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Livestock: Genomics, Genetics and Breeding
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Livestock: Genomics, Genetics and Breeding

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 February 2024) | Viewed by 10285

Special Issue Editor

Prof. Dr. Xin Wang

E-Mail Website
Guest Editor
College of Animal Science & Technology, Northwest A&F University, Yangling 712100, China
Interests: lncRNA; miRNA; hair follicle; gene function; epigenetics

Special Issue Information

Dear Colleagues,

Livestock can provide meat, eggs, milk, and fiber for use in daily life. With the development of molecular biology, microarray and sequencing techniques, many major genes and the underlying regulatory mechanisms of these traits will be revealed at transcriptional, post-transcriptional and translational levels, even reaching the epigenetic level. The establishment of the relationships between genes and these traits will be useful for breeding livestock and the promotion of livestock’s performance.

In this Special Issue, we will present state-of-the-art work in livestock breeding, gathering the most recent advancements in our field in one place.

Prof. Dr. Xin Wang
Guest Editor

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Keywords

  • livestock
  • genetics
  • transcriptome
  • epigenetics
  • cattle
  • goat
  • chicken
  • pig
  • gene function

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Published Papers (6 papers)

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Research

15 pages, 2727 KiB  
Article
Genome-Wide DNA Methylation Analysis and Functional Validation of Litter Size Traits in Jining Grey Goats
by Cunming Yang, Junmin He, Jingyi Mao, Yifan Ren, Guifen Liu, Chen Wei, Guoping Zhang, Kechuan Tian and Xixia Huang
Genes 2024, 15(3), 353; https://doi.org/10.3390/genes15030353 - 12 Mar 2024
Viewed by 1708
Abstract
DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat [...] Read more.
DNA methylation (DNAm) is associated with the reproductive system. However, the genetic mechanism through which DNAm regulates gene expression and thus affects litter size in goats is unclear. Therefore, in the present work, genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues were comprehensively analyzed via WGBS, and RNA-Seq data were combined to identify candidate genes associated with litter size traits in the Jining Grey goat. Finally, BSP and RT-qPCR were used to verify the sequencing results of the key genes. Notably, the DNMT genes were downregulated at the expression level in the HP group. Both groups exhibited comparable levels of methylation. A total of 976 differentially methylated regions (DMRs) (973 DMRs for CG and 3 DMRs for CHG) and 310 differentially methylated genes (DMGs) were identified in this study. Through integration of WGBS and RNA-Seq data, we identified 59 differentially methylated and differentially expressed genes (DEGs) and ultimately screened 8 key DMGs (9 DMRS) associated with litter size traits in Jining Grey goats (SERPINB2: chr24_62258801_62259000, NDRG4: chr18_27599201_27599400, CFAP43: chr26_27046601_27046800, LRP1B. chr2_79720201_79720400, EPHA6: chr1_40088601_40088800, TTC29: chr17_59385801_59386000, PDE11A: chr2_117418601_117418800 and PGF: chr10_ 16913801_16914000 and chr10_16916401_16916600). In summary, our research comprehensively analyzed the genome-wide DNAm profiles of HP and LP Jining Grey goat ovary tissues. The data findings suggest that DNAm in goat ovaries may play an important role in determining litter size. Full article
(This article belongs to the Special Issue Livestock: Genomics, Genetics and Breeding)
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13 pages, 7920 KiB  
Article
Comprehensive Analysis of miRNA and mRNA Expression Profiles during Muscle Development of the Longissimus Dorsi Muscle in Gannan Yaks and Jeryaks
by Dashan Guo, Yali Wei, Xupeng Li, Yanbin Bai, Zhanxin Liu, Jingsheng Li, Zongchang Chen, Bingang Shi, Xiaolan Zhang, Zhidong Zhao, Jiang Hu, Xiangmin Han, Jiqing Wang, Xiu Liu, Shaobin Li and Fangfang Zhao
Genes 2023, 14(12), 2220; https://doi.org/10.3390/genes14122220 - 15 Dec 2023
Cited by 2 | Viewed by 1259
Abstract
A hybrid offspring of Gannan yak and Jersey cattle, the Jeryak exhibits apparent hybrid advantages over the Gannan yak in terms of production performance and other factors. The small non-coding RNAs known as miRNAs post-transcriptionally exert a significant regulatory influence on gene expression. [...] Read more.
A hybrid offspring of Gannan yak and Jersey cattle, the Jeryak exhibits apparent hybrid advantages over the Gannan yak in terms of production performance and other factors. The small non-coding RNAs known as miRNAs post-transcriptionally exert a significant regulatory influence on gene expression. However, the regulatory mechanism of miRNA associated with muscle development in Jeryak remains elusive. To elucidate the regulatory role of miRNAs in orchestrating skeletal muscle development in Jeryak, we selected longissimus dorsi muscle tissues from Gannan yak and Jeryak for transcriptome sequencing analysis. A total of 230 (DE) miRNAs were identified in the longissimus dorsi muscle of Gannan yak and Jeryak. The functional enrichment analysis revealed a significant enrichment of target genes from differentially expressed (DE)miRNAs in signaling pathways associated with muscle growth, such as the Ras signaling pathway and the MAPK signaling pathway. The network of interactions between miRNA and mRNA suggest that some (DE)miRNAs, including miR-2478-z, miR-339-x, novel-m0036-3p, and novel-m0037-3p, played a pivotal role in facilitating muscle development. These findings help us to deepen our understanding of the hybrid dominance of Jeryaks and provide a theoretical basis for further research on the regulatory mechanisms of miRNAs associated with Jeryak muscle growth and development. Full article
(This article belongs to the Special Issue Livestock: Genomics, Genetics and Breeding)
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11 pages, 8799 KiB  
Article
Population Structure and Genetic Diversity of Yunling Cattle Determined by Whole-Genome Resequencing
by Jian Chen, Lilian Zhang, Lutao Gao, Zaichao Wei, Dong Dang and Linnan Yang
Genes 2023, 14(12), 2141; https://doi.org/10.3390/genes14122141 - 27 Nov 2023
Cited by 2 | Viewed by 1247
Abstract
The Yunling cattle breed, a three-breed crossbreed, which comprises 50% Brahman cattle, 25% Murray Grey cattle and 25% Yunnan Yellow cattle, has several advantageous traits, including rapid growth, superior meat quality, ability to improve tolerance in hot and humid climates, tick resistance and [...] Read more.
The Yunling cattle breed, a three-breed crossbreed, which comprises 50% Brahman cattle, 25% Murray Grey cattle and 25% Yunnan Yellow cattle, has several advantageous traits, including rapid growth, superior meat quality, ability to improve tolerance in hot and humid climates, tick resistance and rough feed. It can be rightfully stated that Yunling cattle serve as vital genetic repositories of the local Yunnan cattle. Gaining insights into the genetic information of Yunling cattle plays a significant role in the formulation of sound breeding strategies for this breed, safeguarding genetic resources and mitigating the risks associated with inbreeding depression. In this study, we constructed the Yunling cattle standard reference genome and aligned the whole genomes of 129 Yunling cattle individuals to the constructed reference genome to estimate the current genetic status of Yunling cattle in Yunnan Province, China. The average alignment rate and the average percentage of properly paired are both 99.72%. The average nucleotide diversity in Yunling cattle is 0.000166, which indicates a lower level of diversity. Population structure analysis classified Yunling cattle into two subgroups. Inbreeding analysis revealed that inbreeding events did occur in the Yunling cattle, which may have contributed to the low genetic diversity observed. This study presents a comprehensive assessment of the genetic structure and diversity among the Yunling cattle and provides a theoretical foundation for the preservation and exploitation of these precious germplasm resources. Full article
(This article belongs to the Special Issue Livestock: Genomics, Genetics and Breeding)
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18 pages, 888 KiB  
Article
Investigation of lncRNA in Bos taurus Mammary Tissue during Dry and Lactation Periods
by Alexis Marceau, Junjian Wang, Victoria Iqbal, Jicai Jiang, George E. Liu and Li Ma
Genes 2023, 14(9), 1789; https://doi.org/10.3390/genes14091789 - 12 Sep 2023
Cited by 2 | Viewed by 1283
Abstract
This study aims to collect RNA-Seq data from Bos taurus samples representing dry and lactating mammary tissue, identify lncRNA transcripts, and analyze findings for their features and functional annotation. This allows for connections to be drawn between lncRNA and the lactation process. RNA-Seq [...] Read more.
This study aims to collect RNA-Seq data from Bos taurus samples representing dry and lactating mammary tissue, identify lncRNA transcripts, and analyze findings for their features and functional annotation. This allows for connections to be drawn between lncRNA and the lactation process. RNA-Seq data from 103 samples of Bos taurus mammary tissue were gathered from publicly available databases (60 dry, 43 lactating). The samples were filtered to reveal 214 dry mammary lncRNA transcripts and 517 lactating mammary lncRNA transcripts. The lncRNAs met common lncRNA characteristics such as shorter length, fewer exons, lower expression levels, and less sequence conservation when compared to the genome. Interestingly, several lncRNAs showed sequence similarity to genes associated with strong hair keratin intermediate filaments. Human breast cancer research has associated strong hair keratin filaments with mammary tissue cellular resilience. The lncRNAs were also associated with several genes/proteins that linked to pregnancy using expression correlation and gene ontology. Such findings indicate that there are crucial relationships between the lncRNAs found in mammary tissue and the development of the tissue, to meet both the animal’s needs and our own production needs; these relationships should be further investigated to ensure that we continue to breed the most resilient, efficient dairy cattle. Full article
(This article belongs to the Special Issue Livestock: Genomics, Genetics and Breeding)
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13 pages, 4130 KiB  
Article
The Synchronized Progression from Mitosis to Meiosis in Female Primordial Germ Cells between Layers and Broilers
by Yuxiao Ma, Wenhui Wu, Yun Zhang, Xuzhao Wang, Jiahui Wei, Xiaotong Guo, Man Xue and Guiyu Zhu
Genes 2023, 14(4), 781; https://doi.org/10.3390/genes14040781 - 23 Mar 2023
Cited by 1 | Viewed by 1925
Abstract
Layer and broiler hens show a dramatic difference in the volume and frequency of egg production. However, it is unclear whether the intrinsic competency of oocyte generation is also different between the two types of chicken. All oocytes were derived from the primordial [...] Read more.
Layer and broiler hens show a dramatic difference in the volume and frequency of egg production. However, it is unclear whether the intrinsic competency of oocyte generation is also different between the two types of chicken. All oocytes were derived from the primordial germ cells (PGC) in the developing embryo, and female PGC proliferation (mitosis) and the subsequent differentiation (meiosis) determine the ultimate ovarian pool of germ cells available for future ovulation. In this study, we systematically compared the cellular phenotype and gene expression patterns during PGC mitosis (embryonic day 10, E10) and meiosis (E14) between female layers and broilers to determine whether the early germ cell development is also subjected to the selective breeding of egg production traits. We found that PGCs from E10 showed much higher activity in cell propagation and were enriched in cell proliferation signaling pathways than PGCs from E14 in both types of chicken. A common set of genes, namely insulin-like growth factor 2 (IGF2) and E2F transcription factor 4 (E2F4), were identified as the major regulators of cell proliferation in E10 PGCs of both strains. In addition, we found that E14 PGCs from both strains showed an equal ability to initiate meiosis, which was associated with the upregulation of key genes for meiotic initiation. The intrinsic cellular dynamics during the transition from proliferation to differentiation of female germ cells were conserved between layers and broilers. Hence, we surmise that other non-cell autonomous mechanisms involved in germ-somatic cell interactions would contribute to the divergence of egg production performance between layers and broilers. Full article
(This article belongs to the Special Issue Livestock: Genomics, Genetics and Breeding)
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18 pages, 4052 KiB  
Article
Whole-Genome Sequencing Data Reveal New Loci Affecting Milk Production in German Black Pied Cattle (DSN)
by Paula Korkuć, Guilherme B. Neumann, Deike Hesse, Danny Arends, Monika Reißmann, Siham Rahmatalla, Katharina May, Manuel J. Wolf, Sven König and Gudrun A. Brockmann
Genes 2023, 14(3), 581; https://doi.org/10.3390/genes14030581 - 25 Feb 2023
Cited by 5 | Viewed by 1973
Abstract
German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in [...] Read more.
German Black Pied (DSN) is considered an ancestral population of the Holstein breed. The goal of the current study was to fine-map genomic loci for milk production traits and to provide sequence variants for selection. We studied genome-wide associations for milk-production traits in 2160 DSN cows. Using 11.7 million variants from whole-genome sequencing of 304 representative DSN cattle, we identified 1980 associated variants (−log10(p) ≥ 7.1) in 13 genomic loci on 9 chromosomes. The highest significance was found for the MGST1 region affecting milk fat content (−log10(p) = 11.93, MAF = 0.23, substitution effect of the minor allele (ßMA) = −0.151%). Different from Holstein, DGAT1 was fixed (0.97) for the alanine protein variant for high milk and protein yield. A key gene affecting protein content was CSN1S1 (−log10(p) = 8.47, MAF = 049, ßMA = −0.055%) and the GNG2 region (−log10(p) = 10.48, MAF = 0.34, ßMA = 0.054%). Additionally, we suggest the importance of FGF12 for protein and fat yield, HTR3C for milk yield, TLE4 for milk and protein yield, and TNKS for milk and fat yield. Selection for favored alleles can improve milk yield and composition. With respect to maintaining the dual-purpose type of DSN, unfavored linkage to genes affecting muscularity has to be investigated carefully, before the milk-associated variants can be applied for selection in the small population. Full article
(This article belongs to the Special Issue Livestock: Genomics, Genetics and Breeding)
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