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Wijayanti D, Luo Y, Bai Y, Pan C, Qu L, Guo Z, Lan X. New insight into copy number variations of goat SMAD2 gene and their associations with litter size and semen quality. Theriogenology 2023; 206:114-122. [PMID: 37229957 DOI: 10.1016/j.theriogenology.2023.05.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/27/2023]
Abstract
Copy number variations (CNV) contribute significantly to genetic variations. Numerous studies have shown that CNV affects phenotypic traits in livestock. The SMAD family member 2 (SMAD2) is a leading candidate gene in reproduction and has a crucial effect on litter size. Additionally, SMAD2 is also required for male reproduction and influences male germ cell development. However, there are no reports on investigating the effect of CNVs in the SMAD2 gene on reproductive traits in goat. Therefore, the goal of this study was to explore associations between CNV of the SMAD2 gene and litter size and semen quality in Shaanbei white cashmere (SBWC) goats. In this study, two CNVs within the SMAD2 were identified in 352 SBWC goats (50 males and 302 females). The association analysis revealed that only CNV2 was significantly associated with female goat first-born litter size (P = 3.59 × 10-4), male semen concentration (P < 0.01), ejaculation volume, live sperm count, and sperm deformity rate (P < 0.05). In terms of phenotypic performance, the individuals with loss genotypes outperformed those with other genotypes. CNV1 and CNV2 genotype combinations containing their dominant genotypes were also associated with goat litter size (P = 1.7 × 10-5), but no differences in semen quality were found. In summary, CNV2 of the SMAD2 gene is useful for molecular marker-assisted selection breeding, as it is associated with essential goat reproductive traits.
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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, Shaanxi, 712100, China; Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, 46115, Indonesia.
| | - Yunyun Luo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yangyang Bai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, 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, Shaanxi, 712100, 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.
| | - Zhengang Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China; Institute of Animal Husbandry and Veterinary Science of Bijie City, Guizhou, 551700, 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, Shaanxi, 712100, China.
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Talouarn E, Bardou P, Palhière I, Oget C, Clément V, Tosser-Klopp G, Rupp R, Robert-Granié C. Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats. BMC Genet 2020; 21:19. [PMID: 32085723 PMCID: PMC7035711 DOI: 10.1186/s12863-020-0826-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/13/2020] [Indexed: 01/17/2023] Open
Abstract
Background Goats were domesticated 10,500 years ago to supply humans with useful resources. Since then, specialized breeds that are adapted to their local environment have been developed and display specific genetic profiles. The VarGoats project is a 1000 genomes resequencing program designed to cover the genetic diversity of the Capra genus. In this study, our main objective was to assess the use of sequence data to detect genomic regions associated with traits of interest in French Alpine and Saanen breeds. Results Direct imputation from the GoatSNP50 BeadChip genotypes to sequence level was investigated in these breeds using FImpute and different reference panels: within-breed, all Capra hircus sequenced individuals, European goats and French mainland goats. The best results were obtained with the French goat panel with allele and genotype concordance rates reaching 0.86 and 0.75 in the Alpine and 0.86 and 0.73 in the Saanen breed respectively. Mean correlations tended to be low in both breeds due to the high proportion of variants with low frequencies. For association analysis, imputation was performed using FImpute for 1129 French Alpine and Saanen males using within-breed and French panels on 23,338,436 filtered variants. The association results of both imputation scenarios were then compared. In Saanen goats, a large region on chromosome 19 was significantly linked to semen volume and milk yield in both scenarios. Significant variants for milk yield were annotated for 91 genes on chromosome 19 in Saanen goats. For semen volume, the annotated genes include YBOX2 which is related to azoospermia or oligospermia in other species. New signals for milk yield were detected on chromosome 2 in Alpine goats and on chromosome 5 in Saanen goats when using a multi-breed panel. Conclusion Even with very small reference populations, an acceptable imputation quality can be achieved in French dairy goats. GWAS on imputed sequences confirmed the existence of QTLs and identified new regions of interest in dairy goats. Adding identified candidates to a genotyping array and sequencing more individuals might corroborate the involvement of identified regions while removing potential imputation errors.
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Affiliation(s)
- Estelle Talouarn
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France.
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France.,Sigenae, INRAE, 31326, Castanet-Tolosan, France
| | - Isabelle Palhière
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Claire Oget
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | | | | | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
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Semen characteristics of purebred and crossbred male rabbits. PLoS One 2015; 10:e0128435. [PMID: 26020961 PMCID: PMC4447379 DOI: 10.1371/journal.pone.0128435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2015] [Accepted: 04/27/2015] [Indexed: 11/19/2022] Open
Abstract
The aim of this investigation was to evaluate the semen quality traits of purebred male rabbits and their crosses under subtropical Egyptian conditions. A full 3 x 3 diallel crossing was performed for producing the first generation progeny of New Zealand White (N), Flander (F) and Rex (R) breeds. The highest ejaculate volume (p< 0.05) and percentage of live sperms (p<0.01) with the lowest percentage of sperm cell morphological abnormalities (p<0.05) had been recorded in the NF bucks. Moreover, they possessed positive estimates of direct heterosis for ejaculate volume, mass motility (Mm), individual motility (Im) and sperm cell concentration (SCC). On the contrary, pH had negative estimates of direct heterosis in all crosses and their reciprocal. Semen pH was negatively correlated with SCC (r = -0.18), Mm (r = -0.13) and Im (r = -0.23). In conclusion, the superiority of crossbreeding was particularly obvious in the New Zealand White x Flander males, which cumulated heterosis and favorable maternal effects of the Flander dams.
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