1
|
Wang XG, Shen MM, Lu J, Dou TC, Ma M, Guo J, Wang KH, Qu L. Genome-wide association analysis of eggshell color of an F2 generation population reveals candidate genes in chickens. Animal 2024; 18:101167. [PMID: 38762993 DOI: 10.1016/j.animal.2024.101167] [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] [Received: 10/26/2023] [Revised: 04/11/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024] Open
Abstract
Eggshell color is an important visual characteristic that affects consumer preferences for eggs. Eggshell color, which has moderate to high heritability, can be effectively enhanced through molecular marker selection. Various studies have been conducted on eggshell color at specific time points. However, few longitudinal data are available on eggshell color. Therefore, the objective of this study was to investigate eggshell color using the Commission International de L'Eclairage L*a*b* system with multiple measurements at different ages (age at the first egg and at 32, 36, 40, 44, 48, 52, 56, 60, 66, and 72 weeks) within the same individuals from an F2 resource population produced by crossing White Leghorn and Dongxiang Blue chicken. Using an Affymetrix 600 single nucleotide polymorphism (SNP) array, we estimated the genetic parameters of the eggshell color trait, performed genome-wide association studies (GWASs), and screened for the potential candidate genes. The results showed that pink-shelled eggs displayed a significant negative correlation between L* values and both a* and b* values. Genetic heritability based on SNPs showed that the heritability of L*, a*, and b* values ranged from 0.32 to 0.82 for pink-shelled eggs, indicating a moderate to high level of genetic control. The genetic correlations at each time point were mostly above 0.5. The major-effect regions affecting the pink eggshell color were identified in the 10.3-13.0 Mb interval on Gallus gallus chromosome 20, and candidate genes were selected, including SLC35C2, PCIF1, and SLC12A5. Minor effect polygenic regions were identified on chromosomes 1, 6, 9, 12, and 15, revealing 11 candidate genes, including MTMR3 and SLC35E4. Members of the solute carrier family play an important role in influencing eggshell color. Overall, our findings provide valuable insights into the phenotypic and genetic aspects underlying the variation in eggshell color. Using GWAS analysis, we identified multiple quantitative trait loci (QTLs) for pink eggshell color, including a major QTL on chromosome 20. Genetic variants associated with eggshell color may be used in genomic breeding programs.
Collapse
Affiliation(s)
- X G Wang
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - M M Shen
- Jiangsu Key Laboratory of Sericultural and Animal Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - J Lu
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - T C Dou
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - M Ma
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - J Guo
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - K H Wang
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - L Qu
- Jiangsu Institute of Poultry Science, Yangzhou 225125, China.
| |
Collapse
|
2
|
Zhao Z, Wu J, Liu Y, Zhuang Y, Yan H, Xiao M, Zhang L, An L. Dietary Canthaxanthin Supplementation Promotes the Laying Rate and Follicular Development of Huaixiang Hens. BIOLOGY 2023; 12:1375. [PMID: 37997976 PMCID: PMC10669059 DOI: 10.3390/biology12111375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/17/2023] [Accepted: 10/21/2023] [Indexed: 11/25/2023]
Abstract
Canthaxanthin(CX) is a ketocarotenoid, which is widely used in poultry production as a lipophilic antioxidant. Huaixiang chickens are a local breed in China famous for their excellent meat quality; improving their laying rate via nutritional regulation has attracted extensive attention. The aim of this study was to evaluate the effects of dietary CX on the laying rate and follicular development in Huaixiang hens. A total of 180 Huaixiang hens were randomly divided into five groups with six replicates, and six chickens per replication. The control group (CON) were fed a basal diet, and the treatment group (NT) were fed a basal diet supplemented with 4, 6, 8 and 10 mg/kg CX. All chickens were 26 weeks old, living at an average environmental temperature of 25 ± 2 °C with a relative humidity of 65-75%. The results showed that supplementing the CX improved the laying rate and large white follicles (LWF) number (p < 0.05) and increased the concentration of reproductive hormones (LH, FSH, E2 and Prog) (p < 0.05), and the basal diet supplemented with 6 mg/kg CX worked best. Moreover, CX could increase the activities of antioxidant enzymes SOD and GSH-Px (p < 0.05) and reduce the content of the lipid peroxidation product MDA in Huaixiang chickens (p < 0.05); again, 6 mg/kg CX was best. In conclusion, dietary CX had positive effects on the laying rate, ovarian structure, reproductive hormone secretion, follicle development, and the antioxidant capacity of Huaixiang hens, and 6 mg/kg CX was recommended to be added to the diet of Huaixiang chickens.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Lilong An
- Department of Animal Science, College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; (Z.Z.); (J.W.)
| |
Collapse
|
3
|
Zhong C, Liu Z, Li D, Kang L, Jiang Y. Long-read sequencing reveals the effect of follicle-stimulating hormone on the mRNA profile of chicken granulosa cells from prehierarchical follicles. Poult Sci 2023; 102:102600. [PMID: 36913754 PMCID: PMC10023945 DOI: 10.1016/j.psj.2023.102600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/11/2023] [Accepted: 02/13/2023] [Indexed: 02/18/2023] Open
Abstract
Follicle selection is an important step in the laying process of chicken, which is closely related to the laying performance and fecundity of hens. Follicle selection mainly depends on the regulation of follicle-stimulating hormone (FSH) secreted by pituitary gland and the expression of follicle stimulation hormone receptor. To uncover the role of FSH in chicken follicle selection, in this study, we analyzed the changes in the mRNA transcriptome profiles of FSH-treated chicken granulosa cells from prehierarchical follicles by long-read sequencing Oxford Nanopore Technologies (ONT) approach. Among the 10,764 genes detected, 31 differentially expressed (DE) transcripts of 28 DE genes were significantly upregulated by FSH treatment. These DE transcripts (DETs) were mainly related to the steroid biosynthetic process by GO analysis and enriched in pathways of ovarian steroidogenesis and aldosterone synthesis and secretion by KEGG analysis. Among these genes, the mRNA and protein expression of TNF receptor associated factor 7 (TRAF7) was upregulated after FSH treatment. Further study revealed that TRAF7 stimulated the mRNA expression of steroidogenic enzymes steroidogenic acute regulatory protein (StAR) and cytochrome P450 family 11 subfamily A member 1 (CYP11A1) genes and the proliferation of granulosa cells. This is the first study to investigate differences in chicken prehierarchical follicular granulosa cells before and after FSH treatment by using ONT transcriptome sequencing, which provides a reference for a more comprehensive understanding of the molecular mechanism of follicle selection in chicken.
Collapse
Affiliation(s)
- Conghao Zhong
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China; College of Animal Science and Technology, China Agricultural University, Beijing 100194, China
| | - Zhansheng Liu
- Deparment of Animal Gerplasm Resources, Shandong General Station of Animal Husbandry, Jinan 250000, China
| | - Dandan Li
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Li Kang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China
| | - Yunliang Jiang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Veterinary Medicine, Shandong Agricultural University, Tai'an 271018, China.
| |
Collapse
|
4
|
Ramesha KP, Jeyakumar S, Mall S, Vedamurthy GV, Kumaresan A, Devadasn MJ, Kataktalware MA, Arul D, Das DN, Manimaran A. Anti-Müllerian hormone as an endocrine biomarker of reproductive longevity and assessment of Single Nucleotide Polymorphisms in AMH gene of Bos indicus breeds of cattle. Reprod Domest Anim 2022; 57:1450-1464. [PMID: 35916244 DOI: 10.1111/rda.14222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 08/01/2022] [Indexed: 11/29/2022]
Abstract
Anti-Müllerian hormone (AMH) is a member of the TGF-β superfamily produced by follicular granulosa cells (GCs) in women and cattle and is considered an endocrine biomarker of ovarian follicular reserve. The study examined how age and parity influence serum AMH concentration and investigated the presence of Single Nucleotide Polymorphisms in AMH gene in Bos indicus breeds viz Malnad Gidda Amritmahal and Hallikar. All five exons of AMH gene amplified by Polymerase Chain Reaction (PCR) were subjected to Sanger sequencing and identified important SNP and its effects. We observed a highly significant relationship between parity and AMH concentration in Amritmahal cattle, whereas Malnad Gidda and Hallikar breeds did not show a significant difference. We identified one SNP located in exon 5 (rs21402788) with base change A>G, a non-synonymous mutation resulting in a change in amino acid Q>R and the protein product. It is concluded that AMH level could be considered as an indicator of the ovarian reserve and productive herd life (longevity) irrespective of age/parity, especially in Bos indicus breeds of cattle.
Collapse
Affiliation(s)
- K P Ramesha
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - S Jeyakumar
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - Shweta Mall
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - G V Vedamurthy
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - A Kumaresan
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - M Joel Devadasn
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - Mukund A Kataktalware
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - D Arul
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - D N Das
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| | - A Manimaran
- Protegenomics Laboratory, Dairy Production Section, ICAR - National Dairy Research Institute, Southern Regional Station, Adugodi, Bengaluru, India
| |
Collapse
|
5
|
Shen M, Li T, Feng Y, Chen Z, Dou T, Wu P, Wang K, Lu J, Qu L. Exploring the expression and preliminary function of chicken regulator of G protein signalling 3 ( RGS3) gene in follicular development. Br Poult Sci 2022; 63:613-620. [PMID: 35522181 DOI: 10.1080/00071668.2022.2071597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. The following study explored the expression and preliminary function of RGS3. The spatial and temporal expression patterns of the RGS3 gene were analysed in the ovarian stroma of Shendan No. 6 Green shell hens and Hy-line Brown hens at four time points (6, 28, 40 and 52 weeks old), as well as in various organs and follicles of Hy-line Brown hens.2. Based on the genomic and protein sequences of RGS3 in NCBI database, phylogenetic trees were constructed using MEGA-X. The protein interaction network was analysed using STRING. According to the results of protein-protein interaction network and pathways, the mRNA expression levels of RGS3 and three interaction proteins were explored by qRT-PCR in vitro.3. Spatio-temporal expression data revealed that RGS3 mRNA was expressed in all the organs tested, being highest in the hypothalamus. In different follicles, RGS3 mRNA was highly expressed in post-ovulatory follicles, followed by ovarian stroma and large white follicles. The expression levels of RGS3 mRNA in the ovarian stroma were significantly higher in Shendan No. 6 Green shell hens than that in the Hy-line Brown hens at all egg-laying stages.4. The phylogenetic tree results showed that ducks, geese and chickens had higher homology based on the genomic and protein sequence of RGS3. Moreover, chicken RGS3 interacted with GSK3B, RAF1 and BRAF based on STRING prediction. In vitro follicle stimulating hormone (FSH) treatment showed that mRNA expression levels of RGS3 and those of its predicted interacting proteins BRAF and GSK3B decreased with increasing FSH concentration. The results suggested that RGS3 responds to FSH and may play an important role in the regulation follicular development in chicken.
Collapse
Affiliation(s)
- Manman Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 225108, China.,Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China.,Jiangsu Key Laboratory of Animal genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tao Li
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 225108, China
| | - Yuan Feng
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 225108, China
| | - Zikang Chen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 225108, China
| | - Taocun Dou
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China
| | - Ping Wu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, 225108, China
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China
| | - Jian Lu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, 225125, China
| |
Collapse
|
6
|
Expression of Oocyte Vitellogenesis Receptor Was Regulated by C/EBPα in Developing Follicle of Wanxi White Goose. Animals (Basel) 2022; 12:ani12070874. [PMID: 35405862 PMCID: PMC8997188 DOI: 10.3390/ani12070874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/29/2022] Open
Abstract
Yolk precursor was synthesized under regulation of hormone secretion, while the mechanism of its incorporation into follicle is still unknown. The reproductive hormones, oocyte vitellogenesis receptor (OVR) expression at pre-, early-, peak- and ceased-laying period, and localization of Wanxi White goose were determined in this study. The results showed that the concentration of LH was lowest in serum at peak laying period compared to the other periods (p < 0.01). Moreover, the concentration of E2 was highest (p < 0.01) in serum at early laying period than that of other periods. Moreover, the gene expression level of OVR was highest at ceased laying period compared to other periods (p = 0.014) and was higher in developing follicles than other follicles (p < 0.01). The OVR was distributed in the granular cell layer and decreased with the maturation of follicles. Five transcription factors were predicted in the promoter of OVR, then were screened and verified by overexpression in granulosa cells. C/EBPα and MF3 significantly stimulated the expression of OVR. The combined overexpression of C/EBPα and OVR significantly stimulated the transportation of lipid from culture medium to cytoplasm. In conclusion, C/EBPα is the key transcription factor promoting OVR expression in goose follicle granulosa cells.
Collapse
|
7
|
Liu D, Chen Z, Zhao W, Guo L, Sun H, Zhu K, Liu G, Shen X, Zhao X, Wang Q, Ma P, Pan Y. Genome-wide selection signatures detection in Shanghai Holstein cattle population identified genes related to adaption, health and reproduction traits. BMC Genomics 2021; 22:747. [PMID: 34654366 PMCID: PMC8520274 DOI: 10.1186/s12864-021-08042-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/28/2021] [Indexed: 12/26/2022] Open
Abstract
Background Over several decades, a wide range of natural and artificial selection events in response to subtropical environments, intensive pasture and intensive feedlot systems have greatly changed the customary behaviour, appearance, and important economic traits of Shanghai Holstein cattle. In particular, the longevity of the Shanghai Holstein cattle population is generally short, approximately the 2nd to 3rd lactation. In this study, two complementary approaches, integrated haplotype score (iHS) and runs of homozygosity (ROH), were applied for the detection of selection signatures within the genome using genotyping by genome-reduced sequence data from 1092 cows. Results In total, 101 significant iHS genomic regions containing selection signatures encompassing a total of 256 candidate genes were detected. There were 27 significant |iHS| genomic regions with a mean |iHS| score > 2. The average number of ROH per individual was 42.15 ± 25.47, with an average size of 2.95 Mb. The length of 78 % of the detected ROH was within the range of 1–2 MB and 2–4 MB, and 99 % were shorter than 8 Mb. A total of 168 genes were detected in 18 ROH islands (top 1 %) across 16 autosomes, in which each SNP showed a percentage of occurrence > 30 %. There were 160 and 167 genes associated with the 52 candidate regions within health-related QTL intervals and 59 candidate regions within reproduction-related QTL intervals, respectively. Annotation of the regions harbouring clustered |iHS| signals and candidate regions for ROH revealed a panel of interesting candidate genes associated with adaptation and economic traits, such as IL22RA1, CALHM3, ITGA9, NDUFB3, RGS3, SOD2, SNRPA1, ST3GAL4, ALAD, EXOSC10, and MASP2. In a further step, a total of 1472 SNPs in 256 genes were matched with 352 cis-eQTLs in 21 tissues and 27 trans-eQTLs in 6 tissues. For SNPs located in candidate regions for ROH, a total of 108 cis-eQTLs in 13 tissues and 4 trans-eQTLs were found for 1092 SNPs. Eighty-one eGenes were significantly expressed in at least one tissue relevant to a trait (P value < 0.05) and matched the 256 genes detected by iHS. For the 168 significant genes detected by ROH, 47 gene-tissue pairs were significantly associated with at least one of the 37 traits. Conclusions We provide a comprehensive overview of selection signatures in Shanghai Holstein cattle genomes by combining iHS and ROH. Our study provides a list of genes associated with immunity, reproduction and adaptation. For functional annotation, the cGTEx resource was used to interpret SNP-trait associations. The results may facilitate the identification of genes relevant to important economic traits and can help us better understand the biological processes and mechanisms affected by strong ongoing natural or artificial selection in livestock populations. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08042-x.
Collapse
Affiliation(s)
- Dengying Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Zhenliang Chen
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Wei Zhao
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Longyu Guo
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Hao Sun
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China
| | - Kai Zhu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Guanglei Liu
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Xiuping Shen
- Shanghai Agricultural Development Promotion Center, 200335, Shanghai, PR China
| | - Xiaoduo Zhao
- Shanghai Dairy Cattle Breeding Centre Co., Ltd, 201901, Shanghai, P.R. China
| | - Qishan Wang
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China
| | - Peipei Ma
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, 200240, Shanghai, PR China.
| | - Yuchun Pan
- Department of Animal Breeding and Reproduction, College of Animal Science, Zhejiang University, 310058, Hangzhou, PR China.
| |
Collapse
|
8
|
Tarekegn GM, Khayatzadeh N, Liu B, Osama S, Haile A, Rischkowsky B, Zhang W, Tesfaye K, Dessie T, Mwai OA, Djikeng A, Mwacharo JM. Ethiopian indigenous goats offer insights into past and recent demographic dynamics and local adaptation in sub-Saharan African goats. Evol Appl 2021; 14:1716-1731. [PMID: 34295359 PMCID: PMC8287980 DOI: 10.1111/eva.13118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 07/15/2020] [Accepted: 08/13/2020] [Indexed: 12/13/2022] Open
Abstract
Knowledge on how adaptive evolution and human socio-cultural and economic interests shaped livestock genomes particularly in sub-Saharan Africa remains limited. Ethiopia is in a geographic region that has been critical in the history of African agriculture with ancient and diverse human ethnicity and bio-climatic conditions. Using 52K genome-wide data analysed in 646 individuals from 13 Ethiopian indigenous goat populations, we observed high levels of genetic variation. Although runs of homozygosity (ROH) were ubiquitous genome-wide, there were clear differences in patterns of ROH length and abundance and in effective population sizes illustrating differences in genome homozygosity, evolutionary history, and management. Phylogenetic analysis incorporating patterns of genetic differentiation and gene flow with ancestry modelling highlighted past and recent intermixing and possible two deep ancient genetic ancestries that could have been brought by humans with the first introduction of goats in Africa. We observed four strong selection signatures that were specific to Arsi-Bale and Nubian goats. These signatures overlapped genomic regions with genes associated with morphological, adaptation, reproduction and production traits due possibly to selection under environmental constraints and/or human preferences. The regions also overlapped uncharacterized genes, calling for a comprehensive annotation of the goat genome. Our results provide insights into mechanisms leading to genome variation and differentiation in sub-Saharan Africa indigenous goats.
Collapse
Affiliation(s)
- Getinet M. Tarekegn
- Department of Animal Production and TechnologySchool of Animal Sciences and Veterinary MedicineBahir Dar UniversityBahir DarEthiopia
- Department of Animal Breeding and GeneticsSwedish University of Agricultural Sciences (SLU)UppsalaSweden
| | - Negar Khayatzadeh
- Department of Sustainable Agricultural SystemsDivision of Livestock SciencesUniversity of Natural Resources and Life SciencesViennaAustria
| | - Bin Liu
- Inner Mongolia Agricultural UniversityHohhotChina
| | - Sarah Osama
- The University of QueenslandSaint LuciaQLDAustralia
| | - Aynalem Haile
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | - Barbara Rischkowsky
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
| | | | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular BiologyAddis Ababa UniversityAddis AbabaEthiopia
| | - Tadelle Dessie
- International Livestock Research Institute (ILRI)Addis AbabaEthiopia
| | - Okeyo A. Mwai
- International Livestock Research Institute (ILRI)NairobiKenya
| | - Appolinaire Djikeng
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| | - Joram M. Mwacharo
- Small Ruminant GenomicsInternational Centre for Agricultural Research in the Dry Areas (ICARDA)Addis AbabaEthiopia
- Animal and Veterinary Sciences Group, SRUC and Centre for Tropical Livestock Genetics and Health (CTLGH)The Roslin InstituteEaster BushMidlothianUK
| |
Collapse
|
9
|
Wu Y, Shen M, Yin X, Duan Y, Zhang S, Ding H, Chen L, Zhang T, Zhang G, Wang J. The anti-Müllerian hormone gene's second exon is associated with the reproductive performance of Jinghai Yellow chickens. Arch Anim Breed 2021; 64:45-52. [PMID: 34084903 PMCID: PMC8130546 DOI: 10.5194/aab-64-45-2021] [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: 06/01/2020] [Accepted: 12/17/2020] [Indexed: 11/22/2022] Open
Abstract
Anti-Müllerian hormone (AMH), a member of the transforming growth
factor-β superfamily, plays important regulatory roles in follicular
development and sex differentiation. Although much has been learned about
the impact of polymorphisms of AMH on reproduction in animals, the effect on
chicken reproduction is not well explored. In this study, the polymorphism
of five exons of AMH gene and its effect on the reproductive performance of Jinghai
Yellow chickens were studied. Primers for the amplification of AMH exons were
designed, and Sanger sequencing was performed. Finally, only the polymorphism
in the second exon of the AMH gene was found in the present population. Polymorphisms
in the second exon of the AMH gene in 246 Jinghai Yellow hens and their
associations with reproductive traits were analyzed. In total, four single nucleotide polymorphism (SNP)
mutations were detected in the second exon of the AMH gene: g.1868A>C (AA, aa and Aa); g.1883G>A (BB, bb and Bb);
g.1987G>A (CC, cc and Cc); and g.1996A>G (DD, dd and
Dd). Only the mutation of g.1996A>G affected the reproductive
traits: the age of laying first egg (AFE) of dd genotype was
significantly (p<0.01) earlier than that in the DD and Dd hens. Moreover, the egg
number by 300 d old (EN300) of dd individuals was significantly
higher than that of DD and Dd individuals (p<0.01). Thus, we inferred that the dd
genotype is the beneficial genotype. Additionally, AFE and EN300 showed
significantly better performance in both the H2H2 and H7H7 diplotypes
compared with other diplotype individuals (p<0.01). Thus, the H2H2 and H7H7
genotype had the best combination of AFE and EN300. Our study may allow for
molecular marker section in poultry breeding.
Collapse
Affiliation(s)
- Yulin Wu
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Manman Shen
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China.,College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, China
| | - Xuemei Yin
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yanjun Duan
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanshan Zhang
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao Ding
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Lan Chen
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tao Zhang
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Genxi Zhang
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jinyu Wang
- Jiangsu Key Laboratory of Animal Genetic Breeding and Molecular Design, College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| |
Collapse
|
10
|
Qu L, Shen MM, Dou TC, Ma M, Lu J, Wang XG, Guo J, Hu YP, Li YF, Wang KH. Genome-wide association studies for mottled eggs in chickens using a high-density single-nucleotide polymorphism array. Animal 2020; 15:100051. [PMID: 33516007 DOI: 10.1016/j.animal.2020.100051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 10/22/2022] Open
Abstract
Mottled eggs in layer chickens are gaining increasing attention because of the economic impact on the egg industry caused by the reduced sale value of commodity eggs. However, the genetic architecture underlying mottled eggs is not well understood. The genetic architecture underlying the mottled egg trait was investigated using genome-wide association studies (GWAS) by high-density arrays, using a total of 407 pink eggs and 799 blue eggs from an F2 resource population generated by crossing Dongxiang Blue-shelled and White Leghorn chickens. The mottled egg score in blue eggs was found to be higher than that in pink eggs. The single-nucleotide polymorphism heritability of mottled egg at laying day and storage for 7 days was 0.18 and 0.20, respectively. Bivariate GWAS provided 29 significant loci, mainly located on GGA2, GGA3, GGA8, GGA10, GGA15, GGA17, and GGA23, affecting mottled egg on laying day. Candidate genes RIMS2, SLC25A32, RIMBP2, VPS13B, and RGS3 were obtained for mottled eggshell by bivariate GWAS and gene annotation. Our findings provide new insights into the genetic architecture of mottled egg in hens, and demonstrate that a genomic selection method would be profitable for breeding out the mottled egg trait.
Collapse
Affiliation(s)
- L Qu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - M M Shen
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China; College of Biotechnology, Jiangsu University of Science and Technology, 212003 Zhenjiang, Jiangsu, China
| | - T C Dou
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - M Ma
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - J Lu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - X G Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - J Guo
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - Y P Hu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - Y F Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China
| | - K H Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, 225125 Yangzhou, Jiangsu, China.
| |
Collapse
|
11
|
The relationship between the mTOR signaling pathway and ovarian aging in peak-phase and late-phase laying hens. Poult Sci 2020; 100:334-347. [PMID: 33357698 PMCID: PMC7772700 DOI: 10.1016/j.psj.2020.10.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 08/21/2020] [Accepted: 10/06/2020] [Indexed: 11/23/2022] Open
Abstract
The molecular mechanisms underlying reproductive aging in avian species are poorly understood. Previous studies have shown the importance of mechanistic target of rapamycin (mTOR) signaling pathway in aging. In this study, we investigated the relationship between the mTOR signaling pathway and ovarian aging in the peak phase and late phase of egg production in laying hens. The egg production rate and egg quality were tracked for 5 consecutive weeks in 30-week-old and 70-week-old Dawu Jinfeng hens (N = 30/group). During the peak phase (week 35) and late phase (week 75), antioxidant and immune indicators were detected by enzyme-linked immunosorbent assay, and mTOR signaling-related genes (CLIP-170, GRB10, LIPIN-1, ATG1, 4E-BP1, S6K, PKC, RHO, and SGK1) were detected in the follicles by quantitative reverse transcription-PCR technology. The protein expression of key genes (mTOR, PKC, 4EBP1) was evaluated by Western blot analysis. The egg production rate and the antioxidant indexes superoxide dismutase and glutathione peroxidase and the levels of total antioxidant capacity and immunoglobulins (IgM and IgG) were significantly higher at week 35 than those at week 75 (P < 0.01), while malondialdehyde levels were significantly lower (P < 0.01). At week 75, there were fewer follicles in the different stages of development than were detected at week 35. The number of white follicles (large and small) and primary follicles were significantly higher at week 75 than those detected at week 35 (P < 0.01). The mRNA expression of avTOR, CLIP-170, GRB10, LIPIN-1, 4E-BP1, S6K, RHO, and SGK genes in small white follicles (SWF), large white follicles (LWF), F3, F1, and ovary at week 75 was lower than that in the hens at week 35 (P < 0.05). The mRNA expression in small yellow follicle (SYF) was significantly higher than that at week 35 (P < 0.05), while the mRNA expression of ULK1 in SWF, LWF, F3, F1, and ovary at week 75 was higher than that of hens at week 35 (P<0.01), and SYF was lower (P < 0.05). Treatment of chicken granulosa cells with the mTOR agonist MHY1485 significantly enhanced granulocyte proliferation (P < 0.01) and inhibited apoptosis (P < 0.01) and significantly increased avTOR, S6K, 4E-BP1, and PKC gene expression (P < 0.01). The protein expression levels of mTOR, S6K, p-mTOR, and p-S6K were consistent with mRNA expression levels. The mTOR activity is age-specific, and a compensatory enhancement of the mTOR signaling cascade can regulate ovarian follicular development in aged laying hens.
Collapse
|
12
|
Effect of a Diet Supplemented with the Moringa oleifera Seed Powder on the Performance, Egg Quality, and Gene Expression in Japanese Laying Quail under Heat-Stress. Animals (Basel) 2020; 10:ani10050809. [PMID: 32392810 PMCID: PMC7278701 DOI: 10.3390/ani10050809] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/01/2020] [Accepted: 04/04/2020] [Indexed: 01/04/2023] Open
Abstract
This study was conducted to evaluate the effect of three concentrations of the Moringa oleifera seed powder as a feed supplement on the productive performance and egg quality traits of laying Japanese quail (Coturnix japonica) exposed to heat stress. The expression patterns of the genes estrogen receptors (ESR2), follicle-stimulating hormone receptor (FSHR), prolactin receptor (PRLR), and steroidogenic acute regulatory protein (STAR) were estimated in ovaries, using a quantitative real-time polymerase chain reaction. A total of 200 laying quail aged seven weeks were randomly allocated to the following four experimental groups-the control (CNT), T1, T2, and T3 groups; each group comprised 50 quail females with 5 replicates (10 per group). The CNT group was fed a basal diet, whereas the T1, T2, and T3 groups were fed the basal diet supplemented with 0.1%, 0.2%, and 0.3% M. oleifera seed powder, respectively. The results revealed that the T3 group showed the highest hen-day egg production (%) as well as the highest egg yolk index. Feed intake and feed conversion ratio improved significantly (p < 0.05) with increased concentrations of the M. oleifera seed powder supplementation. Furthermore, the mRNA expressions of ESR2, FSHR, and STAR increased significantly in the T3 group, compared to those in the CNT group. Alterations in ovarian gene expressions corresponded to the reproductive patterns of the treated Japanese quail. Thus, it was concluded that the supplementation of the Japanese quail feed with 0.3% M. oleifera seed powder during the laying period might enhance resistance to heat stress and consequently improve egg productivity.
Collapse
|
13
|
Promoter Identification and Transcriptional Regulation of the Goose AMH Gene. Animals (Basel) 2019; 9:ani9100816. [PMID: 31623192 PMCID: PMC6826907 DOI: 10.3390/ani9100816] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 09/28/2019] [Accepted: 10/10/2019] [Indexed: 12/22/2022] Open
Abstract
Simple Summary Anti-Müllerian hormone (AMH) plays a vital role in the development of follicles. We found that the cloning nucleotide sequence of AMH was high homology in geese with other species. Several regulatory elements were identified and transcriptional factors were predicted in the AMH promoter sequence. Through a double-luciferase reporter assay, potential regulatory relationship spanning from −637 to −87 bp were identified. In addition, the mRNA expression of AMH gradually decreased during the development of follicles in geese. In the Chinese hamster ovary (CHO) cell line, the luciferase activity significantly increased by co-expression of AMH and GATA-4. However, when the binding sites of GATA-4 to the promoter of AMH were mutated, the luciferase activity significantly decreased. These results indicated that the transcription of AMH was activated by GATA-4 to inhibit the development of follicles in geese. Abstract Anti-Müllerian hormone (AMH) is recognized as a reliable marker of ovarian reserve. However, the regulatory mechanism of goose AMH gene remains poorly understood. In the present study, both the full-length coding sequence (CDS) and promoter sequence of goose AMH have been cloned. Its CDS consisted of 2013 nucleotides encoding 670 amino acids and the amino acid sequence contained two structural domain: AMH-N and transforming growth factor beta (TGF-β) domain. The obtained promoter sequence spanned from the −2386 bp to its transcription start site (ATG). Core promoter regions and regulatory elements were identified as well as transcription factors were predicted in its promoter sequence. The luciferase activity was the highest spanning from the −331 to −1 bp by constructing deletion promoter reporter vectors. In CHO cells, the luciferase activity significantly increased by co-expression of AMH and GATA binding protein 4 (GATA-4), while that significantly decreased by mutating the binding sites of GATA-4 located in the −778 and −1477 bp. Results from quantitative real-time polymerase chain reaction (qPCR) indicated that levels of AMH mRNA in geese granulosa layers decreased gradually with the increasing follicular diameter. Taken together, it could be concluded that the transcriptional activity of AMH was activated by GATA-4 to inhibit the development of small follicles in goose.
Collapse
|
14
|
Bovo S, Mazzoni G, Bertolini F, Schiavo G, Galimberti G, Gallo M, Dall'Olio S, Fontanesi L. Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes. Sci Rep 2019; 9:7003. [PMID: 31065004 PMCID: PMC6504931 DOI: 10.1038/s41598-019-43297-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 04/16/2019] [Indexed: 12/20/2022] Open
Abstract
Haematological and clinical-biochemical parameters are considered indicators of the physiological/health status of animals and might serve as intermediate phenotypes to link physiological aspects to production and disease resistance traits. The dissection of the genetic variability affecting these phenotypes might be useful to describe the resilience of the animals and to support the usefulness of the pig as animal model. Here, we analysed 15 haematological and 15 clinical-biochemical traits in 843 Italian Large White pigs, via three genome-wide association scan approaches (single-trait, multi-trait and Bayesian). We identified 52 quantitative trait loci (QTLs) associated with 29 out of 30 analysed blood parameters, with the most significant QTL identified on porcine chromosome 14 for basophil count. Some QTL regions harbour genes that may be the obvious candidates: QTLs for cholesterol parameters identified genes (ADCY8, APOB, ATG5, CDKAL1, PCSK5, PRL and SOX6) that are directly involved in cholesterol metabolism; other QTLs highlighted genes encoding the enzymes being measured [ALT (known also as GPT) and AST (known also as GOT)]. Moreover, the multivariate approach strengthened the association results for several candidate genes. The obtained results can contribute to define new measurable phenotypes that could be applied in breeding programs as proxies for more complex traits.
Collapse
Affiliation(s)
- Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Gianluca Mazzoni
- Department of Health Technology, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Francesca Bertolini
- National Institute of Aquatic Resources, Technical University of Denmark (DTU), Lyngby, 2800, Denmark
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Giuliano Galimberti
- Department of Statistical Sciences "Paolo Fortunati", University of Bologna, Via delle Belle Arti 41, 40126, Bologna, Italy
| | - Maurizio Gallo
- Associazione Nazionale Allevatori Suini (ANAS), Via Nizza 53, 00198, Roma, Italy
| | - Stefania Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127, Bologna, Italy.
| |
Collapse
|
15
|
Shen M, Li T, Zhang G, Wu P, Chen F, Lou Q, Chen L, Yin X, Zhang T, Wang J. Dynamic expression and functional analysis of circRNA in granulosa cells during follicular development in chicken. BMC Genomics 2019; 20:96. [PMID: 30700247 PMCID: PMC6354403 DOI: 10.1186/s12864-019-5462-2] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 01/17/2019] [Indexed: 01/17/2023] Open
Abstract
Background Circular RNA (circRNA) is a type of noncoding RNA involved in a variety of biological processes, especially in post-transcriptional regulation. The granulosa cells of follicles play a determining role in ovarian development. However, the function of circRNA in chicken follicles is unclear. To better understand the molecular mechanism underlying follicular development and granulosa cell function, we performed a strategy of second-generation sequencing and linear RNA depletion for granulosa cells from small yellow follicles (SYF, 5–8 mm), the smallest hierarchal follicles (F6, 9–12 mm), and the largest hierarchal follicles (F1, ~ 40 mm). Results We predicted a total of 11,642 circRNAs that distributed on almost all chromosomes. The majority of the splice lengths of circRNAs were 200–500 nt and mainly produced from intron and CDS regions. During follicle growth, differentially expressed (DE) circRNAs showed dynamic changes which were tissue- and stage-specific. The host genes of DE circRNAs were functionally enriched in GTPase activity and several pathways involved in reproduction. Moreover, bioinformatic prediction analysis for circRalGPS2 demonstrated that circRNAs from the same genes may share common miRNA to act as a sponge. The predicted target genes were enriched in various biological processes including cognition, cell communication, and regulation of signaling, and several pathways related to reproduction such as tight junction, oocyte meiosis, progesterone-mediated oocyte maturation, and GnRH signaling. Conclusions This study provides a starting point for further experimental investigations into chicken circRNAs and casts a light on the understanding of follicle development. Electronic supplementary material The online version of this article (10.1186/s12864-019-5462-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Manman Shen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.,Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Science, Yangzhou, 225216, China
| | - Tingting Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| | - Pengfei Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Fuxiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Qiuhong Lou
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Lan Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Xuemei Yin
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
| |
Collapse
|
16
|
Dou T, Shen M, Ma M, Qu L, Li Y, Hu Y, Lu J, Guo J, Wang X, Wang K. Genetic architecture and candidate genes detected for chicken internal organ weight with a 600 K single nucleotide polymorphism array. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:341-349. [PMID: 30056651 PMCID: PMC6409475 DOI: 10.5713/ajas.18.0274] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/23/2018] [Indexed: 12/22/2022]
Abstract
Objective Internal organs indirectly affect economic performance and well-being of animals. Study of internal organs during later layer period will allow full utilization of layer hens. Hence, we conducted a genome-wide association study (GWAS) to identify potential quantitative trait loci or genes that potentially contribute to internal organ weight. Methods A total of 1,512 chickens originating from White Leghorn and Dongxiang Blue-Shelled chickens were genotyped using high-density Affymetrix 600 K single nucleotide polymorphism (SNP) array. We conducted a GWAS, linkage disequilibrium analysis, and heritability estimated based on SNP information by using GEMMA, Haploview and GCTA software. Results Our results displayed that internal organ weights show moderate to high (0.283 to 0.640) heritability. Variance partitioned across chromosomes and chromosome lengths had a linear relationship for liver weight and gizzard weight (R2 = 0.493, 0.753). A total of 23 highly significant SNPs that associated with all internal organ weights were mainly located on Gallus gallus autosome (GGA) 1 and GGA4. Six SNPs on GGA2 affected heart weight. After the final analysis, five top SNPs were in or near genes 5-Hydroxytryptamine receptor 2A, general transcription factor IIF polypeptide 2, WD repeat and FYVE domain containing 2, non-SMC condensin I complex subunit G, and sonic hedgehog, which were considered as candidate genes having a pervasive role in internal organ weights. Conclusion Our findings provide an understanding of the underlying genetic architecture of internal organs and are beneficial in the selection of chickens.
Collapse
Affiliation(s)
- Taocun Dou
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| | - Manman Shen
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Meng Ma
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| | - Liang Qu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China.,College of Animal Science and Technology, Nanjing Agriculture University, Nanjing, Jiangsu 210095, China
| | - Yongfeng Li
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| | - Yuping Hu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| | - Jian Lu
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| | - Jun Guo
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| | - Xingguo Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| | - Kehua Wang
- Jiangsu Institute of Poultry Science, Chinese Academy of Agricultural Sciences, Yangzhou, Jiangsu 225216, China
| |
Collapse
|