Assessing the Diversity and Population Substructure of Sarda Breed Bucks by Using Mtdna and Y-Chromosome Markers

A sample of 146 Sarda bucks from eight subregions of Sardinia, Italy (Nuorese, Barbagia, Baronia, Ogliastra, Sarrabus, Guspinese, Iglesiente, Sulcis) were characterized for Y-chromosome and mtDNA markers to assess the levels of population substructure. Five polymorphic loci (SRY, AMELY, ZFY, and DDX3Y) on the Y-chromosome were genotyped. The control region of mtDNA was sequenced as a source of complementary information. Analysis of Y-chromosome data revealed the segregation of 5 haplotypes: Y1A (66.43%), Y2 (28.57%), Y1C (3.57%), Y1B1 (0.71%), and Y1B2 (0.71%). High levels of Y-chromosome diversity were observed in populations from Southwest Sardinia. The FST values based on Y-chromosome and mtDNA data were low, although a paternal genetic differentiation was observed when comparing the Nuorese and Barbagia populations (Central Sardinia) with the Sulcis, Iglesiente, and Sarrabus populations (Southern Sardinia). AMOVA analysis supported the lack of population substructure. These results suggest the occurrence of a historical and extensive gene flow between Sarda goat populations from different locations of Sardinia, despite the fact that this island is covered by several large mountain ranges. Introgression with foreign caprine breeds in order to improve milk production might have also contributed to avoiding the genetic differentiation amongst Sarda populations

Identification of novel genetic variants for KAP1.1, KAP1.3 and K33 genes in some of indigenous goat breeds of Turkey

The animal fibres such as mohair, cashmere and cashgora have a complex structure and affected by genetic variation of keratin associated protein genes as KAP 1.1 (Keratin Associated Protein 1.1, formerly known as B2A), KAP1.3 (Keratin Associated Protein 1.3, formerly known as B2C) and K33 (Keratin Intermediate Filaments Type I, formerly known as KRT1.2). Keratin-associated proteins play a significant role in identifying structural and mechanical properties of the hair and wool fibres. This study was conducted to detect genetic variation at the KAP1.1, KAP1.3 and K33 genes in indigenous Turkish goat populations using DNA sequencing method. The DNA of 100 individuals selected from 5 different native goat breeds (Hair, Honamli, Kilis, Norduz, and Angora) that reared different regions of Turkey were used as materials. A total of 59 nucleotide variations and indels (insertion/deletion) of KAP1.1 gene, 15 nucleotide variations and indels of KAP1.3 gene, 16 nucleotide variations of K33 gene were determined in the studied samples. These nucleotide variations and indels have been causing changes in the number and sequence of amino acids. It is necessary to determine the relationships with mohair yield, quality and polymorphisms that are determined in KAP1.1, KAP1.3 and KRT1.2 genes

Microsatellite diversity of the Nordic type of goats in relation to breed conservation: how relevant is pure ancestry?

In the last decades, several endangered breeds of livestock species have been re-established effectively. However, the successful revival of the Dutch and Danish Landrace goats involved crossing with exotic breeds and the ancestry of the current populations is therefore not clear. We have generated genotypes for 27 FAO-recommended microsatellites of these landraces and three phenotypically similar Nordic-type landraces and compared these breeds with central European, Mediterranean and south-west Asian goats. We found decreasing levels of genetic diversity with increasing distance from the south-west Asian domestication site with a south-east-to-north-west cline that is clearly steeper than the Mediterranean east-to-west cline. In terms of genetic diversity, the Dutch Landrace comes next to the isolated Icelandic breed, which has an extremely low diversity. The Norwegian coastal goat and the Finnish and Icelandic landraces are clearly related. It appears that by a combination of mixed origin and a population bottleneck, the Dutch and Danish Land-races are separated from the other breeds. However, the current Dutch and Danish populations with the multicoloured and long-horned appearance effectively substitute for the original breed, illustrating that for conservation of cultural heritage, the phenotype of a breed is more relevant than pure ancestry and the genetic diversity of the original breed. More in general, we propose that for conservation, the retention of genetic diversity of an original breed and of the visual phenotype by which the breed is recognized and defined needs to be considered separately

Genetska karakterizacija istarske koze: polazište dugoročnog očuvanja

Istrian goat is an autochthonous Croatian breed which inhabited Istrian peninsula and was important in milk production and human nutrition, especially for poor people. For centuries Istrian goat was a recognizable heraldic symbol of Istria, but in her real form almost disappeared from the breeding area. The revitalization and reaffirmation of Istrian goat began with several dozen remaining breeding animals, after a decade-long breeding ban. Genetic characterization of the Istrian goat population is necessary for providing insight into the state of genetically preserved structure within population as well as positioning Istrian goats within phylogenetically related breeds. Microsatellite and mtDNA analysis of reproductive individuals of Istrian goat and related breeds, Croatian White goat and Saanen goat was carried out. In the population of Istrian goat, higher allelic variability (nA = 9.7; AR = 7.4) were found as well as significant genetic distance (FST = 0.068 - 0.086) in relation to other two breeds. Such results indicated that Istrian goat constitutes a separate genetic identity. The observed ten haplotype sequences of the D-loop mtDNA also confirm the significant genetic richness of the maternal hereditary component. The observed haplotypes in the population of Istrian goat belong to lineage A. A smaller number of haplotypes shows similarity to the group of “white” goats, indicating traces of earlier limited but targeted crossing of Istrian goats. The genetic profile analysis of Istrian goats indicates a high level of genetic variability and provides guidelines for a long-term conservation program. The preserved genetic and promising potential of milk production of Istrian goat makes a significant basis for her economic reaffirmation. Orientation of the breed towards milk production could be an efficient strategy for its effective preservation.Istarska koza jedna je od autohtonih pasmina koja je nastanjivala područje Istarskog poluotoka i bila važna u proizvodnji mlijeka te prehrani, posebice siromašnog stanovništva. Kroz stoljeća je činila prepoznatljivi heraldički simbol Istre, no u svojem stvarnom obličju gotovo je iščezla iz uzgojnog područja. Revitalizacija i reafirmacija istarske koze započela je nakon višedesetljetne zabrane uzgoja na uzgojnoj bazi od nekoliko desetaka preostalih rasplodnih jedinki. Genetska karakterizacija preostale populacije istarske koze nužna je za uvid u stanje unutar populacijske genetske očuvanosti kao i pozicioniranje naspram filogenetski srodnih pasmina koza. Provedena je analiza strukture mikrosatelita i mtDNA rasplodnih jedinki istarske koze te srodnih pasmina koza, hrvatske bijele i sanske koze. U populaciji istarske koze naspram druge dvije pasmine koza utvrđena je veća alelna varijabilnost (nA = 9,7; AR = 7,4) te značajna genetska udaljenost (FST=0,068-0,086) što ukazuje da istarska koza čini zaseban genetski identitet. Zapaženih deset haplotipova sekvenci D-loop regije mtDNA također potvrđuje značajno genetsko bogatstvo maternalne nasljedne komponente. Uočeni haplotipovi u populaciji istarske koze pripadaju haplogrupi A. Manji broj haplotipova pokazuje srodnost naspram pasmina iz skupine bijelih koza, što indicira na tragove ranijih ograničenih ciljanih oplemenjivanja istarske koze. Analiza genetskog profila ukazuje na visoku razinu očuvanosti genetske varijabilnosti te nudi smjernice dugoročno održivog konzervacijskog programa. Očuvani genetski i izgledni proizvodni (mliječni) potencijal istarske koze čini značajnu osnovu njene gospodarske reafirmacije

Signatures of selection and environmental adaptation across the goat genome post-domestication

Background: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. Results: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. Conclusions: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide

Phylogenetic relationships of Turkish indigenous donkey populations determined by mitochondrial DNA D-loop region

In this study, to analyze the mtDNA D-loop region and the origin of the maternal lineages of 16 different donkey populations, and to assess the domestication of Turkish indigenous donkeys in seven geographical regions, we investigated the DNA sequences of the D-loop region of 315 indigenous donkeys from Turkey. A total of 54 haplotypes, resulting from 35 polymorphic regions (27 parsimoniously informative and 6 singleton sites), were defined. Twenty-eight of these haplotypes are unique (51.85%), and 26 are shared among different Turkish indigenous donkey populations. The most frequent haplotype was Hap 1 (45.71%), followed by two haplotypes (Hap 4, 15.55% and Hap 7, 5.39%). The breed genetic diversity, evaluated by the haplotype diversity (HD ) and nucleotide diversity (?D ), for the Turkish donkey populations ranged from 0.533 ± 0.180 (Tekirdağ–Malkara, MAL) to 0.933 ± 0.122 (Aydin, AYD), and from 0.01196 ± 0.0026 (Antalya, ANT) to 0.02101 ± 0.0041 (Aydin, AYD), respectively. We observed moderate-to-high levels of haplotype diversity and moderate nucleotide diversity, indicating plentiful genetic diversity in all of the Turkish indigenous donkey populations. Phylogenetic analysis (NJT) and median-joining network analysis established that all haplotypes were distinctly grouped into two major haplogroups. The results of AMOVA analyses, based on geographic structuring of Turkish native donkey populations, highlighted that the majority of the observed variance is due to differences among samples within populations. The observed differences between groups were found to be statistically significant. Comparison among Turkish indigenous donkey mtDNA D-loop regions and haplotypes, and different countries’ donkey breeds and wild asses, identified two clades and which is named Somali (Clade IV) and Nubian (Clade V) lineages. The results can be used to understand the origin of Turkish donkey populations clearly, and to resolve the phylogenetic relationship among all of the different regions. © 2020 by the authors. Licensee MDPI, Basel, Switzerland.Türkiye Bilimsel ve Teknolojik Araştirma Kurumu, TÜBITAK: 215O555This research was funded by TUBITAK (The Scientific and Technological Research Council of Turkey), grant number 215O555, project leader Fulya ?zdil. The authors would like to kindly thank to Selen Yatkin who provide help during the sample collection. We are also grateful to all farmers and pastoralists for allowing us to use their animal to collect blood samples for free. Many thanks to our lab team ?eref M?cahit Topalo?lu and Ayla Fidan for helping laboratory experiment. The authors want to thank four anonymous reviewers for comments on this work

Genetic Characterization of the “Chusca Lojana”, a Creole Goat Reared in Ecuador, and Its Relationship with Other Goat Breeds

The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named “Chusca Lojana”, has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of the genetic information of the Creole goat is important to determine intra-racial diversity, the degree of genetic distance among other breeds of goats, and the possible substructure of the population, which is valuable for the conservation of such a species’ genetic resources. A total of 145 samples of the Creole goat was taken from the four biotypes previously identified. Genetic analyses were performed using 38 microsatellites recommended for studies of goat genetic diversity (FAO-ISAG). The results of within-breed genetic diversity showed a mean number of alleles per locus (MNA) of 8, an effective number of alleles (Ae) of 4.3, an expected heterozygosity (He) of 0.71, an observed heterozygosity (Ho) of 0.63, polymorphic information content (PIC) of 0.67, and an FIS value of 0.11. Between-breed genetic diversity among 43 goat populations (native of Spain, American Creole, Europeans, and Africans) showed the following values: FIS = 0.087, FIT = 0.176, and FST = 0.098. Regarding the analysis of the population structure, the results showed that the Creole Chusca Lojana goat population is homogeneous and no genetic separation was observed between the different biotypes (FST = 0.0073). In conclusion, the Chusca Lojana goat has a high genetic diversity, without exhibiting a genetic substructure. Therefore, it should be considered as a distinct population because crossbreeding with other breeds was not detected