Journal Browser

► Journal Browser

Special Issue Editors

E-Mail Website
Guest Editor

College of Animal Science and Technology, Southwest University, Chongqing 400715, China
Interests: livestock science; genetic improvement; genetic resources protection; animal breeding

Dr. Naiyi Xu
E-Mail Website
Guest Editor Assistant

College of Animal Science and Technology, Southwest University, Chongqing 400715, China
Interests: bioinformatics analysis; multi-omics research

Special Issue Information

Dear Colleagues,

Livestock is important for biodiversity and the development of global animal husbandry. Therefore, this Special Issue, “Livestock Genomics, Genetics and Breeding”, aims to collect high-quality research articles, review articles and communications on the recent advances in molecular genetics, genomics and breeding of livestock. The publication of the accurate livestock reference genome (goat, sheep, cattle, etc.) and the rapid development of the newest wide-range high-throughput techniques have enabled us to reveal the complicated molecular mechanisms of important phenotypic traits and estimate the quantitative traits important for the breeding of livestock. Based on this, we hope to present the state of the art in the field of livestock genetics, genomics and breeding using multi-omics approaches (for GWAS, GS, epigenomics, transcriptomics, proteomics, and metabolomics). With the help of your contribution, We look forward to witnessing more cutting-edge research for the genomics, genetics and the breeding of livestock.

Topics of interest for this Special Issue include but are not limited to the following:

Molecular mechanisms research;
Multi-omics data analysis;
Genome selection;
Genome-wide association analysis;
Gene regulation and expression;
Screening of important loci and genes.

Prof. Dr. Yongju Zhao
Guest Editor
Dr. Naiyi Xu
Guest Editor Assistant

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

goat
sheep
cattle
horse
rabbit
traits
molecular mechanism
molecular breeding
multi-omics
genomics

Published Papers (2 papers)

Download All Papers

Research

Open AccessArticle

Integrated Multi-Tissue Transcriptome Profiling Characterizes the Genetic Basis and Biomarkers Affecting Reproduction in Sheep (Ovis aries)

and

Genes 2023, 14(10), 1881; https://doi.org/10.3390/genes14101881 - 27 Sep 2023

Viewed by 200

Abstract

The heritability of litter size in sheep is low and controlled by multiple genes, but the research on its related genes is not sufficient. Here, to explore the expression pattern of multi-tissue genes in Chinese native sheep, we selected 10 tissues of the three adult ewes with the highest estimated breeding value in the early study of the prolific Xinggao sheep population. The global gene expression analysis showed that the ovary, uterus, and hypothalamus expressed the most genes. Using the Uniform Manifold Approximation and Projection (UMAP) cluster analysis, these samples were clustered into eight clusters. The functional enrichment analysis showed that the genes expressed in the spleen, uterus, and ovary were significantly enriched in the Ataxia Telangiectasia Mutated Protein (ATM) signaling pathway, and most genes in the liver, spleen, and ovary were enriched in the immune response pathway. Moreover, we focus on the expression genes of the hypothalamic–pituitary–ovarian axis (HPO) and found that 11,016 genes were co-expressed in the three tissues, and different tissues have different functions, but the oxytocin signaling pathway was widely enriched. To further explore the differences in the expression genes (DEGs) of HPO in different sheep breeds, we downloaded the transcriptome data in the public data, and the analysis of DEGs (Xinggao sheep vs. Sunite sheep in Hypothalamus, Xinggao sheep vs. Sunite sheep in Pituitary, and Xinggao sheep vs. Suffolk sheep in Ovary) revealed the neuroactive ligand–receptor interactions. In addition, the gene subsets of the transcription factors (TFs) of DEGs were identified. The results suggest that 51 TF genes and the homeobox TF may play an important role in transcriptional variation across the HPO. Altogether, our study provided the first fundamental resource to investigate the physiological functions and regulation mechanisms in sheep. This important data contributes to improving our understanding of the reproductive biology of sheep and isolating effecting molecular markers that can be used for genetic selection in sheep. Full article

(This article belongs to the Special Issue Livestock Genomics, Genetics and Breeding)

► Show Figures

Figure 1

Open AccessArticle

Identifying Candidate Genes for Litter Size and Three Morphological Traits in Youzhou Dark Goats Based on Genome-Wide SNP Markers

and

Genes 2023, 14(6), 1183; https://doi.org/10.3390/genes14061183 - 29 May 2023

Cited by 1 | Viewed by 879

Abstract

This study aimed to reveal the potential genetic basis for litter size, coat colour, black middorsal stripe and skin colour by combining genome-wide association analysis (GWAS) and selection signature analysis and ROH detection within the Youzhou dark (YZD) goat population (n = 206) using the Illumina GoatSNP54 BeadChip. In the GWAS, we identified one SNP (snp54094-scaffold824-899720) on chromosome 11 for litter size, two SNPs on chromosome 26 (snp11508-scaffold142-1990450, SORCS3) and chromosome 12 (snp55048-scaffold842-324525, LOC102187779) for coat colour and one SNP on chromosome 18 (snp56013-scaffold873-22716, TCF25) for the black middorsal stripe. In contrast, no SNPs were identified for skin colour. In selection signature analysis, 295 significant iHS genomic regions with a mean |iHS| score > 2.66, containing selection signatures encompassing 232 candidate genes were detected. In particular, 43 GO terms and one KEGG pathway were significantly enriched in the selected genes, which may contribute to the excellent environmental adaptability and characteristic trait formation during the domestication of YZD goats. In ROH detection, we identified 4446 ROH segments and 282 consensus ROH regions, among which nine common genes overlapped with those detected using the iHS method. Some known candidate genes for economic traits such as reproduction (TSHR, ANGPT4, CENPF, PIBF1, DACH1, DIS3, CHST1, COL4A1, PRKD1 and DNMT3B) and development and growth (TNPO2, IFT80, UCP2, UCP3, GHRHR, SIM1, CCM2L, CTNNA3 and CTNNA1) were revealed by iHS and ROH detection. Overall, this study is limited by the small population size, which affects the results of GWAS to a certain extent. Nevertheless, our findings could provide the first overview of the genetic mechanism underlying these important traits and provide novel insights into the future conservation and utilisation of Chinese goat germplasm resources. Full article

(This article belongs to the Special Issue Livestock Genomics, Genetics and Breeding)

► Show Figures

Figure 1

Journal Menu

Journal Browser

Special Issue "Livestock Genomics, Genetics and Breeding"

Share This Special Issue

Special Issue Editors

Special Issue Information

Keywords

Published Papers (2 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI