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Liu X, Zhang W, Jing C, Gao L, Fu C, Ren C, Hao Y, Cao M, Ma K, Pan W, Li D. Corrigendum: Mutation of Gemin5 causes defective hematopoietic stem/progenitor cells proliferation in zebrafish embryonic hematopoiesis. Front Cell Dev Biol 2024; 12:1407675. [PMID: 38655064 PMCID: PMC11035865 DOI: 10.3389/fcell.2024.1407675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Abstract
[This corrects the article DOI: 10.3389/fcell.2021.670654.].
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Affiliation(s)
- Xiaofen Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjuan Zhang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Changbin Jing
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Lei Gao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Cong Fu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chunguang Ren
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yimei Hao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Mengye Cao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Ke Ma
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Clinical Research and Translation Center, The First Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Weijun Pan
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Dantong Li
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
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Mei X, Huang T, Chen A, Liu W, Jiang L, Zhong S, Shen D, Qiao P, Zhao Q. BmC/EBPZ gene is essential for the larval growth and development of silkworm, Bombyx mori. Front Physiol 2024; 15:1298869. [PMID: 38523808 PMCID: PMC10959570 DOI: 10.3389/fphys.2024.1298869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 03/26/2024] Open
Abstract
The genetic male sterile line (GMS) of the silkworm Bombyx mori is a recessive mutant that is naturally mutated from the wild-type 898WB strain. One of the major characteristics of the GMS mutant is its small larvae. Through positional cloning, candidate genes for the GMS mutant were located in a region approximately 800.5 kb long on the 24th linkage group of the silkworm. One of the genes was Bombyx mori CCAAT/enhancer-binding protein zeta (BmC/EBPZ), which is a member of the basic region-leucine zipper transcription factor family. Compared with the wild-type 898WB strain, the GMS mutant features a 9 bp insertion in the 3'end of open reading frame sequence of BmC/EBPZ gene. Moreover, the high expression level of the BmC/EBPZ gene in the testis suggests that the gene is involved in the regulation of reproduction-related genes. Using the CRISPR/Cas9-mediated knockout system, we found that the BmC/EBPZ knockout strains had the same phenotypes as the GMS mutant, that is, the larvae were small. However, the larvae of BmC/EBPZ knockout strains died during the development of the third instar. Therefore, the BmC/EBPZ gene was identified as the major gene responsible for GMS mutation.
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Affiliation(s)
- Xinglin Mei
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Tianchen Huang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Anli Chen
- Key Sericultural Laboratory of Shaanxi, Ankang University, Ankang, Shaanxi, China
| | - Weibin Liu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Li Jiang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Shanshan Zhong
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Dongxu Shen
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
| | - Peitong Qiao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
| | - Qiaoling Zhao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, China
- Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, China
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3
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Watanabe S, Omagari A, Yamada R, Matsumoto A, Kimura Y, Makita N, Hiyama E, Okamoto Y, Okabe R, Sano T, Sato T, Suzuki M, Saito S, Anai T. Mutations in the genes responsible for the synthesis of furan fatty acids resolve the light-induced off-odor in soybean oil. Plant J 2024; 117:1239-1249. [PMID: 38016933 DOI: 10.1111/tpj.16560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/30/2023]
Abstract
Soybean oil is the second most produced edible vegetable oil and is used for many edible and industrial materials. Unfortunately, it has the disadvantage of 'reversion flavor' under photooxidative conditions, which produces an off-odor and decreases the quality of edible oil. Reversion flavor and off-odor are caused by minor fatty acids in the triacylglycerol of soybean oil known as furan fatty acids, which produce 3-methyl-2,4-nonanedione (3-MND) upon photooxidation. As a solution to this problem, a reduction in furan fatty acids leads to a decrease in 3-MND, resulting in a reduction in the off-odor induced by light exposure. However, there are no reports on the genes related to the biosynthesis of furan fatty acids in soybean oil. In this study, four mutant lines showing low or no furan fatty acid levels in soybean seeds were isolated from a soybean mutant library. Positional cloning experiments and homology search analysis identified two genes responsible for furan fatty acid biosynthesis in soybean: Glyma.20G201400 and Glyma.04G054100. Ectopic expression of both genes produced furan fatty acids in transgenic soybean hairy roots. The structure of these genes is different from that of the furan fatty acid biosynthetic genes in photosynthetic bacteria. Homologs of these two group of genes are widely conserved in the plant kingdom. The purified oil from the furan fatty acid mutant lines had lower amounts of 3-MND and reduced off-odor after light exposure, compared with oil from the wild-type.
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Affiliation(s)
- Satoshi Watanabe
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga, 840-8502, Japan
| | - Ayako Omagari
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga, 840-8502, Japan
| | - Risa Yamada
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga, 840-8502, Japan
| | - Akane Matsumoto
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga, 840-8502, Japan
| | - Yuta Kimura
- Faculty of Agriculture, Saga University, 1 Honjo-machi, Saga, Saga, 840-8502, Japan
| | - Naruto Makita
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Erina Hiyama
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Yuki Okamoto
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Ryo Okabe
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Takashi Sano
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Toshiro Sato
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Mototaka Suzuki
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Sanshiro Saito
- Research & Development Center, J-Oil Mills, Inc., 7-41 Daikoku-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0053, Japan
| | - Toyoaki Anai
- Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, Fukuoka, 819-0395, Japan
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4
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Chen X, Liu C, Guo P, Hao X, Pan Y, Zhang K, Liu W, Zhao L, Luo W, He J, Su Y, Jin T, Jiang F, Wang S, Liu F, Xie R, Zhen C, Han W, Xing G, Wang W, Zhao S, Li Y, Gai J. Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication. J Integr Plant Biol 2023. [PMID: 36916709 DOI: 10.1111/jipb.13480] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 03/06/2023] [Indexed: 05/13/2023]
Abstract
Although seed weight has increased following domestication from wild soybean (Glycine soja) to cultivated soybean (Glycine max), the genetic basis underlying this change is unclear. Using mapping populations derived from chromosome segment substitution lines of wild soybean, we identified SW16.1 as the causative gene underlying a major quantitative trait locus controlling seed weight. SW16.1 encodes a nucleus-localized LIM domain-containing protein. Importantly, the GsSW16.1 allele from wild soybean accession N24852 had a negative effect on seed weight, whereas the GmSW16.1 allele from cultivar NN1138-2 had a positive effect. Gene expression network analysis, reverse-transcription quantitative polymerase chain reaction, and promoter-luciferase reporter transient expression assays suggested that SW16.1 regulates the transcription of MT4, a positive regulator of seed weight. The natural variations in SW16.1 and other known seed weight genes were analyzed in soybean germplasm. The SW16.1 polymorphism was associated with seed weight in 247 soybean accessions, showing much higher frequency of positive-effect alleles in cultivated soybean than in wild soybean. Interestingly, gene allele matrix analysis of the known seed weight genes revealed that G. max has lost 38.5% of the G. soja alleles and that most of the lost alleles had negative effects on seed weight. Our results suggest that eliminating negative alleles from G. soja led to a higher frequency of positive alleles and changed genetic backgrounds in G. max, which contributed to larger seeds in cultivated soybean after domestication from wild soybean. Our findings provide new insights regarding soybean domestication and should assist current soybean breeding programs.
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Affiliation(s)
- Xianlian Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Cheng Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Pengfei Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiaoshuai Hao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yongpeng Pan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kai Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wusheng Liu
- Department of Horticultural Science, North Carolina State University, Raleigh, North Carolina, 27606, USA
| | - Lizhi Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Luo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jianbo He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanzhu Su
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Jin
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fenfen Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Si Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fangdong Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Rongzhou Xie
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Changgen Zhen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wei Han
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Guangnan Xing
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Wubin Wang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shancen Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Yan Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Junyi Gai
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
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Altenhofen D, Khuong JM, Kuhn T, Lebek S, Görigk S, Kaiser K, Binsch C, Griess K, Knebel B, Belgardt BF, Cames S, Eickelschulte S, Stermann T, Rasche A, Herwig R, Weiss J, Vogel H, Schürmann A, Chadt A, Al-Hasani H. E96V Mutation in the Kdelr3 Gene Is Associated with Type 2 Diabetes Susceptibility in Obese NZO Mice. Int J Mol Sci 2023; 24. [PMID: 36614300 DOI: 10.3390/ijms24010845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/16/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
Type 2 diabetes (T2D) represents a multifactorial metabolic disease with a strong genetic predisposition. Despite elaborate efforts in identifying the genetic variants determining individual susceptibility towards T2D, the majority of genetic factors driving disease development remain poorly understood. With the aim to identify novel T2D risk genes we previously generated an N2 outcross population using the two inbred mouse strains New Zealand obese (NZO) and C3HeB/FeJ (C3H). A linkage study performed in this population led to the identification of the novel T2D-associated quantitative trait locus (QTL) Nbg15 (NZO blood glucose on chromosome 15, Logarithm of odds (LOD) 6.6). In this study we used a combined approach of positional cloning, gene expression analyses and in silico predictions of DNA polymorphism on gene/protein function to dissect the genetic variants linking Nbg15 to the development of T2D. Moreover, we have generated congenic strains that associated the distal sublocus of Nbg15 to mechanisms altering pancreatic beta cell function. In this sublocus, Cbx6, Fam135b and Kdelr3 were nominated as potential causative genes associated with the Nbg15 driven effects. Moreover, a putative mutation in the Kdelr3 gene from NZO was identified, negatively influencing adaptive responses associated with pancreatic beta cell death and induction of endoplasmic reticulum stress. Importantly, knockdown of Kdelr3 in cultured Min6 beta cells altered insulin granules maturation and pro-insulin levels, pointing towards a crucial role of this gene in islets function and T2D susceptibility.
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Kuramoto T. Positional cloning of rat mutant genes reveals new functions of these genes. Exp Anim 2023; 72:1-8. [PMID: 36058846 PMCID: PMC9978133 DOI: 10.1538/expanim.22-0089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
The laboratory rat (Rattus norvegicus) is a key model organism for biomedical research. Rats can be subjected to strict genetic and environmental controls. The rat's large body size is suitable for both surgical operations and repeated measurements of physiological parameters. These advantages have led to the development of numerous rat models for genetic diseases. Forward genetics is a proven approach for identifying the causative genes of these disease models but requires genome resources including genetic markers and genome sequences. Over the last few decades, rat genome resources have been developed and deposited in bioresource centers, which have enabled us to perform positional cloning in rats. To date, more than 100 disease-related genes have been identified by positional cloning. Since some disease models are more accessible in rats than mice, the identification of causative genes in these models has sometimes led to the discovery of novel functions of genes. As before, various mutant rats are also expected to be discovered and developed as disease models in the future. Thus, the forward genetics continues to be an important approach to find genes involved in disease phenotypes in rats. In this review, I provide an overview the development of rat genome resources and describe examples of positional cloning in rats in which novel gene functions have been identified.
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Affiliation(s)
- Takashi Kuramoto
- Laboratory of Animal Nutrition, Department of Animal Science, Faculty of Agriculture, Tokyo University of Agriculture, 1737 Funako, Atsugi, Kanagawa 243-0034, Japan
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Lv T, Wang L, Zhang C, Liu S, Wang J, Lu S, Fang C, Kong L, Li Y, Li Y, Hou X, Liu B, Kong F, Li X. Identification of two quantitative genes controlling soybean flowering using bulked-segregant analysis and genetic mapping. Front Plant Sci 2022; 13:987073. [PMID: 36531378 PMCID: PMC9749486 DOI: 10.3389/fpls.2022.987073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Photoperiod responsiveness is important to soybean production potential and adaptation to local environments. Varieties from temperate regions generally mature early and exhibit extremely low yield when grown under inductive short-day (SD) conditions. The long-juvenile (LJ) trait is essentially a reduction and has been introduced into soybean cultivars to improve yield in tropical environments. In this study, we used next-generation sequencing (NGS)-based bulked segregant analysis (BSA) to simultaneously map qualitative genes controlling the LJ trait in soybean. We identified two genomic regions on scaffold_32 and chromosome 18 harboring loci LJ32 and LJ18, respectively. Further, we identified LJ32 on the 228.7-kb scaffold_32 as the soybean pseudo-response-regulator gene Tof11 and LJ18 on a 301-kb region of chromosome 18 as a novel PROTEIN FLOWERING LOCUS T-RELATED gene, Glyma.18G298800. Natural variants of both genes contribute to LJ trait regulation in tropical regions. The molecular identification and functional characterization of Tof11 and LJ18 will enhance understanding of the molecular mechanisms underlying the LJ trait and provide useful genetic resources for soybean molecular breeding in tropical regions.
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Affiliation(s)
- Tianxiao Lv
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Lingshuang Wang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Chunyu Zhang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Shu Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jinxing Wang
- Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, Heilongjiang, China
| | - Sijia Lu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Chao Fang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Lingping Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Yunlong Li
- Suihua Branch Institute, Heilongjiang Academy of Agricultural Sciences, Suihua, Heilongjiang, China
| | - Yuge Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Xingliang Hou
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
| | - Baohui Liu
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Fanjiang Kong
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou Higher Education Mega Center, Guangzhou University, Guangzhou, China
| | - Xiaoming Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Innovative Academy of Seed Design, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
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8
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Thomelin P, Bonneau J, Brien C, Suchecki R, Baumann U, Kalambettu P, Langridge P, Tricker P, Fleury D. The wheat Seven in absentia gene is associated with increases in biomass and yield in hot climates. J Exp Bot 2021; 72:3774-3791. [PMID: 33543261 PMCID: PMC8096608 DOI: 10.1093/jxb/erab044] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 02/01/2021] [Indexed: 05/27/2023]
Abstract
Wheat (Triticum aestivum L.) productivity is severely reduced by high temperatures. Breeding of heat-tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits when high temperatures occur and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We advanced the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene, Seven in absentia, TaSINA. This was associated with the QTL's effects on early vigour, root growth, plant biomass, and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL underexpressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number, and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.
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Affiliation(s)
- Pauline Thomelin
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Julien Bonneau
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Chris Brien
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Radoslaw Suchecki
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Ute Baumann
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Priyanka Kalambettu
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Penny Tricker
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
| | - Delphine Fleury
- School of Agriculture, Food and Wine, The University of Adelaide, PMB1, Glen Osmond, SA, 5064, Australia
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9
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Liu X, Zhang W, Jing C, Gao L, Fu C, Ren C, Hao Y, Cao M, Ma K, Pan W, Li D. Mutation of Gemin5 Causes Defective Hematopoietic Stem/Progenitor Cells Proliferation in Zebrafish Embryonic Hematopoiesis. Front Cell Dev Biol 2021; 9:670654. [PMID: 33996826 PMCID: PMC8120239 DOI: 10.3389/fcell.2021.670654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/13/2021] [Indexed: 12/11/2022] Open
Abstract
Fate determination and expansion of Hematopoietic Stem and Progenitor Cells (HSPCs) is tightly regulated on both transcriptional and post-transcriptional level. Although transcriptional regulation of HSPCs have achieved a lot of advances, its post-transcriptional regulation remains largely underexplored. The small size and high fecundity of zebrafish makes it extraordinarily suitable to explore novel genes playing key roles in definitive hematopoiesis by large-scale forward genetics screening. Here, we reported a novel zebrafish mutant line gemin5 cas008 with a point mutation in gemin5 gene obtained by ENU mutagenesis and genetic screening, causing an earlier stop codon next to the fifth WD repeat. Gemin5 is an RNA-binding protein with multifunction in post-transcriptional regulation, such as regulating the biogenesis of snRNPs, alternative splicing, stress response, and translation control. The mutants displayed specific deficiency in definitive hematopoiesis without obvious defects during primitive hematopoiesis. Further analysis showed the impaired definitive hematopoiesis was due to defective proliferation of HSPCs. Overall, our results indicate that Gemin5 performs an essential role in regulating HSPCs proliferation.
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Affiliation(s)
- Xiaofen Liu
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Wenjuan Zhang
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Changbin Jing
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Lei Gao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Cong Fu
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Chunguang Ren
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Yimei Hao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Mengye Cao
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Ke Ma
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
- Clinical Research and Translation Center, The First Affiliated Hospital of Fujian Medical University, Fujian, China
| | - Weijun Pan
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
| | - Dantong Li
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences, Shanghai, China
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10
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Xia Z, Zhai H, Wu H, Xu K, Watanabe S, Harada K. The Synchronized Efforts to Decipher the Molecular Basis for Soybean Maturity Loci E1, E2, and E3 That Regulate Flowering and Maturity. Front Plant Sci 2021; 12:632754. [PMID: 33995435 PMCID: PMC8113421 DOI: 10.3389/fpls.2021.632754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
The general concept of photoperiodism, i.e., the photoperiodic induction of flowering, was established by Garner and Allard (1920). The genetic factor controlling flowering time, maturity, or photoperiodic responses was observed in soybean soon after the discovery of the photoperiodism. E1, E2, and E3 were named in 1971 and, thereafter, genetically characterized. At the centennial celebration of the discovery of photoperiodism in soybean, we recount our endeavors to successfully decipher the molecular bases for the major maturity loci E1, E2, and E3 in soybean. Through systematic efforts, we successfully cloned the E3 gene in 2009, the E2 gene in 2011, and the E1 gene in 2012. Recently, successful identification of several circadian-related genes such as PRR3a, LUX, and J has enriched the known major E1-FTs pathway. Further research progresses on the identification of new flowering and maturity-related genes as well as coordinated regulation between flowering genes will enable us to understand profoundly flowering gene network and determinants of latitudinal adaptation in soybean.
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Affiliation(s)
- Zhengjun Xia
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hong Zhai
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Hongyan Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | - Kun Xu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Harbin, China
| | | | - Kyuya Harada
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
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11
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Colasuonno P, Marcotuli I, Gadaleta A, Soriano JM. From Genetic Maps to QTL Cloning: An Overview for Durum Wheat. Plants (Basel) 2021; 10:315. [PMID: 33562160 PMCID: PMC7914919 DOI: 10.3390/plants10020315] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 01/26/2021] [Accepted: 02/02/2021] [Indexed: 12/17/2022]
Abstract
Durum wheat is one of the most important cultivated cereal crops, providing nutrients to humans and domestic animals. Durum breeding programs prioritize the improvement of its main agronomic traits; however, the majority of these traits involve complex characteristics with a quantitative inheritance (quantitative trait loci, QTL). This can be solved with the use of genetic maps, new molecular markers, phenotyping data of segregating populations, and increased accessibility to sequences from next-generation sequencing (NGS) technologies. This allows for high-density genetic maps to be developed for localizing candidate loci within a few Kb in a complex genome, such as durum wheat. Here, we review the identified QTL, fine mapping, and cloning of QTL or candidate genes involved in the main traits regarding the quality and biotic and abiotic stresses of durum wheat. The current knowledge on the used molecular markers, sequence data, and how they changed the development of genetic maps and the characterization of QTL is summarized. A deeper understanding of the trait architecture useful in accelerating durum wheat breeding programs is envisioned.
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Affiliation(s)
- Pasqualina Colasuonno
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Ilaria Marcotuli
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Agata Gadaleta
- Department of Agricultural and Environmental Science, University of Bari ‘Aldo Moro’, Via G. Amendola 165/A, 70126 Bari, Italy; (P.C.); (I.M.)
| | - Jose Miguel Soriano
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain
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12
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Zhang H, Tang S, Schnable JC, He Q, Gao Y, Luo M, Jia G, Feng B, Zhi H, Diao X. Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety "SSR41" and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1. Front Plant Sci 2021; 12:743782. [PMID: 34858451 PMCID: PMC8632227 DOI: 10.3389/fpls.2021.743782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/13/2021] [Indexed: 05/03/2023]
Abstract
Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the "Yugu1" variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, "SSR41", which is morphologically similar to, and readily cross-pollinates with, "Yugu1". High-throughput resequencing of "SSR41" identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used "SSR41" and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.
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Affiliation(s)
- Hui Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Sha Tang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - James C. Schnable
- Department of Agronomy and Horticulture, University of Nebraska–Lincoln, Lincoln, NE, United States
| | - Qiang He
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuanzhu Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingzhao Luo
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guanqing Jia
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Baili Feng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Hui Zhi
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xianmin Diao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Xianmin Diao,
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13
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Li M, Dong L, Li B, Wang Z, Xie J, Qiu D, Li Y, Shi W, Yang L, Wu Q, Chen Y, Lu P, Guo G, Zhang H, Zhang P, Zhu K, Li Y, Zhang Y, Wang R, Yuan C, Liu W, Yu D, Luo MC, Fahima T, Nevo E, Li H, Liu Z. A CNL protein in wild emmer wheat confers powdery mildew resistance. New Phytol 2020; 228:1027-1037. [PMID: 32583535 DOI: 10.1111/nph.16761] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 05/29/2020] [Indexed: 05/18/2023]
Abstract
Powdery mildew, a fungal disease caused by Blumeria graminis f. sp. tritici (Bgt), has a serious impact on wheat production. Loss of resistance in cultivars prompts a continuing search for new sources of resistance. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW), the progenitor of both modern tetraploid and hexaploid wheats, harbors many powdery mildew resistance genes. We report here the positional cloning and functional characterization of Pm41, a powdery mildew resistance gene derived from WEW, which encodes a coiled-coil, nucleotide-binding site and leucine-rich repeat protein (CNL). Mutagenesis and stable genetic transformation confirmed the function of Pm41 against Bgt infection in wheat. We demonstrated that Pm41 was present at a very low frequency (1.81%) only in southern WEW populations. It was absent in other WEW populations, domesticated emmer, durum, and common wheat, suggesting that the ancestral Pm41 was restricted to its place of origin and was not incorporated into domesticated wheat. Our findings emphasize the importance of conservation and exploitation of the primary WEW gene pool, as a valuable resource for discovery of resistance genes for improvement of modern wheat cultivars.
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Affiliation(s)
- Miaomiao Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Lingli Dong
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Beibei Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Jingzhong Xie
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dan Qiu
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yahui Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wenqi Shi
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Lijun Yang
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Qiuhong Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongxing Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ping Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Guanghao Guo
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huaizhi Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Panpan Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Keyu Zhu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yiwen Li
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yan Zhang
- China Agricultural University, Beijing, 100193, China
| | - Rongge Wang
- Hebei Gaoyi Seeds Farm, Gaoyi, Hebei, 051330, China
| | | | - Wei Liu
- Beijing Dabeinong Technology Group Co. Ltd, Beijing, 100080, China
| | - Dazhao Yu
- Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, 3498838, Israel
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mt. Carmel, 3498838, Israel
| | - Hongjie Li
- The National Engineering Laboratory of Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhiyong Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
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14
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Aga H, Hallahan N, Gottmann P, Jaehnert M, Osburg S, Schulze G, Kamitz A, Arends D, Brockmann G, Schallschmidt T, Lebek S, Chadt A, Al-Hasani H, Joost HG, Schürmann A, Vogel H. Identification of Novel Potential Type 2 Diabetes Genes Mediating β-Cell Loss and Hyperglycemia Using Positional Cloning. Front Genet 2020; 11:567191. [PMID: 33133152 PMCID: PMC7561370 DOI: 10.3389/fgene.2020.567191] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/28/2020] [Indexed: 12/27/2022] Open
Abstract
Type 2 diabetes (T2D) is a complex metabolic disease regulated by an interaction of genetic predisposition and environmental factors. To understand the genetic contribution in the development of diabetes, mice varying in their disease susceptibility were crossed with the obese and diabetes-prone New Zealand obese (NZO) mouse. Subsequent whole-genome sequence scans revealed one major quantitative trait loci (QTL), Nidd/DBA on chromosome 4, linked to elevated blood glucose and reduced plasma insulin and low levels of pancreatic insulin. Phenotypical characterization of congenic mice carrying 13.6 Mbp of the critical fragment of DBA mice displayed severe hyperglycemia and impaired glucose clearance at week 10, decreased glucose response in week 13, and loss of β-cells and pancreatic insulin in week 16. To identify the responsible gene variant(s), further congenic mice were generated and phenotyped, which resulted in a fragment of 3.3 Mbp that was sufficient to induce hyperglycemia. By combining transcriptome analysis and haplotype mapping, the number of putative responsible variant(s) was narrowed from initial 284 to 18 genes, including gene models and non-coding RNAs. Consideration of haplotype blocks reduced the number of candidate genes to four (Kti12, Osbpl9, Ttc39a, and Calr4) as potential T2D candidates as they display a differential expression in pancreatic islets and/or sequence variation. In conclusion, the integration of comparative analysis of multiple inbred populations such as haplotype mapping, transcriptomics, and sequence data substantially improved the mapping resolution of the diabetes QTL Nidd/DBA. Future studies are necessary to understand the exact role of the different candidates in β-cell function and their contribution in maintaining glycemic control.
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Affiliation(s)
- Heja Aga
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Nicole Hallahan
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Pascal Gottmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Markus Jaehnert
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Sophie Osburg
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Gunnar Schulze
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Anne Kamitz
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Gudrun Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Tanja Schallschmidt
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,German Diabetes Center (DDZ), Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sandra Lebek
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,German Diabetes Center (DDZ), Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Alexandra Chadt
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,German Diabetes Center (DDZ), Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hadi Al-Hasani
- German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,German Diabetes Center (DDZ), Medical Faculty, Institute for Clinical Biochemistry and Pathobiochemistry, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Hans-Georg Joost
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Annette Schürmann
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,Institute of Nutritional Science, University of Potsdam, Potsdam, Germany
| | - Heike Vogel
- Department of Experimental Diabetology, German Institute of Human Nutrition Potsdam-Rehbrücke, Potsdam, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany.,Molecular and Clinical Life Science of Metabolic Diseases, University of Potsdam, Potsdam, Germany
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15
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Abstract
Genetic alleles that contribute to enhanced susceptibility or resistance to viral infections and virally induced diseases have often been first identified in mice before humans due to the significant advantages of the murine system for genetic studies. Herein we review multiple discoveries that have revealed significant insights into virus-host interactions, all made using genetic mapping tools in mice. Factors that have been identified include innate and adaptive immunity genes that contribute to host defense against pathogenic viruses such as herpes viruses, flaviviruses, retroviruses, and coronaviruses. Understanding the genetic mechanisms that affect infectious disease outcomes will aid the development of personalized treatment and preventive strategies for pathogenic infections.
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Affiliation(s)
- Melissa Kane
- Center for Microbial Pathogenesis, Department of Pediatrics, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15224, USA
| | - Tatyana V Golovkina
- Department of Microbiology, University of Chicago, Chicago, Illinois 60637, USA;
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16
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Bryant CD, Smith DJ, Kantak KM, Nowak TS Jr, Williams RW, Damaj MI, Redei EE, Chen H, Mulligan MK. Facilitating Complex Trait Analysis via Reduced Complexity Crosses. Trends Genet 2020; 36:549-62. [PMID: 32482413 DOI: 10.1016/j.tig.2020.05.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 05/05/2020] [Accepted: 05/12/2020] [Indexed: 01/02/2023]
Abstract
Genetically diverse inbred strains are frequently used in quantitative trait mapping to identify sequence variants underlying trait variation. Poor locus resolution and high genetic complexity impede variant discovery. As a solution, we explore reduced complexity crosses (RCCs) between phenotypically divergent, yet genetically similar, rodent substrains. RCCs accelerate functional variant discovery via decreasing the number of segregating variants by orders of magnitude. The simplified genetic architecture of RCCs often permit immediate identification of causal variants or rapid fine-mapping of broad loci to smaller intervals. Whole-genome sequences of substrains make RCCs possible by supporting the development of array- and targeted sequencing-based genotyping platforms, coupled with rapid genome editing for variant validation. In summary, RCCs enhance discovery-based genetics of complex traits.
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17
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Ruan QT, Yazdani N, Reed ER, Beierle JA, Peterson LP, Luttik KP, Szumlinski KK, Johnson WE, Ash PEA, Wolozin B, Bryant CD. 5' UTR variants in the quantitative trait gene Hnrnph1 support reduced 5' UTR usage and hnRNP H protein as a molecular mechanism underlying reduced methamphetamine sensitivity. FASEB J 2020; 34:9223-9244. [PMID: 32401417 DOI: 10.1096/fj.202000092r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 04/17/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022]
Abstract
We previously identified a 210 kb region on chromosome 11 (50.37-50.58 Mb, mm10) containing two protein-coding genes (Hnrnph1, Rufy1) that was necessary for reduced methamphetamine-induced locomotor activity in C57BL/6J congenic mice harboring DBA/2J polymorphisms. Gene editing of a small deletion in the first coding exon supported Hnrnph1 as a quantitative trait gene. We have since shown that Hnrnph1 mutants also exhibit reduced methamphetamine-induced reward, reinforcement, and dopamine release. However, the quantitative trait variants (QTVs) that modulate Hnrnph1 function at the molecular level are not known. Nine single nucleotide polymorphisms and seven indels distinguish C57BL/6J from DBA/2J within Hnrnph1, including four variants within the 5' untranslated region (UTR). Here, we show that a 114 kb introgressed region containing Hnrnph1 and Rufy1 was sufficient to cause a decrease in MA-induced locomotor activity. Gene-level transcriptome analysis of striatal tissue from 114 kb congenics vs Hnrnph1 mutants identified a nearly perfect correlation of fold-change in expression for those differentially expressed genes that were common to both mouse lines, indicating functionally similar effects on the transcriptome and behavior. Exon-level analysis (including noncoding exons) revealed decreased 5' UTR usage of Hnrnph1 and immunoblot analysis identified a corresponding decrease in hnRNP H protein in 114 kb congenic mice. Molecular cloning of the Hnrnph1 5' UTR containing all four variants (but none of them individually) upstream of a reporter induced a decrease in reporter signal in both HEK293 and N2a cells, thus, identifying a set of QTVs underlying molecular regulation of Hnrnph1.
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Affiliation(s)
- Qiu T Ruan
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA.,Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.,Transformative Training Program in Addiction Science, Boston University School of Medicine, Boston, MA, USA
| | - Neema Yazdani
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA.,Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.,Transformative Training Program in Addiction Science, Boston University School of Medicine, Boston, MA, USA
| | - Eric R Reed
- Ph.D. Program in Bioinformatics, Boston University, Boston, MA, USA
| | - Jacob A Beierle
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA.,Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.,Transformative Training Program in Addiction Science, Boston University School of Medicine, Boston, MA, USA
| | - Lucy P Peterson
- Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA
| | - Kimberly P Luttik
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA
| | - Karen K Szumlinski
- Department of Psychological and Brain Sciences, Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara, CA, USA
| | - William E Johnson
- Department of Medicine, Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA
| | - Peter E A Ash
- Laboratory of Neurodegeneration, Department of Pharmacology and Experimental Therapeutics and Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Benjamin Wolozin
- Laboratory of Neurodegeneration, Department of Pharmacology and Experimental Therapeutics and Neurology, Boston University School of Medicine, Boston, MA, USA
| | - Camron D Bryant
- Laboratory of Addiction Genetics, Department of Pharmacology and Experimental Therapeutics and Psychiatry, Boston University School of Medicine, Boston, MA, USA.,Biomolecular Pharmacology Training Program, Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, USA.,Transformative Training Program in Addiction Science, Boston University School of Medicine, Boston, MA, USA
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18
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Klymiuk V, Fatiukha A, Raats D, Bocharova V, Huang L, Feng L, Jaiwar S, Pozniak C, Coaker G, Dubcovsky J, Fahima T. Three previously characterized resistances to yellow rust are encoded by a single locus Wtk1. J Exp Bot 2020; 71:2561-2572. [PMID: 31942623 PMCID: PMC7210774 DOI: 10.1093/jxb/eraa020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/12/2020] [Indexed: 05/21/2023]
Abstract
The wild emmer wheat (Triticum turgidum ssp. dicoccoides; WEW) yellow (stripe) rust resistance genes Yr15, YrG303, and YrH52 were discovered in natural populations from different geographic locations. They all localize to chromosome 1B but were thought to be non-allelic based on differences in resistance response. We recently cloned Yr15 as a Wheat Tandem Kinase 1 (WTK1) and show here that these three resistance loci co-segregate in fine-mapping populations and share an identical full-length genomic sequence of functional Wtk1. Independent ethyl methanesulfonate (EMS)-mutagenized susceptible yrG303 and yrH52 lines carried single nucleotide mutations in Wtk1 that disrupted function. A comparison of the mutations for yr15, yrG303, and yrH52 mutants showed that while key conserved residues were intact, other conserved regions in critical kinase subdomains were frequently affected. Thus, we concluded that Yr15-, YrG303-, and YrH52-mediated resistances to yellow rust are encoded by a single locus, Wtk1. Introgression of Wtk1 into multiple genetic backgrounds resulted in variable phenotypic responses, confirming that Wtk1-mediated resistance is part of a complex immune response network. WEW natural populations subjected to natural selection and adaptation have potential to serve as a good source for evolutionary studies of different traits and multifaceted gene networks.
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Affiliation(s)
- Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Dina Raats
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Valeria Bocharova
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lin Huang
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Lihua Feng
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Samidha Jaiwar
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | - Gitta Coaker
- Department of Plant Pathology, University of California, One Shields Avenue, Davis, CA, USA
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, One Shields Avenue, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, Haifa, Israel
- Correspondence:
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19
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Wang Y, Singh R, Tong E, Tang M, Zheng L, Fang H, Li R, Guo L, Song J, Srinivasan R, Sharma A, Lin L, Trujillo JA, Manshardt R, Chen LY, Ming R, Yu Q. Positional cloning and characterization of the papaya diminutive mutant reveal a truncating mutation in the CpMMS19 gene. New Phytol 2020; 225:2006-2021. [PMID: 31733154 DOI: 10.1111/nph.16325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Accepted: 10/19/2019] [Indexed: 06/10/2023]
Abstract
The papaya diminutive mutant exhibits miniature stature, retarded growth and reduced fertility. This undesirable mutation appeared in the variety 'Sunset', the progenitor of the transgenic line 'SunUp', and was accidentally carried forward into breeding populations. The diminutive mutation was mapped to chromosome 2 and fine mapped to scaffold 25. Sequencing of a bacterial artificial chromosome in the fine mapped region led to the identification of the target gene responsible for the diminutive mutant, a gene orthologous to MMS19 with a 36.8 kb deletion co-segregating with the diminutive mutant. The genomic sequence of CpMMS19 is 62 kb, consisting of 20 exons and 19 introns. It encodes a protein of 1143 amino acids while the diminutive allele encodes a truncated protein of 287 amino acids. Expression of the full-length CpMMS19 was able to complement the thermosensitive growth of the yeast mms19 deletion mutant while expression of the diminutive allele resulted in increased thermosensitivity. Over-expression of the diminutive allele in Arabidopsis met18 mutant results in a high frequency of seed abortion. The papaya diminutive phenotype is caused by an alteration in gene function rather than a loss-of-function mutation. SCAR (sequence characterized amplified region) markers were developed for rapid detection of the diminutive allele in breeding populations.
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Affiliation(s)
- Ying Wang
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ratnesh Singh
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Eric Tong
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Min Tang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Liwei Zheng
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Hongkun Fang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruoyu Li
- College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Lin Guo
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jinjin Song
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rajeswari Srinivasan
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Anupma Sharma
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Lianyu Lin
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jorge A Trujillo
- Department of Biology, University of Texas Rio Grande Valley, Edinburg, TX, 78539, USA
| | - Richard Manshardt
- Department of Tropical Plant & Soil Sciences, University of Hawaii, Honolulu, HI, 96822, USA
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
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20
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DeWitt N, Guedira M, Lauer E, Sarinelli M, Tyagi P, Fu D, Hao Q, Murphy JP, Marshall D, Akhunova A, Jordan K, Akhunov E, Brown‐Guedira G. Sequence-based mapping identifies a candidate transcription repressor underlying awn suppression at the B1 locus in wheat. New Phytol 2020; 225:326-339. [PMID: 31465541 PMCID: PMC6916393 DOI: 10.1111/nph.16152] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/16/2019] [Indexed: 05/27/2023]
Abstract
Awns are stiff, hair-like structures which grow from the lemmas of wheat (Triticum aestivum) and other grasses that contribute to photosynthesis and play a role in seed dispersal. Variation in awn length in domesticated wheat is controlled primarily by three major genes, most commonly the dominant awn suppressor Tipped1 (B1). This study identifies a transcription repressor responsible for awn inhibition at the B1 locus. Association mapping was combined with analysis in biparental populations to delimit B1 to a distal region of 5AL colocalized with QTL for number of spikelets per spike, kernel weight, kernel length, and test weight. Fine-mapping located B1 to a region containing only two predicted genes, including C2H2 zinc finger transcriptional repressor TraesCS5A02G542800 upregulated in developing spikes of awnless individuals. Deletions encompassing this candidate gene were present in awned mutants of an awnless wheat. Sequence polymorphisms in the B1 coding region were not observed in diverse wheat germplasm whereas a nearby polymorphism was highly predictive of awn suppression. Transcriptional repression by B1 is the major determinant of awn suppression in global wheat germplasm. It is associated with increased number of spikelets per spike and decreased kernel size.
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Affiliation(s)
- Noah DeWitt
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Mohammed Guedira
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Edwin Lauer
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Martin Sarinelli
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Priyanka Tyagi
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - Daolin Fu
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
| | - QunQun Hao
- Department of Plant SciencesUniversity of IdahoMoscowID83844USA
| | - J. Paul Murphy
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
| | - David Marshall
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
- USDA‐ARS SAAPlant Science ResearchRaleighNC27695USA
| | - Alina Akhunova
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Katherine Jordan
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Eduard Akhunov
- Department of Plant PathologyKansas State UniversityManhattanKS66506USA
| | - Gina Brown‐Guedira
- Department of Crop and Soil SciencesNorth Carolina State UniversityRaleighNC27695USA
- USDA‐ARS SAAPlant Science ResearchRaleighNC27695USA
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21
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Schallschmidt T, Lebek S, Altenhofen D, Damen M, Schulte Y, Knebel B, Herwig R, Rasche A, Stermann T, Kamitz A, Hallahan N, Jähnert M, Vogel H, Schürmann A, Chadt A, Al-Hasani H. Two Novel Candidate Genes for Insulin Secretion Identified by Comparative Genomics of Multiple Backcross Mouse Populations. Genetics 2018; 210:1527-42. [PMID: 30341086 DOI: 10.1534/genetics.118.301578] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 10/16/2018] [Indexed: 12/28/2022] Open
Abstract
To identify novel disease genes for type 2 diabetes (T2D) we generated two backcross populations of obese and diabetes-susceptible New Zealand Obese (NZO/HI) mice with the two lean mouse strains 129P2/OlaHsd and C3HeB/FeJ. Subsequent whole-genome linkage scans revealed 30 novel quantitative trait loci (QTL) for T2D-associated traits. The strongest association with blood glucose [12 cM, logarithm of the odds (LOD) 13.3] and plasma insulin (17 cM, LOD 4.8) was detected on proximal chromosome 7 (designated Nbg7p, NZO blood glucose on proximal chromosome 7) exclusively in the NZOxC3H crossbreeding, suggesting that the causal gene is contributed by the C3H genome. Introgression of the critical C3H fragment into the genetic NZO background by generating recombinant congenic strains and metabolic phenotyping validated the phenotype. For the detection of candidate genes in the critical region (30-46 Mb), we used a combined approach of haplotype and gene expression analysis to search for C3H-specific gene variants in the pancreatic islets, which appeared to be the most likely target tissue for the QTL. Two genes, Atp4a and Pop4, fulfilled the criteria from our candidate gene approaches. The knockdown of both genes in MIN6 cells led to decreased glucose-stimulated insulin secretion, indicating a regulatory role of both genes in insulin secretion, thereby possibly contributing to the phenotype linked to Nbg7p In conclusion, our combined- and comparative-cross analysis approach has successfully led to the identification of two novel diabetes susceptibility candidate genes, and thus has been proven to be a valuable tool for the discovery of novel disease genes.
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22
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Kane M, Deiss F, Chervonsky A, Golovkina TV. A Single Locus Controls Interferon Gamma-Independent Antiretroviral Neutralizing Antibody Responses. J Virol 2018; 92:e00725-18. [PMID: 29875252 DOI: 10.1128/JVI.00725-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/01/2018] [Indexed: 11/20/2022] Open
Abstract
An essential step in the development of effective antiviral humoral responses is cytokine-triggered class switch recombination resulting in the production of antibodies of a specific isotype. Most viral and parasitic infections in mice induce predominantly IgG2a-specific antibody responses that are stimulated by interferon gamma (IFN-γ). However, in some mice deficient in IFN-γ, class switching to IgG2a antibodies is relatively unaffected, indicating that another signal(s) can be generated upon viral or parasitic infections that trigger this response. Here, we found that a single recessive locus, provisionally called IFN-γ-independent IgG2a (Igii), confers the ability to produce IFN-γ-independent production of IgG2a antibodies upon retroviral infection. The Igii locus was mapped to chromosome 9 and was found to function in the radiation-resistant compartment. Thus, our data implicate nonhematopoietic cells in activation of antiviral antibody responses in the absence of IFN-γ.IMPORTANCE Understanding the signals that stimulate antibody production and class switch recombination to specific antibody isotypes is crucial for the development of novel vaccines and adjuvants. While an interferon gamma-mediated switch to the IgG2a isotype upon viral infection in mice has been well established, this investigation reveals a noncanonical, interferon gamma-independent pathway for antiretroviral antibody production and IgG2a class switch recombination that is controlled by a single recessive locus. Furthermore, this study indicates that the radiation-resistant compartment can direct antiviral antibody responses, suggesting that detection of infection by nonhematopoietic cells is involved is stimulating adaptive immunity.
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23
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Wang RX, Tong XL, Gai TT, Li CL, Qiao L, Hu H, Han MJ, Xiang ZH, Lu C, Dai FY. A serine protease homologue Bombyx mori scarface induces a short and fat body shape in silkworm. Insect Mol Biol 2018; 27:319-332. [PMID: 29441628 DOI: 10.1111/imb.12373] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Body shape is one of the most prominent and basic characteristics of any organism. In insects, abundant variations in body shape can be observed both within and amongst species. However, the molecular mechanism underlying body shape fine-tuning is very complex and has been largely unknown until now. In the silkworm Bombyx mori, the tubby (tub) mutant has an abnormal short fat body shape and the abdomen of tub larvae expands to form a fusiform body shape. Morphological investigation revealed that the body length was shorter and the body width was wider than that of the Dazao strain. Thus, this mutant is a good model for studying the molecular mechanisms of body shape fine-tuning. Using positional cloning, we identified a gene encoding the serine protease homologue, B. mori scarface (Bmscarface), which is associated with the tub phenotype. Sequence analysis revealed a specific 312-bp deletion from an exon of Bmscarface in the tub strain. In addition, recombination was not observed between the tub and Bmscarface loci. Moreover, RNA interference of Bmscarface resulted in the tub-like phenotype. These results indicate that Bmscarface is responsible for the tub mutant phenotype. This is the first study to report that mutation of a serine protease homologue can induce an abnormal body shape in insects.
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Affiliation(s)
- R-X Wang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - X-L Tong
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - T-T Gai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - C-L Li
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - L Qiao
- Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Chongqing, China
| | - H Hu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - M-J Han
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - Z-H Xiang
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - C Lu
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
| | - F-Y Dai
- State Key Laboratory of Silkworm Genome Biology, Key Laboratory of Sericultural Biology and Genetic Breeding, Ministry of Agriculture, Southwest University, Chongqing, China
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24
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Wang T, Chen Y, Zhang M, Chen J, Liu J, Han H, Hua X. Arabidopsis AMINO ACID PERMEASE1 Contributes to Salt Stress-Induced Proline Uptake from Exogenous Sources. Front Plant Sci 2017; 8:2182. [PMID: 29312416 PMCID: PMC5743684 DOI: 10.3389/fpls.2017.02182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 12/12/2017] [Indexed: 05/03/2023]
Abstract
Stress-induced proline accumulation in plants is thought to result primarily from enhanced proline biosynthesis and decreased proline degradation. To identify regulatory components involved in proline transport, we screened for Arabidopsis thaliana T-DNA mutants with enhanced tolerance to toxic levels of exogenous proline (45 mM). We isolated the proline resistant 1-1 (pre1-1) mutant and map-based cloning identified PRE1 as AMINO ACID PERMEASE1 (AAP1, At1g58360), which encodes a plasma membrane-localized amino acid permease. AAP1 expression is induced by salt stress and abscisic acid, but not by proline. In pre1-1 mutants, a 19-nucleotide deletion in the AAP1 coding region produced a premature stop codon. When grown on proline-containing medium, pre1-1 mutants accumulated significantly less proline than did the wild type. Under salt stress, proline uptake decreased significantly in pre1-1 mutants. By contrast, proline uptake increased significantly in the wild type. These results suggest that AAP1 functions in the increase of proline uptake during salt stress. In addition, proline uptake promotes salt tolerance in Arabidopsis seedlings. We conclude that plants can increase proline accumulation by AtAAP1-mediated proline uptake from exogenous source, which help to improve the salt tolerance of seedlings.
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Affiliation(s)
- Ting Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Ying Chen
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Min Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
| | - Jiugeng Chen
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
| | - Jie Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Huiling Han
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Xuejun Hua
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences (CAS), Beijing, China
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25
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Zhao J, Chen L, Zhao T, Gai J. Chicken Toes-Like Leaf and Petalody Flower (CTP) is a novel regulator that controls leaf and flower development in soybean. J Exp Bot 2017; 68:5565-5581. [PMID: 29077868 DOI: 10.1093/jxb/erx358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A soybean mutant displaying chicken toes-like leaves and petalody flowers was identified as being caused by a single recessive gene, termed ctp. Using heterozygous-inbred recombinants, this gene was fine-mapped to a 37-kb region harbouring three predicted genes on chromosome 5. The gene Glyma05g022400.1 was detected to have a 33-bp deletion in its first exon that was responsible for ctp. Validation for this gene was provided by the fact that the 33-bp deletion-derived marker I2 completely co-segregated with the phenotypes of 96 F10-derived residual heterozygous lines and 2200 fine-mapping individuals, and by the fact that the orthologue NbCTP in Nicotiana benthamiana also influenced leaf and flower development under virus-induced gene silencing. In terms of characterization, the CTPs shared highly conserved domains specifically in higher plants, GmCTP was alternatively spliced, and it was expressed in multiple organs, especially in lateral meristems. GmCTP was localized to the nucleus and other regions and performed transcriptional activity. In ctp, the expression levels and splicing patterns were dramatically disrupted, and many key regulators in leaf and/or floral developmental pathways were interrupted. Thus, CTP is a novel and critical pleiotropic regulator of leaf and flower development that participates in multiple regulation pathways, and may play key roles in lateral organ differentiation as a putative novel transcription regulator.
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Affiliation(s)
- Jing Zhao
- Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, China
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing 210095, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Lei Chen
- Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, China
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing 210095, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Tuanjie Zhao
- Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, China
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing 210095, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Junyi Gai
- Soybean Research Institute, Nanjing Agricultural University, Nanjing 210095, China
- National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Biology and Genetic Improvement of Soybean, Nanjing Agricultural University, Nanjing 210095, China
- National Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
- Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
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26
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Abstract
In this Commentary, I describe the events that led from an NINDS-sponsored Workshop on Parkinson Disease Research in 1995, where I was asked to speak about the genetics of Parkinson disease, to the identification a mere two years later of a mutation in alpha-synuclein as the cause of autosomal dominant Parkinson disease in the Contursi kindred. I review the steps we took to first map and then find the mutation in the alpha-synuclein locus and describe the obstacles and the role of serendipity in facilitating the work. Although alpha-synuclein mutations are a rare cause of hereditary PD, the importance of this finding goes far beyond the rare families with hereditary disease because it pinpointed alpha-synuclein as a key contributor to the far more common sporadic form of Parkinson disease. This work confirms William Harvey's observation from 350 years ago that studying rarer forms of a disease is an excellent way to understand the more common forms of that disease. The identification of synuclein's role in hereditary Parkinson disease has opened new avenues of research into the pathogenesis and potential treatments of the common form of Parkinson disease that affects many millions of Americans and tens of millions of human beings worldwide.
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Affiliation(s)
- Robert L. Nussbaum
- Correspondence to: Robert L. Nussbaum, MD, Chief Medical Officer, Invitae Corporation and former Holly Smith Professor, University of California San Francisco, CA, USA. Tel.: +1 415 264 2589; Fax: +1 415 230 4991; E-mail:
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Denzin LK, Khan AA, Virdis F, Wilks J, Kane M, Beilinson HA, Dikiy S, Case LK, Roopenian D, Witkowski M, Chervonsky AV, Golovkina TV. Neutralizing Antibody Responses to Viral Infections Are Linked to the Non-classical MHC Class II Gene H2-Ob. Immunity 2017; 47:310-322.e7. [PMID: 28813660 DOI: 10.1016/j.immuni.2017.07.013] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 05/23/2017] [Accepted: 07/19/2017] [Indexed: 01/08/2023]
Abstract
Select humans and animals control persistent viral infections via adaptive immune responses that include production of neutralizing antibodies. The precise genetic basis for the control remains enigmatic. Here, we report positional cloning of the gene responsible for production of retrovirus-neutralizing antibodies in mice of the I/LnJ strain. It encodes the beta subunit of the non-classical major histocompatibility complex class II (MHC-II)-like molecule H2-O, a negative regulator of antigen presentation. The recessive and functionally null I/LnJ H2-Ob allele supported the production of virus-neutralizing antibodies independently of the classical MHC haplotype. Subsequent bioinformatics and functional analyses of the human H2-Ob homolog, HLA-DOB, revealed both loss- and gain-of-function alleles, which could affect the ability of their carriers to control infections with human hepatitis B (HBV) and C (HCV) viruses. Thus, understanding of the previously unappreciated role of H2-O (HLA-DO) in immunity to infections may suggest new approaches in achieving neutralizing immunity to viruses.
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Affiliation(s)
- Lisa K Denzin
- Child Health Institute of NJ, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of NJ, New Brunswick, NJ 08901, USA
| | - Aly A Khan
- Toyota Technological Institute at Chicago, Chicago, IL 60637, USA
| | - Francesca Virdis
- Child Health Institute of NJ, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of NJ, New Brunswick, NJ 08901, USA
| | - Jessica Wilks
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Melissa Kane
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Helen A Beilinson
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Stanislav Dikiy
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | - Laure K Case
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA
| | | | - Michele Witkowski
- Child Health Institute of NJ, Department of Pediatrics, Rutgers Robert Wood Johnson Medical School, Rutgers, The State University of NJ, New Brunswick, NJ 08901, USA
| | | | - Tatyana V Golovkina
- Department of Microbiology, The University of Chicago, Chicago, IL 60637, USA.
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Chen TD, Rotival M, Chiu LY, Bagnati M, Ko JH, Srivastava PK, Petretto E, Pusey CD, Lai PC, Aitman TJ, Cook HT, Behmoaras J. Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function. Genetics 2017; 206:1139-51. [PMID: 28450461 DOI: 10.1534/genetics.116.197376] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 04/05/2017] [Indexed: 12/31/2022] Open
Abstract
Crescentic glomerulonephritis (Crgn) is a complex disorder where macrophage activity and infiltration are significant effector causes. In previous linkage studies using the uniquely susceptible Wistar Kyoto (WKY) rat strain, we have identified multiple crescentic glomerulonephritis QTL (Crgn) and positionally cloned genes underlying Crgn1 and Crgn2, which accounted for 40% of total variance in glomerular inflammation. Here, we have generated a backcross (BC) population (n = 166) where Crgn1 and Crgn2 were genetically fixed and found significant linkage to glomerular crescents on chromosome 2 (Crgn8, LOD = 3.8). Fine mapping analysis by integration with genome-wide expression QTLs (eQTLs) from the same BC population identified ceruloplasmin (Cp) as a positional eQTL in macrophages but not in serum. Liquid chromatography-tandem mass spectrometry confirmed Cp as a protein QTL in rat macrophages. WKY macrophages overexpress Cp and its downregulation by RNA interference decreases markers of glomerular proinflammatory macrophage activation. Similarly, short incubation with Cp results in a strain-dependent macrophage polarization in the rat. These results suggest that genetically determined Cp levels can alter susceptibility to Crgn through macrophage function and propose a new role for Cp in early macrophage activation.
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Kim JY, Moon JC, Kim HC, Shin S, Song K, Kim KH, Lee BM. Identification of downy mildew resistance gene candidates by positional cloning in maize (Zea mays subsp. mays; Poaceae). Appl Plant Sci 2017; 5:apps1600132. [PMID: 28224059 PMCID: PMC5315382 DOI: 10.3732/apps.1600132] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 12/21/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Positional cloning in combination with phenotyping is a general approach to identify disease-resistance gene candidates in plants; however, it requires several time-consuming steps including population or fine mapping. Therefore, in the present study, we suggest a new combined strategy to improve the identification of disease-resistance gene candidates. METHODS AND RESULTS Downy mildew (DM)-resistant maize was selected from five cultivars using a spreader row technique. Positional cloning and bioinformatics tools were used to identify the DM-resistance quantitative trait locus marker (bnlg1702) and 47 protein-coding gene annotations. Eventually, five DM-resistance gene candidates, including bZIP34, Bak1, and Ppr, were identified by quantitative reverse-transcription PCR (RT-PCR) without fine mapping of the bnlg1702 locus. CONCLUSIONS The combined protocol with the spreader row technique, quantitative trait locus positional cloning, and quantitative RT-PCR was effective for identifying DM-resistance candidate genes. This cloning approach may be applied to other whole-genome-sequenced crops or resistance to other diseases.
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Affiliation(s)
- Jae Yoon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Republic of Korea
| | - Jun-Cheol Moon
- Agriculture and Life Science Research Institute, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Hyo Chul Kim
- Department of Life Science, Dongguk University–Seoul, Seoul 04620, Republic of Korea
| | - Seungho Shin
- Department of Life Science, Dongguk University–Seoul, Seoul 04620, Republic of Korea
| | - Kitae Song
- Department of Life Science, Dongguk University–Seoul, Seoul 04620, Republic of Korea
| | - Kyung-Hee Kim
- Department of Life Science, Dongguk University–Seoul, Seoul 04620, Republic of Korea
| | - Byung-Moo Lee
- Department of Life Science, Dongguk University–Seoul, Seoul 04620, Republic of Korea
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Doitsidou M, Jarriault S, Poole RJ. Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans. Genetics 2016; 204:451-474. [PMID: 27729495 PMCID: PMC5068839 DOI: 10.1534/genetics.115.186197] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Accepted: 08/05/2016] [Indexed: 02/07/2023] Open
Abstract
The use of next-generation sequencing (NGS) has revolutionized the way phenotypic traits are assigned to genes. In this review, we describe NGS-based methods for mapping a mutation and identifying its molecular identity, with an emphasis on applications in Caenorhabditis elegans In addition to an overview of the general principles and concepts, we discuss the main methods, provide practical and conceptual pointers, and guide the reader in the types of bioinformatics analyses that are required. Owing to the speed and the plummeting costs of NGS-based methods, mapping and cloning a mutation of interest has become straightforward, quick, and relatively easy. Removing this bottleneck previously associated with forward genetic screens has significantly advanced the use of genetics to probe fundamental biological processes in an unbiased manner.
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Affiliation(s)
- Maria Doitsidou
- Centre for Integrative Physiology, University of Edinburgh, EH8 9XD, Scotland
| | - Sophie Jarriault
- L'Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique UMR 7104/Institut National de la Santé et de la Recherche Médicale U964, Université de Strasbourg, 67404, France
| | - Richard J Poole
- Department of Cell and Developmental Biology, University College London, WC1E 6BT, United Kingdom
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Hua Y, Zhang D, Zhou T, He M, Ding G, Shi L, Xu F. Transcriptomics-assisted quantitative trait locus fine mapping for the rapid identification of a nodulin 26-like intrinsic protein gene regulating boron efficiency in allotetraploid rapeseed. Plant Cell Environ 2016; 39:1601-18. [PMID: 26934080 DOI: 10.1111/pce.12731] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 02/17/2016] [Accepted: 02/23/2016] [Indexed: 05/03/2023]
Abstract
Allotetraploid rapeseed (Brassica napus L., An An Cn Cn , 2n = 4x = 38) is extraordinarily susceptible to boron (B) deficiency, a ubiquitous problem causing severe losses in seed yield. The breeding of B-efficient rapeseed germ plasm is a cost-effective and environmentally friendly strategy for the agricultural industry; however, genes regulating B efficiency in allotetraploid rapeseed have not yet been isolated. In this research, quantitative trait locus (QTL) fine mapping and digital gene expression (DGE) profiling were combined to identify the candidate genes underlying the major-effect QTL qBEC-A3a, which regulates B efficiency. Comparative phenotype analyses of the near-isogenic lines (NILs) indicated that qBEC-A3a plays a significant role in improving B efficiency under B deficiency. Exploiting QTL fine mapping and DGE analyses revealed a nodulin 26-like intrinsic protein (NIP) gene, which encodes a likely boric acid channel. The gene co-expression network for putative B transporters also highlighted its central role in the efficiency of B uptake. An integration of whole-genome re-sequencing (WGS) with bulked segregant analysis (BSA) authenticated the emerging availability of QTL-seq for the QTL analyses in allotetraploid rapeseed. Transcriptomics-assisted QTL mapping and comparative genomics provided novel insights into the rapid identification of quantitative trait genes (QTGs) in plant species with complex genomes.
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Affiliation(s)
- Yingpeng Hua
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Didi Zhang
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ting Zhou
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mingliang He
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070, China
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Sarnowski C, Laprise C, Malerba G, Moffatt MF, Dizier MH, Morin A, Vincent QB, Rohde K, Esparza-Gordillo J, Margaritte-Jeannin P, Liang L, Lee YA, Bousquet J, Siroux V, Pignatti PF, Cookson WO, Lathrop M, Pastinen T, Demenais F, Bouzigon E. DNA methylation within melatonin receptor 1A (MTNR1A) mediates paternally transmitted genetic variant effect on asthma plus rhinitis. J Allergy Clin Immunol 2016; 138:748-753. [PMID: 27038909 DOI: 10.1016/j.jaci.2015.12.1341] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Revised: 11/10/2015] [Accepted: 12/15/2015] [Indexed: 12/23/2022]
Abstract
BACKGROUND Asthma and allergic rhinitis (AR) are common allergic comorbidities with a strong genetic component in which epigenetic mechanisms might be involved. OBJECTIVE We aimed to identify novel risk loci for asthma and AR while accounting for parent-of-origin effect. METHODS We performed a series of genetic analyses, taking into account the parent-of-origin effect in families ascertained through asthma: (1) genome-wide linkage scan of asthma and AR in 615 European families, (2) association analysis with 1233 single nucleotide polymorphisms (SNPs) covering the significant linkage region in 162 French Epidemiological Study on the Genetics and Environment of Asthma families with replication in 154 Canadian Saguenay-Lac-Saint-Jean asthma study families, and (3) association analysis of disease and significant SNPs with DNA methylation (DNAm) at CpG sites in 40 Saguenay-Lac-Saint-Jean asthma study families. RESULTS We detected a significant paternal linkage of the 4q35 region to asthma and allergic rhinitis comorbidity (AAR; P = 7.2 × 10(-5)). Association analysis in this region showed strong evidence for the effect of the paternally inherited G allele of rs10009104 on AAR (P = 1.1 × 10(-5), reaching the multiple-testing corrected threshold). This paternally inherited allele was also significantly associated with DNAm levels at the cg02303933 site (P = 1.7 × 10(-4)). Differential DNAm at this site was found to mediate the identified SNP-AAR association. CONCLUSION By integrating genetic and epigenetic data, we identified that a differentially methylated CpG site within the melatonin receptor 1A (MTNR1A) gene mediates the effect of a paternally transmitted genetic variant on the comorbidity of asthma and AR. This study provides a novel insight into the role of epigenetic mechanisms in patients with allergic respiratory diseases.
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Affiliation(s)
- Chloé Sarnowski
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | | | - Giovanni Malerba
- Section of Biology and Genetics, Department of Mother and Child, and Biology-Genetics, University of Verona, Verona, Italy
| | - Miriam F Moffatt
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Marie-Hélène Dizier
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Andréanne Morin
- Université du Québec, à Chicoutimi, Québec, Canada; McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Quentin B Vincent
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM, UMR1163, Paris, France; Université Paris Descartes, Imagine Institute, Paris, France
| | - Klaus Rohde
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Jorge Esparza-Gordillo
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany; Clinic for Pediatric Allergy, Experimental and Clinical Research Centre, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Patricia Margaritte-Jeannin
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Liming Liang
- Department of Epidemiology, Harvard School of Public Health, Boston, Mass
| | - Young-Ae Lee
- Max-Delbrück-Center for Molecular Medicine (MDC), Berlin, Germany
| | - Jean Bousquet
- Hôpital Arnaud de Villeneuve, Service des Maladies Respiratoires, Montpellier, France
| | - Valérie Siroux
- Université Grenoble Alpes, IAB, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France; INSERM, IAB, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France; CHU de Grenoble, IAB, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France
| | - Pier Franco Pignatti
- Section of Biology and Genetics, Department of Mother and Child, and Biology-Genetics, University of Verona, Verona, Italy
| | - William O Cookson
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Tomi Pastinen
- McGill University and Génome Québec Innovation Centre, Montreal, Québec, Canada
| | - Florence Demenais
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France
| | - Emmanuelle Bouzigon
- INSERM, UMR946, Genetic Variation and Human Diseases Unit, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, Institut Universitaire d'Hématologie, Paris, France.
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Tian J, Keller MP, Oler AT, Rabaglia ME, Schueler KL, Stapleton DS, Broman AT, Zhao W, Kendziorski C, Yandell BS, Hagenbuch B, Broman KW, Attie AD. Identification of the Bile Acid Transporter Slco1a6 as a Candidate Gene That Broadly Affects Gene Expression in Mouse Pancreatic Islets. Genetics 2015; 201:1253-62. [PMID: 26385979 DOI: 10.1534/genetics.115.179432] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 09/16/2015] [Indexed: 12/15/2022] Open
Abstract
We surveyed gene expression in six tissues in an F2 intercross between mouse strains C57BL/6J (abbreviated B6) and BTBR T(+) tf/J (abbreviated BTBR) made genetically obese with the Leptin(ob) mutation. We identified a number of expression quantitative trait loci (eQTL) affecting the expression of numerous genes distal to the locus, called trans-eQTL hotspots. Some of these trans-eQTL hotspots showed effects in multiple tissues, whereas some were specific to a single tissue. An unusually large number of transcripts (∼8% of genes) mapped in trans to a hotspot on chromosome 6, specifically in pancreatic islets. By considering the first two principal components of the expression of genes mapping to this region, we were able to convert the multivariate phenotype into a simple Mendelian trait. Fine mapping the locus by traditional methods reduced the QTL interval to a 298-kb region containing only three genes, including Slco1a6, one member of a large family of organic anion transporters. Direct genomic sequencing of all Slco1a6 exons identified a nonsynonymous coding SNP that converts a highly conserved proline residue at amino acid position 564 to serine. Molecular modeling suggests that Pro564 faces an aqueous pore within this 12-transmembrane domain-spanning protein. When transiently overexpressed in HEK293 cells, BTBR organic anion transporting polypeptide (OATP)1A6-mediated cellular uptake of the bile acid taurocholic acid (TCA) was enhanced compared to B6 OATP1A6. Our results suggest that genetic variation in Slco1a6 leads to altered transport of TCA (and potentially other bile acids) by pancreatic islets, resulting in broad gene regulation.
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Labonne JDJ, Vogt J, Reali L, Kong IK, Layman LC, Kim HG. A microdeletion encompassing PHF21A in an individual with global developmental delay and craniofacial anomalies. Am J Med Genet A 2015; 167A:3011-8. [PMID: 26333423 DOI: 10.1002/ajmg.a.37344] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Accepted: 08/12/2015] [Indexed: 11/09/2022]
Abstract
In Potocki-Shaffer syndrome (PSS), the full phenotypic spectrum is manifested when deletions are at least 2.1 Mb in size at 11p11.2. The PSS-associated genes EXT2 and ALX4, together with PHF21A, all map to this region flanked by markers D11S1393 and D11S1319. Being proximal to EXT2 and ALX4, a 1.1 Mb region containing 12 annotated genes had been identified by deletion mapping to explain PSS phenotypes except multiple exostoses and parietal foramina. Here, we report a male patient with partial PSS phenotypes including global developmental delay, craniofacial anomalies, minor limb anomalies, and micropenis. Using microarray, qPCR, RT-qPCR, and Western blot analyses, we refined the candidate gene region, which harbors five genes, by excluding two genes, SLC35C1 and CRY2, which resulted in a corroborating role of PHF21A in developmental delay and craniofacial anomalies. This microdeletion contains the least number of genes at 11p11.2 reported to date. Additionally, we also discuss the phenotypes observed in our patient with respect to those of published cases of microdeletions across the Potocki-Shaffer interval.
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Affiliation(s)
- Jonathan D J Labonne
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Georgia Regents University, Augusta, Georgia.,Department of Neuroscience and Regenerative Medicine, Georgia Regents University, Augusta, Georgia
| | - Julie Vogt
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Lisa Reali
- West Midlands Regional Genetics Service, Birmingham Women's Hospital, Birmingham, United Kingdom
| | - Il-Keun Kong
- Department of Animal Science, Division of Applied Life Science, Gyeongsang National University, Jinju, Gyeongsangnam-do, Republic of Korea
| | - Lawrence C Layman
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Georgia Regents University, Augusta, Georgia.,Department of Neuroscience and Regenerative Medicine, Georgia Regents University, Augusta, Georgia.,Department of Physiology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia
| | - Hyung-Goo Kim
- Section of Reproductive Endocrinology, Infertility and Genetics, Department of Obstetrics and Gynecology, Georgia Regents University, Augusta, Georgia.,Department of Neuroscience and Regenerative Medicine, Georgia Regents University, Augusta, Georgia
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Billoud B, Jouanno É, Nehr Z, Carton B, Rolland É, Chenivesse S, Charrier B. Localization of causal locus in the genome of the brown macroalga Ectocarpus: NGS-based mapping and positional cloning approaches. Front Plant Sci 2015; 6:68. [PMID: 25745426 PMCID: PMC4333798 DOI: 10.3389/fpls.2015.00068] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 01/26/2015] [Indexed: 05/12/2023]
Abstract
Mutagenesis is the only process by which unpredicted biological gene function can be identified. Despite that several macroalgal developmental mutants have been generated, their causal mutation was never identified, because experimental conditions were not gathered at that time. Today, progresses in macroalgal genomics and judicious choices of suitable genetic models make mutated gene identification possible. This article presents a comparative study of two methods aiming at identifying a genetic locus in the brown alga Ectocarpus siliculosus: positional cloning and Next-Generation Sequencing (NGS)-based mapping. Once necessary preliminary experimental tools were gathered, we tested both analyses on an Ectocarpus morphogenetic mutant. We show how a narrower localization results from the combination of the two methods. Advantages and drawbacks of these two approaches as well as potential transfer to other macroalgae are discussed.
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Affiliation(s)
- Bernard Billoud
- Sorbonne Université, UPMC University Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de RoscoffCS 90074, F-29688, Roscoff cedex, France
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Gallavotti A, Whipple CJ. Positional cloning in maize (Zea mays subsp. mays, Poaceae). Appl Plant Sci 2015; 3:apps1400092. [PMID: 25606355 PMCID: PMC4298233 DOI: 10.3732/apps.1400092] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Accepted: 12/11/2014] [Indexed: 05/20/2023]
Abstract
PREMISE OF THE STUDY Positional (or map-based) cloning is a common approach to identify the molecular lesions causing mutant phenotypes. Despite its large and complex genome, positional cloning has been recently shown to be feasible in maize, opening up a diverse collection of mutants to molecular characterization. • METHODS AND RESULTS Here we outline a general protocol for positional cloning in maize. While the general strategy is similar to that used in other plant species, we focus on the unique resources and approaches that should be considered when applied to maize mutants. • CONCLUSIONS Positional cloning approaches are appropriate for maize mutants and quantitative traits, opening up to molecular characterization the large array of genetic diversity in this agronomically important species. The cloning approach described should be broadly applicable to other species as more plant genomes become available.
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Affiliation(s)
- Andrea Gallavotti
- Waksman Institute of Microbiology, Rutgers University, Piscataway, New Jersey 08854-8020 USA
- Department of Plant Biology and Pathology, Rutgers University, New Brunswick, New Jersey 08901 USA
| | - Clinton J. Whipple
- Department of Biology, Brigham Young University, Provo, Utah 84602 USA
- Author for correspondence:
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Settles AM, Bagadion AM, Bai F, Zhang J, Barron B, Leach K, Mudunkothge JS, Hoffner C, Bihmidine S, Finefield E, Hibbard J, Dieter E, Malidelis IA, Gustin JL, Karoblyte V, Tseung CW, Braun DM. Efficient molecular marker design using the MaizeGDB Mo17 SNPs and Indels track. G3 (Bethesda) 2014; 4:1143-5. [PMID: 24747759 DOI: 10.1534/g3.114.010454] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Positional cloning in maize (Zea mays) requires development of markers in the region of interest. We found that primers designed to amplify annotated insertion–deletion polymorphisms of seven base pairs or greater between B73 and Mo17 produce polymorphic markers at a 97% frequency with 49% of the products showing co-dominant fragment length polymorphisms. When the same polymorphisms are used to develop markers for B73 and W22 or Mo17 and W22 mapping populations, 22% and 31% of markers are co-dominant, respectively. There are 38,223 Indel polymorphisms that can be converted to markers providing high-density coverage throughout the maize genome. This strategy significantly increases the efficiency of marker development for fine-mapping in maize.
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Abstract
Asthma is a multifactorial disorder, primarily resulting from interactions between genetic and environmental factors. ADAM33 gene (located on chromosome 20p13) has been reported to play an important role in asthma. This review article is intended to include all of the publications, to date, which have assessed the association of ADAM33 gene polymorphisms as well as have shown the role of ADAM33 gene in airway remodeling and their expression with asthma. A PubMed search was performed for studies published between 1990 and 2010. The terms “ADAM33,” “ADAM33 gene and asthma,” and “ADAM33 gene polymorphisms” were used as search criteria. Based on available literature we can only speculate its role in the morphogenesis and functions of the lung. Fourteen studies conducted in different populations were found showing an association of ADAM33 gene polymorphisms with asthma. However, none of the single nucleotide polymorphisms (SNPs) of ADAM33 gene had found association with asthma across all ethnic groups. Because higher expression of ADAM33 is found in the fibroblast and smooth muscle cells of the lung, over- or underexpression of ADAM33 gene may result in alterations in airway remodeling and repair processes. However, no SNP of ADAM33 gene showed significant associations with asthma across all ethnic groups; the causative polymorphism, if any, still has to be identified.
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Affiliation(s)
- Neeraj Sharma
- Department of Pediatrics, Chhatrapati Shahuji Maharaj Medical University, Lucknow, Uttar Pradesh, India
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Liu KH, McCormack M, Sheen J. Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis. Plant Methods 2012; 8:12. [PMID: 22462410 PMCID: PMC3348062 DOI: 10.1186/1746-4811-8-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 03/30/2012] [Indexed: 05/07/2023]
Abstract
Large-scale genetic screens in Arabidopsis are a powerful approach for molecular dissection of complex signaling networks. However, map-based cloning can be time-consuming or even hampered due to low chromosomal recombination. Current strategies using next generation sequencing for molecular identification of mutations require whole genome sequencing and advanced computational devises and skills, which are not readily accessible or affordable to every laboratory. We have developed a streamlined method using parallel massive sequencing for mutant identification in which only targeted regions are sequenced. This targeted parallel sequencing (TPSeq) method is more cost-effective, straightforward enough to be easily done without specialized bioinformatics expertise, and reliable for identifying multiple mutations simultaneously. Here, we demonstrate its use by identifying three novel nitrate-signaling mutants in Arabidopsis.
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Affiliation(s)
- Kun-hsiang Liu
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Matthew McCormack
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
| | - Jen Sheen
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
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Shi X, Zeng H, Xue Y, Luo M. A pair of new BAC and BIBAC vectors that facilitate BAC/BIBAC library construction and intact large genomic DNA insert exchange. Plant Methods 2011; 7:33. [PMID: 21985432 PMCID: PMC3213141 DOI: 10.1186/1746-4811-7-33] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2011] [Accepted: 10/11/2011] [Indexed: 05/25/2023]
Abstract
BACKGROUND Large-insert BAC and BIBAC libraries are important tools for structural and functional genomics studies of eukaryotic genomes. To facilitate the construction of BAC and BIBAC libraries and the transfer of complete large BAC inserts into BIBAC vectors, which is desired in positional cloning, we developed a pair of new BAC and BIBAC vectors. RESULTS The new BAC vector pIndigoBAC536-S and the new BIBAC vector BIBAC-S have the following features: 1) both contain two 18-bp non-palindromic I-SceI sites in an inverted orientation at positions that flank an identical DNA fragment containing the lacZ selection marker and the cloning site. Large DNA inserts can be excised from the vectors as single fragments by cutting with I-SceI, allowing the inserts to be easily sized. More importantly, because the two vectors contain different antibiotic resistance genes for transformant selection and produce the same non-complementary 3' protruding ATAA ends by I-SceI that suppress self- and inter-ligations, the exchange of intact large genomic DNA inserts between the BAC and BIBAC vectors is straightforward; 2) both were constructed as high-copy composite vectors. Reliable linearized and dephosphorylated original low-copy pIndigoBAC536-S and BIBAC-S vectors that are ready for library construction can be prepared from the high-copy composite vectors pHZAUBAC1 and pHZAUBIBAC1, respectively, without the need for additional preparation steps or special reagents, thus simplifying the construction of BAC and BIBAC libraries. BIBAC clones constructed with the new BIBAC-S vector are stable in both E. coli and Agrobacterium. The vectors can be accessed through our website http://GResource.hzau.edu.cn. CONCLUSIONS The two new vectors and their respective high-copy composite vectors can largely facilitate the construction and characterization of BAC and BIBAC libraries. The transfer of complete large genomic DNA inserts from one vector to the other is made straightforward.
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Affiliation(s)
- Xue Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haiyang Zeng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yadong Xue
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meizhong Luo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
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Magnan DR, Spacek DV, Ye N, Lu YC, King TR. The male sterility and histoincompatibility (mshi) mutation in mice is a natural variant of microtubule-associated protein 7 (Mtap7). Mol Genet Metab 2009; 97:155-62. [PMID: 19329343 PMCID: PMC2680479 DOI: 10.1016/j.ymgme.2009.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 02/26/2009] [Accepted: 02/26/2009] [Indexed: 12/14/2022]
Abstract
Males homozygous for the mouse male sterility and histoincompatibility (mshi) mutation exhibit small testes and produce no sperm. In addition, mshi generates an "antigen-loss" histoincompatibility barrier, such that homozygous mutants reject skin grafts from wild type co-isogenic BALB/cByJ donors. To facilitate the molecular characterization of the pleiotropic mshi mutation, we genetically mapped mshi into a 0.68 megabasepair region which contains fewer than 10 candidate genes. Complementation testing showed that one of these, Mtap7, is disrupted in mshi mice. Sequence analysis has revealed a 13 kilobasepair deletion in BALB/cByJ-mshi/J mice that begins in Intron 10-11 of Mtap7, and ends less than 2000 base pairs downstream of the wild type gene. Analysis of the mutant cDNA predicts that Mtap7(mshi) encodes a 457 amino acid protein, the first 423 of which are identical to wild type, and the last 34 of which are due to aberrant mRNA splicing with two cryptic exons in the Mtap7 to P04Rik intergenic region. This molecular assignment for the mshi mutation further supports an essential role for microtubule stabilization in spermatogenesis and indicates a new role in allograft transplantation.
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Affiliation(s)
- D. R. Magnan
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT 06053, USA
| | - D. V. Spacek
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT 06053, USA
| | - N. Ye
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT 06053, USA
| | - Y.-C. Lu
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT 06053, USA
| | - T. R. King
- Department of Biomolecular Sciences, Central Connecticut State University, 1615 Stanley Street, New Britain, CT 06053, USA
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Aiyar RS, Gagneur J, Steinmetz LM. Identification of mitochondrial disease genes through integrative analysis of multiple datasets. Methods 2008; 46:248-55. [PMID: 18930150 PMCID: PMC2774125 DOI: 10.1016/j.ymeth.2008.10.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Revised: 10/03/2008] [Accepted: 10/08/2008] [Indexed: 11/24/2022] Open
Abstract
Determining the genetic factors in a disease is crucial to elucidating its molecular basis. This task is challenging due to a lack of information on gene function. The integration of large-scale functional genomics data has proven to be an effective strategy to prioritize candidate disease genes. Mitochondrial disorders are a prevalent and heterogeneous class of diseases that are particularly amenable to this approach. Here we explain the application of integrative approaches to the identification of mitochondrial disease genes. We first examine various datasets that can be used to evaluate the involvement of each gene in mitochondrial function. The data integration methodology is then described, accompanied by examples of common implementations. Finally, we discuss how gene networks are constructed using integrative techniques and applied to candidate gene prioritization. Relevant public data resources are indicated. This report highlights the success and potential of data integration as well as its applicability to the search for mitochondrial disease genes.
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Affiliation(s)
- Raeka S. Aiyar
- European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Julien Gagneur
- European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
| | - Lars M. Steinmetz
- European Molecular Biology Laboratory, Meyerhofstraβe 1, 69117 Heidelberg, Germany
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Wassink TH, Vieland VJ, Sheffield VC, Bartlett CW, Goedken R, Childress D, Piven J. Posterior probability of linkage analysis of autism dataset identifies linkage to chromosome 16. Psychiatr Genet 2008; 18:85-91. [PMID: 18349700 PMCID: PMC4442314 DOI: 10.1097/ypg.0b013e3282f9b48e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To apply phenotypic and statistical methods designed to account for heterogeneity to linkage analyses of the autism Collaborative Linkage Study of Autism (CLSA) affected sibling pair families. METHOD The CLSA contains two sets of 57 families each; Set 1 has been analyzed previously, whereas this study presents the first analyses of Set 2. The two sets were analyzed independently, and were further split based on the degree of phrase speech delay in the siblings. Linkage analysis was carried out using the posterior probability of linkage (PPL), a Bayesian statistic that provides a mathematically rigorous mechanism for combining linkage evidence across multiple samples. RESULTS Two-point PPLs from Set 1 led to the follow-up genotyping of 18 markers around linkage peaks on 1q, 13p, 13q, 16q, and 17q in both sets of families. Multipoint PPLs were then calculated for the entire CLSA sample. These analyses identified four regions with at least modest evidence in support of linkage: 1q at 173 cM, PPL=0.12; 13p at 21 cM, PPL=0.16; 16q at 63 cM, PPL=0.36; Xq at 40 cM, PPL=0.11. CONCLUSION We find strengthened evidence for linkage of autism to chromosomes 1q, 13p, 16q, and Xq, and diminished evidence for linkage to 7q and 13q. The verity of these findings will be tested by continuing to update our PPL analyses with data from additional autism datasets.
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Affiliation(s)
- Thomas H Wassink
- Department of Psychiatry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA.
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Szalai C, Ungvári I, Pelyhe L, Tölgyesi G, Falus A. Asthma from a pharmacogenomic point of view. Br J Pharmacol 2008; 153:1602-14. [PMID: 18311188 PMCID: PMC2438267 DOI: 10.1038/bjp.2008.55] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Revised: 01/28/2008] [Accepted: 02/01/2008] [Indexed: 12/25/2022] Open
Abstract
Pharmacogenomics, a fascinating, emerging area of biomedical research is strongly influenced by growing availability of genomic databases, high-throughput genomic technologies, bioinformatic tools and artificial computational modelling approaches. One main area of pharmacogenomics is the discovery of new drugs and drug targets with molecular genetic, genomic or even bioinformatic methods; the other is the study of how genomic differences influence the variability in patients' responses to drugs. From a genetic point of view, asthma is multifactorial, which means that the susceptibility to the disease is determined by interactions between multiple genes, and involves important non-genetic factors such as the environment for their expression. In this review, we summarize collective evidence from linkage and association studies that have consistently reported suggestive linkage or association of asthma or its associated phenotypes to polymorphic markers and single nucleotide polymorphisms in selected chromosomes. Genes that have been found implicated in the disease are potential new drug targets and several pharmacological investigations are underway to utilize these new discoveries. Next, we will focus on the inter-individual variability in anti-asthmatic drug responses and review the recent results in this topic.
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Affiliation(s)
- C Szalai
- Laboratory of Molecular Biology, Heim Pál Pediatric Hospital Budapest, Hungary
- Inflammation Biology and Immunogenomics Research Group, Hungarian Academy of Sciences, Semmelweis University Budapest, Hungary
| | - I Ungvári
- Department of Genetics, Cell and Immunobiology, Semmelweis University Budapest, Hungary
| | - L Pelyhe
- Faculty of Biology, Eötvös Lóránd University Budapest, Hungary
| | - G Tölgyesi
- Department of Genetics, Cell and Immunobiology, Semmelweis University Budapest, Hungary
| | - A Falus
- Inflammation Biology and Immunogenomics Research Group, Hungarian Academy of Sciences, Semmelweis University Budapest, Hungary
- Department of Genetics, Cell and Immunobiology, Semmelweis University Budapest, Hungary
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Puliti A, Caridi G, Ravazzolo R, Ghiggeri GM. Teaching molecular genetics: chapter 4- positional cloning of genetic disorders. Pediatr Nephrol 2007; 22:2023-9. [PMID: 17661092 PMCID: PMC2908434 DOI: 10.1007/s00467-007-0548-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2007] [Revised: 05/17/2007] [Accepted: 05/22/2007] [Indexed: 11/26/2022]
Abstract
Positional cloning is the approach of choice for the identification of genetic mutations underlying the pathological development of diseases with simple Mendelian inheritance. It consists of different consecutive steps, starting with recruitment of patients and DNA collection, that are critical to the overall process. A genetic analysis of the enrolled patients and their families is performed, based on genetic recombination frequencies generated by meiotic cross-overs and on genome-wide molecular studies, to define a critical DNA region of interest. This analysis culminates in a statistical estimate of the probability that disease features may segregate in the families independently or in association with specific molecular markers located in known regions. In this latter case, a marker can be defined as being linked to the disease manifestations. The genetic markers define an interval that is a function of their recombination frequencies with the disease, in which the disease gene is localised. The identification and characterisation of chromosome abnormalities as translocations, deletions and duplications by classical cytogenetic methods or by the newly developed microarray-based comparative genomic hybridisation (array CGH) technique may define extensions and borders of the genomic regions involved. The step following the definition of a critical genomic region is the identification of candidate genes that is based on the analysis of available databases from genome browsers. Positional cloning culminates in the identification of the causative gene mutation, and the definition of its functional role in the pathogenesis of the disorder, by the use of cell-based or animal-based experiments. More often, positional cloning ends with the generation of mice with homologous mutations reproducing the human clinical phenotype. Altogether, positional cloning has represented a fundamental step in the research on genetic renal disorders, leading to the definition of several disease mechanisms and allowing a proper diagnostic approach to many conditions.
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Affiliation(s)
- Aldamaria Puliti
- Laboratory of Molecular Genetics, Istituto G. Gaslini, Genoa, Italy
- Department of Pediatric Sciences and CEBR, University of Genoa, Genoa, Italy
| | - Gianluca Caridi
- Laboratory on Pathophysiology of Uraemia, Istituto Giannina Gaslini, Largo G. Gaslini, 5, 16147 Genoa, Italy
| | - Roberto Ravazzolo
- Laboratory of Molecular Genetics, Istituto G. Gaslini, Genoa, Italy
- Department of Pediatric Sciences and CEBR, University of Genoa, Genoa, Italy
| | - Gian Marco Ghiggeri
- Laboratory on Pathophysiology of Uraemia, Istituto Giannina Gaslini, Largo G. Gaslini, 5, 16147 Genoa, Italy
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Meng H, Vera I, Che N, Wang X, Wang SS, Ingram-Drake L, Schadt EE, Drake TA, Lusis AJ. Identification of Abcc6 as the major causal gene for dystrophic cardiac calcification in mice through integrative genomics. Proc Natl Acad Sci U S A 2007; 104:4530-5. [PMID: 17360558 PMCID: PMC1838635 DOI: 10.1073/pnas.0607620104] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2006] [Indexed: 11/18/2022] Open
Abstract
The genetic factors contributing to the complex disorder of myocardial calcification are largely unknown. Using a mouse model, we fine-mapped the major locus (Dyscalc1) contributing to the dystrophic cardiac calcification (DCC) to an 840-kb interval containing 38 genes. We then identified the causal gene by using an approach integrating genetic segregation and expression array analyses to identify, on a global scale, cis-acting DNA variations that perturb gene expression. By studying two intercrosses, in which the DCC trait segregates, a single candidate gene (encoding the ATP-binding cassette transporter ABCC6) was identified. Transgenic complementation confirmed Abcc6 as the underlying causal gene for Dyscalc1. We demonstrate that in the cross, the expression of Abcc6 is highly correlated with the local mineralization regulatory system and the BMP2-Wnt signaling pathway known to be involved in the systemic regulation of calcification, suggesting potential pathways for the action of Abcc6 in DCC. Our results demonstrate the power of the integrative genomics in discovering causal genes and pathways underlying complex traits.
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Affiliation(s)
- Haijin Meng
- Departments of *Medicine, Cardiology Division
| | - Iset Vera
- Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461; and
| | - Nam Che
- Departments of *Medicine, Cardiology Division
| | - Xuping Wang
- Departments of *Medicine, Cardiology Division
| | | | | | - Eric E. Schadt
- Rosetta Inpharmatics LLC, Merck & Co., Inc., Seattle, WA 98109
| | | | - Aldons J. Lusis
- Microbiology, Immunology, Molecular Genetics, Medicine, and Human Genetics, University of California, Los Angeles, CA 90095
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Abstract
The recent advances in understanding the pathophysiology of focal segmental glomerulosclerosis (FSGS) and molecular function of glomerular filtration barrier come directly from genetic linkage and positional cloning studies. The exact role and function of the newly discovered genes and proteins are being investigated by in vitro and in vivo mechanistic studies. Those genes and proteins interactions seem to change susceptibility to kidney disease progression. Better understanding of their exact role in the development of FSGS may influence future therapies and outcomes in this complex disease.
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Watanabe M, Iwashita M, Ishii M, Kurachi Y, Kawakami A, Kondo S, Okada N. Spot pattern of leopard Danio is caused by mutation in the zebrafish connexin41.8 gene. EMBO Rep 2006; 7:893-7. [PMID: 16845369 PMCID: PMC1559663 DOI: 10.1038/sj.embor.7400757] [Citation(s) in RCA: 151] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2005] [Revised: 06/20/2006] [Accepted: 06/20/2006] [Indexed: 11/08/2022] Open
Abstract
Leopard, a well-known zebrafish mutant that has a spotted skin pattern instead of stripes, is a model for the study of pigment patterning. To understand the mechanisms underlying stripe formation, as well as the spot variation observed in leopard, we sought to identify the gene responsible for this phenotype. Using positional cloning, we identified the leopard gene as an orthologue of the mammalian connexin 40 gene. A variety of different leopard alleles, such as leo(t1), leo(tq270) and leo(tw28), show different skin-pattern phenotypes. In this manuscript we show that the mutation in allele leo(t1) is a nonsense mutation, whereas alleles leo(tq270) and leo(tw28) contain the missense mutations I202F and I31F, respectively. Patch-clamp experiments of connexin hemichannels demonstrated that the I202F substitution in allele leo(tq270) disrupted the channel function of connexin41.8. These results demonstrate that mutations in this gene lead to a variety of leopard spot patterns.
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Affiliation(s)
- Masakatsu Watanabe
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Motoko Iwashita
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Center of Developmental Biology, Riken, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0077, Japan
| | - Masaru Ishii
- Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Yoshihisa Kurachi
- Graduate School of Medicine, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan
| | - Atsushi Kawakami
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Shigeru Kondo
- Center of Developmental Biology, Riken, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe 650-0077, Japan
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Norihiro Okada
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, 4259-B21, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- National Institute for Basic Biology, Nishigonaka, Myodaiji, Okazaki 444-8585, Japan
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Perincheri S, Dingle RWC, Peterson ML, Spear BT. Hereditary persistence of alpha-fetoprotein and H19 expression in liver of BALB/cJ mice is due to a retrovirus insertion in the Zhx2 gene. Proc Natl Acad Sci U S A 2005; 102:396-401. [PMID: 15626755 PMCID: PMC544306 DOI: 10.1073/pnas.0408555102] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2004] [Indexed: 11/18/2022] Open
Abstract
The alpha-fetoprotein (AFP) and H19 genes are transcribed at high levels in the mammalian fetal liver but are rapidly repressed postnatally. This repression in the liver is controlled, at least in part, by the Afr1 gene. Afr1 was defined >25 years ago when BALB/cJ mice were found to have 5- to 20-fold higher adult serum AFP levels compared with all other mouse strains; subsequent studies showed that this elevation was due to higher Afp expression in the liver. H19, which has become a model for genomic imprinting, was identified initially in a screen for Afr1-regulated genes. The BALB/cJ allele (Afr1(b)) is recessive to the wild-type allele (Afr1(a)), consistent with the idea that Afr1 functions as a repressor. By high-resolution mapping, we identified a gene that maps to the Afr1 interval on chromosome 15 and encodes a putative zinc fingers and homeoboxes (ZHX) protein. In BALB/cJ mice, this gene contains a murine endogenous retrovirus within its first intron and produces predominantly an aberrant transcript that no longer encodes a functional protein. Liver-specific overexpression of a Zhx2 transgene restores wild-type H19 repression on a BALB/cJ background, confirming that this gene is responsible for hereditary persistence of Afp and H19 in the livers of BALB/cJ mice. Thus we have identified a genetically defined transcription factor that is involved in developmental gene silencing in mammals. We present a model to explain the liver-specific phenotype in BALB/cJ mice, even though Afr1 is a ubiquitously expressed gene.
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Affiliation(s)
- Sudhir Perincheri
- Department of Microbiology, Immunology, and Molecular Genetics and Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536
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Nolte D, Niemann S, Müller U. Specific sequence changes in multiple transcript system DYT3 are associated with X-linked dystonia parkinsonism. Proc Natl Acad Sci U S A 2003; 100:10347-52. [PMID: 12928496 PMCID: PMC193564 DOI: 10.1073/pnas.1831949100] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
X-linked dystonia parkinsonism (XDP) is an X-linked recessive adult onset movement disorder characterized by both dystonia and parkinsonism. We report delineation of the disease gene within a 300-kb interval of Xq13.1 by allelic association. Sequencing of this region in a patient revealed five disease-specific single-nucleotide changes (here referred to as DSC) and a 48-bp deletion unique to XDP. One of the DSCs is located within an exon of a not previously described multiple transcript system that is composed of at least 16 exons. There is a minimum of three different transcription start sites that encode four different transcripts. Two of these transcripts include distal portions of the TAF1 gene (TATA-box binding protein-associated factor 1) and are alternatively spliced. Three exons overlap with ING2 (a putative tumor suppressor) and with a homologue of CIS4 (cytokine-inducible SH2 protein 4), both of which are encoded by the opposite strand. Although all DSCs are located within this multiple transcript system, only DSC3 lies within an exon. This exon is used by all alternative transcripts making a pathogenic role of DSC3 in XDP likely. The multiple transcript system is therefore referred to as DYT3 (disease locus in XDP).
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Affiliation(s)
- Dagmar Nolte
- Institut für Humangenetik, Justus-Liebig-Universität, Schlangenzahl 14, 35392 Giessen, Germany
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