ABSTRACT
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.
Subject(s)
Equidae , Inbreeding , Polymorphism, Single Nucleotide , Animals , Equidae/genetics , Male , Female , Gene Frequency , Genome/genetics , Whole Genome Sequencing/methods , Breeding , Heterozygote , GenotypeABSTRACT
In view of the severe reduction in Bactrian camel germplasm resources, scientific evaluation, protection, and utilization is particularly important. Therefore, it is necessary to investigate the genetic diversity and genetic structure of this species, and identify the genes that have played important roles in its evolution. In this study, 21,971 SNPs were identified in 118 domestic Bactrian camels from the Tarim (n = 60) and Junggar (n = 58) populations using simplified GBS genome sequencing. The results show that Tarim and Junggar Bactrian camels have high nucleotide diversity. A phylogenetic tree constructed using structural analysis, principal component analysis (PCA), and the adjacency method (NJ) showed that Tarim and Junggar Bactrian camels were clustered together. The selection signals revealed that the Tarim and Junggar Bactrian camels shared 108 genes under positive selection, including WNT1, WNT10B, CD14, SEC61A2, DPAGT1, FOXO6, etc. These selected genes were widely involved in the immune system, embryonic development, lipid metabolism, and other processes. From a genomic analysis perspective, the genetic relationship between TLM and ZGE camels is close, with an average Fst of 0.048 and a relatively low average differentiation coefficient between the two populations. In addition, shared selected genes in the long-term depression pathway were significantly enriched in Tarim and Junggar. These findings will offer support and assistance for the exploration of genetic resource preservation, economically significant traits, and the mechanisms underlying biological characteristics, molecular breeding, and disease.
ABSTRACT
Understanding the genetic basis of native cattle populations that have adapted to the local environment is of great significance for formulating appropriate strategies and programs for genetic improvement and protection. Therefore, it is necessary to understand the genetic diversity and population structure of Altay white-headed cattle so as to meet the current production needs under various environments, carry out continuous genetic improvement, and promote rapid adaptation to changing environments and breeding objectives. A total of 46 individual samples of endangered Xinjiang Altay white-headed cattle were collected in this study, including nine bulls and 37 cows. To collect genotype data, 100 k SNP markers were used, and then studies of genetic diversity, genetic structure, inbreeding degree, and family analysis were carried out. A total of 101,220 SNP loci were detected, and the genotype detection rate for individuals was ≥90%. There were 85,993 SNP loci that passed quality control, of which 93.5% were polymorphic. The average effective allele number was 0.036, the Polymorphism Information Content was 0.304 and the minimum allele frequency was 0.309, the average observed heterozygosity was 0.413, and the average expected heterozygosity was 0.403. The average genetic distance of Idengtical By State (IBS) was 0.3090, there were 461 ROH (genome-length homozygous fragments), 76.1% of which were between 1 and 5 MB in length, and the average inbreeding coefficient was 0.016. The 46 Altay white-headed cattle were divided into their families, and the individual numbers of each family were obviously different. To sum up, the Altay white-headed cattle conservation population had low heterozygosity, a high inbreeding degree, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the follow-up seed conservation process, seed selection and matching should be carried out according to the divided families to ensure the long-term protection of Altay white-headed cattle genetic resources.
ABSTRACT
The aim of this study was to study the relationship between the methylation level of the promoter region of follicle-stimulating hormone receptor (FSHR) gene and the mRNA expression of Duolang sheep fed different energy diets. In this experiment, three groups of diets with different energy levels (dietary nutrient level reference (NY/T816 - 2004)) were designed to obtain medium energy level diets with metabolic energy of 10.88 MJ/d. The treatments with high and low energy levels increased and decreased by 15%, 12.51, and 9.25 MJ/d, respectively, on the basis of medium energy level. Total RNA and genomic DNA were extracted from the ovaries of Duolang sheep, and qPCR was performed. Bisulfite genomic sequencing PCR and sequence alignment were used to detect the relationship between the relative expression level of FSHR and methylation. The results showed that the expression of FSHR in high-energy group and medium-energy group was significantly higher than that in low-energy group (p < 0.01), and there was no significant difference between high-energy group and medium-energy group (p > 0.05). The methylation rate of the target fragment in the promoter region of FSHR gene was 41.67% in the high-energy group, 75.00% in the medium-energy group, and 83.33% in the low-energy group. This study revealed that different dietary energy levels had certain effects on DNA methylation level of FSHR gene and then affected gene expression, and the expression level was negatively correlated with methylation level.
Subject(s)
DNA Methylation , Receptors, FSH , Animals , Diestrus , Diet , Female , Promoter Regions, Genetic/genetics , RNA, Messenger/genetics , RNA, Messenger/metabolism , Receptors, FSH/genetics , Sheep/geneticsABSTRACT
BACKGROUND: The aim of this study was to study the relationship between the methylation level of the promoter region of follicle-stimulating hormone receptor (FSHR) gene and the mRNA expression of Duolang sheep fed different energy diets. METHODS: In this study, polyembryo estrus Duolang sheep under different energy levels were selected as the experimental subjects. Dietary nutrient level reference (NY/T 816-2004), medium energy level was 10.88 MJ/day, high and low energy groups were increased and decreased by 15% on the basis of medium energy level, respectively 12.51 MJ/day, 9.25 MJ/day. Through RNA and DNA extraction, qPCR, bisulfitegenomicse-quencing PCR (BSP), sequence matching and other analysis of ovarian tissue of Duolang sheep. The difference of DNA methylation level and mRNA expression of FSHR gene during estrus in Duolang sheep fed with different energy diets was detected. RESULTS: The results showed the expression level of FSHR in high energy group was significantly higher than that in low energy group (P < 0.01), the expression level of FSHR in high energy group was significantly higher than that in medium energy group (P < 0.05), and the expression level of FSHR in medium energy group was significantly higher than that in low energy group (P < 0.05). In the target fragment of the promoter region of the FSHR gene, the methylation rate was 25% in the high energy group, 50% in the normal group, and 75% in the low energy group. CONCLUSIONS: This study revealed that different dietary energy levels had certain effects on the FSHR gene DNA methylation level and mRNA expression, and the expression level was negatively correlated with methylation level.