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Ma T, Liu Y, Wei X, Xue Q, Zheng Z, Xu X. Polymorphism of coupled indels in porcine TNNC2 alters its transcript splicing and is associated with meat quality traits. Anim Genet 2022; 53:175-182. [PMID: 34989011 DOI: 10.1111/age.13167] [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: 06/28/2021] [Revised: 11/29/2021] [Accepted: 12/16/2021] [Indexed: 11/30/2022]
Abstract
The TNNC2 gene encodes the fast-skeletal C subunit of the troponin complex that plays a vital role in the regulation of striated muscle contraction and could be a candidate gene for pork quality. Here, we identified coupled insertion/deletion (indel) variants, a 17-bp insertion and an 11-bp deletion, in porcine TNNC2. The coupled indel variants provide an alternative splicing donor site and cause a 42-bp truncation in the first exon of TNNC2-201, leading to increased expression of TNNC2-201. Polymorphism of the two indel variants is associated with the average backfat thickness (p = 3.16 × 10-3 ), pH value 24 h post-slaughter (p = 4.31 × 10-4 ), intramuscular fat (IMF) content (p = 1.54 × 10-2 ), and myofiber cross-sectional area (p = 2.86 × 10-2 ) of longissimus dorsi in a population of 425 Duroc (♂) × Luchuan (♀) pigs. In an independent population of 1,304 commercial hybrid pigs, we further confirmed that it is associated with the IMF content (p = 1.75 × 10-4 ), pH value 45 min post-slaughter (p = 6.34 × 10-3 ), and drip loss (p = 2.88 × 10-2 ) of the longissimus dorsi muscle. An increased frequency of the mutant allele is linked to increased IMF content, smaller myofibers, and a relatively moderate pH value. Furthermore, we detected a mutant allele frequency of 96.67% in Luchuan pigs and 86.67% in Tongcheng pigs, whereas the frequency was 0.91% in Duroc pigs, 2.04% in Landrace pigs, and 0% in Yorkshire and Pietrain pigs, indicating its opposing distributions in lean-type and Chinese local pig breeds. The present results establish coupled indel variants of TNNC2 as a novel molecular marker for meat quality improvement.
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Affiliation(s)
- Tingting Ma
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yan Liu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xingyu Wei
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qianjin Xue
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Zhiwei Zheng
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xuewen Xu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China.,The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.,Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Wuhan, China
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Guglielmi C, Scarpitta R, Gambino G, Conti E, Bellè F, Tancredi M, Cervelli T, Falaschi E, Cosini C, Aretini P, Congregati C, Marino M, Patruno M, Pilato B, Spina F, Balestrino L, Tenedini E, Carnevali I, Cortesi L, Tagliafico E, Tibiletti MG, Tommasi S, Ghilli M, Vivanet C, Galli A, Caligo MA. Detection of Germline Variants in 450 Breast/Ovarian Cancer Families with a Multi-Gene Panel Including Coding and Regulatory Regions. Int J Mol Sci 2021; 22:ijms22147693. [PMID: 34299313 PMCID: PMC8305371 DOI: 10.3390/ijms22147693] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Revised: 07/10/2021] [Accepted: 07/14/2021] [Indexed: 12/24/2022] Open
Abstract
With the progress of sequencing technologies, an ever-increasing number of variants of unknown functional and clinical significance (VUS) have been identified in both coding and non-coding regions of the main Breast Cancer (BC) predisposition genes. The aim of this study is to identify a mutational profile of coding and intron-exon junction regions of 12 moderate penetrance genes (ATM, BRIP1, CDH1, CHEK2, NBN, PALB2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53) in a cohort of 450 Italian patients with Hereditary Breast/Ovarian Cancer Syndrome, wild type for germline mutation in BRCA1/2 genes. The analysis was extended to 5′UTR and 3′UTR of all the genes listed above and to the BRCA1 and BRCA2 known regulatory regions in a subset of 120 patients. The screening was performed through NGS target resequencing on the Illumina platform MiSeq. 8.7% of the patients analyzed is carriers of class 5/4 coding variants in the ATM (3.6%), BRIP1 (1.6%), CHEK2 (1.8%), PALB2 (0.7%), RAD51C (0.4%), RAD51D (0.4%), and TP53 (0.2%) genes, while variants of uncertain pathological significance (VUSs)/class 3 were identified in 9.1% of the samples. In intron-exon junctions and in regulatory regions, variants were detected respectively in 5.1% and in 32.5% of the cases analyzed. The average age of disease onset of 44.4 in non-coding variant carriers is absolutely similar to the average age of disease onset in coding variant carriers for each proband’s group with the same cancer type. Furthermore, there is not a statistically significant difference in the proportion of cases with a tumor onset under age of 40 between the two groups, but the presence of multiple non-coding variants in the same patient may affect the aggressiveness of the tumor and it is worth underlining that 25% of patients with an aggressive tumor are carriers of a PTEN 3′UTR-variant. This data provides initial information on how important it might be to extend mutational screening to the regulatory regions in clinical practice.
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Affiliation(s)
- Chiara Guglielmi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Rosa Scarpitta
- Division of Pathology, University of Pisa, 56126 Pisa, Italy;
| | - Gaetana Gambino
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy;
| | - Eleonora Conti
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Francesca Bellè
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
| | - Mariella Tancredi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Tiziana Cervelli
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
| | - Elisabetta Falaschi
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Cinzia Cosini
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
| | - Paolo Aretini
- Section of Oncological Genomics, Fondazione Pisana per la Scienza, 56017 Pisa, Italy;
| | - Caterina Congregati
- Division of Internal Medicine, University Hospital of Pisa, 56126 Pisa, Italy;
| | - Marco Marino
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | - Margherita Patruno
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Brunella Pilato
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Francesca Spina
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Luisa Balestrino
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Elena Tenedini
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | - Ileana Carnevali
- Ospedale di Circolo ASST Settelaghi, 21100 Varese, Italy; (I.C.); (M.G.T.)
| | - Laura Cortesi
- Department of Oncology, Haematology and Respiratory Diseases, University Hospital of Modena, 41124 Modena, Italy;
| | - Enrico Tagliafico
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy; (M.M.); (E.T.); (E.T.)
| | | | - Stefania Tommasi
- IRCCS Istituto Tumori “Giovanni Paolo II”, 70124 Bari, Italy; (M.P.); (B.P.); (S.T.)
| | - Matteo Ghilli
- Breast Cancer Center, University Hospital, 56126 Pisa, Italy;
| | - Caterina Vivanet
- SC Medical Genetics, ASSL Cagliari, 09126 Cagliari, Italy; (F.S.); (L.B.); (C.V.)
| | - Alvaro Galli
- Functional Genetics and Genomics Laboratory, Institute of Clinical Physiology, IFC-CNR, 56127 Pisa, Italy; (F.B.); (T.C.)
- Correspondence: (A.G.); (M.A.C.)
| | - Maria Adelaide Caligo
- SOD Molecular Genetics, University Hospital of Pisa, 56126 Pisa, Italy; (C.G.); (E.C.); (M.T.); (E.F.); (C.C.)
- Correspondence: (A.G.); (M.A.C.)
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