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Volkova NA, Romanov MN, Abdelmanova AS, Larionova PV, German NY, Vetokh AN, Shakhin AV, Volkova LA, Sermyagin AA, Anshakov DV, Fisinin VI, Griffin DK, Sölkner J, Brem G, McEwan JC, Brauning R, Zinovieva NA. Genome-Wide Association Study Revealed Putative SNPs and Candidate Genes Associated with Growth and Meat Traits in Japanese Quail. Genes (Basel) 2024; 15:294. [PMID: 38540354 PMCID: PMC10970133 DOI: 10.3390/genes15030294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/08/2024] [Accepted: 02/23/2024] [Indexed: 06/14/2024] Open
Abstract
The search for SNPs and candidate genes that determine the manifestation of major selected traits is one crucial objective for genomic selection aimed at increasing poultry production efficiency. Here, we report a genome-wide association study (GWAS) for traits characterizing meat performance in the domestic quail. A total of 146 males from an F2 reference population resulting from crossing a fast (Japanese) and a slow (Texas White) growing breed were examined. Using the genotyping-by-sequencing technique, genomic data were obtained for 115,743 SNPs (92,618 SNPs after quality control) that were employed in this GWAS. The results identified significant SNPs associated with the following traits at 8 weeks of age: body weight (nine SNPs), daily body weight gain (eight SNPs), dressed weight (33 SNPs), and weights of breast (18 SNPs), thigh (eight SNPs), and drumstick (three SNPs). Also, 12 SNPs and five candidate genes (GNAL, DNAJC6, LEPR, SPAG9, and SLC27A4) shared associations with three or more traits. These findings are consistent with the understanding of the genetic complexity of body weight-related traits in quail. The identified SNPs and genes can be used in effective quail breeding as molecular genetic markers for growth and meat characteristics for the purpose of genetic improvement.
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Affiliation(s)
- Natalia A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Michael N. Romanov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK;
| | - Alexandra S. Abdelmanova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Polina V. Larionova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Nadezhda Yu. German
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Anastasia N. Vetokh
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Alexey V. Shakhin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Ludmila A. Volkova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Alexander A. Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
| | - Dmitry V. Anshakov
- Breeding and Genetic Center “Zagorsk Experimental Breeding Farm”—Branch of the Federal Research Center “All-Russian Poultry Research and Technological Institute”, Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Vladimir I. Fisinin
- Federal Research Center “All-Russian Poultry Research and Technological Institute” of the Russian Academy of Sciences, Sergiev Posad 141311, Moscow Oblast, Russia;
| | - Darren K. Griffin
- School of Biosciences, University of Kent, Canterbury CT2 7NJ, Kent, UK;
| | - Johann Sölkner
- Institute of Livestock Sciences (NUWI), University of Natural Resources and Life Sciences Vienna, 1180 Vienna, Austria;
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, 1210 Vienna, Austria;
| | - John C. McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Rudiger Brauning
- AgResearch, Invermay Agricultural Centre, Mosgiel 9053, New Zealand; (J.C.M.); (R.B.)
| | - Natalia A. Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk 142132, Moscow Oblast, Russia; (N.A.V.); (A.S.A.); (P.V.L.); (N.Y.G.); (A.N.V.); (A.V.S.); (L.A.V.); (A.A.S.)
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Wang X, Zhao Y, Bai J. Research Note: Association of LEPR gene polymorphism with growth and carcass traits in Savimalt and French Giant meat-type quails. Poult Sci 2023; 102:103047. [PMID: 37812872 PMCID: PMC10568288 DOI: 10.1016/j.psj.2023.103047] [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: 07/07/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 10/11/2023] Open
Abstract
The leptin receptor (LEPR) gene is a member of the class I cytokine receptor family, which plays an important role in weight regulation, fat accumulation and neuroendocrine function in animals. This study aimed to explore the association of single nucleotide polymorphisms (SNPs) of the LEPR gene with growth and carcass traits in meat-type quail by PCR amplification and DNA direct sequencing. In this study, genomic DNA was extracted from blood samples of 36 female Savimalt (SV) quails and 49 female French Giant (FG) quails. Growth traits (measured at 3 or 5 wk) and carcass traits (measured at 5 wk) were used for LEPR gene association analysis. The results showed the existence of 9 SNPs (T81C, G90T, C187A, A191G, A219G, G258A, C286T, G346A, and G373A) of the LEPR gene in the 2 quail strains. The statistical analyses indicated that these SNPs of LEPR gene was significantly associated with shank circumference (SC), shank length (SL), breastbone length (BBL), heart rate (HR), and whole net carcass rate (WNCR) of FG (P < 0.05); chest width (CW), body length (BL), leg muscle rate (LMR), whole net carcass rate (WNCR), and heart rate (HR) of SV (P < 0.05). While haplotypes showed significant effect on SL, BBL, heart weight (HW), WNCR, and HR of FG (P < 0.05). Therefore, the LEPR gene may serve as a molecular genetic marker for improving growth and carcass traits in quails.
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Affiliation(s)
- Xinle Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, 471023, China
| | - Yonggang Zhao
- China Animal Health and Epidemiology Center, Qingdao, Shandong, 266032, China
| | - Junyan Bai
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, Henan, 471023, China.
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Ramos Z, Garrick DJ, Blair HT, Vera B, Ciappesoni G, Kenyon PR. Genomic Regions Associated with Wool, Growth and Reproduction Traits in Uruguayan Merino Sheep. Genes (Basel) 2023; 14:167. [PMID: 36672908 PMCID: PMC9858812 DOI: 10.3390/genes14010167] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 12/29/2022] [Accepted: 01/04/2023] [Indexed: 01/11/2023] Open
Abstract
The aim of this study was to identify genomic regions and genes associated with the fiber diameter (FD), clean fleece weight (CFW), live weight (LW), body condition score (BCS), pregnancy rate (PR) and lambing potential (LP) of Uruguayan Merino sheep. Phenotypic records of approximately 2000 mixed-age ewes were obtained from a Merino nucleus flock. Genome-wide association studies were performed utilizing single-step Bayesian analysis. For wool traits, a total of 35 genomic windows surpassed the significance threshold (PVE ≥ 0.25%). The proportion of the total additive genetic variance explained by those windows was 4.85 and 9.06% for FD and CFW, respectively. There were 42 windows significantly associated with LWM, which collectively explained 43.2% of the additive genetic variance. For BCS, 22 relevant windows accounted for more than 40% of the additive genetic variance, whereas for the reproduction traits, 53 genomic windows (24 and 29 for PR and LP, respectively) reached the suggestive threshold of 0.25% of the PVE. Within the top 10 windows for each trait, we identified several genes showing potential associations with the wool (e.g., IGF-1, TGFB2R, PRKCA), live weight (e.g., CAST, LAP3, MED28, HERC6), body condition score (e.g., CDH10, TMC2, SIRPA, CPXM1) or reproduction traits (e.g., ADCY1, LEPR, GHR, LPAR2) of the mixed-age ewes.
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Affiliation(s)
- Zully Ramos
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Dorian J. Garrick
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Hugh T. Blair
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
| | - Brenda Vera
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Gabriel Ciappesoni
- National Research Program on Meat and Wool Production, Instituto Nacional de Investigación Agropecuaria, INIA Las Brujas, Ruta 48 Km 10, Canelones 90100, Uruguay
| | - Paul R. Kenyon
- School of Agriculture and Environment, Massey University, Palmerston North 4410, New Zealand
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Zhao YX, Gao GX, Zhou Y, Guo CX, Li B, El-Ashram S, Li ZL. Genome-wide association studies uncover genes associated with litter traits in the pig. Animal 2022; 16:100672. [PMID: 36410176 DOI: 10.1016/j.animal.2022.100672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 10/17/2022] [Accepted: 10/18/2022] [Indexed: 12/24/2022] Open
Abstract
Litter traits are critical economic variables in the pig industry as they represent a production indicator that can serve to determine sow fertility. In this study, a genome-wide association study on litter traits, including total number born (TNB), number born alive (NBA), litter birth weight (LBW), average birth weight (ABW), and piglet uniformity (PU), was carried out on two pig breeds (Yorkshire and Landrace). A total of 3 637 pigs of both breeds were genotyped using the GeneSeek GGP Porcine 50K SNP BeadChip. A mixed linear model (MLM) and fixed and random model circulating probability unification (FarmCPU) were employed in the genome-wide association studies for litter traits using combined data from the two pig breeds and data from each breed separately. Additionally, the heritability of traits was estimated using three methods-pedigree-based best linear unbiased prediction (PBLUP), genomic best linear unbiased prediction (GBLUP), and single-step best linear unbiased prediction (ssGBLUP)-and was found to lie between 0.065 and 0.1289, 0.0478 and 0.0938, 0.0793 and 0.0935, 0.1862 and 0.2163, and 0.0327 and 0.0419 for TNB, NBA, LBW, ABW, and PU, respectively. We also compared the genomic prediction accuracies and unbiasedness for litter traits of the three BLUP models. Our results indicated that the ssGBLUP method provided higher predictive accuracies and more rational unbiasedness compared with the PBLUP and GBLUP methodologies. Furthermore, based on their possible roles, eight candidate genes (INHBA, LEPR, HDHD2, CTNND2, RNF216, HMX1, PAPPA2, and NTN1) were identified as being linked with litter traits. In the middle of the test, these genes were found to be connected with pig metabolism and ovulation rate. Our results provide the insights into the genetic architecture of litter traits in pigs, and the potential single nucleotide polymorphisms (SNPs) and candidate genes identified may benefit economic profits in pig-breeding industry and contribute to improve litter traits.
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Affiliation(s)
- Y X Zhao
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China; Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - G X Gao
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China
| | - Y Zhou
- Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - C X Guo
- Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - B Li
- Guangxi Yangxiang Agricultural and Animal Husbandry Co, Ltd, Guigang, Guangxi 537100, China
| | - S El-Ashram
- Faculty of Science, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt
| | - Z L Li
- School of Life Science and Engineering, Foshan University, Foshan, Guangdong 528000, China.
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Lakhssassi K, Lahoz B, Sarto P, Iguácel LP, Folch J, Alabart JL, Serrano M, Calvo JH. Genome-Wide Association Study Demonstrates the Role Played by the CD226 Gene in Rasa Aragonesa Sheep Reproductive Seasonality. Animals (Basel) 2021; 11:ani11041171. [PMID: 33921837 PMCID: PMC8074133 DOI: 10.3390/ani11041171] [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: 02/23/2021] [Revised: 04/14/2021] [Accepted: 04/15/2021] [Indexed: 01/02/2023] Open
Abstract
Simple Summary To elucidate the genetic basis of reproductive seasonality in Rasa Aragonesa sheep breed, we performed a genome-wide association study (GWAS) in order to detect single nucleotide polymorphisms (SNPs) or regions associated with traits related to ovarian function and behavioural signs of estrous. The GWAS included 205 ewes with genotypes for 583882 SNPs. Only one SNP overcame the genome-wide significance level. Nine potential SNPs overcame the chromosome-wise significance level (FDR 10%). Gene annotation demonstrated that CD226molecule (CD226) and neuropeptide Y (NPY) genes that could be involved in reproductive seasonality were close to the significant SNPs. To validate the results, we sequenced the entire coding region of the NPY gene and four exons of the CD226 gene to search for polymorphisms that could be involved in the phenotypes studied. Two synonymous and two nonsynonymous SNPs in the NPY and CD226 genes, respectively, were genotyped in the whole population. We demonstrated that the AA genotype of the SNP rs404360094 located in exon 3 of the CD226 gene was associated with higher and lower total days of anoestrus and oestrous cycling months, respectively. Therefore, this SNP could be utilized as a genetic marker for assisted selection marker to reduce seasonality. Abstract A genome-wide association study (GWAS) was used to identify genomic regions influencing seasonality reproduction traits in Rasa Aragonesa sheep. Three traits associated with either ovarian function based on blood progesterone levels (total days of anoestrus and progesterone cycling months) or behavioral signs of oestrous (oestrous cycling months) were studied. The GWAS included 205 ewes genotyped using the 50k and 680k Illumina Ovine Beadchips. Only one SNP associated with the progesterone cycling months overcame the genome-wide significance level (rs404991855). Nine SNPs exhibited significant associations at the chromosome level, being the SNPs rs404991855 and rs418191944, that are located in the CD226 molecule (CD226) gene, associated with the three traits. This gene is related to reproductive diseases. Two other SNPs were located close to the neuropeptide Y (NPY) gene, which is involved in circadian rhythms. To validate the GWAS, partial characterization of both genes by Sanger sequencing, and genotyping of two synonymous and two nonsynonymous SNPs in the NPY and CD226 genes, respectively, were performed. SNP association analysis showed that only SNP rs404360094 in the exon 3 of the CD226 gene, which produces an amino acid substitution from asparagine (uncharged polar) to aspartic acid (acidic), was associated with the three seasonality traits. Our results suggest that the CD226 gene may be involved in the reproductive seasonality in Rasa Aragonesa.
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Affiliation(s)
- Kenza Lakhssassi
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
- INRA, Instituts Morocco, 6356 Rabat, Morocco
| | - Belén Lahoz
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Pilar Sarto
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Laura Pilar Iguácel
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - José Folch
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - José Luis Alabart
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
| | - Malena Serrano
- Departamento de Mejora Genética Animal INIA, 28040 Madrid, Spain;
| | - Jorge Hugo Calvo
- Centro de Investigación y Tecnología Agroalimentaria de Aragón, Instituto Agroalimentario de Aragón (IA2) (CITA–Zaragoza University), 50059 Zaragoza, Spain; (K.L.); (B.L.); (P.S.); (L.P.I.); (J.F.); (J.L.A.)
- The Aragonese Foundation for Research and Development (ARAID), 50018 Zaragoza, Spain
- Correspondence: ; Tel.: +34976716471
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