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Pan TY, Kou HS, Wu SM, Wang CC. Identifiable universal fluorescent multiplex PCR equipped with capillary electrophoresis for genotyping of exons 1 to 5 in human red and green pigment genes. Talanta 2022; 241:123199. [PMID: 35033897 DOI: 10.1016/j.talanta.2021.123199] [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: 10/05/2021] [Revised: 12/24/2021] [Accepted: 12/30/2021] [Indexed: 11/27/2022]
Abstract
Congenital red and green color blindness is the most X-linked recessive disorder in humans caused by deletions or gross structural rearrangements of the visual pigment gene array that lead to altered the functions of visual pigments in their retina differ from normal. The incidence is about 7-10% in male and close association of X-linked recessive disorders (such as: hemophilia A, hemophilia B, duchenne muscular dystrophy). However, the traditional genetic analysis methods are time-consuming and low-efficiencies. Therefore, the purpose of the study is to develop a rapid method for genotyping of red and green pigment genes. We describe herein the first method for simultaneous evaluation of ten exons in the red and green pigment genes for genetic analysis. A forward specific primers with identifiable universal fluorescent multiplex PCR (FSIUFM-PCR) method utilized one universal primer (containing two universal non-human sequences) and forward specific primers in the multiplex PCR reaction system for simultaneously fluorescent labeling of eleven gene fragments (ten exons in red and green pigment genes and one internal standard). All the PCR products were analyzed on capillary electrophoresis with short-end injection, which had the advantage of high resolution and rapid separation. Of all 80 detected individuals, 7 subjects with color vision deficiencies (including 3 subjects only had red exons 1-5, 4 subjects had a specific red-green or green-red hybrid gene and 73 subjects with normal color vision). All genotyping results showed good agreement with DNA sequencing data. This method provided a better potential technique for genotyping and identifying of red and green pigment genes. In addition, FSIUFM-PCR method will be useful in many fields, such as diagnosis of diseases, analysis of polymorphisms and quantitative assay.
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Affiliation(s)
- Tzu-Yu Pan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Hwang-Shang Kou
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC
| | - Shou-Mei Wu
- Department of Fragrance and Cosmetic Science, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC.
| | - Chun-Chi Wang
- School of Pharmacy, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan, ROC; Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC; Drug Development and Value Creation Research Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan, ROC.
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Yang Y, Wu L, Wu X, Li B, Huang W, Weng Z, Lin Z, Song L, Guo Y, Meng Z, Liu X, Xia J. Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:153-166. [PMID: 31927644 DOI: 10.1007/s10126-019-09940-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
Brown-marbled grouper, Epinephelus fuscoguttatus, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which, bmp2k, wasf1, and acyp2 involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of bmp2k was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Lina Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Xi Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Bijun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Wenhua Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Zhuoying Weng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Zixuan Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Leling Song
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Yin Guo
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China.
- Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, 510275, People's Republic of China.
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China.
- Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, 510275, People's Republic of China.
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
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