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Animals
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Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains
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Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains

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

Deadline for manuscript submissions: closed (31 October 2021) | Viewed by 24998

Special Issue Editor

Dr. Takeshi Igawa

E-Mail Website
Guest Editor
Amphibian Research Center, Hiroshima University, 1-3-1 Kagamiyama, Higashi-hiroshima 739-8526, Japan
Interests: evolution and genetics of non-model amphibian species; animal models

Special Issue Information

Dear Colleagues,

Breeds, varieties, and strains have been established and maintained in various animal species for their beneficial traits or useful experimental models. Isolation, hybridization, and human-mediated selection of numerous traits has led to a wide range of distinct phenotypes in a comparatively short time, and some of these are extreme and never seen in the wild. They are invaluable genetic resources and important materials to understand the molecular mechanisms of phenotypic diversity. The recent revolution in sequencing technology has enhanced the field, enabling a genomic level approach. This Special Issue will illustrate current integrative research on diversification, phenotypic traits, and biological phenomena of breeds, varieties, and strains maintained in various animal species. Contributions on any of these topics including original research papers and literature reviews, are welcome for this Special Issue.

Dr. Takeshi Igawa
Guest Editor

Manuscript Submission Information

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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

  • Phenotypic diversity
  • Individuality
  • Genetic relationships
  • Genomics
  • Human-mediated selection
  • Inbreeding
  • Hybridization
  • Experimental models

Published Papers (7 papers)

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Research

15 pages, 2053 KiB  
Article
Microsatellite-Based Genetic Characterization of the Indigenous Katjang Goat in Peninsular Malaysia
by Mohd Adhan Ernie Muneerah, Nur Aida Md Tamrin, Mohd Shahrom Salisi, Shahrizim Zulkifly, Siti Shaidatul Maisarah Ghazali, Jackson Jenun Temuli, Mohd Hifzan Rosali, Shariffah Nazari, Wan Mohd Kamil Wan Nik and Kamalludin Mamat-Hamidi
Animals 2021, 11(5), 1328; https://doi.org/10.3390/ani11051328 - 7 May 2021
Cited by 7 | Viewed by 3660
Abstract
The Katjang goat is the only indigenous domestic goat breed in Malaysia. Following a national baseline survey from 2001 to 2002, this breed was reported to the FAO as being at risk of extinction. In this study, 36 microsatellite markers were screened, and [...] Read more.
The Katjang goat is the only indigenous domestic goat breed in Malaysia. Following a national baseline survey from 2001 to 2002, this breed was reported to the FAO as being at risk of extinction. In this study, 36 microsatellite markers were screened, and 25 polymorphic markers were used to analyze the genetic structure of the Katjang goat breed in Peninsular Malaysia. A sample set of data derived from another 10 populations from three published research studies was used as an outgroup for an inter-population genetic study. The analysis showed that the mean value of the observed heterozygosity was 0.29 ± 0.14, and the expected heterozygosity was 0.72 ± 0.14, which indicated low genetic diversity. The inbreeding coefficient, FIS, was high, at 0.46. Significant (p < 0.01) deviations from the Hardy Weinberg equilibrium were noted for all loci. The bottleneck analysis using the Wilcoxon Rank test under the two-phase model of mutation was significant (p < 0.01) for heterozygosity excess, which suggested that the Katjang breed had undergone significant population reduction in the past. Through combined analysis of data from publicly available research, almost the entire population of Katjang goats represent the centroid and are grouped together on a multidimensional scaling plot, except for the Terengganu population. Network analysis revealed that the goat population from Pahang formed the centrality of the network. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains)
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9 pages, 9526 KiB  
Article
Increasing Fat Deposition Via Upregulates the Transcription of Peroxisome Proliferator-Activated Receptor Gamma in Native Crossbred Chickens
by Supanon Tunim, Yupin Phasuk, Samuel E. Aggrey and Monchai Duangjinda
Animals 2021, 11(1), 90; https://doi.org/10.3390/ani11010090 - 5 Jan 2021
Cited by 14 | Viewed by 2580
Abstract
This study aimed to study the role of PPARs on fat deposition in native crossbred chicken. We studied the growth, abdominal, subcutaneous, and intramuscular fat, and mRNA expression of PPARA and PPARG in adipose and muscle tissues of four chicken breeds (CH breed [...] Read more.
This study aimed to study the role of PPARs on fat deposition in native crossbred chicken. We studied the growth, abdominal, subcutaneous, and intramuscular fat, and mRNA expression of PPARA and PPARG in adipose and muscle tissues of four chicken breeds (CH breed (100% Thai native chicken), KM1 (50% CH background), KM2 (25% CH background), and broiler (BR)). The result shows that the BR chickens had higher abdominal fat than other breeds (p < 0.05) and the KM2 had an abdominal fat percentage higher than KM1 and CH respectively (p < 0.05). The intramuscular fat of BR was greater than KM1 and CH (p < 0.05). In adipose tissue, PPARA expression was different among the chicken breeds. However, there were breed differences in PPARG expression. Study of abdominal fat PPARG expression showed the BR breed, KM1, and KM2 breed significantly greater (p < 0.05) than CH. In 8 to 12 weeks of age, the PPARG expression of the CH breed is less than (p < 0.05) KM2. Crossbreeding improved the growth of the Thai native breed, there was also a corresponding increase in carcass fatness. However, there appears to be a relationship between PPARG expression and fat deposition traits. therefore, PPARG activity hypothesized to plays a key role in lipid accumulation by up-regulation. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains)
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12 pages, 1567 KiB  
Article
Genome-Wide Association Analysis Identified BMPR1A as a Novel Candidate Gene Affecting the Number of Thoracic Vertebrae in a Large White × Minzhu Intercross Pig Population
by Qian Liu, Jingwei Yue, Naiqi Niu, Xin Liu, Hua Yan, Fuping Zhao, Xinhua Hou, Hongmei Gao, Lijun Shi, Lixian Wang, Ligang Wang and Longchao Zhang
Animals 2020, 10(11), 2186; https://doi.org/10.3390/ani10112186 - 22 Nov 2020
Cited by 14 | Viewed by 2466
Abstract
The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies [...] Read more.
The number of vertebrae (NV), especially the number of thoracic vertebrae (NTV), varies among pig breeds. The NTV is controlled by vertebral segmentation and the number of somites during embryonic development. Although there is a high correlation between the NTV and NV, studies on a fixed NV have mainly considered the absolute numbers of thoracic vertebrae instead of vertebral segmentation. Therefore, this study aimed to discover variants associated with the NTV by considering the effect of the NV in pigs. The NTV and NV of 542 F2 individuals from a Large White × Minzhu pig crossbreed were recorded. All animals were genotyped for VRTN g.19034 A > C, LTBP2 c.4481A > C, and 37 missense or splice variants previously reported in a 951-kb interval on SSC7 and 147 single nucleotide polymorphisms (SNPs) on SSC14. To identify NTV-associated SNPs, we firstly performed a genome-wide association study (GWAS) using the Q + K (population structure + kinship matrix) model in TASSEL. With the NV as a covariate, the obtained data were used to identify the SNPs with the most significant genome-wide association with the NTV by performing a GWAS on a PorcineSNP60K Genotyping BeadChip. Finally, a conditional GWAS was performed by fixing this SNP. The GWAS showed that 31 SNPs on SSC7 have significant genome-wide associations with the NTV. No missense or splice variants were found to be associated with the NTV significantly. A linkage disequilibrium analysis suggested the existence of quantitative trait loci (QTL) in a 479-Kb region on SSC7, which contained a critical candidate gene FOS for the NTV in pigs. Subsequently, a conditional GWAS was performed by fixing M1GA0010658, the most significant of these SNPs. Two SNPs in BMPR1A were found to have significant genome-wide associations and a significant dominant effect. The leading SNP, S14_87859370, accounted for 3.86% of the phenotypic variance. Our study uncovered that regulation variants in FOS on SSC7 and in BMPR1A on SSC14 might play important roles in controlling the NTV, and thus these genetic factors may be harnessed for increasing the NTV in pigs. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains)
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23 pages, 1776 KiB  
Article
Geographic Origin and Genetic Characteristics of Japanese Indigenous Chickens Inferred from Mitochondrial D-Loop Region and Microsatellite DNA Markers
by Ayano Hata, Atsushi Takenouchi, Keiji Kinoshita, Momomi Hirokawa, Takeshi Igawa, Mitsuo Nunome, Takayuki Suzuki and Masaoki Tsudzuki
Animals 2020, 10(11), 2074; https://doi.org/10.3390/ani10112074 - 9 Nov 2020
Cited by 8 | Viewed by 3093
Abstract
Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not [...] Read more.
Japanese indigenous chickens have a long breeding history, possibly beginning 2000 years ago. Genetic characterization of Japanese indigenous chickens has been performed using mitochondrial D-loop region and microsatellite DNA markers. Their phylogenetic relationships with chickens worldwide and genetic variation within breeds have not yet been examined. In this study, the genetic characteristics of 38 Japanese indigenous chicken breeds were assessed by phylogenetic analyses of mitochondrial D-loop sequences compared with those of indigenous chicken breeds overseas. To evaluate the genetic relationships among Japanese indigenous chicken breeds, a STRUCTURE analysis was conducted using 27 microsatellite DNA markers. D-loop sequences of Japanese indigenous chickens were classified into five major haplogroups, A–E, among 15 haplogroups found in chickens worldwide. The haplogroup composition suggested that Japanese indigenous chickens originated mainly from China, with some originating from Southeast Asia. The STRUCTURE analyses revealed that Japanese indigenous chickens are genetically differentiated from chickens overseas; Japanese indigenous chicken breeds possess distinctive genetic characteristics, and Jidori breeds, which have been reared in various regions of Japan for a long time, are genetically close to each other. These results provide new insights into the history of chickens around Asia in addition to novel genetic data for the conservation of Japanese indigenous chickens. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains)
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13 pages, 2240 KiB  
Article
Novel InDels of GHR, GHRH, GHRHR and Their Association with Growth Traits in Seven Chinese Sheep Breeds
by Mingli Wu, Haidong Zhao, Xiaoqin Tang, Qi Li, Xiaohua Yi, Shirong Liu and Xiuzhu Sun
Animals 2020, 10(10), 1883; https://doi.org/10.3390/ani10101883 - 15 Oct 2020
Cited by 12 | Viewed by 2288
Abstract
The GH growth axis plays an important role in the growth and development of animals and runs through the whole life of animals. Many studies have shown that molecular mutations in key genes of the GH axis will affect the growth and development [...] Read more.
The GH growth axis plays an important role in the growth and development of animals and runs through the whole life of animals. Many studies have shown that molecular mutations in key genes of the GH axis will affect the growth and development of animals. The purpose of this study was to explore the distribution characteristics of InDels of GHR, GHRH, and GHRHR in seven Chinese sheep populations, and to further explore the relationship between InDels and sheep growth traits. GHR showed high variation in Chinese sheep, and GHR-53 showed the highest minimum allele frequency (MAF). There was only one InDel mutation site in both GHRH and GHRHR. The genotype frequencies of Hu sheep (HS), Tong sheep (TS), and Lanzhou fat-tail sheep (LFTS) were quite different from other breeds. The association between GHR, GHRH, and GHRHR InDels and body size traits in seven varieties were analyzed. The results showed that there was no significant relationship between GHRH and body size traits in the seven sheep populations. There was a positive association between GHR-21 and hip height of LFSH (p < 0.05). GHR-43 reduced body height and chest depth of Small tail han sheep (STHS) and hip width of TS. GHR-44 significantly affected the body weight of HS, the body height of STHS and the head depth of TS. GHR-53 significantly reduced cannon girth of HS, chest of STHS and forehead width of TS. GHRHR-2 significantly reduced the body weight of LFHS. To sum up, this study revealed the effects of GHR, GHRH, and GHRHR InDels on sheep phenotypic traits, which indicated their potential application prospects in the genetic improvement of mutton sheep. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains)
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11 pages, 1610 KiB  
Article
Genomic Scan for Selection Signature Reveals Fat Deposition in Chinese Indigenous Sheep with Extreme Tail Types
by Fuping Zhao, Tianyu Deng, Liangyu Shi, Wenwen Wang, Qin Zhang, Lixin Du and Lixian Wang
Animals 2020, 10(5), 773; https://doi.org/10.3390/ani10050773 - 29 Apr 2020
Cited by 29 | Viewed by 4646
Abstract
It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n [...] Read more.
It is a unique feature that fat can be deposited in sheep tails and rumps. To elucidate the genetic mechanism underlying this trait, we collected 120 individuals from three Chinese indigenous sheep breeds with extreme tail types, namely large fat-tailed sheep (n = 40), Altay sheep (n = 40), and Tibetan sheep (n = 40), and genotyped them using the Ovine Infinium HD SNP BeadChip. Then genomic scan for selection signatures was performed using the hapFLK. In total, we identified 25 genomic regions exhibiting evidence of having been under selection. Bioinformatic analysis of the genomic regions showed that selection signatures related to multiple candidate genes had a demonstrated role in phenotypic variation. Nine genes have documented association with sheep tail types, including WDR92, TBX12, WARS2, BMP2, VEGFA, PDGFD, HOXA10, ALX4, and ETAA1. Moreover, a number of genes were of particular interest, including RXFP2 associated with the presence/absence and morphology of horns; MITF involved in coat color; LIN52 and SYNDIG1L related to the number of teats; MSRB3 gene associated with ear sizes; LTBP2 considered as a positional candidate genes for number of ribs; JAZF1 regulating lipid metabolism; PGRMC2, SPAG17, TSHR, GTF2A1, and LARP1B implicated with reproductive traits. Our findings provide insights into fat tail formation and a reference for carrying out molecular breeding and conservation in sheep. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains)
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17 pages, 1351 KiB  
Article
Genome-Wide Association Study Reveals Candidate Genes for Litter Size Traits in Pelibuey Sheep
by Wilber Hernández-Montiel, Mario Alberto Martínez-Núñez, Julio Porfirio Ramón-Ugalde, Sergio Iván Román-Ponce, Rene Calderón-Chagoya and Roberto Zamora-Bustillos
Animals 2020, 10(3), 434; https://doi.org/10.3390/ani10030434 - 4 Mar 2020
Cited by 35 | Viewed by 5036
Abstract
The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of [...] Read more.
The Pelibuey sheep has adaptability to climatic variations, resistance to parasites, and good maternal ability, whereas some ewes present multiple births, which increases the litter size in farm sheep. The litter size in some wool sheep breeds is associated with the presence of mutations, mainly in the family of the transforming growth factor β (TGF-β) genes. To explore genetic mechanisms underlying the variation in litter size, we conducted a genome-wide association study in two groups of Pelibuey sheep (multiparous sheep with two lambs per birth vs. uniparous sheep with a single lamb at birth) using the OvineSNP50 BeadChip. We identified a total of 57 putative SNPs markers (p < 3.0 × 10−3, Bonferroni correction). The candidate genes that may be associated with litter size in Pelibuey sheep are CLSTN2, MTMR2, DLG1, CGA, ABCG5, TRPM6, and HTR1E. Genomic regions were also identified that contain three quantitative trait loci (QTLs) for aseasonal reproduction (ASREP), milk yield (MY), and body weight (BW). These results allowed us to identify SNPs associated with genes that could be involved in the reproductive process related to prolificacy. Full article
(This article belongs to the Special Issue Genetic and Phenotypic Diversity of Animal Breeds, Varieties and Strains)
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