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Animals
Special Issues
Breeding of Livestock in the Age of Genomics
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Breeding of Livestock in the Age of Genomics

A special issue of Animals (ISSN 2076-2615). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 June 2019) | Viewed by 29268

Special Issue Editor

Prof. Joel Ira Weller

E-Mail Website
Guest Editor
Department of Ruminant Science, Institute of Animal Sciences, Agricultural Research Organization, The Volcani Center, 68 HaMaccabim Road, P.O.B 15159, Rishon LeZion 7505101, Israel
Interests: statistical analysis of quantitative trait loci; breeding and genetics of dairy cattle; economic aspects of animal breeding; statistical methods of genetic evaluation

Special Issue Information

Dear Colleagues,

With the development of SNP-chips (a type of DNA microarray which is used to detect polymorphisms) over 10 years ago, breeding of livestock has undergone a revolution. In the past, genetic evaluations of animals were based only on phenotypes for the traits of interest and relationships among animals. Today, it is possible to derive accurate genetic values for individuals based on genetic markers, even though the trait has not been expressed in the individual, and information on relatives is limited. This Special Issue will consider how genomics has changed animal breeding and attempt to predict future trends.

Prof. Joel Ira Weller
Guest Editor

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. Animals is an international peer-reviewed open access semimonthly 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 2400 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

  • Animal breeding
  • SNP-chips
  • Genomic evaluation
  • Livestock
  • Cattle
  • Poultry

Published Papers (5 papers)

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Research

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9 pages, 1091 KiB  
Article
A study of Genomic Prediction across Generations of Two Korean Pig Populations
by Beatriz Castro Dias Cuyabano, Hanna Wackel, Donghyun Shin and Cedric Gondro
Animals 2019, 9(9), 672; https://doi.org/10.3390/ani9090672 - 11 Sep 2019
Cited by 6 | Viewed by 2506
Abstract
Genomic models that incorporate dense marker information have been widely used for predicting genomic breeding values since they were first introduced, and it is known that the relationship between individuals in the reference population and selection candidates affects the prediction accuracy. When genomic [...] Read more.
Genomic models that incorporate dense marker information have been widely used for predicting genomic breeding values since they were first introduced, and it is known that the relationship between individuals in the reference population and selection candidates affects the prediction accuracy. When genomic evaluation is performed over generations of the same population, prediction accuracy is expected to decay if the reference population is not updated. Therefore, the reference population must be updated in each generation, but little is known about the optimal way to do it. This study presents an empirical assessment of the prediction accuracy of genomic breeding values of production traits, across five generations in two Korean pig breeds. We verified the decay in prediction accuracy over time when the reference population was not updated. Additionally we compared the prediction accuracy using only the previous generation as the reference population, as opposed to using all previous generations as the reference population. Overall, the results suggested that, although there is a clear need to continuously update the reference population, it may not be necessary to keep all ancestral genotypes. Finally, comprehending how the accuracy of genomic prediction evolves over generations within a population adds relevant information to improve the performance of genomic selection. Full article
(This article belongs to the Special Issue Breeding of Livestock in the Age of Genomics)
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17 pages, 1650 KiB  
Article
A Transcriptomic Study of the Tail Fat Deposition in Two Types of Hulun Buir Sheep According to Tail Size and Sex
by Hongying Fan, Yali Hou, Goutam Sahana, Hongding Gao, Caiye Zhu, Lixin Du, Fuping Zhao and Lixian Wang
Animals 2019, 9(9), 655; https://doi.org/10.3390/ani9090655 - 5 Sep 2019
Cited by 13 | Viewed by 3338
Abstract
Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism of fat deposition in sheep tails, we firstly evaluated the morphology and transcription level differences of tail fat [...] Read more.
Hulun Buir sheep of similar genetic background were divided into two lines based on tail types: Small- and big fat-tailed. To explore the molecular mechanism of fat deposition in sheep tails, we firstly evaluated the morphology and transcription level differences of tail fat between these two lines. RNA-Seq technology was used to identify differentially expressed genes (DEGs) in phenotypic extremes of tail sizes. Five comparisons were performed taking into account two factors, sex and tail type. We screened out 373 DEGs between big-tailed and small-tailed Hulun Buir sheep, and 775 and 578 DEGs between two types of tails in male and female sheep, respectively. The results showed an obvious sex difference in the fat metabolism in sheep based on gene ontology (GO), pathway, and network analyses. Intriguingly, there were two different co-expression networks only respectively shown in male and female sheep, which were insulin-related network acting on upstream pathways and PPARG-related network effect in downstream pathways. Furthermore, these two networks were linked by a classic pathway of regulating adipogenesis. This is the first study to investigate the sex differences of fat metabolism in domestic animals, and it demonstrates a new experimental way to study fat metabolism. Our findings will provide theoretical background in understanding the tail-size phenotype in sheep and can be exploited in breeding small-tailed sheep. Full article
(This article belongs to the Special Issue Breeding of Livestock in the Age of Genomics)
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13 pages, 1195 KiB  
Article
Genome-Wide Profiling of the Microrna Transcriptome Regulatory Network to Identify Putative Candidate Genes Associated with Backfat Deposition in Pigs
by Xin Liu, Jianfei Gong, Ligang Wang, Xinhua Hou, Hongmei Gao, Hua Yan, Fuping Zhao, Longchao Zhang and Lixian Wang
Animals 2019, 9(6), 313; https://doi.org/10.3390/ani9060313 - 1 Jun 2019
Cited by 14 | Viewed by 3674
Abstract
Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were [...] Read more.
Backfat deposition is strongly related to carcass traits, growth rate, feed conversion rate, and reproductive performance in pig production. To understand the molecular mechanisms underlying porcine backfat thickness phenotypes, transcriptome and miRNA profiling of backfat from high-backfat thickness and low-backfat thickness pigs were performed by RNA sequencing. Twenty genes encoding for miRNAs and 126 genes encoding for protein-coding genes were found to be differentially expressed between the two libraries. After integrative analysis of DEMs targets and DEGs, a total of 33 mRNA‒miRNA interaction pairs were identified, and the regulatory networks of these pairs were determined. Among these genes, five (AQP9, DKK3, GLYCTK, GLIPR1, and DUSP2) related to fat deposition were found to be strong candidate genes, and mir-31-5p/AQP9 and mir-31-5p/GLIPR1 may play important roles in fat deposition. Additionally, potential adipogenesis-related genes and miRNAs were identified. These findings improve the current understanding of the molecular genetic mechanisms of subcutaneous fat deposition in pigs and provide a foundation for further studies. Full article
(This article belongs to the Special Issue Breeding of Livestock in the Age of Genomics)
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16 pages, 2863 KiB  
Article
Comparative Transcriptomics Reveal Key Sheep (Ovis aries) Hypothalamus LncRNAs that Affect Reproduction
by Zhuangbiao Zhang, Jishun Tang, Ran Di, Qiuyue Liu, Xiangyu Wang, Shangquan Gan, Xiaosheng Zhang, Jinlong Zhang, Wenping Hu and Mingxing Chu
Animals 2019, 9(4), 152; https://doi.org/10.3390/ani9040152 - 8 Apr 2019
Cited by 24 | Viewed by 4420
Abstract
The diverse functions of long noncoding RNAs (lncRNAs), which execute their functions mainly through modulating the activities of their target genes, have been have been widely studied for many years (including a number of studies involving lncRNAs in the ovary and uterus). Herein, [...] Read more.
The diverse functions of long noncoding RNAs (lncRNAs), which execute their functions mainly through modulating the activities of their target genes, have been have been widely studied for many years (including a number of studies involving lncRNAs in the ovary and uterus). Herein, for the first time, we detect lncRNAs in sheep hypothalami with FecB++ through RNA Sequencing (RNA-Seq) and identify a number of known and novel lncRNAs, with 622 and 809 found to be differentially expressed in polytocous sheep in the follicular phase (PF) vs. monotocous sheep in the follicular phase (MF) and polytocous sheep in the luteal phase (PL) vs. monotocous sheep in the luteal phase (ML), respectively. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed based on the predicted target genes. The most highly enriched GO terms (at the molecular function level) included carbonyl reductase (NADPH), 15-hydroxyprostaglandin dehydrogenase (NADP+), and prostaglandin-E2 9-reductase activity in PF vs. MF, and phosphatidylinositol-3,5-bisphosphate binding in PL vs. ML was associated with sheep fecundity. Interestingly, the phenomena of valine, leucine, and isoleucine degradation in PL vs. ML, and valine, leucine, and isoleucine biosynthesis in PF vs. MF, were present. In addition, the interactome of lncRNA and its targets showed that MSTRG.26777 and its cis-targets ENSOARG00000013744, ENSOARG00000013700, and ENSOARG00000013777, and MSTRG.105228 and its target WNT7A may participate in the sheep reproductive process at the hypothalamus level. Significantly, MSTRG.95128 and its cis-target Forkhead box L1 (FOXG1) were shown to be upregulated in PF vs. MF but downregulated in PL vs. ML. All of these results may be attributed to discoveries of new candidate genes and pathways related to sheep reproduction, and they may provide new views for understanding sheep reproduction without the effects of the FecB mutation. Full article
(This article belongs to the Special Issue Breeding of Livestock in the Age of Genomics)
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Review

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9 pages, 205 KiB  
Review
Adaptation Mechanisms of Small Ruminants to Environmental Heat Stress
by Haile Berihulay, Adam Abied, Xiaohong He, Lin Jiang and Yuehui Ma
Animals 2019, 9(3), 75; https://doi.org/10.3390/ani9030075 - 28 Feb 2019
Cited by 120 | Viewed by 14730
Abstract
Small ruminants are the critical source of livelihood for rural people to the development of sustainable and environmentally sound production systems. They provided a source of meat, milk, skin, and fiber. The several contributions of small ruminants to the economy of millions of [...] Read more.
Small ruminants are the critical source of livelihood for rural people to the development of sustainable and environmentally sound production systems. They provided a source of meat, milk, skin, and fiber. The several contributions of small ruminants to the economy of millions of rural people are however being challenged by extreme heat stress difficulties. Heat stress is one of the most detrimental factors contributing to reduced growth, production, reproduction performance, milk quantity and quality, as well as natural immunity, making animals more vulnerable to diseases and even death. However, small ruminants have successfully adapted to this extreme environment and possess some unique adaptive traits due to behavioral, morphological, physiological, and largely genetic bases. This review paper, therefore, aims to provide an integrative explanation of small ruminant adaptation to heat stress and address some responsible candidate genes in adapting to thermal-stressed environments. Full article
(This article belongs to the Special Issue Breeding of Livestock in the Age of Genomics)
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