Mitochondrial DNA-Based Analyses of Relatedness Among Turkeys, Meleagris gallopavo

Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus)

BACKGROUND

Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species.

RESULTS

From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip.

CONCLUSION

This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.

Traditional sexing methods and external egg characteristics combination allow highly accurate early sex determination in an endangered native turkey breed

Early sex determination methods are not only crucial in the worldwide massive poultry industry, but also for small-holder producers. The profitability of sexing techniques must be accounted for when aiming to boost management, nutrition, and conservation practices in endangered poultry breeds. This becomes pivotal when the local breed dealt with belongs to an understudied species, such as the turkey. So, the main objective of this study is to identify which method combination may report a higher likelihood of successful sex determination in poults across the three-pattern varieties of the Andalusian turkey breed. A total of 84 one to two days old Andalusian turkey poults (42 black, 28 black-roan, and 14 bronze-roan) were evaluated in this study. Sex determination was performed using 15 methods, which included testing external egg metrics and eggshell color, poult morphological appraisal and phaneroptics, and behavioral traits. Possible differences across plumage varieties and the interaction between sex and plumage were observed when external egg quality was measured. Sex determination through behavioral methods in black base feathered (black and black-roan) male sex individuals showed seven times higher sensitivity when compared to the rest of the studied individuals (χ2 = 7.14, df = 1, P < 0.01). In contrast, for the black-roan plumage females, the method based on the color of down feathers was approximately four times more sensitive (χ2 = 3.95, df = 1, P ≤ 0.05). For the bronze-roan pattern, none of the sexing techniques was reported to efficiently predict sex itself. However, the most proper method combination to determine sex, independent of plumage color, was physical external egg characteristics, the color of down feathers, and behavioral approaches (“English method” and “slap technique”). The specificity values were found to be 49.12, 93.33, and 100%, while the sensitivity values were observed to be 74.64, 91.03, and 100%, which translated into accuracy of 63.10, 92.26, and 100% in black, black-roan, and bronze-roan poults, respectively. Our results suggest that the method combination tested in this study could be considered a highly accurate, simple, and affordable alternative for sex determination in turkeys. This could mean a pivotal advance for small producers of turkeys, as early sex detection can help to plan timely conservational management strategies, which is of prominent importance in the context of endangered poultry breeds.

Morphological Characterization of Two Light Italian Turkey Breeds

Simple Summary

Genetic resources on turkeys are scarce, considering both domestic and wild birds. Smaller, dark-colored Italian heritage breeds such as Brianzolo and Nero d’Italia have been selected for centuries in outskirt areas due to their coping ability in poor environments and high brooding ability. However, they are in danger of extinction. EC Council Regulations on organic farming strongly recommend using local genetic resources and conserving biodiversity. Phenotypical characterization is a basic step in biodiversity conservation; therefore, in this article, we present morphometric and colorimetric analysis results of 46 birds belonging to each of the considered breeds. We considered 18 parameters: morphometries, morphological indexes, linear evaluation, and colorimetric indexes as characterizing factors in breeds differentiation. Differences in weight with clear sexual dimorphism were recorded. Massiveness indexes were in favor of the slightly more compact Brianzolo breed. The extremely fair skin and dark shank of the Nero d’Italia turkey were revealed by colorimetric analysis. The effectiveness of morphological analysis in breeds differentiation, useful data in heritage breeds conservation, and characterization were considered control parameters in classifying animal products.

Abstract

We aimed to investigate the variability within turkeys’ phenotypical traits in two Italian heritage breeds: Brianzolo (BRZ) and Nero d’Italia (NIT), as analyzed through morphometry, morphometrical indexes, linear scoring, and colorimetric indexes. A total of 92 birds were measured, weighed, and scored (46 NIT: M/F = 19/27; 46 BRZ: M/F = 19/27). Live weight (LW), total body length (BL, excluding feathers), keel length (KL), chest circumference (BC), wingspan (WS), shank length (SL), shank diameter (SD), and shank circumference (SC). Massiveness (MASS), stockiness (STOCK), and long-leggedness (LLEG) indexes were also calculated. The body condition score (BCS) applied a linear evaluation to nutritional status and muscular development. Colorimetric indexes (L*, a*, b*) were recorded, sampling skin and shank. Data were analyzed using GLM procedures and PCA. NIT was the heaviest breed (4.89 vs. 4.07 kg; p ≤ 0.05). In both breeds, sexual dimorphism was visible in the LW trait with males (M) weighing significantly heavier than females (F) (p ≤ 0.05). NIT birds recorded the highest BL values: 58.44 vs. 57.15 cm (p ≤ 0.05). MASS was higher in NIT (8.26 vs. 7.0; p ≤ 0.05), and STOCK was higher in BRZ (82.62 vs. 85.37; p ≤ 0.05). Colorimetric indexes revealed significant differences in skin lightness (L*) and redness (a*). For shank color, the breed significantly affected differences in the indexes. This study characterizes these breeds at high risk of genetic erosion and extinction, which will help the morphological standardization of birds and the enhancement of genetic variability

A Matrilineal Study on the Origin and Genetic Relations of the Ecuadorian Pillareño Creole Pig Population through D-Loop Mitochondrial DNA Analysis

Domestic pig breeds reached America on the second Columbus trip; from this date, Iberian pig genetic resources were disseminated throughout the continent, forming diverse creole breeds. These Ecuadorian Creole pigs are important for food production but have been genetically eroded since the introduction of transboundary breeds. In this study, we sought to characterize this erosion more thoroughly through mitochondrial DNA D-Loop analysis of Ecuadorian Pillareño Creole pigs from seven regions of Ecuador. To allow comparison, we also included in our analysis sequences from wild species, commercial lines, and domestic pigs, which were obtained from the NCBI GenBank database. Creole pigs' population showed overall moderate Hd values and low π values, and a negative value of Tajima's D was observed. The greatest differentiation from the Ecuadorian Pillareño Creole pigs was observed between Asian wild and Asian domestic pigs. The haplotype analysis revealed three different phylogenetic clades (A, E I, and E II) and 65 haplotypes. Ecuadorian Creole populations were grouped into nine haplotypes for Clade E I and E II, which have not previously been reported for Creole Pillareño populations. Our analysis indicates that in the establishment of Creole Pillareño pigs, individuals most likely separated from the Asian pig population and appear to be genetically influenced by European and Iberian populations raised in Spain.

Hybrid Versus Autochthonous Turkey Populations: Homozygous Genomic Regions Occurrences Due to Artificial and Natural Selection

Simple Summary

In this study we investigate the genomic differentiation of traditional Mexican turkey breeds and commercial hybrid strains. The analysis aimed to identify the effects of different types of selection on the birds’ genome structure. Mexican turkeys are characterized by an adaptive selection to their specific original environment; on the other hand, commercial hybrid strains are directionally selected to maximize productive traits and to reduce production costs. The Mexican turkeys were grouped in two geographic subpopulations, while high genomic homogeneity was found in hybrid birds. Traditional breeds and commercial strains are clearly differentiated from a genetic point of view. Inbreeding coefficients were here calculated with different approaches. A clear effect of selection for productive traits was recorded.

Abstract

The Mexican turkey population is considered to be the descendant of the original domesticated wild turkey and it is distinct from hybrid strains obtained by the intense artificial selection activity that has occurred during the last 40 years. In this study 30 Mexican turkeys were genomically compared to 38 commercial hybrids using 327,342 SNP markers in order to elucidate the differences in genome variability resulting from different types of selection, i.e., only adaptive for Mexican turkey, and strongly directional for hybrids. Runs of homozygosity (ROH) were detected and the two inbreeding coefficients (F and F_ROH) based on genomic information were calculated. Principal component and admixture analyses revealed two different clusters for Mexican turkeys (MEX_cl_1 and MEX_cl_2) showing genetic differentiation from hybrids (HYB) (F_ST equal 0.168 and 0.167, respectively). A total of 3602 ROH were found in the genome of the all turkeys populations. ROH resulted mainly short in length and the ROH_island identified in HYB (n = 9), MEX_cl_1 (n = 1), and MEX_cl_2 (n = 2) include annotated genes related to production traits: abdominal fat (percentage and weight) and egg characteristics (egg shell color and yolk weight). F and F_ROH resulted correlated to each other only for Mexican populations. Mexican turkey genomic variability allows us to separate the birds into two subgroups according to the geographical origin of samples, while the genomic homogeneity of hybrid birds reflected the strong directional selection occurring in this population.

Tracing Worldwide Turkey Genetic Diversity Using D-loop Sequence Mitochondrial DNA Analysis

Simple Summary

The development of new production lines of turkeys has relegated native breeds to a second position. This has increased the need for new research to ensure the conservation of local turkey breeds and the maintenance of biodiversity. The objective of the present study was to identify turkey populations, their origins, and maternal lines through mitochondrial DNA analysis. For this study, mitochondrial DNA samples from 93 turkeys (Meleagris gallopavo) were used. The animals belonged to populations in Brazil, Mexico, Spain (Andalusia and Majorca) Italy, Iran, Egypt, and the United States. The haplogroup network that formed suggested that turkey domestic populations group into a single haplotype. However, genetic differences within the haplogroup were found. The present study may provide a better approach for the implementation of conservation strategies for domestic turkey populations.

Abstract

According to recent archeological evidence, turkey (Meleagris gallopavo gallopavo) domestication may have occurred in Mexico around 2000 years ago. However, little is known about the phylogenetic and genealogical background underlying domestic turkey populations. This study aimed to further understand the domestication process and identify inter- or intraspecific connections between turkey populations to determine their origins, trace their global expansion, and define the species’ genetic value. Ninety-three domestic turkeys (local breeds) were sampled from populations in Brazil, Mexico, USA, Spain, Italy, Iran, and Egypt. Publicly available sequences from previous studies were also included. Standard mitochondrial DNA, genetic diversity, and haplotype network analyses were performed. Seventy-six polymorphic sites were identified. Turkeys from Mexico showed the greatest number of polymorphic sites (40), while turkeys from Italy and Brazil reported only one site each. Nucleotide diversity was also highest in Mexico and the USA (π = 0.0175 and 0.0102, respectively) and lowest in Brazil and Italy. Of the six major haplogroups defined, the Mexican and USA populations appeared to have remained more stable and diverse than the other populations. This may be due to conservative husbandry policies in the rural areas of other populations, which have prevented the introduction of commercial turkey lines.