Genetic diversity and relationships of Chinese donkeys using microsatellite markers

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology

The Hetian Qing donkey is an excellent local donkey breed in Xinjiang. It is of great significance to accelerate breeding and the speed of breeding and rejuvenation, as well as to understand the genetic basis of the strategies and population. This study collected a total of 4 male donkeys and 28 female donkeys. It then obtained genotype data through Simplified Genomic Sequencing (GBS) technology for data analysis. The results detected a total of 55,399 SNP loci, and the genotype detection rate of individuals was ≥90%. A total of 45,557 SNP loci were identified through quality control, of which 95.5% were polymorphic. The average minimum allele frequency was 0.250. The average observed heterozygosity was 0.347. The average expected heterozygosity was 0.340. The average IBS (state homologous) genetic distance was 0.268. ROH: 49 (homozygous fragments), with 73.47% of the length between 1 and 5 Mb. The average per-strip ROH length was 1.75 Mb. The mean inbreeding coefficient was 0.003. The 32 Hetian green donkeys could be divided into six families. The number of individuals in each family is significant. To sum up, the Hetian Qing donkey population has low heterozygosity, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the subsequent process of seed protection, seed selection should be conducted according to the divided pedigree to ensure the long-term protection of the genetic resources of Hetian green donkeys.

Single nucleotide polymorphisms (SNPs) and indels identified from whole-genome re-sequencing of four Chinese donkey breeds

This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs.

An investigation of genetic diversity in three Dezhou donkey original breeding farms

Dezhou donkey is one of the excellent large donkey breeds in China. In our study, eight microsatellite markers were used to genotype from each of three populations of Chinese Dezhou donkeys: 67 individuals in Liaocheng (pop1), 103 individuals in Binzhou 1 (pop2), and 102 individuals in Binzhou 2 (pop3), in order to study the genetic diversity of these populations. A total of 213 alleles were detected, and the PIC results showed that eight loci were all highly polymorphic. The means of Ho and He of pop2 were the highest, which were 0.646 and 0.717, respectively. The PCoA analysis demonstrated that the samples from three conservation farms were mixed together. The phylogenetic tree showed that pop 2 and pop 3 were closely related. The phylogenetic tree results clustered that 272 donkeys were divided into six groups. AMOVA analysis showed that the genetic variation was mainly concentrated within the population and the genetic differentiation among the populations was low. Fst values between populations also indicated that genetic differentiation between populations was too small to be considered. This indicated a low probability of inbreeding within the population. And this also showed that the conservation and breeding of Dezhou donkeys in recent years have achieved excellent results. The investigation of genetic diversity in three Dezhou donkey original breeding farms can provide reference data for the selection and breeding of excellent breeds of Dezhou donkey.

Genome-wide association study to identify SNPs and candidate genes associated with body size traits in donkeys

The Yangyuan donkey is a domestic animal breed mainly distributed in the northwest region of Hebei Province. Donkey body shape is the most direct production index, can fully reflect the donkey's growth status, and is closely related to important economic traits. As one of the main breeding selection criteria, body size traits have been widely used to monitor animal growth and evaluate the selection response. Molecular markers genetically linked to body size traits have the potential to accelerate the breeding process of animals via marker-assisted selection. However, the molecular markers of body size in Yangyuan donkeys have yet to be explored. In this study, we performed a genome-wide association study to identify the genomic variations associated with body size traits in a population of 120 Yangyuan donkeys. We screened 16 single nucleotide polymorphisms that were significantly associated with body size traits. Some genes distributed around these significant SNPs were considered candidates for body size traits, including SMPD4, RPS6KA6, LPAR4, GLP2R, BRWD3, MAGT1, ZDHHC15, and CYSLTR1. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that these genes were mainly involved in the P13K-Akt signaling pathway, Rap1 signaling pathway, regulation of actin cytoskeleton, calcium signaling pathway, phospholipase D signaling pathway, and neuroactive ligand-receptor interactions. Collectively, our study reported on a list of novel markers and candidate genes associated with body size traits in donkeys, providing useful information for functional gene studies and offering great potential for accelerating Yangyuan donkey breeding.

Genetic characterization of donkeys of Braj region of India

The grey type donkeys of Braj region of Uttar Pradesh in India were genetically characterized using ten heterologous microsatellite loci. At these loci the PCR product size ranged from 75-95 bp at locus HTG6 to 251-277 bp at locus COR18. The observed number of alleles varied from 4 (HTG15) to 10 (HTG7 and AHT4) with a mean of 7.50 ± 1.96. The observed heterozygosity ranged from 0.46 (HTG6 and NVHEQ54) to 0.79 (COR18) with a mean of 0.66 ± 0.12. The mean genetic diversity estimate (FIS) was 0.157. When these donkeys were compared on the basis of allelic frequency data at these loci to the brown type donkeys of Ladakh, Spiti and Rayalseema regions in the union territories/states of Ladakh, Himachal Pradesh and Andhra Pradesh, respectively, they clustered independently from these three donkey populations in a dendrogram based on Goldstein's average square distances indicating their genetic distinctness.

Origin, Evolution, and Research Development of Donkeys

Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population.

Donkey Industry in China: Current Aspects, Suggestions and Future Challenges

Donkey domestication has been essential to human culture and development and has played an important role in economic and social life in human history. China is one of the largest donkey breeders worldwide; donkey farming for meat, milk and hide production is becoming an important industry in rural China as it provides income to the rural livelihoods of many people. Currently, the donkey industry in China is small and relatively young, but it is growing fast. The industry is not adequately exploited economically, which means that it requires the diminution of its role in the traditional activities of rural households and a reorientation towards a more profitable industry. Given the growing importance of the donkey industry in rural China, this paper aims to outline the current situations of the donkey industry in China in terms of animal stock, breeds and distribution, donkey products, suggestions and future challenges to the development of the donkey industry.

Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Simple Summary

This study was conducted to evaluate the genetic variability of Turkish native donkey (Equus asinus) populations, using polymorphism of 17 microsatellite markers. The results revealed a highly mixed genotype of all the examined donkeys, suggesting that two different group of breeds can be distinguished from each other on the basis of microsatellite markers.

Abstract

This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean H_O in the Turkish donkey was estimated to be 0.677, while mean H_E was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (G_ST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The G_ST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (H_t) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.

Leptin Receptor Gene Polymorphisms in Some Turkish Donkey Populations

Leptin receptor is a fundamental regulator in physiological functions of the regulation of food intake, energy homeostasis, immune function, and reproduction as well as on ovarian follicular cells on the placenta and lactating mammary glands. The aim of this study was to investigate the LEPR gene polymorphism in 60 donkeys reared in Thrace region of Turkey. A 585 bp long partial intron 6, exon 7, intron 7, and exon 8 regions of LEPR gene were amplified, and polymerase chain reaction products analyzed via DNA sequencing. A novel single-nucleotide polymorphism (SNP) was identified as g.713668A>G in the seventh exon region of LEPR gene. This novel SNP was first identified, and the partial DNA sequence of LEPR gene in donkeys was reported for the first time in this study, and these sequences were deposited to NCBI Genbank database with the accession number: MK807114-MK807115. The A>G transition revealed a silent mutation (CAA-CAG) in glutamine amino acid. This nucleotide mutation could cause the changes of secondary structure of protein and expression level of LEPR hormone. For this reason, additional studies are needed to reveal new SNPs and in the LEPR gene that may affect economic traits and structure of protein in donkey breeds.