Yong-Ju Zhao

Mitochondrial DNA diversity and the origin of Chinese indigenous sheep.

Large-scale mitochondrial DNA (mtDNA) D-loop sequences data from previous studies were investigated to obtain genetic information which contributes to a better understanding of the genetic diversity and history of modern sheep. In this study, we analyzed mtDNA D-loop sequences of 963 individuals from 16 Chinese indigenous breeds that distributed seven geographic regions. Phylogenetic analysis showed that all three previously defined haplogroups A, B, and C were found in all breeds among different regions except in Southwest China mountainous region, which had only the A and B haplogroups. The weak phylogeographic structure was observed among Chinese indigenous sheep breeds distribution regions and this could be attributable to long-term strong gene flow among regions induced by the human migration, commercial trade, and extensive transport of sheep. The estimation of demographic parameters from mismatch analyses showed that haplogroups A and B had at least one demographic expansion of indigenous sheep in China.

Mitochondrial DNA diversity, origin, and phylogenic relationships of three Chinese large-fat-tailed sheep breeds

China is abundant of sheep genetic resources. A total of 55 sequences containing the Ovis aries mtDNA D-loop of three large-fat-tailed sheep breeds, named Lanzhou, Tong, and Han were retrieved from GenBank to investigate their genetic diversity, origin, and phylogenetic evolution. The results showed that the sheep breeds in our study proved to be extremely diverse, the average haplotype diversity and nucleotide diversity were 0.987 ± 0.006 and 0.03956 ± 0.00206, respectively. The 55 sequences gave 39 different haplotypes. Phylogenetic analyses revealed that there were three distinct mtDNA haplogroups: A, B, and C, in which haplogroup A was predominant and had experienced population expansion events. Clustering analysis showed that the large-fat-tailed sheep breeds clustered into one group and were closely related to the Mongolian sheep and then European mouflon sheep (Ovis musimon). The results contribute to the knowledge of Chinese sheep breeds and the plan of conservation programs on large-fat-tailed sheep.

Conservation genetics in Chinese sheep: diversity of fourteen indigenous sheep (Ovis aries) using microsatellite markers.

Abstract The domestic sheep (Ovis aries) has been an economically and culturally important farm animal species since its domestication around the world. A wide array of sheep breeds with abundant phenotypic diversity exists including domestication and selection as well as the indigenous breeds may harbor specific features as a result of adaptation to their environment. The objective of this study was to investigate the population structure of indigenous sheep in a large geographic location of the Chinese mainland. Six microsatellites were genotyped for 611 individuals from 14 populations. The mean number of alleles (±SD) ranged from 7.00 ± 3.69 in Gangba sheep to 10.50 ± 4.23 in Tibetan sheep. The observed heterozygote frequency (±SD) within a population ranged from 0.58 ± 0.03 in Gangba sheep to 0.71 ± 0.03 in Zazakh sheep and Minxian black fur sheep. In addition, there was a low pairwise difference among the Minxian black fur sheep, Mongolian sheep, Gansu alpine merino, and Lanzhou fat‐tailed sheep. Bayesian analysis with the program STRUCTURE showed support for 3 clusters, revealing a vague genetic clustering pattern with geographic location. The results of the current study inferred high genetic diversity within these native sheep in the Chinese mainland.

Scanning of selection signature provides a glimpse into important economic traits in goats ( Capra hircus )

Goats (Capra hircus) are one of the oldest livestock domesticated species, and have been used for their milk, meat, hair and skins over much of the world. Detection of selection footprints in genomic regions can provide potential insights for understanding the genetic mechanism of specific phenotypic traits and better guide in animal breeding. The study presented here has generated 192.747G raw data and identified more than 5.03 million single-nucleotide polymorphisms (SNPs) and 334,151 Indels (insertions and deletions). In addition, we identified 155 and 294 candidate regions harboring 86 and 97 genes based on allele frequency differences in Dazu black goats (DBG) and Inner Mongolia cashmere goats (IMCG), respectively. Populations differentiation reflected by Fst values detected 368 putative selective sweep regions including 164 genes. The top 1% regions of both low heterozygosity and high genetic differentiation contained 239 (135 genes) and 176 (106 genes) candidate regions in DBG and IMCG, respectively. These genes were related to reproductive and productive traits, such as “neurohypophyseal hormone activity” and “adipocytokine signaling pathway”. These findings may be conducive to molecular breeding and the long-term preservation of the valuable genetic resources for this species.

Genetic variability of ten Chinese indigenous goats using MHC-linked microsatellite markers

In this study, the genetic variability of Chinese indigenous goat breeds (Capra hircus) was analyzed using the MHC-associated microsatellite markers BF1, BM1818, BM1258, and DYMS1. To examine genetic variability, the levels of heterozigosity, degrees of inbreeding, and genetic differences among the breeds were analyzed. The mean number of alleles ranged from 5.50±3.70 in Enshi black goats (EB) to 11.50±3.70 in the Jianyang big ear (JE) breed. The mean observed heterozygosity and mean expected heterozygosity varied from 0.25±0.04 in Jining Qing goats (JQ) to 0.54±0.05 in Chuannan black goats (CN) and from 0.49±0.18 in Hechuan white goats (HW) to 0.78±0.05 in JE, respectively. The mean FIS values ranged from 0.23 in HW to 0.51 in JQ. In addition, the genetic variation among populations and geographic location did indicate a correlation of genetic differences with geographic distance, which was revealed by the phylogenetic network. In conclusion, the high variability and population structure among Chinese native goats in the Major Histocompatibility Complex would be caused by co-evolution between MHC alleles and the epidemic history or pathogens in different agro-ecological zones.

Characteristics of the mitochondrial genome of four native goats in China (Capra hircus)

Abstract Here, we describe the complete mitochondrial genome sequences of Jining Gray goat, Fushun black goat, Youzhou black-skin goat, and Hechuan white goat. The mitogenome of those four goats consisted of 16,640 nt, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. The complete mitogenome of these four local breeds of Chinese native goats could provide an important data to further breed improvement and animal genetics resource conservation in China.

A complete mitochondrial genome of Dazu Black goat.

Abstract Dazu Black goat is an indigenous goat genetic resource in Southwest of China. Here, we describe its complete mitochondrial genome sequence. The mitogenome is 16,641 bp in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and a control region. As in other mammals, most mitochondrial genes are encoded on the heavy strand, except for ND6 and eight tRNA genes, which are encoded on the light strand. Its overall base composition is A: 33.5%, T: 27.3%, C: 26.1% and G: 13.1%. The complete mitogenome of the indigenous goat could provide important data to further explore the taxonomic status of the subspecies and also provide a starting point for further phylogenetic studies.

Polymorphisms of osteopontin gene and their association with placental efficiency and prolificacy in goats

In this study, we investigated the polymorphisms of Caprine osteopontin (OPN) gene and their association with placental traits and prolificacy in goats. The placental and reproductive traits of 171 litters on three goat breeds with different prolificacy (Dazu Black, n = 94; Lezhi Black, n = 27; Hexi Cashmere, n = 50) were evaluated. The polymorphisms in the 5′ promoter and exon 7 of OPN gene were detected by PCR-SSCP methods. Their association was further achieved by using least squares means. It showed that the litter size, litter and placenta weight for Dazu Black and Lezhi Black goats were higher significantly than those of Hexi Cashmere goats (P < 0.01). However, the placental efficiency was not significantly different (P > 0.05). Hexi Cashmere does have more cotyledons in placental than that of Dazu Black and Lezhi Black does (P < 0.01). There were only two genotypes (nominated AA and AB) detected whether by the 5′ promoter primer pairs or by exon 7 of OPN gene. They were associated with litter number, with a trend of AA > AB. At the exon 7 locus, the Dazu Black does with genotype AA had 0.88 more litter numbers than those with genotype AB (P < 0.05). It suggested that OPN gene could be a potential candidate gene on goat prolificacy.

Potent effect of KISS1-54 DNA vaccine compared with KISS1-10 DNA vaccine in inhibiting the fertility of female rats

BACKGROUND Most studies on immunocastration currently focused on male animals. However, immunization of male animals does not completely inhibit sexual behavior and fertility. This study aimed to compare the immunocastration effect of KISS1 DNA vaccines encoding different lengths of kisspeptins in female rats for effective castration effects on both male and female rats. METHODS Fifteen female rats were randomly divided into three groups. The rats in T1 group or T2 group was orally given respectively KISS1-54 or KISS1-10 DNA vaccines with fused tPA signal peptide, and the control group (Group C) was orally administered with empty vector vaccine, at a dose of 5 × 109 CFU/rat at weeks 0, 3 and 6 of the study. Blood samples were collected by retroorbital bleeding before primary immunization and at weeks 3 and 9 after primary immunization. RESULTS Both KISS1-54 and KISS1-10 DNA vaccines induced the bodys humoral immune response, and the anti-kisspeptin antibody titres in the T1 group were significantly higher than that in T2 and C groups (p < 0.05). The rats in T1 group has lower serum kisspeptin and estradiol levels than those in T2 and C groups and smaller litter size of rats than those in the control group after mating (p < 0.05). No significant difference was observed between T2 and C groups. The levels of KISS1 and GPR54 mRNA in the hypothalamus and ovaries of the T1 group were significantly lower than that in control group. However, the levels of KISS1 mRNA in the T2 group were significantly lower than that in the control group only in ovaries (p < 0.05). CONCLUSION The oral KISS1-54 DNA vaccine with fused tPA signal peptide was more effective than that KISS1-10 DNA vaccine in suppressing fertility of female rats.

Sheep mitochondrial heteroplasmy arises from tandem motifs and unspecific PCR amplification

Abstract The mitochondrial DNA control region (D-loop) is a widely used molecular marker in evolutionary and phylogeographic research. However, the occurrence of heteroplasmy of the D-loop region within individuals has rarely been investigated. In this study, a total of 85 Chinese sheep were used to amplify a partial D-loop region, and 15 heteroplasmic animals (17.64%) were identified. A comparative analysis of the PCR amplification and cloning of the D-loop sequences from the heteroplasmic samples revealed most of the sequencing profile from the heteroplasmic regions started at the beginning of a 75-bp random repeat motif. In addition, a total of 22 nonsyngeneic sequences with a D-loop were found in 61 of the clones obtained from the 4 random heteroplasmic and 3 homozygote animals, and their genomic locations were compared for homology. In summary, the D-Loop sequencing profiles appear to be heteroplasmic and could arise from tandem repeat motifs and unspecific replication during PCR amplification; however, they are not likely due to the presence of multiple mitochondrial genomes within an individual.