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Bruscadin JJ, Cardoso TF, da Silva Diniz WJ, de Souza MM, Afonso J, Vieira D, Malheiros J, Andrade BGN, Petrini J, Ferraz JBS, Zerlotini A, Mourão GB, Coutinho LL, de Almeida Regitano LC. Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle. Genes (Basel) 2022; 13:genes13122336. [PMID: 36553605 PMCID: PMC9777870 DOI: 10.3390/genes13122336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/03/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.
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Affiliation(s)
- Jennifer Jessica Bruscadin
- Center of Biological Sciences and Health, Federal University of São Carlos, São Carlos 13560-000, SP, Brazil
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | | | | | | | - Juliana Afonso
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
| | - Dielson Vieira
- Embrapa Pecuária Sudeste, São Carlos 13560-000, SP, Brazil
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jessica Malheiros
- Federal University of Latin American Integration-UNILA, Foz do Iguaçu 85851-000, PR, Brazil
| | | | - Juliana Petrini
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - José Bento Sterman Ferraz
- Department of Veterinary Medicine, University of São Paulo (FMVZ—USP), Pirassununga 13630-000, SP, Brazil
| | | | - Gerson Barreto Mourão
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
| | - Luiz Lehmann Coutinho
- Center for Functional Genomics, Department of Animal Science, 13400-000, University of São Paulo (ESALQ—USP), Piracicaba 13400-000, SP, Brazil
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Wijayanti D, Zhang S, Yang Y, Bai Y, Akhatayeva Z, Pan C, Zhu H, Qu L, Lan X. Goat SMAD family member 1 (SMAD1): mRNA expression, genetic variants, and their associations with litter size. Theriogenology 2022; 193:11-19. [PMID: 36116245 DOI: 10.1016/j.theriogenology.2022.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 08/24/2022] [Accepted: 09/02/2022] [Indexed: 12/20/2022]
Abstract
SMAD family member 1 (SMAD1) is phosphorylated and activated by the BMP receptors, which help regulate ovulation rate, cell growth, apoptosis, and development. Previously, the genome-wide association study revealed that it has been associated with fecundity in sheep. However, its effect on litter size has not been investigated in goats. Therefore, this study aimed to determine the level of SMAD1 mRNA expression in various tissues and to identify its polymorphisms and their association with litter size in Shaanbei white cashmere goat (SBWC). As a result, RT-qPCR analysis showed that SMAD1 was expressed in various tissues in female SBWC goats, including the ovary (P < 0.05). Importantly, the mRNA expression level in the ovaries of mothers of multi-lambs had a higher level than the mothers of single lambs (P < 0.05). Moreover, two InDels (18-bp and 7-bp) in intron 1 of SMAD1 were polymorphic among ten potential loci. Both 18-bp and 7-bp InDels were significantly correlated with litter size (P = 0.014) and (P = 0.0001), respectively. As shown by the chi-squared test, genotypic distributions of 18-bp and 7-bp were significantly distinct between single-lamb (P = 0.02) and multi-lamb mothers (P = 0.002). Our findings confirm that two InDels in SMAD1 were significantly associated with litter size and suggest that they could be used to improve fertility traits in goat breeding strategies.
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Affiliation(s)
- Dwi Wijayanti
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China; Department of Animal Science, Perjuangan University of Tasikmalaya, Tasikmalaya, West Java, 46115, Indonesia.
| | - Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yuta Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Yangyang Bai
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
| | - Haijing Zhu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Lei Qu
- Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin University, Yulin, Shaanxi, 719000, PR China; Life Science Research Center, Yulin University, Yulin, Shaanxi, 719000, PR China.
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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