Genome-wide differential expression of long noncoding RNAs and mRNAs in ovarian follicles of two different chicken breeds.

Bashang long-tail chickens are an indigenous breed with dual purpose in China (meat and eggs) but have low egg laying performance. To improve the low egg laying performance, a genome-wide analysis of mRNAs and long noncoding RNAs (lncRNAs) from Bashang long-tail chickens and Hy-Line brown layers was performed. A total of 16,354 mRNAs and 8691 lncRNAs were obtained from ovarian follicles. Between the breeds, 160 mRNAs and 550 lncRNAs were found to be significantly differentially expressed. Integrated network analysis suggested some differentially expressed genes were involved in ovarian follicular development through oocyte meiosis, progesterone-mediated oocyte maturation, and cell cycle. The impact of lncRNAs on cis and trans target genes, indicating some lncRNAs may play important roles in ovarian follicular development. The current results provided a catalog of chicken ovarian follicular lncRNAs and genes for further study to understand their roles in regulation of egg laying performance.

Genetic variations of the coding region of the melanocortin receptor 1 (MC1R) gene in the fox.

BACKGROUND: The melanocortin 1 receptor (MC1R) gene plays an important role in the control of coat colour in mammals. Genetic variation of the MC1R gene and the relationship between genotype and coat colour are not well understood. Studies in the fox may improve our understanding of gene influence on coat colour in dogs and cats. HYPOTHESIS/OBJECTIVES: To investigate coat colour associated mutations in the coding region of MC1R gene in foxes. ANIMALS: A total of 118 foxes, comprising 70 red foxes (Vulpes vulpes) (19 red, 10 white silver, 29 silver and 12 chocolate foxes) and 48 arctic foxes (Vulpes lagopus) (9 dominant white blue foxes and 39 normal blue foxes) were included in the study. METHODS: Evaluation of the DNA sequence of the coding region of MC1R gene and its polymorphisms. RESULTS: Eight polymorphic sites (single nucleotide polymorphisms, SNPs) distributed throughout the 954-bp coding region of the fox MC1R gene were detected. Among them, c.13G>T, c.124A>G, c.289G>A, c.373T>C and c.839 T>G were mis-sense mutations, which resulted in codon change of p.G5C, p.N42D, p.V97I, p.C125R and p.F280C, respectively. Mutation and haplotype analysis indicated that c.373T>C was associated with black and brown pigmented phenotypes in foxes, and c.13G>T and c.839T>G were important in distinguishing V. lagopus and V. vulpes. CONCLUSIONS AND CLINICAL IMPORTANCE: SNP c.373T>C in the coding region of the MC1R gene is probably associated with the brown phenotype of chocolate foxes.

Effects of dietary supplementation with dandelion tannins or soybean isoflavones on growth performance, antioxidant function, intestinal morphology, and microbiota composition in Wenchang chickens.

Many benefits have been found in supplementing tannins or soybean isoflavones to poultry, including increased body weight gain, antioxidant activity, and better intestinal morphology. However, few studies tested the influence of dandelion tannins or soybean isoflavones supplementation on Wenchang chickens. This study investigates the effects of dietary supplementation with dandelion tannins or soybean isoflavones on the growth performance, antioxidant function, and intestinal health of female Wenchang chickens. A total of 300 chickens were randomly divided into five groups, with six replicates per group and 10 broilers per replicate. The chickens in the control group (Con) were fed a basal diet; the four experimental groups were fed a basal diet with different supplements: 300 mg/kg of dandelion tannin (DT1), 500 mg/kg of dandelion tannin (DT2), 300 mg/kg of soybean isoflavone (SI1), or 500 mg/kg of soybean isoflavone (SI2). The experiment lasted 40 days. The results showed that the final body weight (BW) and average daily gain (ADG) were higher in the DT2 and SI1 groups than in the Con group (P < 0.05). In addition, dietary supplementation with dandelion tannin or soybean isoflavone increased the level of serum albumin (P <0.05); the concentrations of serum aspartate aminotransferase and glucose were significantly higher in the SI1 group (P < 0.05) than in the Con group and the concentration of triglycerides in the DT1 group (P < 0.05). The serum catalase (CAT) level was higher in the DT1 and SI1 groups than in the Con group (P < 0.05). The ileum pH value was lower in the DT2 or SI1 group than in the Con group (P < 0.05). The jejunum villus height and mucosal muscularis thickness were increased in the DT2 and SI1 groups (P < 0.05), whereas the jejunum crypt depth was decreased in the DT1 or DT2 group compared to the Con group (P < 0.05). In addition, the messenger RNA (mRNA) expression level of zonula occludens 1 (ZO-1) in the duodenum of the SI1 group and those of occludin, ZO-1, and claudin-1 in the ileum of the DT2 and SI1 groups were upregulated (P < 0.05) compared to the Con group. Moreover, the DT2 and SI1 groups exhibited reduced intestinal microbiota diversity relative to the Con group, as evidenced by decreased Simpson and Shannon indexes. Compared to the Con group, the relative abundance of Proteobacteria was lower and that of Barnesiella was higher in the DT2 group (P < 0.05). Overall, dietary supplementation with 500 mg/kg of dandelion tannin or 300 mg/kg of soybean isoflavone improved the growth performance, serum biochemical indexes, antioxidant function, and intestinal morphology and modulated the cecal microbiota composition of Wenchang chickens.

Mapping quantitative trait loci for T lymphocyte subpopulations in peripheral blood in swine.

BACKGROUND: Increased disease resistance through improved general immune capacity would be beneficial for the welfare and productivity of farm animals. T lymphocyte subpopulations in peripheral blood play an important role in immune capacity and disease resistance in animals. However, very little research to date has focused on quantitative trait loci (QTL) for T lymphocyte subpopulations in peripheral blood in swine. RESULTS: In the study, experimental animals consist of 446 piglets from three different breed populations. To identify QTL for T lymphocyte subpopulations in peripheral blood in swine, the proportions of CD4+, CD8+, CD4+CD8+, CD4+CD8-, CD4-CD8+, and CD4-CD8- T cells and the ratio of CD4+:CD8+ T cells were measured for all individuals before and after challenge with modified live CSF (classical swine fever) vaccine. Based on the combined data of individuals from three breed populations, genome-wide scanning of QTL for these traits was performed based on a variance component model, and the genome wide significance level for declaring QTL was determined via permutation tests as well as FDR (false discovery rate) correction. A total of 27 QTL (two for CD4+CD8+, one for CD4+CD8-, three for CD4-CD8+, two for CD4-CD8-, nine for CD4+, two for CD8+, and eight for CD4+:CD8+ ratio) were identified with significance level of FDR < 0.10, of which 11 were significant at the level of FDR < 0.05, including the five significant at FDR < 0.01. CONCLUSIONS: Within these QTL regions, a number of known genes having potential relationships with the studied traits may serve as candidate genes for these traits. Our findings herein are helpful for identification of the causal genes underlying these immune-related trait and selection for immune capacity of individuals in swine breeding in the future.

Chromosome-level genome assembly of the Arctic fox (Vulpes lagopus) using PacBio sequencing and Hi-C technology.

The Arctic fox (Vulpes lagopus) is the only fox species occurring in the Arctic and has adapted to its extreme climatic conditions. Currently, the molecular basis of its adaptation to the extreme climate has not been characterized. Here, we applied PacBio sequencing and chromosome structure capture technique to assemble the first V. lagopus genome assembly, which is assembled into chromosome fragments. The genome assembly has a total length of 2.345 Gb with a contig N50 of 31.848 Mb and a scaffold N50 of 131.537 Mb, consisting of 25 pseudochromosomal scaffolds. The V. lagopus genome had approximately 32.33% repeat sequences. In total, 21,278 protein-coding genes were predicted, of which 99.14% were functionally annotated. Compared with 12 other mammals, V. lagopus was most closely related to V. Vulpes with an estimated divergence time of ~7.1 Ma. The expanded gene families and positively selected genes potentially play roles in the adaptation of V. lagopus to Arctic extreme environment. This high-quality assembled genome will not only promote future studies of genetic diversity and evolution in foxes and other canids but also provide important resources for conservation of Arctic species.

Detection of quantitative trait loci affecting haematological traits in swine via genome scanning.

BACKGROUND: Haematological traits, which consist of mainly three components: leukocyte traits, erythrocyte traits and platelet traits, play extremely important role in animal immune function and disease resistance. But knowledge of the genetic background controlling variability of these traits is very limited, especially in swine. RESULTS: In the present study, 18 haematological traits (7 leukocyte traits, 7 erythrocyte traits and 4 platelet traits) were measured in a pig resource population consisting of 368 purebred piglets of three breeds (Landrace, Large White and Songliao Black Pig), after inoculation with the swine fever vaccine when the pigs were 21 days old. A whole-genome scan of QTL for these traits was performed using 206 microsatellite markers covering all 18 autosomes and the X chromosome. Using variance component analysis based on a linear mixed model and the false discovery rate (FDR) test, 35 QTL with FDR < 0.10 were identified: 3 for the leukocyte traits, 28 for the erythrocyte traits, and 4 for the platelet traits. Of the 35 QTL, 25 were significant at FDR < 0.05 level, including 9 significant at FDR < 0.01 level. CONCLUSIONS: Very few QTL were previously identified for hematological traits of pigs and never in purebred populations. Most of the QTL detected here, in particular the QTL for the platelet traits, have not been reported before. Our results lay important foundation for identifying the causal genes underlying the hematological trait variations in pigs.

[Activity and transcriptional regulatory elements of the promoter in Arctic fox (Vulpes lagopus) ß-defensin103 gene].

The aim of this study was to screen the active regions and transcription factor binding sites in the promoter of the CBD103 gene related to Arctic fox coat color, and to provide a basis for revealing the molecular genetic mechanism of CBD103 gene regulating the coat color formation. The 5'-flanking region fragment 2 123 bp of Arctic fox CBD103 gene was cloned, and 4 truncated promoter reporter vectors of different lengths were constructed. The promoter activity was detected by the dual-luciferase reporter assay system. Point mutations were performed on the 3 predicted specificity protein 1 (Sp1) transcription factor binding sites in the highest promoter active region, and 3 mutant vectors were constructed. The activity was then detected by the dual-luciferase reporter assay system. The results showed that the region 1 656 (-1 604/+51) had the highest activity in the 4 truncated promoters of different lengths, and the promoter activity of the three mutant vectors constructed in this region were significantly lower than that of the wild type (fragment 1 656). The region of -1 604 /+51 was the core promoter region of CBD103 gene in Arctic fox and -1 552/-1 564, -1 439/-1 454 and -329/-339 regions were positive regulatory regions. This study successfully obtained the core promoter region and positive regulation regions of the Arctic fox CBD103 gene, which laid a foundation for further study on the molecular genetic mechanism of this gene regulating Arctic fox coat color.

Study on tandem repeat sequence variation in sheep mtDNA D-loop region.

The 75-nt-long tandem repeat sequence in the control region of mtDNA of 77 individuals, of which 69 were from different indigenous sheep breeds in China and 8 were from imported breeds, was sequenced and analyzed to investigate the origin and differentiation of Chinese indigenous sheep breeds and also the genetic diversities and relationships among them. A total of 28 variable sites were detected within 309 repeated sequences, among which 7 sites were singleton variable sites with two variants, 1 site was a singleton variable site with three variants, and 20 sites were parsimony informative sites with two variants. A total of 63 haplotypes were sorted from 28 polymorphic sites, among which two main and basic haplotypes, namely, Hap 1 and Hap 3 were present at a much higher proportion, at 12.94% and 30.42%, respectively. It could be inferred that Chinese indigenous sheep breeds originated from two maternal ancestors because of the maternal inheritance characteristics of the mtDNA. Altay sheep and Kazakstan sheep are closely related and do not differentiate significantly. Mongolian sheep and Ujumuqin sheep also share a close relationship. Tibetan sheep, Mongolian sheep, and Ujumuqin sheep have lower genetic diversity than Altay sheep and Kazakstan sheep.

[Study on mtDNA D-loop of Chinese main indigenous sheep breeds using PCR-RFLP].

The polymorphism of mtDNA D-loop of 83 individuals from 9 Chinese indigenous sheep breeds and 2 imported sheep breeds were studied with 5 endonucleases, Hinf I, Msp I, Sau3A I, Xsp I and Taq I, using PCR-RFLP. The results indicated that there existed two basic haplotypes in the region of mtDNA D-loop. It could be inferred that Chinese indigenous sheep breeds originated from two maternal ancestors. The averaged polymorphic degree (Pi value=0.0421%) of mtDNA D-loop showed that the genetic diversity of mtDNA of Chinese indigenous sheep breeds was very poor.

Study on polymorphisms of microsatellites DNA of six Chinese indigenous sheep breeds.

The polymorphisms of 17 microsatellites loci of six indigenous sheep breeds, including Mongolian sheep, Ujumuqin sheep, Kazakstan sheep, Aletai sheep and Tibetan sheep, were studied using polypropylene gel electrophoresis in order to investigate their genetic diversity,origin, differentiation and relationships. The results indicated that there was a significant difference in genetic diversity between different loci (P < 0.01). There was no significant difference in PIC, Fis and observed heterozygosity (Obs. Het) among populations (P > 0.05), but a significant difference in gene diversity and expected heterozygosity (Exp. Het) (P < 0.05). Chinese indigenous sheep breeds had similar genetic diversity as those from Europe,but with higher inbreeding coefficient. It could be inferred from the cluster of individuals and populations that Chinese indigenous sheep breeds might originate from two ancestors. The cluster of populations showed that Mongolian sheep and Ujumuqin sheep had close relationship and did not differentiate obviously. Mongolian sheep and Tibetan sheep had far relationship and differentiated significantly. Aletai sheep differentiated from Kazakstan sheep but not significantly. Tan sheep,Aletai sheep and Tibetan sheep also had close relationships. The Fst of Chinese indigenous sheep breeds was close to some Spanish sheep breeds,but much smaller than that of other European sheep breeds. More loci and samples should be studied in the future in order to obtain more accurate results.

[Inheritance of head and neck color and black hoof of Boer goat].

The inheritance of head and neck color and black hoof of Boer goats and their offspring were analyzed by observing,breeding data and statistic test in the Crossbreeding and Improving Research Center of Boer goat in Qinhuangdao city. The results indicated that the color of head and neck and black hoof of Boer goat were all controlled respectively by two linked recessive genes on one autosome. The rate of crossing-over between the genes of head and neck color and black hoof was 7.5 genetic units.

[Studies of random amplified polymorphic DNA(RAPD) of main indigenous sheep breeds in China].

The genetic polymorphism and relationship of 7 indigenous sheep breeds of China and 3 imported sheep breeds were studied using random amplified polymorphic DNA (RAPD). The results indicated that the RAPD was an effective marker for the analysis of genetic relationship among sheep breeds. Among 43 arbitrary primers,35 were polymorphic. The percentage of polymorphic markers was 66.24%,which indicated that the RAPD had higher efficiency of polymorphism detection and sensitivity in studying the genetic variation among sheep breeds. The average index of genetic polymorphism for whole population (Hsp) was 0.9139,which showed that the genetic polymorphism was abundant between sheep populations. The genetic relationship between different indigenous sheep breeds in China was in accord with their localities,the results from archeology and cytogenetics and the genetic relationship between imported sheep breeds was in accord with their breeding history.

[Studies of genetic structure of genetic relationship of Boer goat and its upgrading offspring to Tangshan Diary goat].

The gentic structure and relationship of Boer goat and its upgrading offspring to Tangshan Dairy goat were studied using the RAPD maker and some statistical program, such as POPGENE, PHYLIP and SPSS. The results indicated that there were the similar percentage of polymorphic loci, observed and effective number of alleles, gene diversity between Boer goat and its upgrading offspring, especially higher upgrading offspring. With the increasing of upgrading, the difference of population structure decreased as well as the genetic distance and differentiation among higher upgrading offspring and their improving parental, but gene flow and genetic identity increased. There was a close genetic relationship between higher upgrading offspring and Boer goat.

Study on SNP of melanocyte stimulating hormone receptor gene in several Chinese indigenous sheep breeds using DHPLC.

Single nucleotide polymorphism (SNP) of melanocyte stimulating hormone receptor (MSHR) gene was studied by sequencing and denaturing high performance liquid chromatography (DHPLC) in Mongolian sheep, Kazakstan sheep, Tan sheep and Tibetan sheep. The results showed that there is a mutation at position 317 (T317C) within the length of 415bp and the DHPLC is a high-throughput and simple method for screening this mutation. The heterozygote (TC) with shoulder peak could be detected quickly at the first time of DHPLC, and two homozygotes (TT or CC) could be discriminated easily through two times of DHPLC when each homozygous DNA was mixed with a known homozygous reference sample at the second time of DHPLC. All of the populations for this site are in Hardy-Weinberg equilibrium. The results also indicated that Mongolian sheep and Kazakstan sheep had close relationship, Tibetan sheep and Tan sheep had close relationship. The relationship among breeds was consistent with that of microsatellite DNA.

SNP identification and analysis in part of intron 2 of goat MSTN gene and variation within and among species.

Part of intron 2 of the myostatin (MSTN) gene of 140 goats from 24 populations and 38 sheep from 8 breeds were sequenced, and similar sequences of different species from Gene bank were also obtained to study MSTN diversity within and among species. The results indicated that there were seven polymorphic sites in the sequenced region of goat, which have not been separated by recombination (or recurrent mutation), presented complete linkage disequilibrium, and could be sorted into three haplotypes. There was no polymorphic site in the sequenced region of sheep. The haplotype diversity, nucleotide diversity, and average number of single nucleotide polymorphism (SNP) differences of goats from the South group are higher than those of North group, and the corresponding value of the Foreign group is also higher than that of Chinese. The genetic differentiation (0.7558) between the Foreign and Chinese group is significant. There are two main haplotypes of the MSTN intron 2 in the goat, which may represent two ancestral types, in support of the theory that domestic goats in the world mainly originated from two ancestors based on morphology, history, archaeology, and molecular markers. The sequence differences of the MSTN intron 2 among species are greater than those within species.