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

Deadline for manuscript submissions: closed (15 October 2022) | Viewed by 8079

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Prof. Dr. Ottmar Distl

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Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
Interests: cattle; domestication; ecotypes; selection signatures; resilience; climate change; genomics; breeding program; genomic evaluation
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Dear Colleagues,

Domestication as well as artificial and natural selection have shaped the cattle genome and resulted in a large number of breeds and ecotypes. Many of these ecotypes are adapted to very different ecosystems and climates. Genome-sequencing data from cattle ecotypes and their integration with genome data from highly selected modern breeds allows us to uncover signatures of selection and likely unique and novel selection events associated with specific environments. These signatures of selection point to important regulators and genes that have evolved as a result of adaptive responses. Several methods have been developed to study selection signatures and to distinguish between unique and common signatures for a variety of traits under very different production systems and environments. Combining different statistics can even improve the discovery of novel genomic regions that are selection signatures. Indicators of resilience help to capture the response of cattle to environmental challenges, and the use of such indicator traits should enable the discovery of genomic regions associated with adaptation to changing climatic conditions, food shortages and emerging diseases. Breeding programs should aim to incorporate newly developed indicator traits for resilience and, on the other hand, to maintain local ecotypes of cattle with lower production, but which represent an important genetic resource for production under harsh conditions.

This Special Issue of “genes” highlights recent advances in the discovery of selection signatures in cattle across a wide range of ecosystems and indicator traits for resilience in different production systems. Research articles, short communications and reviews are invited to present the latest developments and discoveries in understanding adaptation and resilience.

Prof. Dr. Ottmar Distl
Guest Editor

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Keywords

cattle
domestication
ecotypes
selection signatures
resilience
climate change
genomics
breeding program
genomic evaluation

Published Papers (5 papers)

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Research

19 pages, 3241 KiB

Open AccessArticle

A Missense Mutation in the Collagen Triple Helix of EDA Is Associated with X-Linked Recessive Hypohidrotic Ectodermal Dysplasia in Fleckvieh Cattle

by Sina Reinartz, Christine Weiß, Maike Heppelmann, Marion Hewicker-Trautwein, Maren Hellige, Laure Willen, Karsten Feige, Pascal Schneider and Ottmar Distl

Genes 2024, 15(1), 8; https://doi.org/10.3390/genes15010008 - 20 Dec 2023

Viewed by 923

Abstract

Mutations within the ectodysplasin A (EDA) gene have been associated with congenital hypotrichosis and anodontia (HAD/XHED) in humans, mice, dogs and cattle. We identified a three-generation family of Fleckvieh cattle with male calves exhibiting clinical and histopathological signs consistent with an X-linked recessive HAD (XHED). Whole genome and Sanger sequencing of cDNA showed a perfect association of the missense mutation g.85716041G>A (ss2019497443, rs1114816375) within the EDA gene with all three cases following an X-linked recessive inheritance, but normal EDAR and EDARADD. This mutation causes an exchange of glycine (G) with arginine (R) at amino acid position 227 (p.227G>R) in the second collagen triple helix repeat domain of EDA. The EDA variant was associated with a significant reduction and underdevelopment of hair follicles along with a reduced outgrowth of hairs, a complete loss of seromucous nasolabial and mucous tracheal and bronchial glands and a malformation of and reduction in number of teeth. Thermostability of EDA G227R was reduced, consistent with a relatively mild hair and tooth phenotype. However, incisors and canines were more severely affected in one of the calves, which correlated with the presence of a homozygous missense mutation of RNF111 (g.51306765T>G), a putative candidate gene possibly associated with tooth number in EDA-deficient Fleckvieh calves. Full article

(This article belongs to the Special Issue Genomic View of Cattle Breeding and Domestication)

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18 pages, 7239 KiB

Open AccessArticle

Selection Signature and CRISPR/Cas9-Mediated Gene Knockout Analyses Reveal ZC3H10 Involved in Cold Adaptation in Chinese Native Cattle

by Luyu Wang, Yaping Gao, Jinpeng Wang, Ning Huang, Qiang Jiang, Zhihua Ju, Chunhong Yang, Xiaochao Wei, Yao Xiao, Yaran Zhang, Ling Yang and Jinming Huang

Genes 2022, 13(10), 1910; https://doi.org/10.3390/genes13101910 - 20 Oct 2022

Cited by 1 | Viewed by 1853

Abstract

Cold stress is an important factor affecting cattle health, production performance, and reproductive efficiency. Understanding of the potential mechanism underlying genetic adaptation to local environments, particularly extreme cold environment, is limited. Here, by using FLK and hapFLK methods, we found that the Zinc finger CCCH-type containing 10 (ZC3H10) gene underwent positive selection in the Menggu, Fuzhou, Anxi, and Shigatse humped cattle breeds that are distributed in the cold areas of China. Furthermore, ZC3H10 expression significantly increased in bovine fetal fibroblast (BFF) cells at 28 °C for 4 h. ZC3H10 knockout BFFs were generated using CRISPR/Cas9. Wild and ZC3H10-deleted BFFs were treated at two temperatures and were divided into four groups (WT, wild and cultured at 38 °C; KO, ZC3H10^−/− and 38 °C; WT_LT, wild, and 28 °C for 4 h; and KO_LT, ZC3H10^−/− and 28 °C for 4 h. A total of 466, 598, 519, and 650 differently expressed genes (two-fold or more than two-fold changes) were identified by determining transcriptomic difference (KO_LT vs. KO, WT_LT vs. WT, KO vs. WT, and KO_LT vs. WT_LT, respectively). Loss of ZC3H10 dysregulated pathways involved in thermogenesis and immunity, and ZC3H10 participated in immunity-related pathways induced by cold stress and regulated genes involved in glucose and lipid metabolism and lipid transport (PLTP and APOA1), thereby facilitating adaptability to cold stress. Our findings provide a foundation for further studies on the function of ZC3H10 in cold stress and development of bovine breeding strategies for combatting the influences of cold climate. Full article

(This article belongs to the Special Issue Genomic View of Cattle Breeding and Domestication)

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11 pages, 1768 KiB

Open AccessArticle

Assessment of Genetic Diversity, Runs of Homozygosity, and Signatures of Selection in Tropical Milking Criollo Cattle Using Pedigree and Genomic Data

by Ricardo Martínez-Rocha, Jorge Hidalgo, Alberto Cesarani, Rodolfo Ramírez-Valverde, Rafael Núñez-Domínguez, José Guadalupe García-Muñiz and Joel Domínguez-Viveros

Genes 2022, 13(10), 1896; https://doi.org/10.3390/genes13101896 - 19 Oct 2022

Cited by 1 | Viewed by 1587

Abstract

The objective of this study was to evaluate the genetic diversity of the Tropical Milking Criollo cattle (TMC) breed in Mexico through parameters derived from pedigree and genomic information assessment. The pedigree file consisted of 3780 animals. Seventy-nine bovines were genotyped with the medium-density single nucleotide polymorphism chip and considered a reference population for pedigree analysis. The effective population size and the probability of gene origin used to assess the evolution of genetic diversity were calculated with pedigree information. Inbreeding coefficients were evaluated based on pedigree (

F_{P e d}

), the genomic relationship matrix (

F_{G R M}

), and runs of homozygosity (

F_{R O H}

) of different length classes. The average inbreeding was 2.82 ± 2.66%, −0.7 ± 3.8%, and 10.9 ± 3.0% for

F_{P E D}

F_{G R M}

, and

F_{R O H}

, respectively. Correlation between

F_{P E D}

and

F_{R O H}

was significant only for runs of homozygosity > 4 Mb, indicating the

F_{P E D}

of a population with an average equivalent complete generation of five only recovers the most recent inbreeding. The parameters of the probability of gene origin indicated the existence of genetic bottlenecks and the loss of genetic diversity in the history of the TMC cattle population; however, pedigree and genomic information revealed the existence of current sufficient genetic diversity to design a sustainable breeding program. Full article

(This article belongs to the Special Issue Genomic View of Cattle Breeding and Domestication)

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15 pages, 12864 KiB

Open AccessArticle

Blood Transcriptome Analysis of Beef Cow with Different Parity Revealed Candidate Genes and Gene Networks Regulating the Postpartum Diseases

by Yanda Yang, Chencheng Chang, Batu Baiyin, Zaixia Liu, Lili Guo, Le Zhou, Bin Liu, Caixia Shi and Wenguang Zhang

Genes 2022, 13(9), 1671; https://doi.org/10.3390/genes13091671 - 19 Sep 2022

Cited by 1 | Viewed by 1721

Abstract

Maternal parity is an important physiological factor influencing beef cow reproductive performance. However, there are few studies on the influence of different calving periods on early growth and postpartum diseases. Here, we conducted blood transcriptomic analysis on cows of different parities for gene discovery. We used Short Time Series Expression Miner (STEM) analysis to determine gene expression levels in cows of various parities and divided multiple parities into three main periods (nulliparous, primiparous, and multiparous) for subsequent analysis. Furthermore, the top 15,000 genes with the lowest median absolute deviation (MAD) were used to build a co-expression network using weighted correlation network analysis (WGCNA), and six independent modules were identified. Combing with Exon Wide Selection Signature (EWSS) and protein-protein interaction (PPI) analysis revealed that TPCN2, KIF22, MICAL3, RUNX2, PDE4A, TESK2, GPM6A, POLR1A, and KLHL6 involved in early growth and postpartum diseases. The GO and KEGG enrichment showed that the Parathyroid hormone synthesis, secretion, and action pathway and stem cell differentiation function-related pathways were enriched. Collectively, our study revealed candidate genes and gene networks regulating the early growth and postpartum diseases and provided new insights into the potential mechanism of reproduction advantages of different parity selection. Full article

(This article belongs to the Special Issue Genomic View of Cattle Breeding and Domestication)

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11 pages, 279 KiB

Open AccessArticle

Seven Shades of Grey: A Follow-Up Study on the Molecular Basis of Coat Colour in Indicine Grey Cattle Using Genome-Wide SNP Data

by Gabriele Senczuk, Vincenzo Landi, Salvatore Mastrangelo, Christian Persichilli, Fabio Pilla and Elena Ciani

Genes 2022, 13(9), 1601; https://doi.org/10.3390/genes13091601 - 07 Sep 2022

Cited by 1 | Viewed by 1343

Abstract

Shades of grey and brown are a dominant component in mammal coat colours, representing a fundamental trait involved in a great number of processes including cryptism, sexual selection and signalling. The genetic mechanisms of the grey colouration in mammals are very complex and controlled by hundreds of genes whose effects and interactions are still largely unclear. In this study, we adopted a robust multi-cohort F_st outlier approach based on pairwise contrasts between seven grey indicine cattle breeds and both taurine and indicine non-grey cattle breeds in order to find genomic regions potentially related to the grey colouration. On the basis of three main drawn settings, built in order to control both the effect of the sample size and the genetic structure, we have identified some signals common to those obtained in a previous work employing only taurine cattle. In particular, using the top 1% F_st approach, we detected a candidate region (22.6–23.8 megabases) on chromosome 14 in which genes related to pigmentation have been already documented. In addition, when we constructed a phylogenetic tree using the significant markers identified in this study and including also the genotyping data at these loci of both the grey taurine and the extinct wild auroch, we found a topological repartition consistent with breed colour pattern rather than with the known bovine evolutionary history. Thus, on the basis of this evidence, together with the geographical distribution of the current taurine grey cattle, an ancestral indicine origin for the grey phenotype would seem to be a conceivable interpretation. In this context, a higher thermo-tolerance and less UV-induced damage of the grey phenotype might have favoured the retention of advantageous genes into the taurine genome during the post-Neolithic human-mediated cattle expansions. Full article

(This article belongs to the Special Issue Genomic View of Cattle Breeding and Domestication)

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