Research

9 pages, 1094 KiB

Open AccessArticle

Genetic Determination of the Amount of White Spotting: A Case Study in Siberian Cats

by Agnieszka Górska, Wioleta Drobik-Czwarno, Agata Górska and Joanna Bryś

Genes 2022, 13(6), 1006; https://doi.org/10.3390/genes13061006 - 02 Jun 2022

Viewed by 6098

The current hypothesis, along with the opinion of the breeders, is that a cat with two copies of the white spotting allele (SS) has white on more than half of its body, while a cat with only one copy (Ss [...] Read more.

The current hypothesis, along with the opinion of the breeders, is that a cat with two copies of the white spotting allele (SS) has white on more than half of its body, while a cat with only one copy (Ss) has white on less than half of its body. The present study was based on the analysis of two large pedigree databases of Siberian cats (23,905 individuals in PawPeds and 21,650 individuals in Felis Polonia database). The distribution of the amount of white spotting in the offspring of cats with different amounts of white was investigated. Significant differences compared to expected distributions were observed. In many cases the amount of white in cats that were supposed to be homozygous was less than 50% of the body, while in many supposedly heterozygous cats a very large amount of white (over 50%) was observed. This phenomenon was also presented on the verified examples of the specific families excluding possible errors in determining the amount of white by the breeder. The collected evidence suggests that there are other factors involved in the inheritance of the amount of white in cats and the current hypothesis should be revised. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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20 pages, 2072 KiB

Open AccessArticle

Fish as Model Systems to Study Epigenetic Drivers in Human Self-Domestication and Neurodevelopmental Cognitive Disorders

by Dafni Anastasiadi, Francesc Piferrer, Maren Wellenreuther and Antonio Benítez Burraco

Genes 2022, 13(6), 987; https://doi.org/10.3390/genes13060987 - 31 May 2022

Cited by 4 | Viewed by 2378

Abstract

Modern humans exhibit phenotypic traits and molecular events shared with other domesticates that are thought to be by-products of selection for reduced aggression. This is the human self-domestication hypothesis. As one of the first types of responses to a novel environment, epigenetic changes [...] Read more.

Modern humans exhibit phenotypic traits and molecular events shared with other domesticates that are thought to be by-products of selection for reduced aggression. This is the human self-domestication hypothesis. As one of the first types of responses to a novel environment, epigenetic changes may have also facilitated early self-domestication in humans. Here, we argue that fish species, which have been recently domesticated, can provide model systems to study epigenetic drivers in human self-domestication. To test this, we used in silico approaches to compare genes with epigenetic changes in early domesticates of European sea bass with genes exhibiting methylation changes in anatomically modern humans (comparison 1), and neurodevelopmental cognitive disorders considered to exhibit abnormal self-domestication traits, i.e., schizophrenia, Williams syndrome, and autism spectrum disorders (comparison 2). Overlapping genes in comparison 1 were involved in processes like limb morphogenesis and phenotypes like abnormal jaw morphology and hypopigmentation. Overlapping genes in comparison 2 affected paralogue genes involved in processes such as neural crest differentiation and ectoderm differentiation. These findings pave the way for future studies using fish species as models to investigate epigenetic changes as drivers of human self-domestication and as triggers of cognitive disorders. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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16 pages, 11657 KiB

Open AccessArticle

Genomic Diversity Profiling and Breed-Specific Evolutionary Signatures of Selection in Arunachali Yak

by Aneet Kour, Saket Kumar Niranjan, Mohan Malayaperumal, Utsav Surati, Martina Pukhrambam, Jayakumar Sivalingam, Amod Kumar and Mihir Sarkar

Genes 2022, 13(2), 254; https://doi.org/10.3390/genes13020254 - 28 Jan 2022

Cited by 11 | Viewed by 3462

Abstract

Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA [...] Read more.

Arunachali yak, the only registered yak breed of India, is crucial for the economic sustainability of pastoralist Monpa community. This study intended to determine the genomic diversity and to identify signatures of selection in the breed. Previously available double digest restriction-site associated DNA (ddRAD) sequencing data of Arunachali yak animals was processed and 99,919 SNPs were considered for further analysis. The genomic diversity profiled based on nucleotide diversity, π (π = 0.041 in 200 bp windows), effective population size, Ne (Ne = 83) and Runs of homozygosity (ROH) (predominance of shorter length ROHs) was found to be optimum. Subsequently, 207 regions were identified to be under selective sweeps through de-correlated composite of multiple signals (DCMS) statistic which combined three individual test statistics viz. π, Tajima’s D and |iHS| in non-overlapping 100 kb windows. Mapping of these regions revealed 611 protein-coding genes including KIT, KITLG, CDH12, FGG, FGA, FGB, PDGFRA, PEAR1, STXBP3, olfactory receptor genes (OR5K3, OR5H6 and OR1E1) and taste receptor genes (TAS2R1, TAS2R3 and TAS2R4). Functional annotation highlighted that biological processes like platelet aggregation and sensory perception were the most overrepresented and the associated regions could be considered as breed-specific signatures of selection in Arunachali yak. These findings point towards evolutionary role of natural selection in environmental adaptation of Arunachali yak population and provide useful insights for pursuing genome-wide association studies in future. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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25 pages, 3876 KiB

Open AccessArticle

Y-Chromosomal Insights into Breeding History and Sire Line Genealogies of Arabian Horses

by Viktoria Remer, Elif Bozlak, Sabine Felkel, Lara Radovic, Doris Rigler, Gertrud Grilz-Seger, Monika Stefaniuk-Szmukier, Monika Bugno-Poniewierska, Samantha Brooks, Donald C. Miller, Douglas F. Antczak, Raheleh Sadeghi, Gus Cothran, Rytis Juras, Anas M. Khanshour, Stefan Rieder, Maria C. Penedo, Gudrun Waiditschka, Liliya Kalinkova, Valery V. Kalashnikov, Alexander M. Zaitsev, Saria Almarzook, Monika Reißmann, Gudrun A. Brockmann, Gottfried Brem and Barbara Wallner Show full author list Hide full author list

Genes 2022, 13(2), 229; https://doi.org/10.3390/genes13020229 - 26 Jan 2022

Cited by 13 | Viewed by 7529

Abstract

The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data [...] Read more.

The Y chromosome is a valuable genetic marker for studying the origin and influence of paternal lineages in populations. In this study, we conducted Y-chromosomal lineage-tracing in Arabian horses. First, we resolved a Y haplotype phylogeny based on the next generation sequencing data of 157 males from several breeds. Y-chromosomal haplotypes specific for Arabian horses were inferred by genotyping a collection of 145 males representing most Arabian sire lines that are active around the globe. These lines formed three discrete haplogroups, and the same haplogroups were detected in Arabian populations native to the Middle East. The Arabian haplotypes were clearly distinct from the ones detected in Akhal Tekes, Turkoman horses, and the progeny of two Thoroughbred foundation sires. However, a haplotype introduced into the English Thoroughbred by the stallion Byerley Turk (1680), was shared among Arabians, Turkomans, and Akhal Tekes, which opens a discussion about the historic connections between Oriental horse types. Furthermore, we genetically traced Arabian sire line breeding in the Western World over the past 200 years. This confirmed a strong selection for relatively few male lineages and uncovered incongruences to written pedigree records. Overall, we demonstrate how fine-scaled Y-analysis contributes to a better understanding of the historical development of horse breeds. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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15 pages, 3180 KiB

Open AccessArticle

Tracing the Origin of the RSPO2 Long-Hair Allele and Epistatic Interaction between FGF5 and RSPO2 in Sapsaree Dog

by Mingue Kang, Byeongyong Ahn, Seungyeon Youk, Yun-Mi Lee, Jong-Joo Kim, Ji-Hong Ha and Chankyu Park

Genes 2022, 13(1), 102; https://doi.org/10.3390/genes13010102 - 01 Jan 2022

Cited by 2 | Viewed by 2274

Abstract

Genetic analysis of the hair-length of Sapsaree dogs, a Korean native dog breed, showed a dominant mode of inheritance for long hair. Genome-Wide Association Study (GWAS) analysis and subsequent Mendelian segregation analysis revealed an association between OXR1, RSPO2, and PKHD1L1 on [...] Read more.

Genetic analysis of the hair-length of Sapsaree dogs, a Korean native dog breed, showed a dominant mode of inheritance for long hair. Genome-Wide Association Study (GWAS) analysis and subsequent Mendelian segregation analysis revealed an association between OXR1, RSPO2, and PKHD1L1 on chromosome 13 (CFA13). We identified the previously reported 167 bp insertion in RSPO2 3’ untranslated region as a causative mutation for hair length variations. The analysis of 118 dog breeds and wolves revealed the selection signature on CFA13 in long-haired breeds. Haplotype analysis showed the association of only a few specific haplotypes to the breeds carrying the 167 bp insertion. The genetic diversity in the neighboring region linked to the insertion was higher in Sapsarees than in other Asian and European dog breeds carrying the same variation, suggesting an older history of its insertion in the Sapsaree genome than in that of the other breeds analyzed in this study. Our results show that the RSPO2 3’ UTR insertion is responsible for not only the furnishing phenotype but also determining the hair length of the entire body depending on the genetic background, suggesting an epistatic interaction between FGF5 and RSPO2 influencing the hair-length phenotype in dogs. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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9 pages, 2371 KiB

Open AccessArticle

Selection for Reduced Fear of Humans Changes Intra-Specific Social Behavior in Red Junglefowl—Implications for Chicken Domestication

by Johanna Gjøen and Per Jensen

Genes 2022, 13(1), 43; https://doi.org/10.3390/genes13010043 - 24 Dec 2021

Cited by 4 | Viewed by 2488

Abstract

The domestic fowl has a different social behavior compared to their ancestor, the red junglefowl. To examine whether selection for tameness has affected their intra-specific social behavior, 32 red junglefowl from two selection lines, one selected for increased tameness and one selected for [...] Read more.

The domestic fowl has a different social behavior compared to their ancestor, the red junglefowl. To examine whether selection for tameness has affected their intra-specific social behavior, 32 red junglefowl from two selection lines, one selected for increased tameness and one selected for a high fear of humans for ten generations, were kept in a group of two females and two males each and were observed in a semi-natural undisturbed enclosure. Birds selected for a low fear of humans had more social conflict, and the males from this selection crowed more and were more often observed in low social proximity to others. The high-fear birds spent more time close together with the rest of the group and performed more social, non-aggressive pecking. These results are consistent with known differences between ancestral red junglefowl and domesticated laying hens. Our results show that intra-specific social behavior has been affected as a side-effect of selection for increased tameness. This may have interesting implications for the emergence of the domestication syndrome in chickens. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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14 pages, 2463 KiB

Open AccessArticle

Identification of the Key Genes Associated with the Yak Hair Follicle Cycle

by Xiaolan Zhang, Pengjia Bao, Na Ye, Xuelan Zhou, Yongfeng Zhang, Chunnian Liang, Xian Guo, Min Chu, Jie Pei and Ping Yan

Genes 2022, 13(1), 32; https://doi.org/10.3390/genes13010032 - 23 Dec 2021

Cited by 8 | Viewed by 2783

Abstract

The development of hair follicles in yak shows significant seasonal cycles. In our previous research, transcriptome data including mRNAs and lncRNAs in five stages during the yak hair follicles (HFs) cycle were detected, but their regulation network and the hub genes in different [...] Read more.

The development of hair follicles in yak shows significant seasonal cycles. In our previous research, transcriptome data including mRNAs and lncRNAs in five stages during the yak hair follicles (HFs) cycle were detected, but their regulation network and the hub genes in different periods are yet to be explored. This study aimed to screen and identify the hub genes during yak HFs cycle by constructing a mRNA-lncRNA co-expression network. A total of 5000 differently expressed mRNA (DEMs) and 729 differently expressed long noncoding RNA (DELs) were used to construct the co-expression network, based on weighted genes co-expression network analysis (WGCNA). Four temporally specific modules were considered to be significantly associated with the HFs cycle of yak. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the modules are enriched into Wnt, EMC-receptor interaction, PI3K-Akt, focal adhesion pathways, and so on. The hub genes, such as FER, ELMO1, PCOLCE, and HOXC13, were screened in different modules. Five hub genes (WNT5A, HOXC13, DLX3, FOXN1, and OVOL1) and part of key lncRNAs were identified for specific expression in skin tissue. Furthermore, immunofluorescence staining and Western blotting results showed that the expression location and abundance of DLX3 and OVOL1 are changed following the process of the HFs cycle, which further demonstrated that these two hub genes may play important roles in HFs development. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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11 pages, 1118 KiB

Open AccessArticle

LTBP3 Frameshift Variant in British Shorthair Cats with Complex Skeletal Dysplasia

by Gabriela Rudd Garces, Anna Knebel, Kirsten Hülskötter, Vidhya Jagannathan, Theresa Störk, Marion Hewicker-Trautwein, Tosso Leeb and Holger A. Volk

Genes 2021, 12(12), 1923; https://doi.org/10.3390/genes12121923 - 29 Nov 2021

Cited by 1 | Viewed by 3284

Abstract

We investigated a highly inbred family of British Shorthair cats in which two offspring were affected by deteriorating paraparesis due to complex skeletal malformations. Radiographs of both affected kittens revealed vertebral deformations with marked stenosis of the vertebral canal from T11 to L3. [...] Read more.

We investigated a highly inbred family of British Shorthair cats in which two offspring were affected by deteriorating paraparesis due to complex skeletal malformations. Radiographs of both affected kittens revealed vertebral deformations with marked stenosis of the vertebral canal from T11 to L3. Additionally, compression of the spinal cord, cerebellar herniation, coprostasis and hypogangliosis were found. The pedigree suggested monogenic autosomal recessive inheritance of the trait. We sequenced the genome of an affected kitten and compared the data to 62 control genomes. This search yielded 55 private protein-changing variants of which only one was located in a likely functional candidate gene, LTBP3, encoding latent transforming growth factor β binding protein 3. This variant, c.158delG or p.(Gly53Alafs*16), represents a 1 bp frameshift deletion predicted to truncate 95% of the open reading frame. LTBP3 is a known key regulator of transforming growth factor β (TGF-β) and is involved in bone morphogenesis and remodeling. Genotypes at the LTBP3:c.158delG variant perfectly co-segregated with the phenotype in the investigated family. The available experimental data together with current knowledge on LTBP3 variants and their functional impact in human patients and mice suggest LTBP3:c.158delG as a candidate causative variant for the observed skeletal malformations in British Shorthair cats. To the best of our knowledge, this study represents the first report of LTBP3-related complex skeletal dysplasia in domestic animals. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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17 pages, 7113 KiB

Open AccessArticle

Identification, Molecular Characterization, and Tissue Expression Profiles of Three Smad Genes from Water Buffalo (Bubalus bubalis)

by Jie Zhang, Guangle Zhang and Yongwang Miao

Genes 2021, 12(10), 1536; https://doi.org/10.3390/genes12101536 - 28 Sep 2021

Viewed by 1507

Abstract

Smads are involved in a variety of biological activities by mediating bone morphogenetic protein (BMP) signals. The full-length coding sequences (CDSs) of buffalo Smads 1, 4, and 5 were isolated and identified through RT-PCR in this study. Their lengths are 1398 [...] Read more.

Smads are involved in a variety of biological activities by mediating bone morphogenetic protein (BMP) signals. The full-length coding sequences (CDSs) of buffalo Smads 1, 4, and 5 were isolated and identified through RT-PCR in this study. Their lengths are 1398 bp, 1662 bp, and 1398 bp, respectively. In silico analysis showed that their transcriptional region structures, as well as their amino acid sequences, physicochemical characteristics, motifs, conserved domains, and three-dimensional structures of their encoded proteins are highly consistent with their counterparts in the species of Bovidae. The three Smad proteins are all hydrophilic without the signal peptides and transmembrane regions. Each of them has an MH1 domain and an MH2 domain. A nuclear localization sequence was found in the MH1 domain of buffalo Smads 1 and 5. Prediction showed that the function of the three Smads is mainly protein binding, and they can interact with BMPs and their receptors. The three genes were expressed in all 10 buffalo tissues assayed, and their expression in the mammary gland, gonad, and spleen was relatively high. The results here indicate that the three buffalo Smads may be involved in the transcriptional regulation of genes in a variety of tissues. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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13 pages, 907 KiB

Open AccessArticle

Prediction of Genetic Resistance for Scrapie in Ungenotyped Sheep Using a Linear Animal Model

by Mohammed Boareki, Flavio Schenkel, Delma Kennedy and Angela Cánovas

Genes 2021, 12(9), 1432; https://doi.org/10.3390/genes12091432 - 17 Sep 2021

Cited by 3 | Viewed by 2157

Abstract

Selection based on scrapie genotypes could improve the genetic resistance for scrapie in sheep. However, in practice, few animals are genotyped. The objectives were to define numerical values of scrapie resistance genotypes and adjust for their non-additive genetic effect; evaluate prediction accuracy of [...] Read more.

Selection based on scrapie genotypes could improve the genetic resistance for scrapie in sheep. However, in practice, few animals are genotyped. The objectives were to define numerical values of scrapie resistance genotypes and adjust for their non-additive genetic effect; evaluate prediction accuracy of ungenotyped animals using linear animal model; and predict and assess selection response based on estimated breeding values (EBV) of ungenotyped animals. The scrapie resistance (SR) was defined by ranking scrapie genotypes from low (0) to high (4) resistance based on genotype risk groups and was also adjusted for non-additive genetic effect of the haplotypes. Genotypes were simulated for 1,671,890 animals from pedigree. The simulated alleles were assigned to scrapie haplotypes in two scenarios of high (SR_h) and low (SR_l) resistance populations. A sample of 20,000 genotyped animals were used to predict ungenotyped using animal model. Prediction accuracies for ungenotyped animals for SR_h and SR_l were 0.60 and 0.54, and for allele content were from 0.41 to 0.71, respectively. Response to selection on SR_h and SR_l increased SR by 0.52 and 0.28, and on allele content from 0.13 to 0.50, respectively. In addition, the selected animals had large proportion of homozygous for the favorable haplotypes. Thus, pre-selection prior to genotyping could reduce genotyping costs for breeding programs. Using a linear animal model to predict SR makes better use of available information for the breeding programs. Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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12 pages, 2660 KiB

Open AccessArticle

A KRT71 Loss-of-Function Variant Results in Inner Root Sheath Dysplasia and Recessive Congenital Hypotrichosis of Hereford Cattle

by Joana G. P. Jacinto, Alysta D. Markey, Inês M. B. Veiga, Julia M. Paris, Monika Welle, Jonathan E. Beever and Cord Drögemüller

Genes 2021, 12(7), 1038; https://doi.org/10.3390/genes12071038 - 04 Jul 2021

Cited by 2 | Viewed by 3306

Abstract

Genodermatoses, such as heritable skin disorders, mostly represent Mendelian conditions. Congenital hypotrichosis (HY) characterize a condition of being born with less hair than normal. The purpose of this study was to characterize the clinicopathological phenotype of a breed-specific non-syndromic form of HY in [...] Read more.

Genodermatoses, such as heritable skin disorders, mostly represent Mendelian conditions. Congenital hypotrichosis (HY) characterize a condition of being born with less hair than normal. The purpose of this study was to characterize the clinicopathological phenotype of a breed-specific non-syndromic form of HY in Hereford cattle and to identify the causative genetic variant for this recessive disorder. Affected calves showed a very short, fine, wooly, kinky and curly coat over all parts of the body, with a major expression in the ears, the inner part of the limbs, and in the thoracic-abdominal region. Histopathology showed a severely altered morphology of the inner root sheath (IRS) of the hair follicle with abnormal Huxley and Henle’s layers and severely dysplastic hair shafts. A genome-wide association study revealed an association signal on chromosome 5. Homozygosity mapping in a subset of cases refined the HY locus to a 690 kb critical interval encompassing a cluster of type II keratin encoding genes. Protein-coding exons of six positional candidate genes with known hair or hair follicle function were re-sequenced. This revealed a protein-changing variant in the KRT71 gene that encodes a type II keratin specifically expressed in the IRS of the hair follicle (c.281delTGTGCCCA; p.Met94AsnfsX14). Besides obvious phenocopies, a perfect concordance between the presence of this most likely pathogenic loss-of-function variant located in the head domain of KRT71 and the HY phenotype was found. This recessive KRT71-related form of hypotrichosis provides a novel large animal model for similar human conditions. The results have been incorporated in the Online Mendelian Inheritance in Animals (OMIA) database (OMIA 002114-9913). Full article

(This article belongs to the Special Issue Animal Domestication and Breeding)

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