Special Issue "Genomics for Understanding the Architecture of Reproductive Traits in Livestock Animals"

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

Deadline for manuscript submissions: 31 October 2021.

Special Issue Editor

Prof. Dr. Sebastian Demyda Peyrás
E-Mail Website
Guest Editor
IGEVET (CONICET-UNLP), Departamento de Producción Animal, Facultad de Ciencias Veterinarias, Universidad Nacional de La Plata, La Plata, Argentina
Interests: genomics; reproduction; domestic animal; association studies; reproductive traits; genotyping; functional studies; genetic architecture

Special Issue Information

Dear Colleagues,


Reproductive success is a key part of any animal production system. This is an important issue since it is well known that the underlying mechanisms associated with reproductive traits in domestic animals could be species specific and, therefore, the results obtained cannot be extrapolated.


One of the main limitations of studying reproductive traits is the difficulty of obtaining, objective phenotypes of animals. Additionally, many of the characteristics studied in males cannot be studied in females, and vice versa. However, the use of breeding program data, as well as the collaboration between breeders’ associations and scientists could be an interesting path to overcome those limitations and increase the number of individuals phenotyped.


Nowadays, in the age of genomics, an important part of a breeding program in most domestic animals is to produce and analyze genomic data. However, in some species, its use in studies involving reproductive traits is still scarce.


This Special Issue aims to compel research studies that could bring novel insights into the control of the reproductive function on the most common domestic animal species.

Prof. Sebastian Demyda

Keywords

  • genomics
  • reproduction
  • domestic animals
  • association studies
  • reproductive traits
  • genotyping
  • functional studies
  • genetic architecture

Published Papers (2 papers)

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Research

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Article
Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep
Animals 2021, 11(1), 157; https://doi.org/10.3390/ani11010157 - 12 Jan 2021
Cited by 1 | Viewed by 645
Abstract
Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. Here, we focused on detecting candidate genes associated with the increasing of the litter size in this breeds under recent [...] Read more.
Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. Here, we focused on detecting candidate genes associated with the increasing of the litter size in this breeds under recent artificial selection to improve the efficiency of mutton production. We selected five high- and five low-fecundity Bamei mutton sheep for whole-genome resequencing to identify candidate genes for sheep prolificacy. We used the FST and XP-EHH statistical approach to detect the selective sweeps between these two groups. Combining the two selective sweep methods, the reproduction-related genes JUN, ITPR3, PLCB2, HERC5, and KDM4B were detected. JUN, ITPR3, and PLCB2 play vital roles in GnRH (gonadotropin-releasing hormone), oxytocin, and estrogen signaling pathway. Moreover, KDM4B, which had the highest FST value, exhibits demethylase activity. It can affect reproduction by binding the promoters of estrogen-regulated genes, such as FOXA1 (forkhead box A1) and ESR1 (estrogen receptor 1). Notably, one nonsynonymous mutation (p.S936A) specific to the high-prolificacy group was identified at the TUDOR domain of KDM4B. These observations provide a new opportunity to research the genetic variation influencing fecundity traits within a population evolving under artificial selection. The identified genomic regions that are responsible for litter size can in turn be used for further selection. Full article
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Review
Impaired Reproductive Function in Equines: From Genetics to Genomics
Animals 2021, 11(2), 393; https://doi.org/10.3390/ani11020393 - 03 Feb 2021
Cited by 1 | Viewed by 774
Abstract
Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. [...] Read more.
Fertility is one of the key factors in the economic and productive success of the equine industry. Despite this, studies on the genetic causes affecting reproductive performance are scarce, especially in mares, where the genetic architecture of the reproductive traits is extremely complex. Today, with the increasing availability of new genomic methodologies for this species, we are presented with an interesting opportunity to understand the genetic basis of equine reproductive disorders. These include, among others, novel techniques for detecting chromosomal abnormalities, whose association with infertility in horses was established over 50 years ago; new sequencing technologies permitting an accurate detection of point mutations influencing fertility, as well as the study of inbreeding and molecular homozygosity, which has been widely suggested as one of the main causes of low reproductive performance in horses. Finally, over the last few years, reproductive performance has also been associated with copy number variants and candidate genes detected by genome-wide association studies on fertility traits. However, such studies are still scarce, probably because they depend on the existence of large and accurate phenotypic datasets of reproductive and/or fertility traits, which are still difficult to obtain in equines. Full article

Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Genome-Wide Association Study for Fresh and Frozen Semen Quality in Stallions
Authors: Natalia Dementieva; Michael Atroshchenko; Yuri Shcherbakov; Elena Nikitkina; Andrey Kudinov; Marina Pozovnikova; Artem Dysin; Anna Krutikova; Artem Musidray; Olga Mitrofanova; Kirill Plemyashov
Affiliation: Russian Research Institute for Farm Animal Genetics and Breeding – Branch of the L.K. Ernst Federal Science Center for Animal Husbandry (RRIFAGB), 55А, Moskovskoye sh., Tyarlevo, St. Petersburg, Pushkin, 196625, Russian Federation
Abstract: The quality of stallion semen have a high level of individual variability. Genetic factors determining the quality of fresh and cryopreserved semen of stallions have not been studied enough. The aim of our study was to search for genome-wide associations with quality of fresh and cryopreserved stallion semen. The characteristics of fresh semen of stallions were studied: volume (VOL), concentration (SCON), progressive motility (PM), as well as total motility after freezing (FTM), progressive motility after freezing (FPM) and the ratio of progressive motility to total motility (RPM). 96 DNA samples from stallions of 24 breeds were genotyped on an Affymetrix Equine HD high-density chip. GWAS analysis revealed 56 SNPs on the 21th chromosome that were significantly associated with the quality of native and thawed sperm of stallions. 79 candidate genes were identified. VOL-related parts are located on ECA 1, 3, 5, 6, 10-12, 14, 18, 20, 21, 23, 26, 29. SCON-associated loci are located on chromosomes 1, 3, 15, 21, 22, 29, 31; PM - 1, 4, 15, 28, 29. Our studies which carried out on thawed sperm allowed to reveal statistically significant associations with the genes GRM8, PHACTR4 for the first time that functionally affecting energy metabolism in the cell, which affects the preservation of total motility after cryopreservation. Most of the identified significant SNPs were found in the regions of genes associated with the formation of male fertility. The analysis of possible mechanisms of the influence of these genes on the pathology of spermatogenesis, hormonal regulation, and cellular functions has been carried out. The identified genomic regions and candidate genes are a promising basis for studying the biological processes of the formation and functioning of the reproductive system of stallions.

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