Search

With the rapid growth of data driven by high-throughput sequencing technologies, genomics has entered an era characterized by big data, which presents significant challenges for traditional bioinformatics methods in handling complex data patterns. At this critical juncture of technological progress, deep learning-an advanced artificial intelligence technology-offers powerful capabilities for data analysis and pattern recognition, revitalizing genomic research. In this review, we focus on four major deep learning models: Convolutional Neural Network(CNN), Recurrent Neural Network(RNN), Long Short-Term Memory(LSTM), and Generative Adversarial Network(GAN). We outline their core principles and provide a comprehensive review of their applications in DNA, RNA, and protein research over the past five years. Additionally, we also explore the use of deep learning in livestock genomics, highlighting its potential benefits and challenges in genetic trait analysis, disease prevention, and genetic enhancement. By delivering a thorough analysis, we aim to enhance precision and efficiency in genomic research through deep learning and offer a framework for developing and applying livestock genomic strategies, thereby advancing precision livestock farming and genetic breeding technologies.

Litter size is a key indicator of production performance in livestock. However, its genetic basis in goats remains poorly understood. In this work, a genome-wide selection sweep analysis (GWSA) on 100 published goat genomes with different litter rates was performed for the first time to identify candidate genes related to kidding rate. This analysis was combined with the public RNA-sequencing data of ovary tissues (follicular phase) from high- and low-yielding goats. A total of 2278 genes were identified by GWSA. Most of these genes were enriched in signaling pathways related to ovarian follicle development and hormone secretion. Moreover, 208 differentially expressed genes between groups were obtained from the ovaries of goats with different litter sizes. These genes were substantially enriched in the cholesterol and steroid synthesis signaling pathways. Meanwhile, the weighted gene co-expression network was used to perform modular analysis of differentially expressed genes. The results showed that seven modules were reconstructed, of which one module showed a very strong correlation with litter size (r = -0.51 and p-value <0.001). There were 51 genes in this module, and 39 hub genes were screened by Pearson's correlation coefficient between core genes > 0.4, correlation coefficient between module members > 0.80 and intra-module connectivity ≥5. Finally, based on the results of GWSA and hub gene Venn analysis, seven key genes (ACSS2, HECW2, KDR, LHCGR, NAMPT, PTGFR and TFPI) were found to be associated with steroid synthesis and follicle growth development. This work contributes to understanding of the genetic basis of goat litter size and provides theoretical support for goat molecular breeding., (© 2024 Stichting International Foundation for Animal Genetics.)

CRISPR/Cas9 gene editing technology, as a highly efficient genome editing method, has been extensively employed in the realm of animal husbandry for genetic improvement. With its remarkable efficiency and precision, this technology has revolutionized the field of animal husbandry. Currently, CRISPR/Cas9-based gene knockout, gene knock-in and gene modification techniques are widely employed to achieve precise enhancements in crucial production traits of livestock and poultry species. In this review, we summarize the operational principle and development history of CRISPR/Cas9 technology. Additionally, we highlight the research advancements utilizing this technology in muscle growth and development, fiber growth, milk quality composition, disease resistance breeding, and animal welfare within the livestock and poultry sectors. Our aim is to provide a more comprehensive understanding of the application of CRISPR/Cas9 technology in gene editing for livestock and poultry.

This study aimed to explore the genetic basis of muscle development in goats. The transcriptome dataset for differentially expressed lncRNAs (DELs) and differentially expressed genes (DEGs) of goat muscle at different developmental stages were obtained using RNA-Seq. A total of 447,806,481 and 587,559,465 clean reads in the longissimus dorsi muscle of Dazu black goats between 75d embryonic stage and 1d after birth were generated through Illumina paired-end sequencing, and their mapping rates were 89.82 and 90.99%, respectively. Moreover, 4517 DEGs and 648 DELs were identified, and 4784 lncRNA-mRNA targeting relationships were predicted. Gene function annotation results showed that 4101 DEGs were significantly enriched to 1098 GO terms, and 2014 DEGs were significantly enriched to 40 KEGG pathways, including many GO terms and pathways related to muscle development, such as cell differentiation and Wnt signaling pathway. Then, 10 DELs and 20 DEGs were randomly selected for RT-qPCR verification, and the agreement rate between the verification and RNA-Seq results was 90%, indicating the high reliability of the RNA-Seq data analysis. In conclusion, this study obtained several mRNAs and lncRNAs related to the muscle development of Dazu black goats and identified several targeted regulatory pairs of lncRNA-mRNA. This study may serve as a reference to understand the genetic basis and molecular mechanism of muscle development in goats.

The Boer goat is one of the top meat breeds in modern animal husbandry and has attracted widespread attention for its unique growth performance. However, the genetic basis of muscle development in the Boer goat remains obscure. In this study, we identified specific structural variants in the Boer goat based on genome-wide selection signals and analyzed the basis of the molecular heredity of related candidate genes in muscle development. A total of 9 959 autosomal copy number variations (CNVs) were identified through selection signal analysis in 127 goat genomes. Specifically, we confirmed that the highest signal CNV (HSV) was a chromosomal arrangement containing an approximately 1.11 Mb (CHIR17: 60062304-61171840 bp) duplicated fragment inserted in reverse orientation and a 5 362 bp deleted region (CHIR17:60145940-60151302 bp) with overlapping genes (e.g., ARHGAP10 , NR3C2 , EDNRA , PRMT9 , and TMEM184C ). The homozygous duplicated HSV genotype (+/+) was found in 96% of Boer goats but was not detected in Eurasian goats and was only detected in 4% of indigenous African goats. The expression network of three candidate genes ( ARHGAP10 , NR3C2 , and EDNRA ) regulating dose transcription was constructed by RNA sequencing. Results indicated that these genes were involved in the proliferation and differentiation of skeletal muscle satellite cells (SMSCs) and their overexpression significantly increased the expression of SAA3 . The HSV of the Boer goat contributed to superior skeletal muscle growth via the dose effects of overlapping genes.

This study compared and analyzed the genetic diversity and population structure of exon 2 of the DQB1 gene and 13 autosomal neutral microsatellite markers from 14 Chinese goat breeds to explore the potential evolutionary mechanism of the major histocompatibility complex (MHC). A total of 287 haplotypes were constructed from MHC-DQB1 exon 2 from 14 populations, and 82 nucleotide polymorphic sites (SNPs, 31.78%) and 172 heterozygous individuals (79.12%) were identified. The F ST values of the microsatellites and MHC-DQB ranged between 0.01831-0.26907 and 0.00892-0.38871, respectively. Furthermore, 14 goat populations showed rich genetic diversity in the microsatellite loci and MHC-DQB1 exon 2. However, the population structure and phylogenetic relationship represented by the two markers were different. Positive selection and Tajima's D test results showed the occurrence of a diversified selection mechanism, which was primarily based on a positive and balancing selection in goat DQB. This study also found that the DQB sequences of bovines exhibited trans-species polymorphism (TSP) among species and families. In brief, this study indicated that positive and balancing selection played a major role in maintaining the genetic diversity of DQB, and TSP of MHC in bovines was common, which enhanced the understanding of the MHC evolution.

AMH , KISS1R and GDF9 genes play a vital role in human and animal reproduction and might be used as the genetic markers for the reproduction traits selection. The aim of this study was to screen the single nucleotide polymorphisms (SNPs) within the AMH , KISS1R and GDF9 genes and to determine the correlations between these SNPs and the litter size in goats. Nine single SNPs within these genes were used for genotyping of the 190 Dazu black goat populations by SNaPshot technique. The polymorphisms of nine SNPs within these genes were detected in Dazu black goats. The significant correlation was observed between one SNP (g.89172108A > C) within the AMH gene and the litter size of second born in Dazu black goats ( p  < 0.05). The SNP was located in exon 4 (XM&#95;018050765.1) of the AMH gene and was one nonsynonymous substitution, which resulted in a change of an amino acid from Glutamine to Proline (Gln38Pro). These results suggested that the nonsynonymous SNP g.89172108A > C of AMH gene could be used as a potential genetic marker for Marker-assisted selection (MAS) in goats breeding programs.

As the aging process is springing up around the whole world, the problem of sit-to-stand (STS) for the elderly has become the focal point of older people themselves, their families, and society. The key challenge in solving this problem is developing and applying the technology of auxiliary robots for standing up and auxiliary stands. The research is not only to find the appropriate fundamentals from a healthcare perspective in the center of gravity movement (COM) curve of the elderly during STS but also to meet the psychological needs of the elderly during STS in a comfortable, pleasant, and safe way. To obtain the skeleton tracking technology used in this study, we used the Vicon optical motion capture system and automatic moving target indicator (AMTI) 3-D force measuring table to obtain a COM curve of the elderly during STS. The stationary process, speed, and sitting posture analysis during STS were combined in this paper to seek a solution to the psychological needs of the elderly. The analysis is conducted with the integration of medicine, engineering, art, and science into this research. Finally, a movement curve and related dynamic parameters that can truly reflect the STS of the elderly are obtained, and the discussion is provided. The research result can provide theoretical and technical support for the later development of auxiliary robots for standing up and auxiliary stands technology products, so that the elderly can STS comfortably, happily, and safely with the assistance of human-robot interaction., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Wang, Xu, Fu, Xu, Wang and Na.)

This study aims to identify the relative Copy number variation (CNV) associated with the litter size of Dazu black goats based on the unpublished CNV analytical results of our previously published sequencing data, in which the litter-size groups were classified into extreme low- and high-yield groups. Firstly, to compare the existence of valuable CNV in Dazu black goats with different fertility levels with mixed pools. We obtained 4992 and 4888 CNVs from the HY and LY, which overlapping 1461 genes, and classified on the original CNV type. Three genes [ LOC108633278 , PPP1R12A , and YIPF4 ] were observed in the intersection between the HY deletion and the LY duplication groups. Secondly, on individuals level, we identified a novel candidate CNV (Chr1&#95;50215501, F ST = 0.148, V ST = 0.347) from 214 autosomal credible CNVs to be significant with litter size in the Dazu black goat, which located in the CBLB gene. This finding indicates the CBLB gene may affect the litter size of the Dazu black goats through structural variations, and Chr1&#95;50215501 can be an effective genetic marker for marker-assisted selection breeding, and this study was also helps understand the molecular mechanism related to the goat litter size.

The aim of this study was to analyse the association between single-nucleotide polymorphisms within INHA and ACVR2B and litter size in Dazu black goats. In total, twenty-two SNPs were genotyped in 190 individuals by SNaPshot and resequencing. The results showed that three SNPs (SNP&#95;1, SNP&#95;12 and SNP&#95;13 in this study) were detected to have significant additive genetic effect on the recorded goat litter size (p < .05). The SNP&#95;1 (NC&#95;030809.1), a non-synonymous substitution of G for T at chr2-g. 28314990 in the exon 2 of INHA gene (NM&#95;001285606.1), resulted in homozygote 2 (HOM2) contributed 0.25 and heterozygote (HET) contributed 0.12 larger litter than homozygote 1 (HOM1). Meanwhile, SNP&#95;12 (Chr22-g. 11721225 A > T) and SNP&#95;13 (Chr22-g. 11721227 A > C) (NC&#95;030829.1) simultaneously mutated at the first and third position of a triplet AAA (lysine, K) in the exon 4 of ACVR2B gene (XM&#95;018066623.1) had estimated genetic effects of HOM1 (0.00) and HOM2 (0.03) larger than HET (-0.12). In conclusion, one SNPs (chr2-g. 28314990 T > G) within the exon 2 of INHA and two SNPs (Chr22-g. 11721225 A > T and Chr22-g. 11721227 A > C) in the exon 4 of ACVR2B gene were highly recommended as candidate markers of litter size in Dazu black goats. A large-scale association study to assess the impact of these variants on litter size is still necessary., (© 2021 Wiley-VCH GmbH.)

Background: Polled intersex syndrome (PIS) leads to reproductive disorders in goats and exerts a heavy influence on goat breeding. Since 2001, the core variant of an 11.7 kb deletion at ~129 Mb on chromosome 1 (CHI1) has been widely used as a genetic diagnostic criterion. In 2020, a ~0.48 Mb insertion within the PIS deletion was identified by sequencing in XX intersex goats. However, the suitability of this variation for the diagnosis of intersex goats worldwide and its further molecular genetic mechanism need to be clarified. Results: The whole-genome selective sweep of intersex goats from China was performed with whole-genome next-generation sequencing technology for large sample populations and a case-control study on interbreeds. A series of candidate genes related to the goat intersexuality phenotype were found. We further confirmed that a ~0.48 Mb duplicated fragment (including ERG and KCNJ15 ) downstream of the ~20 Mb PIS region was reversely inserted into the PIS locus in intersex Chinese goats and was consistent with that in European Saanen and Valais black-necked goats. High-throughput chromosome conformation capture (Hi-C) technology was then used to compare the 3D structures of the PIS variant neighborhood in CHI1 between intersex and non-intersex goats. A newly found structure was validated as an intrachromosomal rearrangement. This inserted duplication changed the original spatial structure of goat CHI1 and caused the appearance of several specific loop structures in the adjacent ~20 kb downstream region of FOXL2 . Conclusions: Results suggested that the novel complex PIS variant genome was sufficient as a broad-spectrum clinical diagnostic marker of XX intersexuality in goats from Europe and China. A series of private dense loop structures caused by segment insertion into the PIS deletion might affect the expression of FOXL2 or other neighboring novel candidate genes. However, these structures require further in-depth molecular biological experimental verification. In general, this study provided new insights for future research on the molecular genetic mechanism underlying female-to-male sex reversal in goats., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 E, Zhou, Zheng, Yang, Li, Li, Zhou, Nai, Jiang, Zhang, Hong, Ma, Chu, Gao, Zhao, Duan, He, Na, Han, Zeng, Jiang and Huang.)

Major histocompatibility complex (MHC) genes are critical for disease resistance or susceptibility responsible for host-pathogen interactions determined mainly by extensive polymorphisms in the MHC genes. Here, we examined the diversity and phylogenetic pattern of MHC haplotypes reconstructed using three MHC-linked microsatellite markers in 55 populations of five Bovidae species and compared them with those based on neutral autosomal microsatellite markers (NAMs). Three-hundred-and-forty MHC haplotypes were identified in 1453 Bovidae individuals, suggesting significantly higher polymorphism and heterozygosity compared with those based on NAMs. The ambitious boundaries in population differentiation (phylogenetic network, pairwise F ST and STRUCTURE analyses) within and between species assessed using the MHC haplotypes were different from those revealed by NAMs associated closely with speciation, geographical distribution, domestication and management histories. In addition, the mean F ST was significantly correlated negatively with the number of observed alleles (N A ), observed (H O ) and expected (H E ) heterozygosity and polymorphism information content (PIC) (P < 0.05) in the MHC haplotype dataset while there was no correction of the mean F ST estimates (P> 0.05) between the MHC haplotype and NAMs datasets. Analysis of molecular variance (AMOVA) revealed a lower percentage of total variance (PTV) between species/groups based on the MHC-linked microsatellites than NAMs. Therefore, it was inferred that individuals within populations accumulated as many MHC variants as possible to increase their heterozygosity and thus the survival rate of their affiliated populations and species, which eventually reduced population differentiation and thereby complicated their classification and phylogenetic relationship inference. In summary, host-pathogen coevolution and heterozygote advantage, rather than demographic history, act as key driving forces shaping the MHC diversity within the populations and determining the interspecific MHC diversity., Competing Interests: Declaration of competing interest Authors declare no conflict of interest., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Droughtmaster is a tropical breed of beef cattle that can survive in hot climates and easily adapt to torrid environments. These traits are important in livestock breeding. In this study, we genotyped five single-nucleotide polymorphisms (SNPs) of the AHSA2 gene from 190 cattle belonging to three different breeds (Droughtmaster, Angus and Simmental) by using snapshot technology. This work aimed to identify the valuable molecular marker of heat resistance in cattle. Results showed that Droughtmaster exhibited higher expected heterozygosity and polymorphic information content compared with the two other breeds. The AHSA2 -1 locus deviated from the Hardy-Weinberg equilibrium in the Droughtmaster breed (P < 0.05). Two SNPs in Droughtmaster diverged significantly from Angus and Simmental. The SNPs were identified as AHSA2 -3 and AHSA2 -4, which were closely linked to the three breeds based on pair-wise FST. AHSA2 -4 involved a missense mutation. In summary, the GG genotypes in AHSA2 -3 and AHSA2 -4 may be candidate genotypes associated with heat resistance traits and may serve as valuable genetic markers for breeding of heat-tolerant beef cattle in the future.

Objective: In order to investigate the effect of secretagogin (SCGN) on colorectal cancer (CRC) cells apoptosis, invasion and migration in vitro., Methods: Expression of SCGN in CRC tissues and the paired adjacent non-tumorous tissues (n = 36) and four human CRC cell lines (HT29, HCT116, SW480 and SW620) were detected. SW480 cells were transfected with the SCGN overexpression plasmid (eGFP-SCGN), si-SCGN-773, and the corresponding negative controls (NCs). Then, cell-cycle distribution, cell apoptosis, migration, invasion and expression of apoptosis- and metastasis-related proteins were detected., Results: SCGN was significantly downregulated in CRC tissues as compared with the adjacent non-tumorous tissues. The expression of SCGN in HT29 and SW480 cells were lower than those in HT116 and SW620 cells. We transfected SW480 cells with SCGN overexpression plasmid eGFP-SCGN and found the increased cell apoptosis, with cell arresting at G0/G1 phase. SW480 cells with SCGN overexpression showed wider wound width and fewer invaded cells than control and blank cells, with upregulated Bax, cleaved Caspase 3 and E-cadherin, and downregulated Bcl-2 and Vimentin. We also transfected SW480 cells with si-SCGN-773 and found si-SCGN increased cell migration and invasion, but did not affect cell apoptosis and expression of related proteins., Conclusion: We concluded that the overexpression of SCGN in SW480 cells promoted cell apoptosis and inhibited cell migration and invasion., (Copyright © 2018. Published by Elsevier Masson SAS.)

The primarily metabolic abnormality in type 2 diabetes mellitus (T2DM) is the defect in gluconeogenesis and glucose uptake. Itraconazole (ITCZ) is a traditional azole drug with anti-fungal and anticancer properties. However, limited attention has been directed towards the contribution of ITCZ to hepatic gluconeogenesis and glucose uptake in T2DM. The present study aimed to investigate the potential effects of ITCZ on hepatic gluconeogenesis and glucose uptake as well as the underlying mechanisms. No obvious change in cell viability was detected by MTT assay in HepG2 cells with ITCZ treatment at gradually increasing concentrations. Western blot analysis demonstrated that the phosphorylation level of 5' adenosine monophosphate-activated protein kinase (AMPK) was significantly elevated by ITCZ treatment at ≥5 µg/ml (P<0.05). Moreover, ITCZ repressed the gluconeogenesis of HepG2 cells, as evidenced by the dose-dependently increased glycogen synthase kinase 3β phosphorylation level and a notably decreased glucose production rate (P<0.05). Simultaneously, the expression of peroxisome proliferator-activated receptor γ co-activator 1α, phosphoenolpyruvate carboxykinase (PEPCK) and glucose-6-phosphatase (G6Pase) in HepG2 cells was reduced by ITCZ in a dose-dependent manner (P<0.001). Furthermore, a 2-deoxyglucose uptake assay revealed that the glucose uptake of HepG2 cells was notably enhanced, accompanied by the ITCZ dose-dependent upregulation of glucose transporter-4 (GLUT-4) (P<0.05). Conversely, silencing of AMPK by small interfering RNA resulted in an increase of ITCZ-reduced gluconeogenesis and inhibition of ITCZ-induced glucose uptake with relative upregulation of PEPCK and G6Pase and downregulation of GLUT4 in the presence of 50 µg/ml ITCZ (P<0.05). Overall, the results indicated that AMPK has an important role in regulating ITCZ-induced glucose uptake by stimulating GLUT4 in HepG2 cells. Therefore, ITCZ may become a promising candidate for T2DM therapy.

The Chinese Yakow, Bos primigenius taurus × Bos grunniens, is a large and commercially important hybrid in family Bovidae. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,322 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: 33.7%, T: 27.3%, C: 25.8% and G: 13.2%. The complete mitogenome of Yakow (B. p. taurus × B. grunniens) could provide an important data to further explore the taxonomic status of Yakow (B. p. taurus × B. grunniens) in B. grunniens and enrich the genetic information or evolutionary history of the Bovidae.

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.

The Hechuan white goat (Capra hircus), an indigenous of China. Here, we describe the complete mitochondrial genome sequence of Hechuan white goat. The mitogenome is 16,640 nt 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 local subspecies of Hechuan white goat could provide an important data to further explore the breed improvement in Chinese goat.

The Chuanzhong black goat (Capra hircus) is a breed native to southwest of China. Its complete mitochondrial genome is 16,641 nt in length, consisting of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a non-coding 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 Chinese indigenous breed of goat could provide a basic data for further phylogenetics analysis.

The Youzhou black-skin goat (Capra hircus), an indigenous breed of Chinese southwest. Here, we describe the complete mitochondrial genome sequence of Hechuan white goat. The mitogenome is 16,640 nt 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 local subspecies of Hechuan white goat could provide an important data to further breed improvement and animal genetics resource conservation in China.

The population of domestic yak, Tianzhu white yak, from Tibetan area in China is considered as a rare Bos grunniens species. We first determined and annotated its complete mitochondrial genome. The mitogenome is 16,319 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: 33.7%, T: 27.2%, C: 25.8% and G: 13.2%. The complete mitogenome of the new subspecies of Bos grunniens could provide an important data to further explore the taxonomic status of the subspecies.

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., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Background: Capra hircus is an important economic livestock animal, and therefore, it is necessary to discover transcriptome information about their reproductive performance. In this study, we performed de novo transcriptome sequencing to produce the first transcriptome dataset for the goat ovary using high-throughput sequencing technologies. The result will contribute to research on goat reproductive performance., Method and Results: RNA-seq analysis generated more than 38.8 million clean paired end (PE) reads, which were assembled into 80,069 unigenes (mean size = 619 bp). Based on sequence similarity searches, 64,824 (60.6%) genes were identified, among which 29,444 and 11,271 unigenes were assigned to Gene Ontology (GO) categories and Clusters of Orthologous Groups (COG), respectively. Searches in the Kyoto Encyclopedia of Genes and Genomes pathway database (KEGG) showed that 27,766 (63.4%) unigenes were mapped to 258 KEGG pathways. Furthermore, we investigated the transcriptome differences of goat ovaries at two different ages using a tag-based digital gene expression system. We obtained a sequencing depth of over 5.6 million and 5.8 million tags for the two ages and identified a large number of genes associated with reproductive hormones, ovulatory cycle and follicle. Moreover, many antisense transcripts and novel transcripts were found; clusters with similar differential expression patterns, enriched GO terms and metabolic pathways were revealed for the first time with regard to the differentially expressed genes., Conclusions: The transcriptome provides invaluable new data for a functional genomic resource and future biological research in Capra hircus, and it is essential for the in-depth study of candidate genes in breeding programs.

Traditional culture-dependent method and PCR-DGGE were adopted to investigate the amount of microorganism and bacterial diversity in rhizospheric soil of transgenic Bt cotton in four provinces of Yellow River basin at four growth stages, i.e., 30, 60, 90, and 120 days after sowing. In the same province and at the same growth stage, no significant difference was observed in the amount of microorganism in rhizospheric soils of transgenic and non-transgenic Bt cottons. Within the same province the amount of microorganism was mainly affected by growth stage; while in different provinces, it was greatly affected by regional conditions. In the four provinces, the bacterial diversity in rhizospheric soil of transgenic Bt cotton was abundant; and in the same province and at the same growth stage, there were no significant differences in the Shannon index, evenness, and richness of bacteria in rhizospheric soils of transgenic and non-transgenic Bt cottons. In different provinces, the bacterial diversity in rhizospheric soils was dependent on regional conditions, but the difference was rather small.

Objective: To investigate the proliferation effects of arsenic trioxide (As2O3) on salivary adenoid cystic carcinoma-2 (ACC-2) cells in vitro and to study the role of Survivin on the apoptosis of ACC-2 induced by As2O3., Methods: ACC-2 cells were treated with different concentration of As2O3 for different time. The inhibitory effects on cell's viability were assayed with methyl thiazolyl tetrazolium (MTT) test. Apoptosis was determined by flow cytometry. The expression of Survivin mRNA and protein were investigated by reverse transcription-polymerase chain raction (RT-PCR) and Western blot analysis respectively., Results: Cell viability after As2O3 treatment was markedly suppressed and exhibited as a dose- and time-dependent pattern. The apoptotic index showed the similar trend. The results of RT-PCR revealed gene expression of Survivin was suppressed significantly. Through Western blot analysis, a negative correlation between concentration and amount of protein product of Survivin was determined., Conclusion: As2O3 might markedly suppressed ACC-2 cell's viability in vitro. The inhibition of Survivin gene expression may play a critical role on ACC-2 cell apoptosis induced by As2O3.

The present study aimed to predict the dry matter digestibility (DMD) of animals fed complex diet using the spectra difference between diets and feces by near infrared reflectance spectroscopy (NIRS). Four indoor experiments were carried out with artificial mixed complex diets in the state field observatory stations located at Hebei province. The sheep were used as tested animals. One hundred and four parts of "diet-feces" were obtained and divided into a calibration sample set (70 samples) and a validation sample set (34 samples). The spectra difference between diets and feces, and the partial least square (PLS) were used to calibrate the models of DMD of sheep. The results indicated that the optimum range of spectrum was 8 656-4 310 cm(-1). The optimum proceeding method was multivariate scattering correction + first derivative + Norris smoothing. The optimum number of factors was 7. The root mean square error of prediction (RMSEP) was 2.46%, and the RPD value of validation was above 2.5. The coefficient of correlation between the actual and predicted DMD using the NIRS was 0.8339, indicating that the NIRS could be used to evaluate dry matter digestibility of sheep fed complex diets.

A Ujumqin sheep ear marginal tissue (USEM) fibroblast line, frozen in 147 cryovials with 4 x 10(6) cell each, was successfully established from 33 Ujumqin sheep ear marginal tissues using explant culture and cryopreservation techniques. The cells were morphologically consistent with fibroblasts. The growth curve was typical S-shape and the cell population passed through a lag phase, a logarithmic phase and a plateau phase. The population doubling time (PDT) was approximately 72 h. Tests for bacteria, fungi, viruses and mycoplasma were all negative. Isoenzyme polymorphism indicated that the genetic characteristics of the cell line were stable in vitro. Karyotyping analysis indicated that the chromosome number of a normal cell was of 2n = 54 and 95.4% of the entire population was diploid. The transfection efficiencies of six fluorescent proteins (pEGFP-N3, pEGFP-C1, pDsRed-N1, pEYFP-N1, pECFP-N1 and pECFP-mito) optimal at 48 h were from 18.5% to 30.1%. The cell line met all criteria from the American Type Culture Collection (ATCC). Not only has the germline of this important sheep breed been preserved at the cell level, but also valuable material had been provided for genome, postgenome and somatic cloning research. Moreover, the establishment of this technical platform may provide both technical and theoretical support for storing the genetic resources of other animals and poultry at the cell level.

By using wavelet transform and remote sensing techniques, the influence of climate change on the unique mosaic landscape of sand land-wetland in middle-east Inner Mongolia in 1961 -2005 was studied. The results showed that in 1961-2005, the annual air temperature in study area had an increment of 0.32 degrees C x (10 a)(-1), the annual precipitation fluctuated with a cycle of 30 years and of 15 years, and the annual average wind speed decreased by 0.26 m x s(-1) x (10 a)(-1). In the southeast part of study area, which located in the places between Hunshandake sand land and Keerqin Deserts, there was a district, in which, the climatic characteristics did not change evidently. Until 2010, the study area would still have an increasing air temperature, lesser precipitation, and decreasing wind speed. Under the influence of warming and drying, the total area of Hunshandake sand land and the wetland around reduced year after year, and, with the vegetation degradation on sand land, wetland shrunk and lake dried up, moving sand land enlarged ceaselessly, while immovable and semi-moving sand lands reduced obviously.

The fluorescence characteristics of the complex of piperine with cation in micellar system were studied. At the same time, the influence of experimental condition on the fluorescence intensity was also studied. The experiments indicated that piperine had very low fluorescence signal itself. But in pH 8.77 Na2 HPO4-NaH2PO4 buffer solution, both Mn(II) and cationic surfactant cetyltrimethylammonium bromide can enhance the fluorescence intensity and stability of piperine. Based on this, a sensitive method has been developed for the quantitative determination of piperine in Mn(II)-piperine-cetyltrimethylammonium bromide ternary system. Under the optimum conditions, there is a linear relationship between the enhancement of fluorescence intensity and the concentration of Mn(II). The optimal conditions are as follows: the concentration of Mn(II) is 2.5 x 10(-4) mol x L(-1) and the concentration of cetyltrimethylammonium bromide is 5 x 10(-4) mol x L(-1). The fluorescence intensity was determined by a 1 cm quartz cell with the excitation wavelength of 352 nm and the emission wavelength of 452 nm. The linear range of concentration of piperine was 2.02-10.1 microg x mL(-1) with the relative coefficient of 0.9985 and the detection limit of 0.0602 microg x mL(-1). The relative standard deviation (RSD) was 1.10%. The proposed method has been successfully applied to the quantitative determination of piperine in the Mongolian medicine Piper longum L, and the recovery was within the range of 97.6%-102.0%. The results were very satisfactory.

PCR-RFLP was applied to analyze the polymorphism of MSTN gene UTR in 345 sheep that comprised of eleven sheep breeds, namely Texel sheep, Charolais sheep, Small-tailed Han sheep, Monggolian sheep, Ujumqin sheep, Altay Fat-rumped sheep, Hulunbeir sheep, Tashikurgan sheep, Duolang sheep, Hu sheep, and Gangba sheep. A 271 bp and a 1 003 bp long PCR products were digested with Mboand Bsato demonstrate polymorphism in the eleven sheep breeds, which were all at Hardy-Weinberg equilibrium (P>0.05). The distribution of 3 genotypes in 11 sheep breeds was significantly different (P<0.01). Digestion of the PCR products with HpyCH4 proved that 9 domestic local sheep breeds were different from Texel sheep in the SNP site that was associated with muscularity. The individual mutation base could generate the motifs for miRNA in the 3'UTR, and sequencing analysis demonstrated high frequency of mutation in the 3'UTR region.