Progress on deep learning in genomics.

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).

Multiomic meta-analysis suggests a correlation between steroid hormone-related genes and litter size in goats.

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.

Progress on CRISPR/Cas9 system in the genetic improvement of livestock and poultry.

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.

A 1.1 Mb duplication CNV on chromosome 17 contributes to skeletal muscle development in Boer 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.

Sit-to-Stand (STS) Movement Analysis of the Center of Gravity for Human-Robot Interaction.

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.

Identification of differentially expressed long non-coding RNAs and messenger RNAs involved with muscle development in Dazu black goats through RNA sequencing.

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.

Three SNPs within exons of INHA and ACVR2B genes are significantly associated with litter size in Dazu black goats.

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_1, SNP_12 and SNP_13 in this study) were detected to have significant additive genetic effect on the recorded goat litter size (p < .

Identification of a Goat Intersexuality-Associated Novel Variant Through Genome-Wide Resequencing and Hi-C.

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.

A nonsynonymous SNP within the gene is associated with litter size in Dazu black goats.

, and 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 , and 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.

SNP of gene in three cattle breeds using snapshot technology.

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 gene from 190 cattle belonging to three different breeds (Droughtmaster, Angus and Simmental) by using snapshot technology.

Evolutionary relationship and population structure of domestic Bovidae animals based on MHC-linked and neutral autosomal microsatellite markers.

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.

Comparative and selection sweep analysis of CNV was associated to litter size in Dazu black goats.

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.

Overexpression of secretagogin promotes cell apoptosis and inhibits migration and invasion of human SW480 human colorectal cancer cells.

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).

Itraconazole attenuates hepatic gluconeogenesis and promotes glucose uptake by regulating AMPK pathway.

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.

Meta-analysis evidence of maternal lineages in Chinese Tibetan sheep using mtDNA D-loop panel.

The Tibetan sheep is an indigenous breed living in the entire Tibetan Plateau, and its origin and phylogenic relationships are still uncertain and controversial. In this study, we analyzed partial mtDNA D-loop sequences of 156 Chinese Tibetan sheep individuals from 12 distributed geographic ecotype populations. Phylogenetic analysis indicated that three maternal lineages (haplogroups A, B and C) were found in this breed and that Ovis vignei and Ovis ammon have possibly contributed to the original Tibetan sheep.

Complete mitochondrial genome of Hechuan white goat in China (Capra hircus).

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.

A complete mitochondrial genome of Youzhou black-skin goat.

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.

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.

Transcriptome analysis of the Capra hircus ovary.

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.

Complete mitochondrial genome of Chuanzhong black goat in southwest of China (Capra hircus).

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.

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

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.

Complete mitochondrial genome of the Yakow (Bos primigenius taurus × Bos grunniens) in China.

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.