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Dos Santos JCG, de Araujo Neto FR, de Oliveira Seno L, de Abreu Santos DJ, de Oliveira KJ, Aspilcueta-Borquis RR, de Oliveira HN, Tonhati H. Genomic analysis of genotype-environment interaction in age at first calving of Murrah buffaloes. J Anim Breed Genet 2024. [PMID: 38837529 DOI: 10.1111/jbg.12885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Revised: 04/24/2024] [Accepted: 05/26/2024] [Indexed: 06/07/2024]
Abstract
Age at first calving (AFC) is a measure of sexual maturity associated with the start of productive life of dairy animals. Additionally, a lower AFC reduces the generation interval and early culling of females. However, AFC has low heritability, making it a trait highly influenced by environmental factors. In this scenario, one way to improve the reproductive performance of buffalo cows is to select robust animals according to estimated breeding value (EBV) using models that include genotype-environment interaction (GEI) with the application of reaction norm models (RNMs). This can be achieved by understanding the genomic basis related to GEI of AFC. Thus, in this study, we aimed to predict EBV considering GEI via the RNM and identify candidate genes related to this component in dairy buffaloes through genome-wide association studies (GWAS). We used 1795 AFC records from three Murrah buffalo herds and formed environmental gradients (EGs) from contemporary group solutions obtained from genetic analysis of 270-day cumulative milk yield. Heritability estimates ranged from 0.15 to 0.39 along the EG. GWAS of the RNM slope parameter identified important genomic regions. The genomic window that explained the highest percentage of genetic variance of the slope (0.67%) was located on BBU1. After functional analysis, five candidate genes were detected, involved in two biological processes. The results suggested the existence of a GEI for AFC in Murrah buffaloes, with reclassification of animals when different environmental conditions were considered. The inclusion of genomic information increased the accuracy of breeding values for the intercept and slope of the reaction norm. GWAS analysis suggested that important genes associated with the AFC reaction norm slope were possibly also involved in biological processes related to lipid metabolism and immunity.
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Affiliation(s)
| | | | | | | | | | | | | | - Humberto Tonhati
- Faculdade de Ciências Agrárias e Veterinárias de Jaboticabal - UNESP, Jaboticabal, São Paulo, Brazil
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Amin AMS, Salem MMI, Ashour AF, El Nagar AG. Principal component analysis of phenotypic and breeding value data for semen traits in Egyptian buffalo bulls. Trop Anim Health Prod 2024; 56:135. [PMID: 38647705 PMCID: PMC11035465 DOI: 10.1007/s11250-024-03975-3] [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: 03/27/2023] [Accepted: 03/28/2024] [Indexed: 04/25/2024]
Abstract
Buffalo bull semen traits are economically important traits that influence farm fertility and profitability. Genetic improvement of semen characteristics is an important detail of the genetic improvement. This study was conducted to assess the relationship between the breeding values as well as the phenotypic values for semen traits (VOL, MM, LS, AS and CONC) of the Egyptian buffalo bulls. A total of 7761 normal semen ejaculates were collected and characterized at ILMTC laboratory from 26 bulls from 2009 to 2019. For VOL, MM, LS, AS, and CONC, the actual means were 3.89 mL, 62.37%, 60.64%, 3.94%, and 0.67 × 109 sperm/mL, respectively. The prediction of breeding values for semen traits was estimated using a Bayesian procedure. The estimated standardized EBVs and phenotypic values were used in the principal component analysis (PCA). Of five PCs, one PC (PC1) had > 1 eigenvalues that was responsible for 87.19% of the total variation of SEBV, and two PCs had > 1 eigenvalues that were responsible for 59.61% and 21.35% of the total variation of the phenotypic values. Together, PC1 and PC2 accounted for 97.97% of the total variance of SEBV and 80.96% of the total variance of phenotypic values. A graphs of the first two components showed the traits separated into two different directions by group. This indicates each group was under similar genetic influence. Therefore, selection can be done separately for each group without influencing the other. Principal component analysis reduced variables to describe the key information in buffalo semen data.
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Affiliation(s)
- Amin M S Amin
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Ministry of Agriculture and Land Reclamation, Dokki, Giza, Egypt.
| | - Mohamed M I Salem
- Department of Animal and Fish Production, Faculty of Agriculture, University of Alexandria, Alexandria, 21545, Egypt
| | - Ayman F Ashour
- Animal Production Research Institute (APRI), Agricultural Research Center (ARC), Ministry of Agriculture and Land Reclamation, Dokki, Giza, Egypt
| | - Ayman G El Nagar
- Department of Animal Production, Faculty of Agriculture at Moshtohor, Benha University, Benha, 13736, Egypt
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Yang Y, Gan M, Yang X, Zhu P, Luo Y, Liu B, Zhu K, Cheng W, Chen L, Zhao Y, Niu L, Wang Y, Zhang H, Wang J, Shen L, Zhu L. Estimation of genetic parameters of pig reproductive traits. Front Vet Sci 2023; 10:1172287. [PMID: 37415962 PMCID: PMC10321596 DOI: 10.3389/fvets.2023.1172287] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 06/01/2023] [Indexed: 07/08/2023] Open
Abstract
Introduction In this study, we aimed to estimate the genetic parameters of the reproductive traits in three popular commercial pig breeds: Duroc, Landrace, and Yorkshire. Additionally, we evaluated the factors that influence these traits. Method We collected data from a large number of litters, including 1,887 Duroc, 21,787 Landrace, and 74,796 Yorkshire litters. Using the ASReml-R software to analyze 11 traits, which included: total number of pigs born (TNB); number of piglets born alive (NBA); number of piglets born healthy (NBH); number of piglets born weak (NBW); number of new stillborn piglets (NS); number of old stillborn piglets (OS); number of piglets born with malformation (NBM); number of mummified piglets (NM); total litter birthweight (LBW); litter average weight (LAW); duration of gestational period (GP). We investigated the effects of 4 fixed factors on the genetic parameters of these traits. Results Among the 11 reproductive-related traits, the gestational period belonged to the medium heritability traits (0.251-0.430), while remaining traits showed low heritability, ranging from 0.005 to 0.159. TNB, NBA, NBH, LBW had positive genetic correlation (0.737 ~ 0.981) and phenotype correlation (0.711 ~ 0.951). There was a negative genetic correlation between NBW and LAW (-0.452 ~ -0.978) and phenotypic correlation (-0.380 ~ -0.873). LBW was considered one of the most reasonable reproductive traits that could be used for breeding improvement. Repeatability of the three varieties was within the range of 0.000-0.097. In addition, the fixed effect selected in this study had a significant effect on Landrace and Yorkshire (p < 0.05). Discussion We found a positive correlation between LBW and TNB, NBA, and NBH, suggesting the potential for multi-trait association breeding. Factors such as farm, farrowing year, breeding season, and parity should be taken into consideration in practical production, as they may impact the reproductive performance of breeding pigs.
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Affiliation(s)
- Yiting Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Mailin Gan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xidi Yang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Peng Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yi Luo
- Sichuan Dekon Livestock Foodstuff Group, Chengdu, China
| | - Bin Liu
- Sichuan Dekon Livestock Foodstuff Group, Chengdu, China
| | - Kangping Zhu
- Sichuan Dekon Livestock Foodstuff Group, Chengdu, China
| | | | - Lei Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Ye Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Hui Zhang
- Sichuan Center for Animal Disease Control, Chengdu, China
| | - Jingyong Wang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Linyuan Shen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-Omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
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Easa AA, El-Aziz AHA, Barbary ASAE, Kostomakhin NM, Nasr MAF, Imbabi TA. Genetic parameters of production and reproduction traits of Egyptian buffaloes under subtropical conditions. Trop Anim Health Prod 2022; 54:270. [PMID: 36001186 PMCID: PMC9402497 DOI: 10.1007/s11250-022-03251-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 07/29/2022] [Indexed: 11/26/2022]
Abstract
This research was aimed to investigate the production and reproduction traits and their genetic parameters of Egyptian buffaloes under subtropical environment. Heritability, phenotypic, and genetic parameters were estimated for productive and reproduction traits of first parity This study revealed the averages TMY, 305-dMY, LL, BW, DP, SP, CI, and AFC were 2260, 2150 kg, 271 days, 38.63 kg, 210.50 days, 195.20 days, 586.86 days, and 36.61 months, respectively. The heritability estimates for productive traits of the first lactation were 0.61, 0.52, 0.47, 0.20, and 0.23 for TMY, 305-dMY, LL, DP, and BW, respectively. Heritability estimates for reproductive traits SP, CI, and AFC were 0.07, 0.09, and 0.35, respectively. Genetic correlations of most of the investigated first parity traits were positive, with an exception of DP. The genetic correlation was negative between SP and BW, and between AFC and LL. Phenotypic correlations of the first parity among all investigated traits were positive except between DP and TMY, 305-dMY, LL, BW, and AFC. High and moderate heritability estimates indicated that the opportunity of genetic upgrading of these parameters could be achieved owing to sire selection. Selection for high milk yield will be associated with genetic improvement in lactation period and birth weight.
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Affiliation(s)
- Ahmed A Easa
- Department of Animal and Poultry Production, Faculty of Agriculture, Damanhour University, Abadiyyat Damanhur, Egypt
| | - Ayman H Abd El-Aziz
- Department of Animal Husbandry and Animal Wealth Development, Faculty of Veterinary Medicine, Damanhour University, Abadiyyat Damanhur, Egypt
| | - Adel S A El Barbary
- Department of Animal Production, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Nikolay M Kostomakhin
- Department of Dairy and Beef Cattle Breeding, Russian State Agrarian University - Moscow Agriculture Academy named After K.A. Timiryazev, Moscow, Russia
| | - Mohammed A F Nasr
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Zagazig University, Sharkia, Egypt.
| | - Tharwat A Imbabi
- Department of Animal Production, Faculty of Agriculture, Benha University, Benha, Egypt
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