Deciphering the Patterns of Genetic Admixture and Diversity in the Ecuadorian Creole Chicken

Studying Genetic Diversity and Relationships between Mountainous Meihua Chickens Using Mitochondrial DNA Control Region

The Mountainous Meihua chicken is a unique regional germplasm resource from Tongjiang County, Bazhong City, China, but its genetic structure and evolutionary relationships with other native chicken breeds in the Sichuan region remain unclear. Here, we analyzed a total of 469 sequences, including 199 Mountainous Meihua chicken sequences generated in this study, together with 30 sequences representing 13 clades and 240 sequences from seven different Sichuan local chicken breeds downloaded from NCBI. These sequences were further used to analyze genetic diversity, patterns of population differentiation, and phylogenetic relationships between groups. We show that Mountainous Meihua chicken mtDNA sequences have high haplotypic and nucleotide diversity (0.876 and 0.012, respectively) and with a T bias that is suggestive of good breeding potential. Phylogenetic analysis showed that Mountainous Meihua chickens belong to clades A, B, E, and G and have a low affinity to other chicken breeds, with a moderate degree of differentiation. A non-significant Tajima's D indicates that no demographic expansions occurred in the past. Finally, the four maternal lineages identified in Mountainous Meihua chicken showed unique genetic characteristics.

Variability of Meat and Carcass Quality from Worldwide Native Chicken Breeds

The present research aimed to determine the differential clustering patterns of carcass and meat quality traits in local chicken breeds from around the world and to develop a method to productively characterize minority bird populations. For this, a comprehensive meta-analysis of 91 research documents that dealt with the study of chicken local breeds through the last 20 years was performed. Thirty-nine traits were sorted into the following clusters: weight-related traits, histological properties, pH, color traits, water-holding capacity, texture-related traits, flavor content-related nucleotides, and gross nutrients. Multicollinearity problems reported for pH 72 h post mortem, L* meat 72 h post mortem, a* meat 72 h post mortem, sex, firmness, and chewiness, were thus discarded from further analyses (VIF < 5). Data-mining cross-validation and chi-squared automatic interaction detection (CHAID) decision tree development allowed us to detect similarities across genotypes. Easily collectable trait, such as shear force, muscle fiber diameter, carcass/pieces weight, and pH, presented high explanatory potential of breed variability. Hence, the aforementioned variables must be considered in the experimental methodology of characterization of carcass and meat from native genotypes. This research enables the characterization of local chicken populations to satisfy the needs of specific commercial niches for poultry meat consumers.

Evaluación de la utilidad de marcadores microsatélites en la población avícola rustipollos

Los marcadores moleculares son una herramienta de gran utilidad para estudios de diversidad genética, que permite identificar poblaciones con características genéticas particulares, que soportan el establecimiento de programas de conservación y mejoramiento genético. El objetivo de este estudio fue evaluar el grado de información generada por un panel de 30 marcadores microsatélites en la población avícola Rustipollos. Se obtuvieron muestras de sangre de 50 individuos, la amplificación de fragmentos se realizó mediante PCR, utilizando 30 microsatélites recomendados por la FAO-ISAG para estudios de biodiversidad en gallinas. La estimación de los tamaños de los fragmentos se realizó en un secuenciador automático ABI Prism 377. Fueron determinados el número de alelos por locus y el Contenido de Información Polimórfica (PIC), mediante el programa Microsatellite-Toolkit. El número total de alelos reportados fue de 99 en los 30 marcadores microsatélites, con un valor medio de 3.3 ±1.06 alelos por locus. La determinación del PIC registró un promedio de 0.46, con un rango de 0.18 a 0.76 en los marcadores MCW016 y ADL278, respectivamente. El 43% de los marcadores empleados resultaron altamente informativos para la población evaluada. En general, los marcadores microsatélites demostraton ser útiles para estudios genéticos en la población avícola Rustipollos.

Morphometric and microsatellite-based comparative genetic diversity analysis in Bubalus bubalis from North India

To understand the similarities and dissimilarities of a breed structure among different buffalo breeds of North India, it is essential to capture their morphometric variation, genetic diversity, and effective population size. In the present study, diversity among three important breeds, namely, Murrah, Nili-Ravi and Gojri were studied using a parallel approach of morphometric characterization and molecular diversity. Morphology was characterized using 13 biometric traits, and molecular diversity through a panel of 22 microsatellite DNA markers recommended by FAO, Advisory Group on Animal Genetic Diversity, for diversity studies in buffaloes. Canonical discriminate analysis of biometric traits revealed different clusters suggesting distinct genetic entities among the three studied populations. Analysis of molecular variance revealed 81.8% of genetic variance was found within breeds, while 18.2% of the genetic variation was found between breeds. Effective population sizes estimated based on linkage disequilibrium were 142, 75 and 556 in Gojri, Nili-Ravi and Murrah populations, respectively, indicated the presence of sufficient genetic variation and absence of intense selection among three breeds. The Bayesian approach of STRUCTURE analysis (at K = 3) assigned all populations into three clusters with a degree of genetic admixture in the Murrah and Nili-Ravi buffalo populations. Admixture analysis reveals introgression among Murrah and Nili-Ravi breeds while identified the Gojri as unique buffalo germplasm, indicating that there might be a common origin of Murrah and Nili-Ravi buffaloes. The study provides important insights on buffalo breeds of North India that could be utilized in designing an effective breeding strategy, with an appropriate choice of breeds for upgrading local non-descript buffaloes along with conservation of unique germplasm.

Genetic and physiological variation in two strains of Japanese quail

Background

Detecting the genetic and physiological variations in two Japanese quail strains could be used to suggest a new avian model for future breeding studies. Consequently, two estimations were performed on two Japanese quail strains: gray quail strain (GJQS) and white jumbo quail strain (WJQS). The first estimation was conducted on carcass characteristics, breast muscles, breast concentration of collagen type I, and body measurements. In contrast, blood samples were collected for the second estimation for genomic DNA extraction and genetic analysis.

Results

A total of 62 alleles out of 97 specific alleles (63.92%) were detected overall loci (14 microsatellite loci) for the two strains. A total of 27 specific alleles of WJQS were observed, and 35 were obtained for GJQS. The percentage of similarity was 48.09% ranged from 4.35 with UBC001 to 100% with GUJ0051. WJQS had greater body weights and a higher value of pectoral muscle and supracoracoideus muscle than GJQS. The breast muscles of GJQS exhibited a higher concentration of type I collagen than the WJQS. Furthermore, males showed higher concentrations of collagen type I than females. WJQS showed a higher body length, chest girth, chest length, thigh length, thigh girth, drumstick length, and drumstick girth (cm) than GJQS. WJQS showed more significant differences in carcass traits compared with GJQS.

Conclusion

The physiological differences between WJQS and GJQS were ascertained with microsatellite markers, which indicated high polymorphism between these strains. These observations provided a scientific basis for evaluating and utilizing the genetic resources of WJQS and GJQS in a future genetic improvement program.

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.

Sexual Dimorphism and Breed Characterization of Creole Hens through Biometric Canonical Discriminant Analysis across Ecuadorian Agroecological Areas

Simple Summary

The first step towards the protection and valorization of the genetic resources of a country is their definition. Although Ecuadorian zootechnical species are very diverse, they are scarcely characterized, and hence the efforts towards their protection are not as fruitful as they could be. The present paper approaches the biometric characterization of the Creole hen population in Ecuador through the study of sexual dimorphism and the differentiation of an agroecologically-based structured population using fourteen zoometric measures as differentiation criteria. Highlands region provinces of Cotopaxi and Tungurahua were the most zoometrically distant from the rest. However, Morona Santiago province population in the Amazonian region slightly differs from those in Guayas, Chimborazo and Bolívar in the Coastal and Highlands regions, respectively. The dual-purpose nature of Ecuadorian Creole hen resources enables the implementation of breeding programs that seek meeting a wider scope of public demands, through the definition of the agroecologically-based breed differentiated production of local hen eggs and meat.

Abstract

Despite Ecuador having a wide biodiversity of zootechnical species, characterization studies of these genetic resources are scarce. The objective of this research was to perform the biometric characterization of the Creole hen population through 14 quantitative zoometric measures. We evaluated 207 hens and 37 roosters from Ecuador’s three agro-ecological regions: the Sierra (highlands) region (Bolivar, Chimborazo, Tungurahua and Cotopaxi provinces); the Costa (coastal) region (Guayas); and the Oriente Amazonian region (Morona Santiago). Sexual dimorphism was assessed using one-way analysis of variance (ANOVA). Body dimensions were generally significantly higher for males (p < 0.05), especially for length of head, beak, neck, dorsum, tarsus, thigh, leg, and middle finger. Then, individuals were biometrically clustered into populations after a stepwise canonical discriminant analysis (CDA) computing interpopulation Mahalanobis distances. Agroecologically-based structured populations were identified when zoometrical criteria were used to classify the animals. Cotopaxi and Tungurahua provinces were reported to be the most distant from the rest, with a slight differentiation of the Morona Santiago province population from those in Guayas, Chimborazo and Bolívar. Conclusively, Ecuadorian Creole hens were higher than longer contrasting light hen breeds, which favors their dual-purpose aptitude. Hence, the development of selection programs aimed at Ecuadorian differentiated entity of production of eggs and meat across agro-ecological areas is feasible.