24 microsatellite markers. A total of 150 alleles were detected across all population. The number of alleles by locus ranged from 2 to 13, with the mean value being 6.25. The mean polymorphic information content was 0.591, ranging from 0.847 to 0.172. The combined parentage exclusion probability of excluding 1 parent or 2 parents was 99 and 100%, respectively. The observed heterozygosity was lower than the expected heterozygosity for all loci, the mean values being 0.461 and 0.637. The observed and expected heterozygosity ranged from 0.003 to 0.735 and 0.181 to 0.863, respectively. Mean deficit of heterozygotes within populations (F(IS)) was 0.056 and mean fixation index of each population (F(ST)) was 0.244. The mean global deficit of heterozygotes across populations (F(IT)) was 0.286. A total of 15 private alleles in 10 microsatellites were observed, and in some populations, fixed alleles were found for 7 microsatellites. A total of 300 birds (83%) were properly assigned to the source population. The average observed heterozygosity for each population was 0.461, ranging from 0.328 (Quail Castellana) to 0.538 (Red Villafranquina), and the average expected heterozygosity was 0.488, ranging from 0.320 (Quail Castellana) to 0.550 (White-Faced Spanish). All of the Spanish breeds except the Quail Castellana were more polymorphic than the White Leghorn population. The mean value of the deviation of heterozygote number was 0.052. Nei's genetic distance showed a range from 0.109 (between White-Faced Spanish and Black Menorca) to 0.437 (between Buff Prat and White Leghorn). A phylogenetic tree constructed by the neighbor-joining method, based on Nei's genetic distance, showed a clear separation between the White Leghorn and the remaining breeds. The results indicate that the panel of microsatellite markers was useful in studying the genetic diversity of chicken breeds.

Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations

Previous studies suggested that multiple domestication events in South and South-East Asia (Yunnan and surrounding areas) and India have led to the genesis of modern domestic chickens. Ha Giang province is a northern Vietnamese region, where local chickens, such as the H'mong breed, and wild junglefowl coexist. The assumption was made that hybridisation between wild junglefowl and Ha Giang chickens may have occurred and led to the high genetic diversity previously observed. The objectives of this study were i) to clarify the genetic structure of the chicken population within the Ha Giang province and ii) to give evidence of admixture with G. gallus. A large survey of the molecular polymorphism for 18 microsatellite markers was conducted on 1082 chickens from 30 communes of the Ha Giang province (HG chickens). This dataset was combined with a previous dataset of Asian breeds, commercial lines and samples of Red junglefowl from Thailand and Vietnam (Ha Noï). Measurements of genetic diversity were estimated both within-population and between populations, and a step-by-step Bayesian approach was performed on the global data set.

RESULTS

The highest value for expected heterozygosity (> 0.60) was found in HG chickens and in the wild junglefowl populations from Thailand. HG chickens exhibited the highest allelic richness (mean A = 2.9). No significant genetic subdivisions of the chicken population within the Ha Giang province were found. As compared to other breeds, HG chickens clustered with wild populations. Furthermore, the neighbornet tree and the Bayesian clustering analysis showed that chickens from 4 communes were closely related to the wild ones and showed an admixture pattern.

CONCLUSION

In the absence of any population structuring within the province, the H'mong chicken, identified from its black phenotype, shared a common gene pool with other chickens from the Ha Giang population. The large number of alleles shared exclusively between Ha Giang chickens and junglefowl, as well as the results of a Bayesian clustering analysis, suggest that gene flow has been taking place from junglefowl to Ha Giang chickens.

Genetic diversity among Turkish native chickens, Denizli and Gerze, estimated by microsatellite markers

The genetic diversity of the Turkish native chicken breeds Denizli and Gerze was evaluated with 10 microsatellite markers. We genotyped a total of 125 individuals from five subpopulations. Among loci, the mean number of alleles was 7.5, expected heterozygosity (H (e)) was 0.665, PIC value was 0.610, and Wright's fixation index was 0.301. H (e) was higher in the Denizli breed (0.656) than in the Gerze breed (0.475). The PIC values were 0.599 and 0.426 for Denizli and Gerze, respectively. A phylogenetic tree was constructed using genetic distance and the neighbor-joining method. Its topology reflects the general pattern of genetic differentiation among the Denizli and Gerze breeds. The present study suggests that Denizli and Gerze subpopulations have a rich genetic diversity. The information about Denizli and Gerze breeds estimated by microsatellite analysis may also be useful as an initial guide in defining objectives for designing future investigations of genetic variation and developing conservation strategies.

Microsatellite-based phylogeny of Indian domestic goats

Background

The domestic goat is one of the important livestock species of India. In the present study we assess genetic diversity of Indian goats using 17 microsatellite markers. Breeds were sampled from their natural habitat, covering different agroclimatic zones.

Results

The mean number of alleles per locus (NA) ranged from 8.1 in Barbari to 9.7 in Jakhrana goats. The mean expected heterozygosity (He) ranged from 0.739 in Barbari to 0.783 in Jakhrana goats. Deviations from Hardy-Weinberg Equilibrium (HWE) were statistically significant (P < 0.05) for 5 loci breed combinations. The D_A measure of genetic distance between pairs of breeds indicated that the lowest distance was between Marwari and Sirohi (0.135). The highest distance was between Pashmina and Black Bengal. An analysis of molecular variance indicated that 6.59% of variance exists among the Indian goat breeds. Both a phylogenetic tree and Principal Component Analysis showed the distribution of breeds in two major clusters with respect to their geographic distribution.

Conclusion

Our study concludes that Indian goat populations can be classified into distinct genetic groups or breeds based on the microsatellites as well as mtDNA information.