Genetic diversity and population structure of six ethiopian cattle breeds from different geographical regions using high density single nucleotide polymorphisms

Genetic diversity and population structure in five Inner Mongolia cashmere goat populations using whole-genome genotyping

OBJECTIVE

As a charismatic species, cashmere goats have rich genetic resources. In the Inner Mongolia Autonomous Region, there are three cashmere goat varieties named and approved by the state. These goats are renowned for their high cashmere production and superior cashmere quality. Therefore, it is vitally important to protect their genetic resources as they will serve as breeding material for developing new varieties in the future.

METHODS

Three breeds including Inner Mongolia cashmere goats (IMCG), Hanshan White cashmere goats (HS), and Ujimqin white cashmere goats (WZMQ) were studied. IMCG were of three types: Aerbas (AEBS), Erlangshan (ELS), and Alashan (ALS). Nine DNA samples were collected for each population, and they were genomically re-sequenced to obtain high-depth data. The genetic diversity parameters of each population were estimated to determine selection intensity. Principal component analysis, phylogenetic tree construction and genetic differentiation parameter estimation were performed to determine genetic relationships among populations.

RESULTS

Samples from the 45 individuals from the five goat populations were sequenced, and 30,601,671 raw single nucleotide polymorphisms (SNPs) obtained. Then, variant calling was conducted using the reference genome, and 17,214,526 SNPs were retained after quality control. Individual sequencing depth of individuals ranged from 21.13× to 46.18×, with an average of 28.5×. In the AEBS, locus polymorphism (79.28) and expected heterozygosity (0.2554) proportions were the lowest, and the homologous consistency ratio (0.1021) and average inbreeding coefficient (0.1348) were the highest, indicating that this population had strong selection intensity. Conversely, ALS and WZMQ selection intensity was relatively low. Genetic distance between HS and the other four populations was relatively high, and genetic exchange existed among the other four populations.

CONCLUSION

The Inner Mongolia cashmere goat (AEBS type) population has a relatively high selection intensity and a low genetic diversity. The IMCG (ALS type) and WZMQ populations had relatively low selection intensity and high genetic diversity. The genetic distance between HS and the other four populations was relatively high, with a moderate degree of differentiation. Overall, these genetic variations provide a solid foundation for resource identification of Inner Mongolia Autonomous Region cashmere goats in the future.

Genetic diversity and positive signatures of selection in indigenous cattle breeds of Iran

Animal domestication, climate changes over time, and artificial selection have played significant roles in shaping the genome structure of various animal species, including cattle. These processes have led to the emergence of several indigenous cattle breeds with distinct genetic characteristics. This study focused on unraveling the genetic diversity and identifying candidate genomic regions in eight indigenous cattle breeds of Iran. The data consisted of ∼777 962 single nucleotide polymorphisms (SNPs) of 89 animals from Iranian indigenous cattle scattered throughout the country. We employed various methods, including integrated haplotype score, FST, and cross-population composite likelihood ratio, to conduct a genome scan for detecting selection signals within and between cattle populations. Average observed heterozygosity across the populations was 0.36, with a range of 0.32-0.40. In addition, negative and low rates of inbreeding (FIS) in the populations were observed. The genome-wide analysis revealed several genomic regions that harbored candidate genes associated with production traits (e.g., MFSD1, TYW5, ADRB2, BLK, and CRTC3), adaptation to local environmental constraints (CACNA2D1, CXCL3, and GRO1), and coat color (DYM). Finally, the study of the reported quantitative trait loci (QTL) regions in the cattle genome demonstrated that the identified regions were associated with QTL related to important traits such as milk composition, body weight, daily gain, feed conversion, and residual feed intake. Overall, this study contributes to a better understanding of the genetic diversity and potential candidate genes underlying important traits in Iranian indigenous cattle breeds, which can inform future breeding and conservation efforts.

Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.