Special Issue "Understanding and Utilizing Populations and Phenotypes in Animal Genomics Research"

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

Deadline for manuscript submissions: 31 January 2022.

Special Issue Editor

Dr. Heather Huson
E-Mail Website
Guest Editor
Department of Animal Science, Cornell University, Ithaca, NY, USA
Interests: animal genetics; genomics; working dogs; livestock; population studies; association studies; performance; aging

Special Issue Information

Dear Colleagues,

Successful genomics studies rely heavily on understanding the population and phenotypes being analysed. Most importantly, interpretation of data and recommendations generated from studies depends upon our understanding of the intricacies, limitations, and strengths of our data. In the face of today’s rapidly changing world of technologies, initiatives, funding, and scientific understanding, researchers are tasked with developing new strategies to understand biology and foster change.

To this end, the strategic use of animal populations and the development of phenotypic assessment is a priority. Analysis methods looking for signatures of selection on the genome rely on calculated use of populations, breeds, and species to infer what selection enacted upon a population to cause genetic change. Similarly, exploring admixed populations for conservation, selection, and management requires in-depth understanding of population structure. In addition, researchers are pursuing new, complex traits and revisiting well-studied traits with new approaches. Digital agriculture, remote sensing, and internal biological sensors are exciting new opportunities to generate novel phenotypes for use in genomics research. These technologies offer an abundance of datapoints collected through minimally invasive measures at a lower cost ratio. They are particularly valuable for capturing data among large livestock populations or sensitive wild populations. Research is also pursuing rigorous, intense, biological phenotyping to refine our understanding of biological regulation of disease and performance. Efforts are aimed at not only identifying causative mutations but also factors such as epigenetic regulation and systems biology.

This special issue of Animals - Understanding and Utilizing Populations and Phenotypes in Animal Genomics Research is aimed at highlighting studies with novel phenotypes or novel approaches for rigorously assessing a phenotype to better understand genetic regulation. This includes but is not limited to novel phenotypic assessment of behaviour and well-being in animals, the use of digital technologies, and intensive longitudinal sample collection over time. It is also aimed at emphasizing strategic use of populations to extrapolate the influences of genetic selection and evolution on the genome. Specific consideration will be given to studies with lower sample sizes of rare species or particularly difficult and intensive phenotyping parameters. We also acknowledge that negative results are important outcomes in scientific literature.  Considering the aim of this special issue, Understanding and Utilizing Populations and Phenotypes in Animal Genomics Research, articles should emphasize the uniqueness of their population and/or phenotypes and both strengths and weaknesses of the data and interpretation of results. Accepted submissions will further our knowledge and use of populations and phenotypes in animal genomics research which will ultimately improve our biological understanding and management of traits in animal species. 

Dr. Heather Huson
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 papers will be 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 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 1800 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 genetics
  • phenotype
  • genome-wide association study
  • signatures of selection
  • cross species comparison
  • longitudinal studies
  • digital agriculture
  • remote sensing
  • behavior

Published Papers (2 papers)

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Research

Article
Direct Phenotyping and Principal Component Analysis of Type Traits Implicate Novel QTL in Bovine Mastitis through Genome-Wide Association
Animals 2021, 11(4), 1147; https://doi.org/10.3390/ani11041147 - 17 Apr 2021
Viewed by 524
Abstract
Our objectives were to robustly characterize a cohort of Holstein cows for udder and teat type traits and perform high-density genome-wide association studies for those traits within the same group of animals, thereby improving the accuracy of the phenotypic measurements and genomic association [...] Read more.
Our objectives were to robustly characterize a cohort of Holstein cows for udder and teat type traits and perform high-density genome-wide association studies for those traits within the same group of animals, thereby improving the accuracy of the phenotypic measurements and genomic association study. Additionally, we sought to identify a novel udder and teat trait composite risk index to determine loci with potential pleiotropic effects related to mastitis. This approach was aimed at improving the biological understanding of the genetic factors influencing mastitis. Cows (N = 471) were genotyped on the Illumina BovineHD777k beadchip and scored for front and rear teat length, width, end shape, and placement; fore udder attachment; udder cleft; udder depth; rear udder height; and rear udder width. We used principal component analysis to create a single composite measure describing type traits previously linked to high odds of developing mastitis within our cohort of cows. Genome-wide associations were performed, and 28 genomic regions were significantly associated (Bonferroni-corrected p < 0.05). Interrogation of these genomic regions revealed a number of biologically plausible genes whicht may contribute to the development of mastitis and whose functions range from regulating cell proliferation to immune system signaling, including ZNF683, DHX9, CUX1, TNNT1, and SPRY1. Genetic investigation of the risk composite trait implicated a novel locus and candidate genes that have potentially pleiotropic effects related to mastitis. Full article
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Article
Genome-Wide Analysis of Nubian Ibex Reveals Candidate Positively Selected Genes That Contribute to Its Adaptation to the Desert Environment
Animals 2020, 10(11), 2181; https://doi.org/10.3390/ani10112181 - 22 Nov 2020
Cited by 2 | Viewed by 923
Abstract
The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting [...] Read more.
The domestic goat (Capra hircus) is an important livestock species with a geographic range spanning all continents, including arid and semi-arid regions of Africa and Asia. The Nubian ibex (Capra nubiana), a wild relative of the domestic goat inhabiting the hot deserts of Northern Africa and the Arabian Peninsula, is well-adapted to challenging environments in hot deserts characterized by intense solar radiation, thermal extremes, and scarce water resources. The economic importance of C. hircus breeds, as well as the current trends of global warming, highlights the need to understand the genetic basis of adaptation of C. nubiana to the desert environments. In this study, the genome of a C. nubiana individual was sequenced at an average of 37x coverage. Positively selected genes were identified by comparing protein-coding DNA sequences of C. nubiana and related species using dN/dS statistics. A total of twenty-two positively selected genes involved in diverse biological functions such as immune response, protein ubiquitination, olfactory transduction, and visual development were identified. In total, three of the twenty-two positively selected genes are involved in skin barrier development and function (ATP binding cassette subfamily A member 12, Achaete-scute family bHLH transcription factor 4, and UV stimulated scaffold protein A), suggesting that C. nubiana has evolved skin protection strategies against the damaging solar radiations that prevail in deserts. The positive selection signatures identified here provide new insights into the potential adaptive mechanisms to hot deserts in C. nubiana. Full article
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