Breeding and Functional Genomics in Animals

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

Deadline for manuscript submissions: 10 June 2024 | Viewed by 4544

Special Issue Editor


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Guest Editor
Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
Interests: livestock genomes and transcriptomes; population genetics; whole-genome sequencing; genome-wide association studies; animal biodiversity

Special Issue Information

Dear Colleagues,

Animal breeding is entering the big data era. With the rapid development of high-throughput sequencing technology, the generation of multi-omics data in livestock has been accelerated, leading to the arrival of a new era of "animal breeding big data". This not only provides new opportunities and challenges for animal breeding, but also provides new possibilities for the genetic analysis of economically important traits in animals. Understanding the economically important traits of animals can be used for management interventions in breeding programs and agricultural innovations.

Large-scale molecular markers and precise phenotypic data provide an important basis for the GWAS application and QTL mapping. Population genetics is a subfield of genetics that deals with genetic differences within and between populations, helping to explain the genetic background of the studied population and provide some key information on the application of GWAS. In addition, omic studies will facilitate and accelerate the breeding process and provide applications for genetic improvement, such as GS and MAS.

This Special issue, "Breeding and Functional Genomics in Animals", will cover a range of research topics and review articles on the latest developments in genomics, transcriptomics, population genetics, and other multi-omics that can strengthen breeding strategies and advance the breeding process of livestock species.

Dr. Tingxian Deng
Guest Editor

Manuscript Submission Information

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Keywords

  • animal breeding
  • genetic marker
  • RNA-seq
  • genome
  • population genetics
  • economical important traits
  • omics

Published Papers (4 papers)

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Research

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18 pages, 7311 KiB  
Article
Transcriptomic Analysis of Newborn Hanwoo Calves: Effects of Maternal Overnutrition during Mid- to Late Pregnancy on Subcutaneous Adipose Tissue and Liver
by Borhan Shokrollahi, Hyun-Jeong Lee, Youl Chang Baek, Shil Jin, Gi-Suk Jang, Sung Jin Moon, Kyung-Hwan Um, Sun Sik Jang and Myung Sun Park
Genes 2024, 15(6), 704; https://doi.org/10.3390/genes15060704 - 28 May 2024
Abstract
This study investigated the transcriptomic responses of subcutaneous adipose tissue (SAT) and liver in newborn Hanwoo calves subjected to maternal overnutrition during mid- to late gestation. Eight Hanwoo cows were randomly assigned to control and treatment groups. The treatment group received a diet [...] Read more.
This study investigated the transcriptomic responses of subcutaneous adipose tissue (SAT) and liver in newborn Hanwoo calves subjected to maternal overnutrition during mid- to late gestation. Eight Hanwoo cows were randomly assigned to control and treatment groups. The treatment group received a diet of 4.5 kg of concentrate and 6.5 kg of rice straw daily, resulting in intake levels of 8.42 kg DMI, 5.69 kg TDN, and 0.93 kg CP—higher than the control group (6.07 kg DMI, 4.07 kg TDN, and 0.65 kg CP), with respective NEm values of 9.56 Mcal and 6.68 Mcal. Following birth, newly born calves were euthanized humanely as per ethical guidelines, and SAT and liver samples from newborn calves were collected for RNA extraction and analysis. RNA sequencing identified 192 genes that were differentially expressed in the SAT (17 downregulated and 175 upregulated); notably, HSPA6 emerged as the most significantly upregulated gene in the SAT and as the singular upregulated gene in the liver (adj-p value < 0.05). Additionally, differential gene expression analysis highlighted extensive changes across genes associated with adipogenesis, fibrogenesis, and stress response. The functional enrichment pathway and protein–protein interaction (PPI) unraveled the intricate networks and biological processes impacted by overnutrition, including extracellular matrix organization, cell surface receptor signaling, and the PI3K-Akt signaling pathway. These findings underscore maternal overnutrition’s substantial influence on developmental pathways, suggesting profound cellular modifications with potential lasting effects on health and productivity. Despite the robust insights that are provided, the study’s limitations (sample size) underscore the necessity for further research. Full article
(This article belongs to the Special Issue Breeding and Functional Genomics in Animals)
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15 pages, 8478 KiB  
Article
Identification of Missense Variants Affecting Carcass Traits for Hanwoo Precision Breeding
by Dong Jae Lee, Yoonsik Kim, Phuong Thanh N. Dinh, Yoonji Chung, Dooho Lee, Yeongkuk Kim, Soo Hyun Lee, Inchul Choi and Seung Hwan Lee
Genes 2023, 14(10), 1839; https://doi.org/10.3390/genes14101839 - 22 Sep 2023
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Abstract
This study aimed to identify causal variants associated with important carcass traits such as weight and meat quality in Hanwoo cattle. We analyzed missense mutations extracted from imputed sequence data (ARS-UCD1.2) and performed an exon-specific association test on the carcass traits [...] Read more.
This study aimed to identify causal variants associated with important carcass traits such as weight and meat quality in Hanwoo cattle. We analyzed missense mutations extracted from imputed sequence data (ARS-UCD1.2) and performed an exon-specific association test on the carcass traits of 16,970 commercial Hanwoo. We found 33, 2, 1, and 3 significant SNPs associated with carcass weight (CW), backfat thickness (BFT), eye muscle area (EMA), and marbling score (MS), respectively. In CW and EMA, the most significant missense SNP was identified at 19,524,263 on BTA14 and involved the PRKDC. A missense SNP in the ZFAND2B, located at 107,160,304 on BTA2 was identified as being involved in BFT. For MS, missense SNP in the ACVR2B gene, located at 11,849,704 in BTA22 was identified as the most significant marker. The contribution of the most significant missense SNPs to genetic variance was confirmed to be 8.47%, 2.08%, 1.73%, and 1.19% in CW, BFT, EMA, and MS, respectively. We generated favorable and unfavorable haplotype combinations based on the significant SNPs for CW. Significant differences in GEBV (Genomic Estimated Breeding Values) were observed between groups with each favorable and unfavorable haplotype combination. In particular, the missense SNPs in PRKDC, MRPL9, and ANKFN1 appear to significantly affect the protein’s function and structure, making them strong candidates as causal mutations. These missense SNPs have the potential to serve as valuable markers for improving carcass traits in Hanwoo commercial farms. Full article
(This article belongs to the Special Issue Breeding and Functional Genomics in Animals)
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11 pages, 3141 KiB  
Article
ranchSATdb: A Genome-Wide Simple Sequence Repeat (SSR) Markers Database of Livestock Species for Mutant Germplasm Characterization and Improving Farm Animal Health
by Naveen Duhan, Simardeep Kaur and Rakesh Kaundal
Genes 2023, 14(7), 1481; https://doi.org/10.3390/genes14071481 - 20 Jul 2023
Cited by 1 | Viewed by 1250
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource [...] Read more.
Microsatellites, also known as simple sequence repeats (SSRs), are polymorphic loci that play an important role in genome research, animal breeding, and disease control. Ranch animals are important components of agricultural landscape. The ranch animal SSR database, ranchSATdb, is a web resource which contains 15,520,263 putative SSR markers. This database provides a comprehensive tool for performing end-to-end marker selection, from SSRs prediction to generating marker primers and their cross-species feasibility, visualization of the resulting markers, and finding similarities between the genomic repeat sequences all in one place without the need to switch between other resources. The user-friendly online interface allows users to browse SSRs by genomic coordinates, repeat motif sequence, chromosome, motif type, motif frequency, and functional annotation. Users may enter their preferred flanking area around the repeat to retrieve the nucleotide sequence, they can investigate SSRs present in the genic or the genes between SSRs, they can generate custom primers, and they can also execute in silico validation of primers using electronic PCR. For customized sequences, an SSR prediction pipeline called miSATminer is also built. New species will be added to this website’s database on a regular basis throughout time. To improve animal health via genomic selection, we hope that ranchSATdb will be a useful tool for mapping quantitative trait loci (QTLs) and marker-assisted selection. The web-resource is freely accessible at https://bioinfo.usu.edu/ranchSATdb/. Full article
(This article belongs to the Special Issue Breeding and Functional Genomics in Animals)
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7 pages, 253 KiB  
Case Report
Demonstration of Parthenogenetic Reproduction in a Pet Ball Python (Python regius) through Analysis of Early-Stage Embryos
by Francesco Di Ianni, Sara Albarella, Alessandro Vetere, Marco Torcello, Michela Ablondi, Mariagiulia Pugliano, Susanna Di Mauro, Pietro Parma and Francesca Ciotola
Genes 2023, 14(9), 1744; https://doi.org/10.3390/genes14091744 - 31 Aug 2023
Viewed by 1840
Abstract
Parthenogenesis is an asexual form of reproduction, normally present in various animal and plant species, in which an embryo is generated from a single gamete. Currently, there are some species for which parthenogenesis is supposed but not confirmed, and the mechanisms that activate [...] Read more.
Parthenogenesis is an asexual form of reproduction, normally present in various animal and plant species, in which an embryo is generated from a single gamete. Currently, there are some species for which parthenogenesis is supposed but not confirmed, and the mechanisms that activate it are not well understood. A 10-year-old, wild-caught female ball python (Python regius) laid four eggs without any prior contact with a male. The eggs were not incubated and, after 3 days, were submitted to the University of Parma for analysis due to the suspicion of potential embryo presence. Examination of the egg content revealed residual blood vessels and a small red spot, indicative of an early-stage embryo. DNA was extracted from the three deceased embryos and from the mother’s blood, five microsatellites were analyzed to ascertain the origin of the embryos. The captive history data, together with the genetic microsatellite analysis approach, demonstrated the parthenogenetic origin of all three embryos. The embryos were homozygous for each of the maternal microsatellites, suggesting a terminal fusion automixis mode of development. Full article
(This article belongs to the Special Issue Breeding and Functional Genomics in Animals)
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