1
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Li C, Wang X, Li H, Ahmed Z, Luo Y, Qin M, Yang Q, Long Z, Lei C, Yi K. Whole-genome resequencing reveals diversity and selective signals in the Wuxue goat. Anim Genet 2024; 55:575-587. [PMID: 38806279 DOI: 10.1111/age.13437] [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: 10/10/2023] [Revised: 04/14/2024] [Accepted: 04/17/2024] [Indexed: 05/30/2024]
Abstract
Animal genetic resources are crucial for ensuring global food security. However, in recent years, a noticeable decline in the genetic diversity of livestock has occurred worldwide. This decline is pronounced in developing countries, where the management of these resources is insufficient. In the current study, we performed whole genome sequencing for 20 Wuxue (WX) and five Guizhou White (GW) goats. Additionally, we utilized the published genomes of 131 samples representing five different goat breeds from various regions in China. We investigated and compared the genetic diversity and selection signatures of WX goats. Whole genome sequencing analysis of the WX and GW populations yielded 120 425 063 SNPs, which resided primarily in intergenic and intron regions. Population genetic structure revealed that WX exhibited genetic resemblance to GW, Chengdu Brown, and Jintang Black and significant differentiation from the other goat breeds. In addition, three methods (nucleotide diversity, linkage disequilibrium decay, and runs of homozygosity) showed moderate genetic diversity in WX goats. We used nucleotide diversity and composite likelihood ratio methods to identify within-breed signatures of positive selection in WX goats. A total of 369 genes were identified using both detection methods, including genes related to reproduction (GRID2, ZNF276, TCF25, and SPIRE2), growth (HMGA2 and GJA3), and immunity (IRF3 and SRSF3). Overall, this study explored the adaptability of WX goats, shedding light on their genetic richness and potential to thrive in challenges posed by climatic changes and diseases. Further investigations are warranted to harness these insights to enhance more efficient and sustainable goat breeding initiatives.
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Affiliation(s)
- Chuanqing Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianglin Wang
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Haobang Li
- Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Zulfiqar Ahmed
- Faculty of Veterinary and Animal Sciences, University of Poonch Rawalakot, Rawalakot, Pakistan
| | - Yang Luo
- Hunan Institute of Animal and Veterinary Science, Changsha, China
| | - Mao Qin
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Qiong Yang
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Zhangcheng Long
- Animal Husbandry and Aquatic Products Affairs Center of Xiangxi Autonomous Prefecture, Jishou, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kangle Yi
- Hunan Institute of Animal and Veterinary Science, Changsha, China
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2
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Cui W, Wang H, Li J, Lv D, Xu J, Liu M, Yin G. Sheep litter size heredity basis using genome-wide selective analysis. Reprod Domest Anim 2024; 59:e14689. [PMID: 39044628 DOI: 10.1111/rda.14689] [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: 03/22/2024] [Revised: 06/19/2024] [Accepted: 07/12/2024] [Indexed: 07/25/2024]
Abstract
Sheep are important herbivorous domestic animal globally, and the Chinese indigenous sheep breed has a multitude of economically significant variations due to the diverse geographical and ecological conditions. In particular, certain native breeds exhibit a visible high litter size phenotype due to the selection pressure of natural and artificial for thousands of years, offering an ideal animal model for investigating sheep's fecundity. In this study, selective signal analysis was performed on public whole-genome sequencing data from 60 sheep across eight breeds to identify candidate genes related to litter size. Results revealed that a total of 34,065,017 single-nucleotide polymorphisms (SNPs) were identified from all sheep, and 65 candidate genes (CDGs) were pinpointed from the top 1% of interacted windows and SNPs between the pairwise fixation index (FST, >0.149543) and cross-population extended haplotype homozygosity (XP-EHH, >0.701551). A total of 41 CDGs (e.g. VRTN, EYA2 and MCPH1) were annotated to 576 GO terms, of which seven terms were directly linked to follicular and embryonic development (e.g. TBXT, BMPR1B, and BMP2). In addition, 73 KEGG pathways were enriched by 21 CDGs (e.g. ENTPD5, ABCD4 and RXFP2), mainly related to Hippo (TCF4, BMPR1B and BMP2), TGF-β (BMPR1B and BMP2), PI3K-Akt (ITGB4, IL4R and PPP2R5A) and Jak-STAT signalling pathways (IL20RA and IL4R). Notably, a series of CDGs was under strong selection in sheep with high litter size traits. These findings result could improve the comprehension of the genetic underpinnings of sheep litter size. Furthermore, it provides valuable CDGS for future molecular breeding.
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Affiliation(s)
- Weiguo Cui
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Hechuan Wang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jingchun Li
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Dongyu Lv
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Jiayi Xu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Mengyu Liu
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Guoan Yin
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, China
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3
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Zhai R, Wang W, Zhang D, Li X, Zhang Y, Zhao Y, Zhao L, Wang J, Xu D, Cheng J, Li W, Zhou B, Lin C, Zeng X, Yang X, Ma Z, Liu J, Cui P, Zhang XX. Novel polymorphism at KLF15 gene and its association with growth traits in Hu sheep. Anim Biotechnol 2023; 34:3287-3293. [PMID: 36346056 DOI: 10.1080/10495398.2022.2138413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Growth traits are important economic characteristics of livestock and poultry. In the present study, the expression features of KLF15 and the relationship between KLF15 gene polymorphisms and growth traits in Hu sheep were investigated by using real-time quantitative PCR technology (qPCR), Sanger sequencing, and Kaspar genotyping technology. The qPCR results showed that the KLF15 gene is expressed widely in the tested tissues of Hu sheep, and the expression level of the KLF15 gene in the heart and the muscle was significantly higher than in other tissues (p < 0.05). Missense mutation c.62565119 A > G was found in KLF15, and an association analysis showed that it was correlated with the growth traits (body weight, body height, and body length) of Hu sheep (p < 0.05). The body weight, body height, and body length of the sheep carrying the AA genotype were remarkably higher than those of the GG and AG genotypes (p < 0.05). These results showed that novel polymorphisms at the KLF15 gene can be used as a genetic marker of growth traits of Hu sheep.
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Affiliation(s)
- Rui Zhai
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, Gansu, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiwen Zeng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Zongwu Ma
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Jia Liu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Panpan Cui
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
| | - Xiao Xue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, China
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4
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Wijayanti D, Bai Y, Hanif Q, Chen H, Zhu H, Qu L, Guo Z, Lan X. Goat CLSTN2 gene: tissue expression profile, genetic variation, and its associations with litter size. Anim Biotechnol 2023; 34:2674-2683. [PMID: 35980330 DOI: 10.1080/10495398.2022.2111311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Calsyntenin-2 (CLSTN2) is involved in cell proliferation, differentiation, cell death, tumorigenesis, and follicular expression. Although CLSTN2 has been identified as a potential candidate gene for sheep prolificacy, no studies have been done on its effect on goat prolificacy. The purpose of this study was to identify mRNA expression and genetic variation within goat CLSTN2, and its association with prolificacy. Herein, we uncovered significant differences in mRNA levels of the CLSTN2 gene in different tissues in female goats (p < 0.01), including ovary tissue. Nine putative indels were designed to investigate their correlation to litter size, but only one 16-bp deletion was discovered in female Shaanbei white cashmere goats (n = 902). We discovered that a 16-bp deletion within the CLSTN2 gene was significantly correlated with first-born litter size (p = 0.0001). As shown by the chi-squared test, the genotypic II of single-lambs and multi-lambs was dramatically higher than with genotype ID (p = 0.005). Our findings suggest that indel within the CLSTN2 gene is a candidate gene affecting prolificacy in goats and may be used for Marker Assisted Selection (MAS) in goats.
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Affiliation(s)
- Dwi Wijayanti
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, Indonesia
| | - Yangyang Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, PR China and Life Science Research Center, Yulin University, Yulin, Shaanxi, PR China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, PR China and Life Science Research Center, Yulin University, Yulin, Shaanxi, PR China
| | - Zhengang Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
- Institute of Animal Husbandry and Veterinary Science of Bijie City, Guizhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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5
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Liu LL, Meng J, Ma HY, Cao H, Liu WJ. Candidate genes for litter size in Xinjiang sheep identified by Specific Locus Amplified Fragment (SLAF) sequencing. Anim Biotechnol 2023; 34:3053-3062. [PMID: 36244020 DOI: 10.1080/10495398.2022.2131561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
The aim of this study was to investigate the selection signatures at a genome-wide level in 'Pishan' sheep using Specific Locus Amplified Fragment (SLAF)-seq. Blood samples from 126 ewes were sequenced using SLAF tags, and the ovarian tissues from 8 ewes (Bashbay sheep, a single litter size group (SG group); 'Pishan' sheep, double litter size group (DG group)) were collected to detect expression levels by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Selection signature analysis was performed using global fixation index (Fst) and nucleotide diversity (π) ratio. A total of 1,192,168 high-quality SLAFs were identified. Notably, 2380 candidate regions under selection using two approaches were identified. A total of 2069 genes were identified, which were involved in dopaminergic synapses, thyroid hormone synthesis, ovarian steroidogenesis and thyroid hormone signalling pathways. Furthermore, Growth Differentiation Factor 9 (GDF9), Period Circadian Regulator 2 (PER2), Thyroid Stimulating Hormone Receptor (TSHR), and Nuclear Receptor Coactivator 1 (NCOA1) reside within these regions and pathways. The expression levels of GDF9 and PER2 genes in sheep tissue of the DG group were significantly higher than those in the SG group. These genes are interesting candidates for litter size and provide a starting point for further identification of conservation strategies for 'Pishan' sheep.
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Affiliation(s)
- Ling-Ling Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jun Meng
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hai-Yu Ma
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hang Cao
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wu-Jun Liu
- Department of Animal Science, Xinjiang Agricultural University, Urumqi, China
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6
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Wan X, Jing JN, Wang DF, Lv FH. Whole-genome selective scans detect genes associated with important phenotypic traits in goat ( Capra hircus). Front Genet 2023; 14:1173017. [PMID: 37144124 PMCID: PMC10151485 DOI: 10.3389/fgene.2023.1173017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. In this study, we focused on the worldwide goat breeds with outstanding traits and used whole-genome resequencing data in 361 samples from 68 breeds to detect genomic selection sweep regions. We identified 210-531 genomic regions with six phenotypic traits, respectively. Further gene annotation analysis revealed 332, 203, 164, 300, 205, and 145 candidate genes corresponding with dairy, wool, high prolificacy, poll, big ear, and white coat color traits. Some of these genes have been reported previously (e.g., KIT, KITLG, NBEA, RELL1, AHCY, and EDNRA), while we also discovered novel genes, such as STIM1, NRXN1, LEP, that may be associated with agronomic traits like poll and big ear morphology. Our study found a set of new genetic markers for genetic improvement in goats and provided novel insights into the genetic mechanisms of complex traits.
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Affiliation(s)
- Xing Wan
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jia-Nan Jing
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Feng-Hua Lv,
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7
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Kang Y, Bi Y, Tang Q, Xu H, Lan X, Zhang Q, Pan C. A 7-nt nucleotide sequence variant within the sheep KDM3B gene affects female reproduction traits. Anim Biotechnol 2022; 33:1661-1667. [PMID: 34081570 DOI: 10.1080/10495398.2021.1929270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Lysine demethylase 3B (KDM3B) gene is a histone demethylase, demonstrating specific demethylation of the histone H3 lysine 9. It was detected as a sheep reproductive candidate gene by genome-wide scans, and related studies also showed its significance in female reproductive process. However, rare study researched its polymorphism. Herein, we hypothesized that the polymorphisms of KDM3B gene were associated with sheep reproduction traits. A 7-nt nucleotide sequence variant (rs1088697156) within KDM3B gene was identified in a total of 888 individuals, including the Australian White (AUW) sheep and Lanzhou Fat-tailed (LFT) sheep. II (insertion/insertion) and ID (insertion/deletion) genotypes of 7-nt variant were detected, which were at Hardy-Weinberg equilibrium (HWE) in detected breeds. Association analysis illustrated the 7-nt variant was significantly associated with the litter size, duration of pregnancy, live lamb number, live lamb rate, stillbirth number, stillbirth rate of average and different parity (P < 0.05) in AUW sheep. Moreover, 'ID' was the dominant genotype with excellent consistency in reproductive traits. It is instrumental to select individuals with ID genotype for improving the sheep reproduction traits. These findings suggest that the 7-nt variant within KDM3B gene can be used as a candidate marker of reproduction traits for sheep breeding improvement by marker-assisted selection.
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Affiliation(s)
- Yuxin Kang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yi Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qi Tang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Hongwei Xu
- College of Life Science and Engineering, Northwest Minzu University, Lanzhou, China.,Gansu Tech Innovation Center of Animal Cell, Biomedical Research Center, Northwest Minzu University, Lanzhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Qingfeng Zhang
- Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd, Tianjin, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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8
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Wijayanti D, Zhang S, Yang Y, Bai Y, Akhatayeva Z, Pan C, Zhu H, Qu L, Lan X. Goat SMAD family member 1 (SMAD1): mRNA expression, genetic variants, and their associations with litter size. Theriogenology 2022; 193:11-19. [PMID: 36116245 DOI: 10.1016/j.theriogenology.2022.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 12/20/2022]
Abstract
SMAD family member 1 (SMAD1) is phosphorylated and activated by the BMP receptors, which help regulate ovulation rate, cell growth, apoptosis, and development. Previously, the genome-wide association study revealed that it has been associated with fecundity in sheep. However, its effect on litter size has not been investigated in goats. Therefore, this study aimed to determine the level of SMAD1 mRNA expression in various tissues and to identify its polymorphisms and their association with litter size in Shaanbei white cashmere goat (SBWC). As a result, RT-qPCR analysis showed that SMAD1 was expressed in various tissues in female SBWC goats, including the ovary (P < 0.05). Importantly, the mRNA expression level in the ovaries of mothers of multi-lambs had a higher level than the mothers of single lambs (P < 0.05). Moreover, two InDels (18-bp and 7-bp) in intron 1 of SMAD1 were polymorphic among ten potential loci. Both 18-bp and 7-bp InDels were significantly correlated with litter size (P = 0.014) and (P = 0.0001), respectively. As shown by the chi-squared test, genotypic distributions of 18-bp and 7-bp were significantly distinct between single-lamb (P = 0.02) and multi-lamb mothers (P = 0.002). Our findings confirm that two InDels in SMAD1 were significantly associated with litter size and suggest that they could be used to improve fertility traits in goat breeding strategies.
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Affiliation(s)
- Dwi Wijayanti
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China; Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, 46115, Indonesia.
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yuta Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yangyang Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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9
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Yao X, El-Samahy MA, Li X, Bao Y, Guo J, Yang F, Wang Z, Li K, Zhang Y, Wang F. LncRNA-412.25 activates the LIF/STAT3 signaling pathway in ovarian granulosa cells of Hu sheep by sponging miR-346. FASEB J 2022; 36:e22467. [PMID: 35929417 DOI: 10.1096/fj.202200632r] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/15/2022] [Accepted: 07/14/2022] [Indexed: 11/11/2022]
Abstract
Although long non-coding RNAs (lncRNAs) are reported to regulate follicular development and reproductive disease pathogenesis, the underlying mechanisms have not been elucidated. In this study, lncRNA expression profiling of different-sized healthy follicles from Hu sheep with different prolificacy revealed 50 613 lncRNAs. Numerous lncRNAs were differentially expressed among different comparison groups. This study characterized one novel transcript, lncRNA-412.25 (from healthy follicles with a diameter of >5 mm), which was predominantly expressed in the high prolificacy group and localized to the cytoplasm of granulosa cells (GCs). LncRNA-412.25 knockdown promoted and inhibited Hu sheep GC apoptosis and proliferation, respectively. Interestingly, lncRNA-412.25 could directly bind to miR-346, which can target the gene of leukemia inhibitory factor (LIF). Knockdown of lncRNA-412.25 promoted GC apoptosis by downregulating LIF expression, where this effect was attenuated by miR-346. Moreover, the miR-346 inhibitor mitigated the lncRNA-412.25 knockdown-induced downregulation of phosphorylated protein of signal transducer and activator of transcription 3 (STAT3), which was validated using immunofluorescence analysis. Our results demonstrated that lncRNA-412.25 regulates GC proliferation and apoptosis in Hu sheep by binding to miR-346 and then activating the LIF/STAT3 pathway. These findings provide novel insights into the mechanisms underlying prolificacy in sheep.
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Affiliation(s)
- Xiaolei Yao
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Mohamed AbdFatah El-Samahy
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China.,Animal Production Research Institute, ARC, Ministry of Agriculture, Giza, Egypt
| | - Xiaodan Li
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Yongjin Bao
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Jiahe Guo
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Fan Yang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Zhibo Wang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Kang Li
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Yanli Zhang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
| | - Feng Wang
- Hu Sheep Academy, Nanjing Agricultural University, Nanjing, China.,Jiangsu Livestock Embryo Engineering Laboratory, Nanjing Agricultural University, Nanjing, China
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10
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Zhang D, Zhang X, Li F, Zhao Y, Li X, Wang J, Zhao L, Yang X, Zhang Y, Xu D, Cheng J, Li W, Lin C, Zhou B, Wang W. Expression Profiles of the Ovine IL18 Gene and Association of Its Polymorphism With Hematologic Parameters in Hu Lambs. Front Vet Sci 2022; 9:925928. [PMID: 35847634 PMCID: PMC9280051 DOI: 10.3389/fvets.2022.925928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/06/2022] [Indexed: 11/29/2022] Open
Abstract
Hematological traits are important indexes to evaluate health status and immunological conditions in human and livestock. In this study, we measured the hematologic indexes of 819 male Hu lambs and performed the descriptive statistical analysis. The results showed the coefficients of variation of partial indexes were >10%, and the heritability for mean erythrocyte volume (MCV), white blood cell count (WBC), hemoglobin concentration (HGB), hematocrit (HCT), and red blood cell (RBC) distribution-standard deviation (RDW_SD) were medium to high, ranging from 0.17 to 0.43. In addition, Interleukin 18 (IL18), as an important regulator of both innate and acquired immune responses, was selected as candidate gene and subjected to the expression profile analysis, single nucleotide polymorphism (SNP) scanning and association analysis by using quantitative real-time PCR (qRT-PCR), PCR amplification, Sanger sequencing, and KASP genotyping. The results of qRT-PCR indicated that IL18 is predominantly expressed in lymph and lung compared with that in the other tested tissues. In addition, three novel polymorphisms (g. 24991544 A > G, g. 24991651 A > G, and g. 24991749 C > T) were identified in IL18, and the three SNPs were in a strong linkage state. Therefore, only a SNP was genotyped and performed association analysis in the enlarged experimental population, the result of association analysis demonstrated that the polymorphism g. 24991651 A > G was significantly associated with RBC, MCV, MCHC, and RDW_CV. These results will provide the reference values and the novel genetic markers of hematological parameters in sheep.
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Affiliation(s)
- Deyin Zhang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Fadi Li
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jianghui Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiaobin Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Wenxin Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Changchun Lin
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bubo Zhou
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Weimin Wang
- The State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
- *Correspondence: Weimin Wang ; orcid.org/0000-0002-6660-4865
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11
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Wang C, Zhao Y, Yuan Z, Wu Y, Zhao Z, Wu C, Hou J, Zhang M. Genome-Wide Identification of mRNAs, lncRNAs, and Proteins, and Their Relationship With Sheep Fecundity. Front Genet 2022; 12:750947. [PMID: 35211149 PMCID: PMC8861438 DOI: 10.3389/fgene.2021.750947] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 12/06/2021] [Indexed: 12/19/2022] Open
Abstract
The exploration of multiple birth-related genes has always been a significant focus in sheep breeding. This study aimed to find more genes and proteins related to the litter size in sheep. Ovarian specimens of Small Tail Han sheep (multiple births) and Xinji Fine Wool sheep (singleton) were collected during the natural estrus cycle. Transcriptome and proteome of ovarian specimens were analyzed. The transcriptome results showed that "steroid hormone biosynthesis" and "ovarian steroidogenesis" were significantly enriched, in which HSD17B1 played an important role. The proteome data also confirmed that the differentially expressed proteins (DEPs) were enriched in the ovarian steroidogenesis pathway, and the CYP17A1 was the candidate DEP. Furthermore, lncRNA MSTRG.28645 was highly expressed in Small Tailed Han sheep but lowly expressed in Xinji fine wool sheep. In addition, MSTRG.28645, a hub gene in the co-expression network between mRNAs and lncRNAs, was selected as one of the candidate genes for subsequent verification. Expectedly, the overexpression and interference of HSD17B1 and MSTRG.28645 showed a significant effect on hormone secretion in granulosa cells. Therefore, this study confirmed that HSD17B1 and MSTRG.28645 might be potential genes related to the fecundity of sheep. It was concluded that both HSD17B1 and MSTRG.28645 were critical regulators in the secretion of hormones that affect the fecundity of the sheep.
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Affiliation(s)
- Chunxin Wang
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yunhui Zhao
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Changchun, China
| | - ZhiYu Yuan
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Yujin Wu
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Zhuo Zhao
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Cuiling Wu
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Changchun, China
| | - Jian Hou
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
| | - Mingxin Zhang
- Institute of Animal Sciences, Jilin Academy of Agricultural Sciences, Changchun, China
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12
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Li M, Zhou Q, Pan Y, Lan X, Zhang Q, Pan C, Mao C. Screen of small fragment mutations within the sheep thyroid stimulating hormone receptor gene associated with litter size. Anim Biotechnol 2021:1-6. [PMID: 34895066 DOI: 10.1080/10495398.2021.1992415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The thyroid stimulating hormone receptor (TSHR), a glycoprotein hormone receptor, plays an important role in metabolic regulation and photoperiod control in the time of reproduction in birds and mammals. Previous genome-wide association studies revealed that the TSHR gene was related to reproduction and its function was identified in female reproduction, but rare studies reported the polymorphism of TSHR gene. However, the molecular mutations of the TSHR gene in sheep have not been reported so far. Herein, we explored potential polymorphisms of the sheep TSHR gene, and a 29 bp nucleotide sequence variant (rs1089565492) was identified in the AUW sheep. There were three genotypes of the 29 bp variant locus detected which named 'II' 'DD' and 'ID' been identified. Association analysis results showed the 29 bp variant was significantly associated with the litter size of the AUW sheep (p < 0.05). This finding suggests that the 29 bp nucleotide sequence variant within TSHR gene could be a candidate marker of reproduction traits for sheep breeding improving through the marker-assisted selection (MAS).
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Affiliation(s)
- Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qian Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yejun Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qingfeng Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Tianjin Aoqun Animal Husbandry Co., Ltd, Tianjin, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Cui Mao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Tianjin Aoqun Sheep Industry Academy Company, Tianjin, China.,Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Ji'nan, China
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13
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Zhang S, Gao X, Jiang Y, Shen Y, Xie H, Pan P, Huang Y, Wei Y, Jiang Q. Population validation of reproductive gene mutation loci and association with the litter size in Nubian goat. Arch Anim Breed 2021; 64:375-386. [PMID: 34584939 PMCID: PMC8461558 DOI: 10.5194/aab-64-375-2021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/20/2021] [Indexed: 01/05/2023] Open
Abstract
Litter size is an important component trait of doe
reproduction. By improving it, production efficiency and economic benefits
can be significantly provided. Genetic marker-assisted selection (MAS) based
on proven molecular indicators could enhance the efficacy of goat selection,
as well as litter size trait. Many molecular markers have been identified
that they can be used to improve litter size in different goat breeds.
However, the presence and value of these markers vary among goat breeds. In
the present study, we used the reported loci on other breeds of goat as
candidate loci to detect whether these loci appear in this Nubian goat
population; then we proceed to genotype and detect surrounding loci (50 bp)
by multiplex PCR and sequencing technology. As a result, 69
mutations (59 SNPs and 10 indels) were screened out from 23 candidate genes
in Nubian goat population, 12 loci were significantly associated with
the litter size of first-parity individuals; 5 loci were significantly
associated with the litter size of second-parity individuals; 3 loci
were significantly associated with the litter size of third-parity
individuals. In addition, five loci were significantly associated with the
average litter size. The additive effect value of KITLG: g.18047318 G>A in first parity, KITLG: g.18152042G>A in third parity, KISS-1: g.1341674
C>G in first parity, and GHR: g.32134187G>A in
second parity exceed more than 0.40, and the preponderant alleles are G, C,
A and G, respectively. Further, linkage disequilibrium analysis of 21 mutation
loci shows that 3 haplotype blocks are formed, and the litter size of
combination type AACC in KISS-1 gene and AAGG in KITLG gene are significantly lower
than that of other combinations genotype in first parity (P<0.05). These findings
can provide effective candidate DNA markers for selecting superior
individuals in Nubian goat breeding.
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Affiliation(s)
- Sanbao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Xiaotong Gao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yuhang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yujian Shen
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Hongyue Xie
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Peng Pan
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yanna Huang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
| | - Yingming Wei
- Institute for New Rural Development, Guangxi University, Nanning 530004, Guangxi, China
| | - Qinyang Jiang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, Guangxi, China
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14
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Gao Y, Hao Q, Cang M, Wang J, Yu H, Liu Y, Zhang W, Tong B. Association between novel variants in BMPR1B gene and litter size in Mongolia and Ujimqin sheep breeds. Reprod Domest Anim 2021; 56:1562-1571. [PMID: 34543455 DOI: 10.1111/rda.14020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/17/2021] [Indexed: 11/27/2022]
Abstract
Prolificacy is an important trait of animals, specifically for sheep. The Bone morphogenetic protein receptor 1B (BMPR1B) is a major gene affecting the litter size of many sheep breeds. The well-known FecB mutation (Q249R) was associated fully with the hyper prolific phenotype of Booroola Merino. However, the identification of variation in all exonic regions of BMPR1B was rare. In this study, we sequenced all exonic regions of BMPR1B gene of Mongolia sheep breed, and ten novel variants were detected by direct sequencing. Among them, the litter size of the Mongolia ewes with the CC genotype was significantly higher (0.34 additional lambs, p < .05) than those with the TT genotype of the g.29346567C>T single nucleotide polymorphism (SNP). The litter size of the Mongolia ewes with the TT genotype was significantly higher (0.19 additional lambs, p < .05 and .31 additional lambs, p < .01, respectively) than those with the GT and GG genotypes of the c.1470G>T SNP. The silent c.1470G>T mutation is predicted to increase the stability of the mRNA secondary structure through reducing minimum free energy and is predicted to change the mRNA secondary structure of BMPR1B. Our findings may give potentially useful genetic markers for increasing litter size in sheep.
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Affiliation(s)
- Yuanyuan Gao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Qi Hao
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Ming Cang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Jianguo Wang
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Haiquan Yu
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
| | - Yongbin Liu
- Institute of Animal Science, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, China
| | - Wenguang Zhang
- College of Animal Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Bin Tong
- The State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, School of Life Sciences, Inner Mongolia University, Hohhot, China
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15
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Tao L, Wang X, Zhong Y, Liu Q, Xia Q, Chen S, He X, Di R, Chu M. Combined approaches identify known and novel genes associated with sheep litter size and non-seasonal breeding. Anim Genet 2021; 52:857-867. [PMID: 34494299 DOI: 10.1111/age.13138] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/26/2021] [Indexed: 01/29/2023]
Abstract
Improvement of ewe reproduction is considerable by appropriately increasing litter size and sustaining non-seasonal breeding. However, their genetic makeups have not been entirely elucidated. Genome-wide analyses of 821 individuals were performed by combining three genomic approaches (genome-wide association study, XP-nSL, and runs of homozygosity). Consequently, 35 candidate genes including three domestication genes (TSHR, GTF2A1, and KITLG) were identified. Other than the FecB mutation at BMPR1B, we described a significant association of a missense mutation rs406686139 at seasonal lambing-associated TSHR gene with litter size. Some promising novel genes may be relevant for sheep reproduction by multitude biological processes, such as FETUB functioning in fertilization, HNRNPA1 in oogenesis, DCUN1D1 in spermatogenesis, and HRG in fertility outcome. The present study suggests that improvement of ewe reproduction is attributed to selective breeding, and casts light on the genetic basis and improvement of sheep reproduction.
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Affiliation(s)
- Lin Tao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiangyu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yingjie Zhong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qiuyue Liu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Qing Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Si Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
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16
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Zhao X, Nie C, Zhang J, Li X, Zhu T, Guan Z, Chen Y, Wang L, Lv XZ, Yang W, Jia Y, Ning Z, Li H, Qu C, Wang H, Qu L. Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study. BMC Genomics 2021; 22:610. [PMID: 34376144 PMCID: PMC8356427 DOI: 10.1186/s12864-021-07755-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 05/25/2021] [Indexed: 02/07/2023] Open
Abstract
Background Since the domestication of chicken, various breeds have been developed for food production, entertainment, and so on. Compared to indigenous chicken breeds which generally do not show elite production performance, commercial breeds or lines are selected intensely for meat or egg production. In the present study, in order to understand the molecular mechanisms underlying the dramatic differences of egg number between commercial egg-type chickens and indigenous chickens, we performed a genome-wide association study (GWAS) in a mixed linear model. Results We obtained 148 single nucleotide polymorphisms (SNPs) associated with egg number traits (57 significantly, 91 suggestively). Among them, 4 SNPs overlapped with previously reported quantitative trait loci (QTL), including 2 for egg production and 2 for reproductive traits. Furthermore, we identified 32 candidate genes based on the function of the screened genes. These genes were found to be mainly involved in regulating hormones, playing a role in the formation, growth, and development of follicles, and in the development of the reproductive system. Some genes such as NELL2 (neural EGFL like 2), KITLG (KIT ligand), GHRHR (Growth hormone releasing hormone receptor), NCOA1 (Nuclear receptor coactivator 1), ITPR1 (inositol 1, 4, 5-trisphosphate receptor type 1), GAMT (guanidinoacetate N-methyltransferase), and CAMK4 (calcium/calmodulin-dependent protein kinase IV) deserve our attention and further study since they have been reported to be closely related to egg production, egg number and reproductive traits. In addition, the most significant genomic region obtained in this study was located at 48.61–48.84 Mb on GGA5. In this region, we have repeatedly identified four genes, in which YY1 (YY1 transcription factor) and WDR25 (WD repeat domain 25) have been shown to be related to oocytes and reproductive tissues, respectively, which implies that this region may be a candidate region underlying egg number traits. Conclusion Our study utilized the genomic information from various chicken breeds or populations differed in the average annual egg number to understand the molecular genetic mechanisms involved in egg number traits. We identified a series of SNPs, candidate genes, or genomic regions that associated with egg number, which could help us in developing the egg production trait in chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07755-3.
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Affiliation(s)
- Xiurong Zhao
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Changsheng Nie
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Jinxin Zhang
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinghua Li
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Tao Zhu
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zi Guan
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Yu Chen
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Liang Wang
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Xue Ze Lv
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Weifang Yang
- Beijing Municipal General Station of Animal Science, Beijing, 100107, China
| | - Yaxiong Jia
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Zhonghua Ning
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Haiying Li
- College of Animal Science, Xinjiang Agricultural University, Urumqi, 830000, China
| | - Changqing Qu
- Engineering Technology Research Center of Anti-aging Chinese Herbal Medicine of Anhui Province, Fuyang Normal University, Fuyang, 236037, Anhui, China
| | - Huie Wang
- College of Animal Science, Tarim University, Alar, 843300, Xingjiang, China.,Key Laboratory of Tarim Animal Husbandry Science and Technology, Xinjiang Production & amp; Construction Corps, Alar, 843300, Xingjiang, China
| | - Lujiang Qu
- Department of Animal Genetics and Breeding, State Key Laboratory of Animal Nutrition, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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17
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Tao L, He X, Wang X, Di R, Chu M. Litter Size of Sheep ( Ovis aries): Inbreeding Depression and Homozygous Regions. Genes (Basel) 2021; 12:109. [PMID: 33477586 PMCID: PMC7831309 DOI: 10.3390/genes12010109] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 02/07/2023] Open
Abstract
Ovine litter size (LS) is an important trait showing variability within breeds. It remains largely unknown whether inbreeding depression on LS exists based on genomic homozygous regions, and whether the homozygous regions resulted from inbreeding are significantly associated with LS in sheep. We here reanalyze a set of single nucleotide polymorphism (SNP) chip of six breeds to characterize the patterns of runs of homozygosity (ROH), to evaluate inbreeding levels and inbreeding depressions on LS, and to identify candidate homozygous regions responsible for LS. Consequently, unique ROH patterns were observed among six sheep populations. Inbreeding depression on LS was only found in Hu sheep, where a significant reduction of 0.016, 0.02, and 0.02 per 1% elevated inbreeding FROH4-8, FROH>8 and the total inbreeding measure was observed, respectively. Nine significantly homozygous regions were found for LS in Hu sheep, where some promising genes for LS possibly via regulation of the development of oocytes (NGF, AKT1, and SYCP1), fertilization (SPAG17, MORC1, TDRD9, ZFYVE21, ADGRB3, and CKB), embryo implantation (PPP1R13B, INF2, and VANGL1) and development (DPPA2, DPPA4, CDCA4, CSDE1, and ADSSL1), and reproductive health (NRG3, BAG5, CKB, and XRCC3) were identified. These results from the present study would provide insights into the genetic management and complementary understandings of LS in sheep.
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Affiliation(s)
| | | | | | | | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.T.); (X.H.); (X.W.); (R.D.)
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18
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Review of Huang-huai sheep, a new multiparous mutton sheep breed first identified in China. Trop Anim Health Prod 2020; 53:35. [PMID: 33230646 PMCID: PMC7683451 DOI: 10.1007/s11250-020-02453-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 10/15/2020] [Indexed: 12/24/2022]
Abstract
Huang-huai sheep are a new multiparous mutton sheep breed that has been cultivated by domestic scientific research institutes, governments, and sheep farms in China. Huang-huai sheep were bred using Dorper sheep as a sire and Small-tailed Han sheep as a dam. The breeding of Huang-huai sheep started in 2003, and three stages have been carried out: crossbreeding innovation, fixation in a two-way-crossbred closed flock, and herd propagation. A pilot test of Huang-huai sheep was conducted on 6 sheep farms from 2017 to 2018, and hereditary properties and production performance were evaluated in 2019. Huang-huai sheep were identified on site by the National Livestock and Poultry Resources Committee of China in December 2019 and approved as a new multiparous mutton sheep breed in China. The genetic distance showed that Huang-huai sheep are most closely related to Dorper sheep, Luxi black-headed sheep, and Small-tailed Han sheep, but the genetic distances are subspecies (0.02–0.20) each other. The body weights of adult Huang-huai sheep are 98.1 ± 5.2 kg (♂) and 71.7 ± 3.5 kg (♀), and those of 6-month-old Huang-huai sheep are 58.50 ± 6.55 kg (♂) and 52.45 ± 5.67 kg (♀). The slaughter rates of 6-month-old sheep are 56.02 ± 1.25% (♂) and 53.19 ± 1.19% (♀). The estrus cycle of Huang-huai sheep is 19.32 ± 2.8 days, the first estrus cycle occurs at 168 ± 12 days, the annual lambing rate of ewes is 252.82% ± 10.69%, the survival rate of lambs is 95.79 ± 0.95%, and the number of weaned lambs per ewe per year is 2.38 ± 0.14. The growth performance, carcass quality, and reproductive performance of Huang-huai sheep have been improved, resulting in considerable economic and social benefits and broader market prospects. This breed represents a new multiparous mutton sheep breed adapted for industrial sheep farms in China.
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Li Z, Wang B, Li H, Jian L, Luo H, Wang B, Zhang C, Zhao X, Xue Y, Peng S, Zuo S. Maternal Folic Acid Supplementation Differently Affects the Small Intestinal Phenotype and Gene Expression of Newborn Lambs from Differing Litter Sizes. Animals (Basel) 2020; 10:E2183. [PMID: 33266421 PMCID: PMC7700240 DOI: 10.3390/ani10112183] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/16/2020] [Accepted: 11/19/2020] [Indexed: 11/16/2022] Open
Abstract
The purpose of this study was to investigate the effect of maternal dietary folic acid (FA) supplementation during gestation on small intestinal development of newborn lambs of different litter sizes, focusing on the intestinal morphology and development-, apoptosis- and digestion-related genes expression. One hundred and twenty Hu ewes (Ovis aries) were inseminated and randomly allotted to three groups. One group received a control diet [without FA supplementation, control (CON)] and the other two groups received control diets supplemented with different amount of FA [16 or 32 mg FA per kg dry matter (DM), i.e., F16 and F32] during pregnancy. After lambing, according to the dietary FA levels and litter size (twins, TW; triplets, TR), the neonatal lambs were divided into 6 (TW-CON, TW-F16, TW-F32, TR-CON, TR-F16, TR-F32) treatment groups. The results showed that the ratio of small intestinal weight to live body weight and the thickness of the intestinal muscle layer in the offspring was enhanced significantly with increasing maternal FA supplementation (p < 0.05). Meanwhile, the expression levels of insulin-like growth factor I (IGF-I), B-cell lymphoma-2 (BCL-2) and sodium/glucose co-transporter-1 (SGLT1) in the small intestines of the newborn lambs were increased, while the opposite was true for Bcl2-associated × (BAX) in response to FA supplementation (p < 0.05). Moreover, the small intestinal weights of twins were significantly higher than those of triplets (p < 0.01), and the expression levels of IGF-I (p < 0.05), sucrase-isomaltase (SI) (p < 0.05) and solute carrier family 2 member 5 (SLC2A5) (p < 0.01) were significantly lower than those in triplets. These findings suggest that maternal FA supplementation could improve the offspring's small intestinal phenotype and the expression of development-, apoptosis- and digestion-related genes, so it could promote the small intestinal development of newborn lambs. Furthermore, the small intestine phenotypic development of twins was generally better than that of triplets, while the expression levels of the above genes of twins were lower than those of triplets.
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Affiliation(s)
| | | | | | | | - Hailing Luo
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (Z.L.); (B.W.); (H.L.); (L.J.); (B.W.); (C.Z.); (X.Z.); (Y.X.); (S.P.); (S.Z.)
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Bi Y, Feng B, Wang Z, Zhu H, Qu L, Lan X, Pan C, Song X. Myostatin (MSTN) Gene Indel Variation and Its Associations with Body Traits in Shaanbei White Cashmere Goat. Animals (Basel) 2020; 10:E168. [PMID: 31963797 PMCID: PMC7022945 DOI: 10.3390/ani10010168] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 12/21/2022] Open
Abstract
Myostatin (MSTN) gene, also known as growth differentiation factor 8 (GDF8), is a member of the transforming growth factor-beta super-family and plays a negative role in muscle development. It acts as key points during pre- and post-natal life of amniotes that ultimately determine the overall muscle mass of animals. There are several studies that concentrate on the effect of a 5 bp insertion/deletion (indel) within the 5' untranslated region (5' UTR) of goat MSTN gene in goats. However, almost all sample sizes were below 150 individuals. Only in Boer goats, the sample sizes reached 482. Hence, whether the 5 bp indel was still associated with the growth traits of goats in large sample sizes which were more reliable is not clear. To find an effective and dependable DNA marker for goat rearing, we first enlarged the sample sizes (n = 1074, Shaanbei White Cashmere goat) which would enhance the robustness of the analysis and did the association analyses between the 5 bp indel and growth traits. Results uncovered that the 5 bp indel was significantly related to body height, height at hip cross, and chest width index (p < 0.05). In addition, individuals with DD genotype had a superior growing performance than those with the ID genotype. These findings suggested that the 5 bp indel in MSTN gene are significantly associated with growth traits and the specific genotype might be promising for maker-assisted selection (MAS) of goats.
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Affiliation(s)
- Yi Bi
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.B.); (B.F.); (Z.W.); (X.L.)
| | - Bo Feng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.B.); (B.F.); (Z.W.); (X.L.)
| | - Zhen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.B.); (B.F.); (Z.W.); (X.L.)
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.B.); (B.F.); (Z.W.); (X.L.)
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (Y.B.); (B.F.); (Z.W.); (X.L.)
| | - Xiaoyue Song
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin 719000, China; (H.Z.); (L.Q.)
- Life Science Research Center, Yulin University, Yulin 719000, China
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