Chinese Donkey Breeds Research Articles

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, F ST, 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.

Genetic diversity and relationships of Chinese donkeys using microsatellite markers.

Donkeys are one important livestock in China because of their nourishment and medical values. To investigate the genetic diversity and phylogenetic relationships of Chinese donkey breeds, a panel of 25 fluorescently labeled microsatellite markers was applied to genotype 504 animals from 12 Chinese donkey breeds. A total of 226 alleles were detected, and the expected heterozygosity ranged from 0.6315 (Guanzhong) to 0.6999 (Jiami). The mean value of the polymorphism information content, observed number of alleles, and expected number of alleles for all the tested Chinese donkeys were 0.6600, 6.890, and 3.700, respectively, suggesting that Chinese indigenous donkeys have relatively abundant genetic diversity. Although there were abundant genetic variations found, the genetic differentiation between the Chinese donkey breeds was relatively low, which displayed only 5.99 % of the total genetic variance among different breeds. The principal coordinates analysis clearly splits 12 donkey breeds into two major groups. The first group included Xiji, Xinjiang, Liangzhou, Kulun, and Guanzhong donkey breeds. In the other group, Gunsha, Dezhou, Biyang, Taihang, Jiami, Qingyang, and Qinghai donkeys were clustered together. This grouping pattern was further supported by structure analysis and neighbor-joining tree analysis. Furthermore, genetic relationships between different donkey breeds identified in this study were corresponded to their geographic distribution and breeding history. Our results provide comprehensive and precise baseline information for further research on preservation and utilization of Chinese domestic donkeys.

Characterization of the complete mitochondrial genome of the Liangzhou donkey (Equus asinus)

Liangzhou donkey (Equus asinus) is one of the most important donkey species in China. In this study, we sequenced the complete mitochondrial genome by next-generation sequencing method, the results show it was 16,560 bp in length, consisting 37 genes: 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a non-coding control region. The base composition of the genome was 32.4% for A, 28.7% for C, 13.2% for G, and 25.7% for T； A + T for 58.1%. The phylogenetic analysis demonstrated that Liangzhou donkey was more closely related to Qingyang donkey and processed distinct relationships with other Chinese donkey breeds. This work characterized the mitochondrial genome of Equus asinus (Liangzhou donkey) and presents significant genetic information for this special species.

Copy number variations of five Y chromosome genes in donkeys

Abstract. In mammals, the Y chromosome plays a pivotal role in male sex determination and is essential for normal sperm production. A number of studies were conducted on Y chromosome genes of various species and identified single-copy and multi-copy genes. However, limited studies about donkey Y chromosome genes have been done. In this study, 263 male samples from 13 Chinese donkey breeds were collected to analyze the copy number variations (CNVs) of five Y chromosome genes using the quantitative PCR (qPCR) method. These five genes (cullin 4 B Y (CUL4BY), equus testis-specific transcript y1 (ETSTY1), equus testis-specific transcript y4 (ETSTY4), equus testis-specific transcript Y 5 (ETSTY5), and sex-determining region Y (SRY) were identified as multi-copy, whose median copy numbers (MCNs) were 5, 45, 2, and 2, and 13 with CNV ranges of 1–57, 1–227, 1–37, 1–86 and 1–152, respectively. The CNVs of these five genes were shared in different breeds. Compared to previous studies, the copy numbers of five genes showed some distinct consequences in this study. In particular, the well-known single-copy SRY gene showed CNVs in donkeys. Our results provided genetic variations of donkey Y chromosome genes.

The genetic diversity analysis in the donkey myostatin gene

Myostatin (MSTN) gene negatively controls skeletal muscle development and growth, variations of which play an important role in the regulation of skeletal muscle growth in mammals. However, study on genetic polymorphism ofMSTN gene in donkey is limited. In this study, we screened the single nucleotide polymorphsims (SNPs) ofMSTN gene in 13 Chinese donkey breeds. Four novel SNPs (g.229T>C, g.872A>G, g.2014G>A, and g.2395C>G) were detected and genotyped by sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) methods. Six haplotypes (H1-H6) were analyzed, which indicated abundant haplotype diversities in Chinese donkeys. The haplotype H1 was the most dominant and ancient in all breeds. Xinjiang donkey displayed the highest haplotype diversity. The Neighbour-Joining (NJ) tree ofMSTN gene among different species was constructed. The clustering result of nine species was consistent with the fact of species differentiation. Our results will provide a reliable theoretical basis for the preservation, exploration and utilization of Chinese donkey genetic resources.

Complete mitochondrial genome of Qingyang donkey (Equus asinus)

The present study aimed to report the entire mitochondrial genome of Qingyang donkey (Equus asinus). Donkeys play an important role in the daily lives of human beings. The population of Chinese donkey breeds has undergone an enormous decline with the advance of agricultural mechanization, rapid development of transportation and introduction of new different breeds over the past few decades. As a result, a large number of donkey breeds are close to extinction, especially Qingyang donkey. Mitochondrial DNA is used as a molecular tool in research on biodiversity conservation and sustainable utilization of biological resources. The circular genome sequenced using the Illumina Hiseq 2500 platform was 16,568 base pairs (bp), containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a non-coding control region. The initiation site of the L-strand replication origin, 32 bp in length, was between tRNA-Asn and tRNA-Cys. The base composition of the genome was A (32.4%), C (28.7%), G (13.2%) and T (25.7%) with an A+T content of 58.1%. Molecular phylogeny demonstrated two separated clades in Equidae and the presence of a distant relationship between the domestic donkey breeds and Asian wild asses, indicating that domestic donkeys might not probably have originated from Asian wild asses. However, African wild asses were grouped as a sister to domestic donkeys. This study presented the complete mitochondrial genome of E. asinus, providing the important genetic background of protection and adequate utilization of domestic donkey breeds.

High polymorphism at microsatellite loci in the Chinese donkey.

To reveal the genetic diversity and phylogenetic relationships between Chinese donkey breeds, 415 individuals representing ten breeds were investigated using ten microsatellite markers. The observed number of alleles, mean effective number of alleles (NE), mean expected heterozygosity (HE), and polymorphic information content (PIC) of each breed and polymorphic locus were analyzed. The results showed that seven (HTG7, HTG10, AHT4, HTG6, HMS6, HMS3, and HMS7) of ten microsatellite loci were polymorphic. The mean PIC, HE, and NE of seven polymorphic loci for the ten donkey breeds were 0.7679, 0.8072, and 6.0275, respectively. These results suggest that domestic Chinese donkey breeds possess higher levels of genetic diversity and heterozygosity than foreign donkeys. A neighbor-joining tree based on Nei's standard genetic distance showed that there was close genetic distance among Xinjiang, Qingyang, Xiji, and Guanzhong donkey breeds. In addition, Mongolia and Dezhou donkey breeds were placed in the same category. The phylogenetic tree revealed that the genetic relationships between Chinese donkey breeds are consistent with their geographic distribution and breeding history.

Maternal genetic diversity and population structure of four Chinese donkey breeds

To be helpful for the conservation, utilization, and exploitation of the genetic resources of the indigenous Chinese donkeys, and analyze genetic diversity and provide some implications for their maternal origins, we first detailedly investigated the nearly whole mitochondrial Cytochrome b gene ( cytb) of four Chinese donkey breeds' populations. In this study, abundant mitochondrial DNA (mtDNA) diversity and two distinct mitochondrial matrenal lineages, lineage Somali and lineage Nubian, were revealed in the four Chinese domestic donkey breed populations we analyzed. A co-existence model of two lineages as same as the previous studies was found in the four analyzed donkey breeds. Moreover, there was no obvious correspondence between the geographic regions, lineage structure, and maternal origins among all four Chinese donkey breeds. The pattern of genetic variation in analyzed donkey cytb gene indicated that the two lineages had not undergone population expansion events.

The association analysis between Cytb polymorphism and growth traits in three Chinese donkey breeds

The aim of this study was to investigate the effects of haplotypes in Cytb (Cytochrome b) gene on growth traits in three Chinese donkey breeds, Yunnan donkey (YN), Dezhou donkey (DZ) and Liangzhou donkey (LZ). The samples were genotyped for the Cytb gene by single strand conformation polymorphism (SSCP), and association analysis was conducted with growth traits. The results show that in most cases the effects of the gene on growth traits were not significant and that for the three different donkey breeds, the effects of the gene are different. For YN donkeys, there was a significant effect of the gene on the rump width ( P < 0.05) and the effect of genotype AA was larger than that of BB genotype (1.6 cm and 5.4% of the trait mean in YN donkeys, P < 0.05). For DZ donkeys, the effect of gene on body height was significant ( P < 0.05). The results also verify that the SSCPs are caused by two cytosine to thymine and one guanine to adenine transitions, corresponding to amino acid substitutions of leucine for proline (L ↔ P) and isoleucine for valine (I ↔ V).

Mitochondrial DNA diversity and population structure of four Chinese donkey breeds

Mitochondrial DNA diversity and population structure of four Chinese donkey breeds