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Zhao J, Liu Z, Wang X, Xin X, Du L, Zhao H, An Q, Ding X, Zhang Z, Wang E, Xu Z, Huang Y. The Identification of Goat KCNJ15 Gene Copy Number Variation and Its Association with Growth Traits. Genes (Basel) 2024; 15:250. [PMID: 38397239 PMCID: PMC10888278 DOI: 10.3390/genes15020250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/06/2024] [Accepted: 02/13/2024] [Indexed: 02/25/2024] Open
Abstract
(1) Background: Copy number variation (CNV) is a critical component of genome structural variation and has garnered significant attention. High-throughput screening of the KCNJ15 gene has revealed a correlation between the CNV region and the growth traits of goats. We aimed to identify the CNV of the KCNJ15 gene in five goat breeds and analyze its association with growth characteristics. (2) Methods: We utilized 706 goats from five breeds: Guizhou black goat (GZB), Guizhou white goat (GZW), Bohuai goat (BH), Huai goat (HH), and Taihang goat (TH). To evaluate the number of copies of the KCNJ15 gene using qPCR, we analyzed the correlation between the CNV and growth characteristics and then used a universal linear model. The findings revealed variations in the distribution of different copy number types among the different goat breeds. (3) Results: Association analysis revealed a positive influence of the CNV in the KCNJ15 gene on goat growth. In GZB, individuals with duplication types exhibited superior performance in terms of cannon bone circumference (p < 0.05). In HH, individuals with duplication types exhibited superior performance in terms of body slanting length (p < 0.05). Conversely, normal TH demonstrated better body height and body weight (p < 0.05), while in GZW, when CN = 3, it performed better than other types in terms of body weight and chest circumference (p < 0.05). However, in BH, it had no significant effect on growth traits. (4) Conclusions: We confirmed that the CNV in the KCNJ15 gene significantly influences the growth characteristics of four distinct goat breeds. The correlation between KCNJ15 gene CNVs and goat growth traits offers valuable insights to breeders, enabling them to employ precise and efficient breeding methods that enhance livestock welfare, productivity, and overall economic benefits in the industry.
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Affiliation(s)
- Jiahao Zhao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Z.); (Z.L.); (L.D.); (H.Z.); (X.D.)
| | - Zhe Liu
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Z.); (Z.L.); (L.D.); (H.Z.); (X.D.)
| | - Xianwei Wang
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China;
| | - Xiaoling Xin
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (X.X.); (Z.Z.); (E.W.)
| | - Lei Du
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Z.); (Z.L.); (L.D.); (H.Z.); (X.D.)
| | - Huangqing Zhao
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Z.); (Z.L.); (L.D.); (H.Z.); (X.D.)
| | - Qingming An
- College of Agriculture and Forestry Engineering, Tongren University, Tongren 554300, China;
| | - Xiaoting Ding
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Z.); (Z.L.); (L.D.); (H.Z.); (X.D.)
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (X.X.); (Z.Z.); (E.W.)
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (X.X.); (Z.Z.); (E.W.)
| | - Zejun Xu
- Henan Provincial Animal Husbandry General Station, Zhengzhou 450008, China;
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (J.Z.); (Z.L.); (L.D.); (H.Z.); (X.D.)
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Heidari F, Rahbaran M, Mirzaei A, Mozafari Tabatabaei M, Shokrpoor S, Mahjoubi F, Ara MS, Akbarinejad V, Gharagozloo F. The study of a hermaphroditic sheep caused by a mutation in the promoter of SRY gene. Vet Anim Sci 2023; 21:100308. [PMID: 37593675 PMCID: PMC10428133 DOI: 10.1016/j.vas.2023.100308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023] Open
Abstract
In mammals, sex-determining region Y (SRY) gene plays vital role as a transcription factor to regulate the expression of the genes contributing to development of male genitals. Any mutation disrupting expression of SRY gene can cause disorders of sex development (DSDs). In this study, the examination of a hermaphroditic (female-like) Shal sheep which was referred for infertility is described. Initially, the reproductive system of the sheep was histologically and anatomically assessed. Karyotyping was used to determine the real gender of the animal. Sex hormones including progesterone, estradiol, and testosterone were measured by enzyme-linked immunosorbent assay (ELISA). Eventually, promoter part and SRY gene were sequenced and aligned to detect any potential mutation using NCBI data base. Although anatomical inspection led to identification of uterus, ovary, and enlarged clitoris as well as testes in the sheep, the karyotyping results interestingly revealed that the animal was genetically a male. Although the sheep had both male and female gonads, there were no overt signs of reproductive behavior and gamete production was not observed. Plasma steroid hormone levels were reported to be at basal levels. Additionally, a mutation was detected on the promoter of the SRY gene. In conclusion, the case implies that mutation on the promoter part of SRY gene could disrupt sexual development of the fetus culminating in DSDs in the sheep.
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Affiliation(s)
- Farid Heidari
- Department of Animal Biotechnology, Faculty of Agriculture Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Tehran, Iran
| | - Mohaddeseh Rahbaran
- Department of Animal Biotechnology, Faculty of Agriculture Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Tehran, Iran
| | - Asieh Mirzaei
- Department of Animal Biotechnology, Faculty of Agriculture Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Tehran, Iran
| | - Mehran Mozafari Tabatabaei
- Department of Animal Biotechnology, Faculty of Agriculture Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Tehran, Iran
- Department of Animal Sciences, Shahid Bahonar University of Kerman, Kerman, Kerman, Iran
| | - Sara Shokrpoor
- Department of Pathology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Tehran, Iran
| | - Frouzandeh Mahjoubi
- Department of Medical Genetic, Institute of Medical Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Tehran, Iran
| | - Mehdi Shams Ara
- Department of Animal Biotechnology, Faculty of Agriculture Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Tehran, Iran
| | - Vahid Akbarinejad
- Department of Theriogenology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Tehran, Iran
| | - Faramarz Gharagozloo
- Department of Theriogenology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Tehran, Iran
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Two Sisters with Kallmann Syndrome, Gonadal Dysgenesis, and Multiple Neuromuscular and Endocrine Disorders: Report of Two Cases with Description of an Unusual Association. Reprod Sci 2022; 29:2859-2863. [PMID: 35199317 PMCID: PMC9537203 DOI: 10.1007/s43032-022-00897-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 02/16/2022] [Indexed: 11/04/2022]
Abstract
Kallmann syndrome (KS) is an uncommon genetic disorder characterized by isolated congenital hypogonadotropic hypogonadism (CHH) and anosmia/hyposmia. KS originates from abnormal embryonic migration of olfactory axons and gonadotropin-releasing hormone (GnRH)-synthesizing neurons. It can be challenging to diagnose due to its heterogeneous clinical presentation and genes implied. Herein, we report a rare phenotype of KS in two sisters accompanied by a variety of nonreproductive disorders such as hypoparathyroidism, hypercortisolism, atrophy of the cerebellum, intellectual disability, and remarkably, ovarian dysgenesis. Additionally, both subjects present muscle weakness, exercise intolerance, marked hypotonia and seizures, being suspected, although not fully confirmed, mitochondrial encephalomyopathy. These cases illustrate the heterogeneous clinical presentation and the diagnostic difficulties often found in patients suffering from this condition. These clinical features have never been described before as associated with KS; therefore, we decided to report this novel KS phenotype.
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Guo J, Jiang R, Mao A, Liu GE, Zhan S, Li L, Zhong T, Wang L, Cao J, Chen Y, Zhang G, Zhang H. Genome-wide association study reveals 14 new SNPs and confirms two structural variants highly associated with the horned/polled phenotype in goats. BMC Genomics 2021; 22:769. [PMID: 34706644 PMCID: PMC8555091 DOI: 10.1186/s12864-021-08089-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 10/14/2021] [Indexed: 12/01/2022] Open
Abstract
Background There is a long-term interest in investigating the genetic basis of the horned/polled phenotype in domestic goats. Here, we report a genome-wide association study (GWAS) to detect the genetic loci affecting the polled phenotype in goats. Results We obtained a total of 13,980,209 biallelic SNPs, using the genotyping-by-sequencing data from 45 Jintang Black (JT) goats, which included 32 female and nine male goats, and four individuals with the polled intersex syndrome (PIS). Using a mixed-model based GWAS, we identified two association signals, which were located at 150,334,857–150,817,260 bp (P = 5.15 × 10− 119) and 128,286,704–131,306,537 bp (P = 2.74 × 10− 15) on chromosome 1. The genotype distributions of the 14 most significantly associated SNPs were completely correlated with horn status in goats, based on the whole-genome sequencing (WGS) data from JT and two other Chinese horned breeds. However, variant annotation suggested that none of the detected SNPs within the associated regions were plausible causal mutations. Via additional read-depth analyses and visual inspections of WGS data, we found a 10.1-kb deletion (CHI1:g. 129424781_129434939del) and a 480-kb duplication (CHI1:150,334,286–150,818,098 bp) encompassing two genes KCNJ15 and ERG in the associated regions of polled and PIS-affected goats. Notably, the 10.1-kb deletion also served as the insertion site for the 480-kb duplication, as validated by PCR and Sanger sequencing. Our WGS genotyping showed that all horned goats were homozygous for the reference alleles without either the structural variants (SVs), whereas the PIS-affected goats were homozygous for both the SVs. We also demonstrated that horned, polled, and PIS-affected individuals among 333 goats from JT and three other Chinese horned breeds can be accurately classified via PCR amplification and agarose gel electrophoresis of two fragments in both SVs. Conclusion Our results revealed that two genomic regions on chromosome 1 are major loci affecting the polled phenotypes in goats. We provided a diagnostic PCR to accurately classify horned, polled, and PIS-affected goats, which will enable a reliable genetic test for the early-in-life prediction of horn status in goats. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08089-w.
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Affiliation(s)
- Jiazhong Guo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Rui Jiang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ayi Mao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Siyuan Zhan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Li Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Zhong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Linjie Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jiaxue Cao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Chen
- Nanjiang Yellow Goat Scientific Research Institute, Bazhong, 635600, China
| | - Guojun Zhang
- Nanjiang Yellow Goat Scientific Research Institute, Bazhong, 635600, China
| | - Hongping Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, China.
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Wold J, Koepfli KP, Galla SJ, Eccles D, Hogg CJ, Le Lec MF, Guhlin J, Santure AW, Steeves TE. Expanding the conservation genomics toolbox: Incorporating structural variants to enhance genomic studies for species of conservation concern. Mol Ecol 2021; 30:5949-5965. [PMID: 34424587 PMCID: PMC9290615 DOI: 10.1111/mec.16141] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 07/28/2021] [Accepted: 08/18/2021] [Indexed: 12/28/2022]
Abstract
Structural variants (SVs) are large rearrangements (>50 bp) within the genome that impact gene function and the content and structure of chromosomes. As a result, SVs are a significant source of functional genomic variation, that is, variation at genomic regions underpinning phenotype differences, that can have large effects on individual and population fitness. While there are increasing opportunities to investigate functional genomic variation in threatened species via single nucleotide polymorphism (SNP) data sets, SVs remain understudied despite their potential influence on fitness traits of conservation interest. In this future-focused Opinion, we contend that characterizing SVs offers the conservation genomics community an exciting opportunity to complement SNP-based approaches to enhance species recovery. We also leverage the existing literature-predominantly in human health, agriculture and ecoevolutionary biology-to identify approaches for readily characterizing SVs and consider how integrating these into the conservation genomics toolbox may transform the way we manage some of the world's most threatened species.
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Affiliation(s)
- Jana Wold
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Klaus-Peter Koepfli
- Smithsonian-Mason School of Conservation, Front Royal, Virginia, USA.,Centre for Species Survival, Smithsonian Conservation Biology Institute, National Zoological Park, Washington, District of Columbia, USA.,Computer Technologies Laboratory, ITMO University, Saint Petersburg, Russia
| | - Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.,Department of Biological Sciences, Boise State University, Boise, Idaho, USA
| | - David Eccles
- Malaghan Institute of Medical Research, Wellington, New Zealand
| | - Carolyn J Hogg
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Marissa F Le Lec
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand
| | - Joseph Guhlin
- Department of Biochemistry, University of Otago, Dunedin, Otago, New Zealand.,Genomics Aotearoa, Dunedin, Otago, New Zealand
| | - Anna W Santure
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
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