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Wang Z, Wang R, Yuan H, Fan F, Li S, Cheng M, Tian Z. Comprehensive identification and analysis of DUF640 genes associated with rice growth. Gene 2024; 914:148404. [PMID: 38521113 DOI: 10.1016/j.gene.2024.148404] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/13/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Protein domains with conserved amino acid sequences and uncharacterized functions are called domains of unknown function (DUF). The DUF640 gene family plays a crucial role in plant growth, particularly in light regulation, floral organ development, and fruit development. However, there exists a lack of systematic understanding of the evolutionary relationships and functional differentiation of DUF640 within the Oryza genus. In this study, 61 DUF640 genes were identified in the Oryza genus. The expression of DUF640s is induced by multiple hormonal stressors including abscisic acid (ABA), cytokinin (CK), ethylene (ETH), and indole-3-acetic acid (IAA). Specifically, OiDUF640-10 expression significantly increased after ETH treatment. Transgenic experiments showed that overexpressing OiDUF640-10 lines were sensitive to ETH, and seedling length was obstructed. Evolutionary analysis revealed differentiation of the OiDUF640-10 gene in O. sativa ssp. indica and japonica varieties, likely driven by natural selection during the domestication of cultivated rice. These results indicate that OiDUF640-10 plays a vital role in the regulation of rice seedling length.
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Affiliation(s)
- Zhikai Wang
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Life Science, Yangtze University, Jingzhou, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China
| | - Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Sciences, Wuhan University, Wuhan, China; Hubei Hongshan Laboratory, Wuhan, China.
| | - Zhihong Tian
- Engineering Research Center of Ecology and Agricultural Use of Wetland, Ministry of Education, College of Life Science, Yangtze University, Jingzhou, China.
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Hu X, Yasir M, Zhuo Y, Cai Y, Ren X, Rong J. Genomic insights into glume pubescence in durum wheat: GWAS and haplotype analysis implicates TdELD1-1A as a candidate gene. Gene 2024; 909:148309. [PMID: 38417687 DOI: 10.1016/j.gene.2024.148309] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 03/01/2024]
Abstract
Glume pubescence is an important morphological trait for the characterization of wheat cultivars. It shows tolerance to biotic and abiotic stresses to some extent. Hg1 (formerly named Hg) locus on chromosome 1AS controls glume pubescence in wheat. Its genetic analysis, fine-mapping and candidate gene analysis have been widely studied recently, however, the cloning of Hg1 has not yet been reported. Here, we conducted a GWAS between a dense panel of 171,103 SNPs and glume pubescence (Gp) in a durum wheat population of 145 lines, and further analyzed the candidate genes of Hg1 combined with the gene expression, functional annotation, and haplotype analysis. As a results, TRITD0Uv1G104670 (TdELD1-1A), encoding glycosyltransferase-like ELD1/KOBITO 1, was detected as the most promising candidate gene of Hg1 for glume pubescence in durum wheat. Our findings not only contribute to a deeper understanding of its cloning and functional validation but also underscore the significance of accurate genome sequences and annotations. Additionally, our study highlights the relevance of unanchored sequences in chrUn and the application of bioinformatics analysis for gene discovery in durum wheat.
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Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Yujie Zhuo
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China
| | - Yijing Cai
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xifeng Ren
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China.
| | - Junkang Rong
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Lin'an, Hangzhou 311300, Zhejiang, China.
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Aloryi KD, Okpala NE, Guo H, Karikari B, Amo A, Bello SF, Saini DK, Akaba S, Tian X. Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice. BMC Genomics 2024; 25:338. [PMID: 38575927 PMCID: PMC10993490 DOI: 10.1186/s12864-024-10219-z] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/13/2024] [Indexed: 04/06/2024] Open
Abstract
BACKGROUND Due to rising costs, water shortages, and labour shortages, farmers across the globe now prefer a direct seeding approach. However, submergence stress remains a major bottleneck limiting the success of this approach in rice cultivation. The merger of accumulated rice genetic resources provides an opportunity to detect key genomic loci and candidate genes that influence the flooding tolerance of rice. RESULTS In the present study, a whole-genome meta-analysis was conducted on 120 quantitative trait loci (QTL) obtained from 16 independent QTL studies reported from 2004 to 2023. These QTL were confined to 18 meta-QTL (MQTL), and ten MQTL were successfully validated by independent genome-wide association studies from diverse natural populations. The mean confidence interval (CI) of the identified MQTL was 3.44 times narrower than the mean CI of the initial QTL. Moreover, four core MQTL loci with genetic distance less than 2 cM were obtained. By combining differentially expressed genes (DEG) from two transcriptome datasets with 858 candidate genes identified in the core MQTL regions, we found 38 common differentially expressed candidate genes (DECGs). In silico expression analysis of these DECGs led to the identification of 21 genes with high expression in embryo and coleoptile under submerged conditions. These DECGs encode proteins with known functions involved in submergence tolerance including WRKY, F-box, zinc fingers, glycosyltransferase, protein kinase, cytochrome P450, PP2C, hypoxia-responsive family, and DUF domain. By haplotype analysis, the 21 DECGs demonstrated distinct genetic differentiation and substantial genetic distance mainly between indica and japonica subspecies. Further, the MQTL7.1 was successfully validated using flanked marker S2329 on a set of genotypes with phenotypic variation. CONCLUSION This study provides a new perspective on understanding the genetic basis of submergence tolerance in rice. The identified MQTL and novel candidate genes lay the foundation for marker-assisted breeding/engineering of flooding-tolerant cultivars conducive to direct seeding.
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Grants
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2023AFA022 Hubei Provincial Natural Science Foundation of China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2020BBB060 Key R&D Project in Hubei Province, China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- 2018YFD0301306 the National Key Research and Development Program of China
- Key R&D Project in Hubei Province, China
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Affiliation(s)
- Kelvin Dodzi Aloryi
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Nnaemeka Emmanuel Okpala
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China
| | - Hong Guo
- University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Benjamin Karikari
- Département de phytologie, Université Laval, Québec, QC, Canada
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Aduragbemi Amo
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, USA
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, USA
| | - Semiu Folaniyi Bello
- Department of Animal Genetics, Breeding and Reproduction, College of Animal Science, South China Agricultural University, Guangzhou, Guangdong, China
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
- Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Selorm Akaba
- School of Agriculture, University of Cape Coast, Cape Coast, Ghana
| | - Xiaohai Tian
- Hubei Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, China.
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Zhang H, Tang S, Wang H, Wang Y, Zhi H, Liu B, Zhang R, Ma Q, Jia G, Feng B, Diao X. Genetic diversity of grain yield traits and identification of a grain weight gene SiTGW6 in foxtail millet. Theor Appl Genet 2024; 137:84. [PMID: 38493242 DOI: 10.1007/s00122-024-04586-0] [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: 10/08/2023] [Accepted: 02/20/2024] [Indexed: 03/18/2024]
Abstract
KEY MESSAGE Agronomic traits were evaluated in 1250 foxtail millet accessions, and a crucial gene SiTGW6 governing grain yield was identified. Elite haplotypes and dCAPS markers developed for SiTGW6 facilitate molecular breeding. A comprehensive evaluation of phenotypic characteristics and genetic diversity in germplasm resources are important for gene discovery and breeding improvements. In this study, we conducted a comprehensive evaluation of 1250 foxtail millet varieties, assessing seven grain yield-related traits and fourteen common agronomic traits over two years. Principal component analysis, correlation analysis, and cluster analysis revealed a strong positive correlation between 1000-grain weight and grain width with grain yield, emphasizing their importance in foxtail millet breeding. Additionally, we found that panicle weight positively correlated with 1000-grain weight but negatively correlated with branch and tiller numbers, indicating selection factors during domestication and breeding. Using this information, we identified 27 germplasm resources suitable for high-yield foxtail millet breeding. Furthermore, through an integration of haplotype variations and phenotype association analysis, we pinpointed a crucial gene, SiTGW6, responsible for governing grain yield in foxtail millet. SiTGW6 encodes an IAA-glucose hydrolase, primarily localized in the cytoplasm and predominantly expressed in flowering panicles. Employing RNAseq analysis, we identified 1439 differentially expressed genes across various SiTGW6 haplotypes. Functional enrichment analysis indicating that SiTGW6 regulates grain yield through the orchestration of auxin and glucan metabolism, as well as plant hormone signaling pathways. Additionally, we have identified elite haplotypes and developed dCAPS markers for SiTGW6, providing valuable technical tools to facilitate molecular breeding efforts in foxtail millet.
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Affiliation(s)
- Hui Zhang
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Sha Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Honglu Wang
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Yannan Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hui Zhi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Bin Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Renliang Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Qian Ma
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi Province, China
| | - Guanqing Jia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Baili Feng
- College of Agronomy, State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi Province, China.
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Abdelraheem A, Zhu Y, Zeng L, Stetina S, Zhang J. A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum. Mol Genet Genomics 2024; 299:30. [PMID: 38472439 DOI: 10.1007/s00438-024-02130-9] [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: 11/09/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. vasinfectum (FOV), is a devastating disease affecting cotton (Gossypium spp.) worldwide. Understanding the genetic basis of resistance in diploid cotton and successfully transferring the resistance to tetraploid Upland cotton (G. hirsutum) are crucial for developing resistant cotton cultivars. Although numerous studies have been conducted to investigate the genetic basis of Fusarium wilt in tetraploid cotton, little research has been conducted on diploid species. In this study, an association mapping panel consisting of 246 accessions of G. arboreum, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings in four greenhouse tests. Through a genome-wide association study (GWAS) based on 7,009 single nucleotide polymorphic (SNP) markers, 24 FOV4 resistance QTLs, including three major QTLs on chromosomes A04, A06, and A11, were detected. A validation panel consisting of 97 diploid cotton accessions was employed, confirming the presence of several QTLs. Evaluation of an introgressed BC2F7 population derived from G. hirsutum/G. aridum/G. arboreum showed significant differences in disease incidence and mortality rate, as compared to susceptible and resistant controls, suggesting that the resistance in G. arboreum and/or G. aridum was transferred into Upland cotton for the first time. The identification of novel major resistance QTLs, along with the transfer of resistance from the diploid species, expands our understanding of the genomic regions involved in conferring resistance to FOV4 and contributes to the development of resilient Upland cotton cultivars.
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Affiliation(s)
- Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Linghe Zeng
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Salliana Stetina
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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Zhang L, Sun W, Gao W, Zhang Y, Zhang P, Liu Y, Chen T, Yang D. Genome-wide identification and analysis of the GGCT gene family in wheat. BMC Genomics 2024; 25:32. [PMID: 38177998 PMCID: PMC10768367 DOI: 10.1186/s12864-023-09934-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND γ-glutamylcyclotransferase (GGCT), an enzyme to maintain glutathione homeostasis, plays a vital role in the response to plant growth and development as well as the adaptation to various stresses. Although the GGCT gene family analysis has been conducted in Arabidopsis and rice, the family genes have not yet been well identified and analyzed at the genome-wide level in wheat (Triticum aestivum L.). RESULTS In the present study, 20 TaGGCT genes were identified in the wheat genome and widely distributed on chromosomes 2A, 2B, 2D, 3A, 4A, 5A, 5B, 5D, 6A, 6B, 6D, 7A, 7B, and 7D. Phylogenetic and structural analyses showed that these TaGGCT genes could be classified into three subfamilies: ChaC, GGGACT, and GGCT-PS. They exhibited similar motif compositions and distribution patterns in the same subgroup. Gene duplication analysis suggested that the expansion of TaGGCT family genes was facilitated by segmental duplications and tandem repeats in the wheat evolutionary events. Identification of diverse cis-acting response elements in TaGGCT promoters indicated their potential fundamental roles in response to plant development and abiotic stresses. The analysis of transcriptome data combined with RT-qPCR results revealed that the TaGGCTs genes exhibited ubiquitous expression across plant organs, with highly expressed in roots, stems, and developing grains. Most TaGGCT genes were up-regulated after 6 h under 20% PEG6000 and ABA treatments. Association analysis revealed that two haplotypes of TaGGCT20 gene displayed significantly different Thousand-kernel weight (TKW), Kernel length (KL), and Kernel width (KW) in wheat. The geographical and annual distribution of the two haplotypes of TaGGCT20 gene further revealed that the frequency of the favorable haplotype TaGGCT20-Hap-I was positively selected in the historical breeding process of wheat. CONCLUSION This study investigated the genome-wide identification, structure, evolution, and expression analysis of TaGGCT genes in wheat. The motifs of TaGGCTs were highly conserved throughout the evolutionary history of wheat. Most TaGGCT genes were highly expressed in roots, stems, and developing grains, and involved in the response to drought stresses. Two haplotypes were developed in the TaGGCT20 gene, where TaGGCT20-Hap-I, as a favorable haplotype, was significantly associated with higher TKW, KL, and KW in wheat, suggesting that the haplotype is used as a function marker for the selection in grain yield in wheat breeding.
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Affiliation(s)
- Long Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Wanting Sun
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Weidong Gao
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Yanyan Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Peipei Zhang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China
| | - Yuan Liu
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China
| | - Tao Chen
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
| | - Delong Yang
- State Key Laboratory of Aridland Crop Science, Lanzhou, Gansu, 730070, China.
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, Gansu, 730070, China.
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Jin Y, Yu Z, Su F, Fang T, Liu S, Xu H, Wang J, Xiao B, Han G, Li H, Ma P. Evaluation and identification of powdery mildew resistance genes in Aegilops tauschii Coss and emmer wheat accessions. Plant Dis 2024. [PMID: 38173259 DOI: 10.1094/pdis-08-23-1667-re] [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] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is a serious threat to wheat (Triticum aestivum L.) production. Narrow genetic basis of common wheat boosted the demand for diversified donors against powdery mildew. Aegilops tauschii Coss (2n = 2x = DD) and emmer wheat (2n = 4x = AABB), as the ancestor species of common wheat, are important gene donors for genetic improvement of common wheat. In this study, a total of 71 Ae. tauschii Coss and 161 emmer wheat accessions were firstly evaluated their powdery mildew resistance using the Bgt isolate E09. Thirty-three Ae. tauschii Coss (46.5%) and 108 emmer wheat accessions (67.1%) were resistant. Then, all these accessions were tested by the diagnostic markers for 21 known Pm genes. The results showed that Pm2 alleles were detected in all the 71 Ae. tauschii Coss and only Pm4 alleles were detected in the 20 of 161 emmer wheat accessions. After haplotype analysis, we identified four Pm4 alleles (Pm4a, Pm4b, Pm4d and Pm4f) in the emmer wheat accessions and three Pm2 alleles (Pm2d, Pm2e and Pm2g) in the Ae. tauschii Coss. Further resistant spectrum analysis indicated that these resistance accessions displayed different resistance reactions to different Bgt isolates, implying they may have other Pm genes apart from Pm2 and/or Pm4 alleles. Notably, a new Pm2 allele Pm2S was identified in the Ae. tauschii Coss, which contained a 64 bp deletion in the first exon and formed a new termination site at the 513th triplet of the shifted reading frame compared to reported Pm2 alleles. The phylogenetic tree of Pm2S showed that the kinship of Pm2S was closed to Pm2h. To efficiently and accurately detect Pm2S and distinguish with other Pm2 alleles in Ae. tauschii Coss background, a diagnostic marker YTU-QS-3 was developed and verified its effectiveness. This study provided valuable Pm alleles and enriched the genetic diversity of the powdery mildew resistance in wheat improvement.
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Affiliation(s)
| | | | | | | | | | - Hongxing Xu
- Henan University, 12411, School of Life Sciences, Jin ming school, Kaifeng, Henan, China, 475001;
| | | | - Bei Xiao
- Yantai University, 12682, Yantai, Shandong, China;
| | | | - Hongjie Li
- Chinese Academy of Agricultural Sciences, Institute of Crop Science, Zhong Guan Cun South Street #12, Beijing, China, 100081;
| | - Pengtao Ma
- Yantai University, No.30, Qingquan Road, Yantai, Shandong, China, 264005;
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8
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Cheng M, Yuan H, Wang R, Wang W, Zhang L, Fan F, Li S. Identification and characterization of BES1 genes involved in grain size development of Oryza sativa L. Int J Biol Macromol 2023; 253:127327. [PMID: 37820910 DOI: 10.1016/j.ijbiomac.2023.127327] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 09/14/2023] [Accepted: 10/07/2023] [Indexed: 10/13/2023]
Abstract
BES1 (BRI1-EMS-SUPPRESSOR1) defines a unique class of plant-specific transcription factors that plays an essential role in response to Brassinosteroids (BRs) signal induction pathways. In our study, we conducted genome-wide scanning and comprehensive characterization of the BES1 gene family in rice and other eukaryotes, leading to valuable findings. Molecular docking experiments showed that all OsBES1 genes in rice could directly bind to BR small molecules. Among the identified genes, OsBES1-4 exhibited a remarkable response as it consistently showed induction upon exposure to various phytohormones after treatment. Further functional verification of OsBES1-4 revealed its impact on grain size. Overexpression of OsBES1-4 resulted in increased grain size, as confirmed by cytological observations showing an increase in cell length and cell number. Moreover, we identified that OsBES1-4 plays a role in rice grain size development by binding to the BR response element in the promoter region of the OsBZR1 gene. Evolutionary analysis indicated differentiation of OsBES1-4 between indica and japonica rice varieties, suggesting natural selection during the domestication process of cultivated rice. Therefore, we conclude that OsBES1-4 plays a crucial role in regulating rice grain size and has the potential to be an important target in rice breeding programs, and haplotype analysis found that all OsBES1 genes were associated with grain size development, either thousand-grain weight, grain length, or grain width. Overall, these findings suggest that the BES1 genes are involved in the regulation of grain size development in rice, and the utilization of SNPs in the OsBES1-4 gene promoter could be a favorable option for distinguishing indica and japonica.
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Affiliation(s)
- Mingxing Cheng
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China; Hongshan Laboratory of Hubei Province, China
| | - Huanran Yuan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China; Hongshan Laboratory of Hubei Province, China
| | - Ruihua Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Wei Wang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Licheng Zhang
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China
| | - Fengfeng Fan
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China; Hongshan Laboratory of Hubei Province, China
| | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China; Hongshan Laboratory of Hubei Province, China.
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9
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Iqbal MS, Peng K, Sardar N, Iqbal MH, Ghani MU, Tanvir F, Gu D, Guohua Z, Duan X. Interleukins-6 -174G/C (rs1800795) and -572C/G (rs1800796) polymorphisms and prostate cancer risk. Mol Immunol 2023; 164:88-97. [PMID: 37989067 DOI: 10.1016/j.molimm.2023.11.005] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/23/2023]
Abstract
Prostate cancer (PCa) is an aggressive cancer influenced by a complex interplay of genetic and environmental factors. Amongst these risk factors, the impact of Interleukin6 (IL6) gene polymorphisms in PCa risk has received a lot of attention. IL-6 is a cytokine that has been implicated in the pathogenesis of several malignancies, including PCa. Two IL-6 gene polymorphisms, - 174 G/C (rs1800795) and - 572 C/G (rs1800796), have received intellectual attention due to their potential role as modulators of prostate cancer risk. The main objective of this research was to comprehensively explore the potential associations between IL-6 rs1800795 and rs1800796 polymorphisms, and their impact on the occurrence of PCa. A case-control study was carried out with a well-defined cohort comprising 110 PCa cases and 110 controls (total n = 220). The genotyping of rs1800795 and rs1800796 was carefully performed using the highly sensitive and accurate Polymerase Chain Reaction-High Resolution Melting Curve (PCR-HRM) technique. The assessment of genetic associations was evaluated using various R packages, such as Haplo-Stats, SNP stat, pheatmap, and LD heatmap. The present study applied odds ratio (OR) analysis to reveal significant evidence of strong associations between the genotypes of rs1800795 and rs1800796 and the susceptibility to PCa. The findings of this study underscore the noteworthy impact of genetic variations in the IL-6 gene on the development of prostate cancer. Specifically, the C/G and G/G genotypes of rs1800795 demonstrated increased PCa risk, with odds ratios (OR) of 1.650 (95% CI = 1.068-2.549, p = 0.032) and 2.475 (95% CI = 1.215-5.043, p < 0.001), respectively. Similarly, the G/C genotype of rs1800796 exhibited an OR of 2.374 (95% CI = 1.363-4.130, p = 0.012) for elevated prostate cancer risk, while the C/C genotype had an OR of 1.81 (95% CI = 1.02-3.22, p = 0.7). Furthermore, our haplotype analysis have revealed an association between haplotype 4 (C-G) and increased risk of PCa (OR = 1.69, 95% CI = 1.05-2.73, p = 0.032). In conclusion, this case-control analysis presents compelling evidence for a significant association between IL-6 variants (rs1800795 and rs1800796) and increased susceptibility to prostate cancer.
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Affiliation(s)
- Muhammad Sarfaraz Iqbal
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Kaoqing Peng
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Nimra Sardar
- Department of Microbiology and Molecular Genetics, School of Applied Sciences, University of Okara, Punjab, Pakistan.
| | | | - Muhammad Usman Ghani
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Pakistan.
| | - Fouzia Tanvir
- Department of Molecularbiology, Institute of Pure and Applied Zoology, University of Okara, Punjab, Pakistan
| | - Di Gu
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Zeng Guohua
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China.
| | - Xiaolu Duan
- Department of Urology, Minimally Invasive Surgery Center, Guangdong Key Laboratory of Urology, Guangzhou Urology Research Institute, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
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10
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Yamasani MR, Pandu VR, Kalluru S, Bommaka RR, Bandela R, Duddu B, Komeri S, Kumbha D, Vemireddy LR. Haplotype analysis of QTLs governing early seedling vigor-related traits under dry-direct-seeded rice (Oryza sativa L.) conditions. Mol Biol Rep 2023; 50:8177-8188. [PMID: 37555871 DOI: 10.1007/s11033-023-08714-9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/26/2023] [Indexed: 08/10/2023]
Abstract
BACKGROUND The eventual shifting of cultivation method from puddle transplanted rice to direct-seeded rice (DSR) to save water prompted researchers to develop DSR-suitable varieties. To achieve this, identification of molecular markers associated with must-have traits for DSR, especially early seedling vigour related traits is crucial. METHODS AND RESULTS In the present investigation, the haplotype analysis using flanking markers of three important quantitative trait loci (QTLs) for early seedling vigour-related traits viz., qSV-6a (RM204 and RM402) for root length; qVI (RM20429 and RM3) for seedling vigour index; qGP-6 (RM528 and RM400) for germination percentage revealed that the marker alleles were found to show significant associations with qVI and qGP-6 QTLs. The majority of genotypes with high early seedling vigour are with qVIHap-1 (220 and 160 bp) and qGPHap-1 (290 and 290 bp). The rice genotypes with superior haplotypes for early seedling vigour are BMF536, BMF540, BMF525, MM129 and MDP2. CONCLUSIONS In conclusion, here we demonstrated that the markers RM20429 and RM3 are associated with seedling vigour index whereas RM528 and RM400 are associated with germination percentage. Therefore, these markers can be utilized to develop varieties suitable for DSR conditions through haplotype-based breeding. In addition, the rice genotypes with superior haplotypes can be of immense value to use as donors or can be released as varieties also under DSR conditions.
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Affiliation(s)
- Mounika Reddy Yamasani
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Vasanthi Raguru Pandu
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Sudhamani Kalluru
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Rupeshkumar Reddy Bommaka
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Ramanamurthy Bandela
- Department of Statistics and Computer Applications, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Bharathi Duddu
- Department of Genetics and Plant Breeding, Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Srikanth Komeri
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Dineshkumar Kumbha
- Department of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India
| | - Lakshminarayana R Vemireddy
- Department of Molecular Biology and Biotechnology, S.V. Agricultural College, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, 517502, Andhra Pradesh, India.
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11
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Zhu X, Chen L, Zhang Z, Li J, Zhang H, Li Z, Pan Y, Wang X. Genetic-based dissection of resistance to bacterial leaf streak in rice by GWAS. BMC Plant Biol 2023; 23:396. [PMID: 37596557 PMCID: PMC10436437 DOI: 10.1186/s12870-023-04412-7] [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: 06/28/2023] [Accepted: 08/14/2023] [Indexed: 08/20/2023]
Abstract
BACKGROUND Rice is the second-largest food crop in the world and vulnerable to bacterial leaf streak disease. A thorough comprehension of the genetic foundation of agronomic traits was essential for effective implementation of molecular marker-assisted selection. RESULTS Our study aimed to evaluate the vulnerability of rice to bacterial leaf streak disease (BLS) induced by the gram-negative bacterium Xanthomonas oryzae pv. oryzicola (Xoc). In order to accomplish this, we first analyzed the population structure of 747 accessions and subsequently assessed their phenotypes 20 days after inoculation with a strain of Xoc, GX01. We conducted genome-wide association studies (GWAS) on a population of 747 rice accessions, consisting of both indica and japonica subpopulations, utilizing phenotypic data on resistance to bacterial leaf streak (RBLS) and sequence data. We identified a total of 20 QTLs associated with RBLS in our analysis. Through the integration of linkage mapping, sequence analysis, haplotype analysis, and transcriptome analysis, we were able to identify five potential candidate genes (OsRBLS1-OsRBLS5) that possess the potential to regulate RBLS in rice. In order to gain a more comprehensive understanding of the genetic mechanism behind resistance to bacterial leaf streak, we conducted tests on these genes in both the indica and japonica subpopulations, ultimately identifying superior haplotypes that suggest the potential utilization of these genes in breeding disease-resistant rice varieties. CONCLUSIONS The findings of our study broaden our comprehension of the genetic mechanisms underlying RBLS in rice and offer significant insights that can be applied towards genetic improvement and breeding of disease-resistant rice in rapidly evolving environmental conditions.
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Affiliation(s)
- Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Lei Chen
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jinjie Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology / Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Yinghua Pan
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China.
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, 530007, China.
| | - Xueqiang Wang
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, People's Republic of China.
- Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China.
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12
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Yuan P, Liu H, Wang X, Hammond JP, Shi L. Genome-wide association study reveals candidate genes controlling root system architecture under low phosphorus supply at seedling stage in Brassica napus. Mol Breed 2023; 43:63. [PMID: 37521313 PMCID: PMC10382450 DOI: 10.1007/s11032-023-01411-2] [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] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 07/18/2023] [Indexed: 08/01/2023]
Abstract
Optimal root system architecture (RSA) is essential for vigorous growth and yield in crops. Plants have evolved adaptive mechanisms in response to low phosphorus (LP) stress, and one of those is changes in RSA. Here, more than five million single-nucleotide polymorphisms (SNPs) obtained from whole-genome re-sequencing data (WGR) of an association panel of 370 oilseed rape (Brassica napus L.) were used to conduct a genome-wide association study (GWAS) of RSA traits of the panel at LP in "pouch and wick" system. Fifty-two SNPs were forcefully associated with lateral root length (LRL), total root length (TRL), lateral root density (LRD), lateral root number (LRN), mean lateral root length (MLRL), and root dry weight (RDW) at LP. There were significant correlations between phenotypic variation and the number of favorable alleles of the associated loci on chromosomes A06 (chrA06_20030601), C03 (chrC03_3535483), and C07 (chrC07_42348561), respectively. Three candidate genes (BnaA06g29270D, BnaC03g07130D, and BnaC07g43230D) were detected by combining transcriptome, candidate gene association analysis, and haplotype analysis. Cultivar carrying "CCGC" at BnaA06g29270DHap1, "CAAT" at BnaC03g07130DHap1, and "ATC" at BnaC07g43230DHap1 had greater LRL, LRN, and RDW than lines carrying other haplotypes at LP supply. The RSA of a cultivar harboring the three favorable haplotypes was further confirmed by solution culture experiments. These findings define exquisite insights into genetic architectures underlying B. napus RSA at LP and provide valuable gene resources for root breeding. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01411-2.
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Affiliation(s)
- Pan Yuan
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
| | - Haijiang Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
| | - Xiaohua Wang
- College of Agriculture and Forestry Science, Linyi University, Linyi, 276000 China
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR UK
| | - Lei Shi
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China
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13
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Irehan B, Celik F, Koroglu E, Tektemur A, Simsek S. Molecular characterization of cattle and sheep isolates of Echinococcus granulosus from elazig province in Turkey and expression analysis of the non-coding RNAs, egr-miR-7, egr-miR-71 and egr-miR-96. Exp Parasitol 2023:108551. [PMID: 37257717 DOI: 10.1016/j.exppara.2023.108551] [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: 01/27/2023] [Revised: 03/29/2023] [Accepted: 05/22/2023] [Indexed: 06/02/2023]
Abstract
Cystic Echinococcosis (CE) is a common zoonotic disease seen in human and animals worldwide, caused by the larval form of Echinococcus granulosus. In this study, E. granulosus s.l. species and haplotypes were determined in hydatid cysts isolated from cattle and sheep, and the expression levels of egr-miR-7, egr-miR-71 and egr-miR-96 miRNAs were compared in different cyst structures. A total of 82 (cattle, n = 41; sheep, n = 41) hydatid cyst isolates (germinal membranes and/or protoscoleces) were collected from a slaughterhouse in Elazig province of Turkey. After mt-CO1 gene sequences were made, 81 out of 82 hydatid cyst isolates were determined as E. granulosus s.s. (G1 and G3), while an isolate of cattle origin was determined as Echinococcus canadensis (G6/7). A total of 26 nucleotide polymorphisms and 29 haplotype groups were identified in the samples. miRNA expressions in germinal membranes of sterile cysts and germinal membrane and protoscoleces of fertile cysts were investigated by qRT-PCR and Real Time PCR analyses. It was determined that miRNAs were expressed at high levels in 79.31% of the 29 haplotype groups and at low levels in the remaining 10.34%. In 10 fertile samples of sheep origin, egr-miR-7, egr-miR-71 and egr-miR-96 miRNAs were found to be 44, 168, and 351-fold higher in expression, respectively, in the germinal membrane compared to the protoscoleces. Especially egr-miR-96 may have the potential to be used as biomarkers in the diagnosis of active CE.
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Affiliation(s)
- Bunyamin Irehan
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Figen Celik
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Ergun Koroglu
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey
| | - Ahmet Tektemur
- Department of Medical Biology, Faculty of Medicine, University of Firat, Elazig, Turkey
| | - Sami Simsek
- Department of Parasitology, Faculty of Veterinary Medicine, University of Firat, Elazig, Turkey.
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14
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Al-Jawabreh A, Ereqat S, Al-Jawabreh H, Dumaidi K, Nasereddin A. Genetic diversity and haplotype analysis of Leishmania tropica identified in sand fly vectors of the genera Phlebotomus and Sergentomyia using next-generation sequencing technology. Parasitol Res 2023; 122:1351-1360. [PMID: 37036520 DOI: 10.1007/s00436-023-07835-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/30/2023] [Indexed: 04/11/2023]
Abstract
Next-generation sequencing (NGS) was used to investigate the genetic diversity of Leishmania tropica in the sand fly vector, targeting the internal transcribed spacer 1 (ITS1) of the genus Leishmania. Bioinformatics analyses were conducted using Galaxy, MEGA version X, DnaSP ver. 6.12.03, and PopART 1.7 software for NGS analysis, phylogenetic tree, genetic diversity, and haplotype networking, respectively. A total of 307 engorged sand flies were trapped, with an overall Leishmania infection rate of 9.4 (29/307) and 6.8% by NGS and ITS1-PCR, respectively. Two Leishmania-infected sand fly genera were identified: Phlebotomus (10.2%, 26/254) and Sergentomyia (5.7% (3/53). The phylogenetic tree showed two clusters, cluster I included the four study sequences along with 25 GenBank-retrieved DNA sequences. Cluster II consisted of three sequences from Iran and Pakistan. The genetic diversity analysis for the 29 L. tropica sequences showed high haplotype (gene) diversity index (Hd) (0.62 ± 0.07) but low nucleotide diversity index (π) (0.04 ± 0.01). Tajima's D, a neutrality test, is more negative in cluster I (D = - 2.0) than in total population (D = - 1.83), but both are equally significant (P < 0.001), indicating that observed variation in cluster I and whole population is less frequent than expected. The median-joining haplotype network produced a total of 11 active haplotypes. In conclusion, L. tropica from sand flies in Palestine is monophyletic that assembled in one main phylogroup and one haplotype.
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Affiliation(s)
- Amer Al-Jawabreh
- Arab American University, Jenin, Palestine
- Leishmaniases Research Unit-Jericho, Jericho, Palestine
| | - Suheir Ereqat
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Deis, East Jerusalem, Palestine.
| | - Hanan Al-Jawabreh
- Leishmaniases Research Unit-Jericho, Jericho, Palestine
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Deis, East Jerusalem, Palestine
| | | | - Abedelmajeed Nasereddin
- Biochemistry and Molecular Biology Department, Faculty of Medicine, Al-Quds University, Abu Deis, East Jerusalem, Palestine
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15
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Jahantigh D, Ghazaey Zidanloo S, Moossavi SZ, Forghani F. Interleukin 12B rs3212227 and rs6887695 single nucleotide polymorphisms are associated with the susceptibility to preeclampsia: Genetic, haplotype and bioinformatics analysis. Cytokine 2023; 164:156166. [PMID: 36842370 DOI: 10.1016/j.cyto.2023.156166] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/26/2023]
Abstract
It is well-known that functional single nucleotide polymorphisms (SNPs) in IL-12B gene might intensely change the protein expression level, or modify its functions, which might result in immune disorders. The association between common IL-12B SNPs with preeclampsia (PE) risk has remained unclear yet. In a case-control study, 253 PE patients and 250 healthy subjects were genotyped for SNPs in IL-12B rs3212227 by PCR-RFLP and in IL-12B rs6887695 by AS-PCR. Novel in-silico analysis were performed to predict the potential functions of these polymorphisms, as well. The rs3212227 variation in IL12B gene showed an association with susceptibility to PE. The AC and CC genotypes and also C allele of this SNP were more frequent in patients. Likewise, they were frequent in early onset and late onset PE. The G allele and GC and CC genotype of rs6887695 SNP correlated negatively with PE development and it shown protective effect on PE risk. In addition, the AG and CC haplotypes of IL-12B were more prevalent in PE patients. Then, IL12B AC haplotype was less frequent in PE compare to healthy pregnant women. In-silico analysis of IL-12B rs3212227 gene polymorphism might not have significant impact on the mRNA structure and transcription of IL-12B. The results of our study revealed a significant relationship between rs3212227A/C and rs6887695G/C polymorphisms in IL-12B gene and the risk of PE in the Iranian population.
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Affiliation(s)
- Danial Jahantigh
- Department of Biology, Faculty of Science, University of Sistan and Baluchestan, Zahedan, Iran.
| | | | | | - Forough Forghani
- Department of Obstetrics and Gynecology, Zabol University of Medical Sciences, Zabol, Iran; Department of Obstetrics and Gynecology, Zahedan University of Medical Sciences, Zahedan, Iran.
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16
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Wang T, Su N, Lu J, Zhang R, Sun X, Weining S. Genome-wide association studies of peduncle length in wheat under rain-fed and irrigating field conditions. J Plant Physiol 2023; 280:153854. [PMID: 36413900 DOI: 10.1016/j.jplph.2022.153854] [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: 07/07/2022] [Revised: 09/29/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Drought is one of the most destructive environmental factors limiting wheat production and food security globally. Peduncle length (PLE) is an important morphological trait to determine plant architecture, photosynthate transport, and yield formation, which is also considered a useful index for drought tolerance in wheat. However, the genetic basis of wheat PLE is not well studied at present. Here, a large-scale genome-wide association study (GWAS) of PLE was performed using a panel of 282 wheat accessions with the Wheat 660K SNP array genotyping under rain-fed and irrigating field conditions. Totally, 1,301 significant marker-trait associations (MTAs) were identified using the threshold of p-value < 4.16 × 10-4, five of which were high-confidence. Furthermore, combining GWAS intervals, previously reported QTLs, expression levels, homologous genes, and selected sweep analysis, a total of 5 candidate genes were detected to associate with drought stress. Moreover, the expression levels of TraesCS2A02G082100 were significantly up-regulated under drought conditions and co-localized in the selected sweep region, suggesting it is a drought-responsive gene. Our results shed light on the genetic basis underlying wheat drought tolerance, which accelerates the marker-assistant selection and genetic improvement through genomic breeding in wheat.
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Affiliation(s)
- Tingting Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, China.
| | - Ning Su
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, China.
| | - Jianan Lu
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, China.
| | - Ruipu Zhang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, China.
| | - Xuming Sun
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, China.
| | - Song Weining
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, China.
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17
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Patel YP, Pandey SN, Patel SB, Parikh A, Soni S, Shete N, Srivastava R, Raval MA, Ganpule AP, Patel SG, Desai MR. Haplotype of CaSR gene is associated with risk of renal stone disease in West Indian population. Urolithiasis 2022; 51:25. [PMID: 36585523 DOI: 10.1007/s00240-022-01394-3] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 12/12/2022] [Indexed: 01/01/2023]
Abstract
Calcium is the most abundant metabolite involved in the stone matrix. The CaSR gene controls calcium homeostasis, and genetic variation in the CaSR gene could lead to the development of renal stone disease. Therefore, the current study has been designed to assess the association of genetic variants of CaSR gene polymorphisms with renal stone disease. A single-centric prospective study has been carried out on a total of 300 participants (150 cases and 150 controls). Serum levels of calcium, creatinine, parathyroid hormone, and 24 h urine metabolites were measured. Two polymorphisms, rs1801725 and rs1042636, of the CaSR gene, have been genotyped for each participant. T test, binary logistic regression, and Chi-square analysis were used for statistical analysis. Renal stone patients had significantly higher levels of serum parathyroid hormone, creatinine, and 24-h urine metabolites in comparison to the controls. CaSR gene variants, rs1801725 (GG) and rs1042636 (AA), both have shown significant association with renal stone disease. In addition, individuals having specific genotypes along with metabolic abnormalities such as hypercalcemia and hyperparathyroidism are found to be at a higher significant risk of developing the renal stone disease. In the present study, the haplotype of the CaSR gene has shown an association with renal stone disease. Individuals with hyperparathyroidism and hypercalcemia and risk genotype have a higher susceptibility to developing renal stone disease.
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Affiliation(s)
- Yash P Patel
- Department of Clinical Pharmacy, Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Anand, Gujarat, 388421, India
| | - Sachchida Nand Pandey
- Department of Pathology, Muljibhai Patel Urological Hospital, Nadiad, Gujarat, 387001, India
| | - Sandip B Patel
- Department of Pharmacology, L.M. College of Pharmacy, Ahmedabad, Gujarat, 380009, India
| | - Aditya Parikh
- Department of Urology, Muljibhai Patel Urological Hospital, Nadiad, Gujarat, 387001, India
| | - Shailesh Soni
- Department of Pathology, Muljibhai Patel Urological Hospital, Nadiad, Gujarat, 387001, India
| | - Nitiraj Shete
- Muljibhai Patel Urological Hospital, Nadiad, Gujarat, 387001, India
| | - Ratika Srivastava
- Department of Biotechnology, School of Life Sciences, Babasaheb Bhimrao Ambedkar University (A Central University), Lucknow, UP, India
| | - Manan A Raval
- Department of Pharmacognosy and Phytochemistry, Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Anand, Gujarat, 388421, India
| | - Arvind P Ganpule
- Department of Urology, Muljibhai Patel Urological Hospital, Nadiad, Gujarat, 387001, India
| | - Samir G Patel
- Department of Pharmaceutical Chemistry and Analysis, Ramanbhai Patel College of Pharmacy, Charotar University of Science and Technology, Changa, Anand, Gujarat, 388421, India.
| | - Mahesh R Desai
- Department of Urology, Muljibhai Patel Urological Hospital, Nadiad, Gujarat, 387001, India
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Liu H, Zou M, Zhang B, Yang X, Yuan P, Ding G, Xu F, Shi L. Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus. Mol Breed 2022; 42:61. [PMID: 37313016 PMCID: PMC10248642 DOI: 10.1007/s11032-022-01332-6] [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: 06/14/2022] [Accepted: 09/19/2022] [Indexed: 06/15/2023]
Abstract
Oilseed rape (Brassica napus L.) is one of the most essential oil crops. Genetic improvement of seed yield (SY) is a major aim of B. napus breeding. Several studies have been reported on the genetic mechanisms of SY of B. napus. Here, a genome-wide association study (GWAS) of SY was conducted using a panel of 403 natural accessions of B. napus, with more than five million high-quality single-nucleotide polymorphisms (SNPs). A total of 1773 significant SNPs were detected associated with SY, and 783 significant SNPs were co-located with previously reported QTLs. The lead SNPs chrA01__8920351 and chrA02__4555979 were jointly detected in Trial 2_2 and Trial 2_mean value, and in Trial 1_2 and Trial 1_mean value, respectively. Subsequently, two candidate genes of BnaA01g17200D and BnaA02g08680D were identified through combining transcriptome, candidate gene association analysis, and haplotype analysis. BnaA09g10430D detected through lead SNP chrA09__5160639 was associated with SY of B. napus. Our results provide valuable information for studying the genetic control of seed yield in B. napus and valuable genes, haplotypes, and cultivars resources for the breeding of high seed yield B. napus cultivars. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01332-6.
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Affiliation(s)
- Haijiang Liu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Maoyan Zou
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Bingbing Zhang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Xinyu Yang
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Pan Yuan
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Guangda Ding
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Fangsen Xu
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
| | - Lei Shi
- National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
- Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 Hubei Province China
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Nisar A, Kayani MA, Nasir W, Mehmood A, Ahmed MW, Parvez A, Mahjabeen I. Fyn and Lyn gene polymorphisms impact the risk of thyroid cancer. Mol Genet Genomics 2022; 297:1649-1659. [PMID: 36058999 DOI: 10.1007/s00438-022-01946-7] [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: 06/27/2021] [Accepted: 08/11/2022] [Indexed: 10/14/2022]
Abstract
Thyroid cancer is the most common malignancy of the endocrine glands, and during last couple of decades, its incidence has risen alarmingly, across the globe. Etiology of thyroid cancer is still debatable. There are a few worth mentioning risk factors which contribute to initiation of abnormalities in thyroid gland leading to cancer. Genetic instability is major risk factors in thyroid carcinogenesis. Among the genetic factors, the Src family of genes (Src, Yes1, Fyn and Lyn) have been implicated in many cancers but there is little data regarding the association of these (Src, Yes1, Fyn and Lyn) genes with thyroid carcinogenesis. Fyn and Lyn genes of Src family found engaged in proliferation, migration, invasion, angiogenesis, and metastasis in different cancers. This study was planned to examine the effect of Fyn and Lyn SNPs on thyroid cancer risk in Pakistani population in 500 patients and 500 controls. Three polymorphisms of Fyn gene (rs6916861, rs2182644 and rs12910) and three polymorphisms of Lyn gene (rs2668011, rs45587541 and rs45489500) were analyzed using Tetra-primer ARMS-PCR followed by DNA sequencing. SNP rs6916861 of Fyn gene mutant genotype (CC) showed statistically significant threefold increased risk of thyroid cancer (P < 0.0001). In case of rs2182644 of Fyn gene, mutant genotype (AA) indicated statistically significant 17-fold increased risk of thyroid cancer (P < 0.0001). Statistically significant threefold increased risk of thyroid cancer was observed in genotype AC (P < 0.0001) of Fyn gene polymorphism rs12910. In SNP rs2668011 of Lyn gene, TT genotype showed statistically significant threefold increased risk of thyroid cancer (P < 0.0001). In case of rs45587541 of Lyn gene, GA genotypes showed statistically significant 11-fold increased risk in thyroid cancer (P < 0.0001). Haplotype analysis revealed that AAATAG*, AGACAG*, AGCCAA*, AGCCAG*, CAATAG*, CGCCAG* and CGCCGA* haplotypes of Fyn and Lyn polymorphisms are associated with increased thyroid cancer risk. These results showed that genotypes and allele distribution of Fyn and Lyn are significantly linked with increased thyroid cancer risk and could be genetic adjuster for said disease.
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Affiliation(s)
- Asif Nisar
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Mahmood Akhtar Kayani
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Wajiha Nasir
- Department of Radiation, Nuclear Oncology Radiation Institute, Islamabad, Pakistan
| | - Azhar Mehmood
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Malik Waqar Ahmed
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan.,Pakistan Institute of Rehabilitation Sciences (PIRS), Isra University Islamabad Campus, Islamabad, Pakistan
| | - Aamir Parvez
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan
| | - Ishrat Mahjabeen
- Cancer Genetics and Epigenetics Lab, Department of Biosciences, COMSATS University Islamabad, Park Road Tarlai Kalan, Islamabad, Pakistan.
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20
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Mao F, Wu D, Lu F, Yi X, Gu Y, Liu B, Liu F, Tang T, Shi J, Zhao X, Liu L, Ji L. QTL mapping and candidate gene analysis of low temperature germination in rice ( Oryza sativa L.) using a genome wide association study. PeerJ 2022; 10:e13407. [PMID: 35578671 PMCID: PMC9107303 DOI: 10.7717/peerj.13407] [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] [Received: 12/20/2021] [Accepted: 04/18/2022] [Indexed: 01/14/2023] Open
Abstract
Low temperature germination (LTG) is a key agronomic trait in rice (Oryza sativa L.). However, the genetic basis of natural variation for LTG is largely unknown. Here, a genome-wide association study (GWAS) was performed using 276 accessions from the 3,000 Rice Genomes (3K-RG) project with 497 k single nucleotide polymorphisms (SNPs) to uncover potential genes for LTG in rice. In total, 37 quantitative trait loci (QTLs) from the 6th day (D6) to the 10th day (D10) were detected in the full population, overlapping with 12 previously reported QTLs for LTG. One novel QTL, namely qLTG1-2, was found stably on D7 in both 2019 and 2020. Based on two germination-specific transcriptome datasets, 13 seed-expressed genes were isolated within a 200 kb interval of qLTG1-2. Combining with haplotype analysis, a functional uncharacterized gene, LOC_Os01g23580, and a seed germination-associated gene, LOC_Os01g23620 (OsSar1a), as promising candidate genes, both of which were significantly differentially expressed between high and low LTG accessions. Collectively, the candidate genes with favorable alleles may be useful for the future characterization of the LTG mechanism and the improvement of the LTG trait in rice breeding.
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Affiliation(s)
- Feng Mao
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China,Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Depeng Wu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fangfang Lu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Xin Yi
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Yujuan Gu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Bin Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Fuxia Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Tang Tang
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Jianxin Shi
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiangxiang Zhao
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lei Liu
- Jiangsu Key Laboratory for Eco-Agriculture Biotechnology around Hongze Lake, Huaiyin Normal University, Huai’an, Jiangsu, China,Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environment Protection, Huaiyin Normal University, Huai’an, Jiangsu, China
| | - Lilian Ji
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, Jiangsu, China
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21
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Jiang C, Rashid MAR, Zhang Y, Zhao Y, Pan Y. Genome wide association study on development and evolution of glutinous rice. BMC Genom Data 2022; 23:33. [PMID: 35508973 PMCID: PMC9066796 DOI: 10.1186/s12863-022-01033-1] [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] [Received: 06/23/2021] [Accepted: 03/02/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Glutinous rice as a special endosperm type is consumed as a staple food in East Asian countries by consumers' preference. Genetic studies on glutinous rice could be conducive to improve rice quality and understand its development and evolution. Therefor, we sought to explore more genes related to glutinous by genome wide association study and research the formation history for glutinous. RESULTS Here, genome-wide association study was performed to explore the associated loci/genes underlying glutinous rice by using 2108 rice accessions. Combining the expression patterns analysis, 127, 81, and 48 candidate genes were identified to be associated with endosperm type in whole rice panel, indica, and japonica sub-populations. There were 32 genes, including three starch synthesis-related genes Wx, SSG6, and OsSSIIa, detected simultaneously in the whole rice panel and subpopulations, playing important role in determining glutinous rice. The combined haplotype analyses revealed that the waxy haplotypes combination of three genes mainly distributed in Southeast Asia (SEA), SEA islands (SER) and East Asia islands (EAR). Through population structure and genetic differentiation, we suggest that waxy haplotypes of the three genes firstly evolved or were directly inherited from wild rice in japonica, and then introgressed into indica in SER, SEA and EAR. CONCLUSIONS The cloning and natural variation analysis of waxy-related genes are of great significance for the genetic improvement of quality breeding and comprehend the history in glutinous rice. This work provides valuable information for further gene discovery and understanding the evolution and formation for glutinous rice in SEA, SER and EAR.
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Affiliation(s)
- Conghui Jiang
- Shandong Rice Engineering Technology Research Center, Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Muhammad Abdul Rehman Rashid
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, 38000, Pakistan.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Research Center of Perennial Rice Engineering and Technology in Yunnan, School of Agriculture, Yunnan University, Kunming, 650500, China
| | - Yanhong Zhang
- Institute of Nuclear and Biological Technologies, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091, China
| | - Yan Zhao
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, PR China.
| | - Yinghua Pan
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, 530007, China.
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22
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Ai Q, Pan W, Zeng Y, Li Y, Cui L. CCCH Zinc finger genes in Barley: genome-wide identification, evolution, expression and haplotype analysis. BMC Plant Biol 2022; 22:117. [PMID: 35291942 PMCID: PMC8922935 DOI: 10.1186/s12870-022-03500-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/25/2021] [Accepted: 03/01/2022] [Indexed: 05/03/2023]
Abstract
BACKGROUND CCCH transcription factors are important zinc finger transcription factors involved in the response to biotic and abiotic stress and physiological and developmental processes. Barley (Hordeum vulgare) is an agriculturally important cereal crop with multiple uses, such as brewing production, animal feed, and human food. The identification and assessment of new functional genes are important for the molecular breeding of barley. RESULTS In this study, a total of 53 protein-encoding CCCH genes unevenly dispersed on seven different chromosomes were identified in barley. Phylogenetic analysis categorized the barley CCCH genes (HvC3Hs) into eleven subfamilies according to their distinct features, and this classification was supported by intron-exon structure and conserved motif analysis. Both segmental and tandem duplication contributed to the expansion of CCCH gene family in barley. Genetic variation of HvC3Hs was characterized using publicly available exome-capture sequencing datasets. Clear genetic divergence was observed between wild and landrace barley populations in HvC3H genes. For most HvC3Hs, nucleotide diversity and the number of haplotype polymorphisms decreased during barley domestication. Furthermore, the HvC3H genes displayed distinct expression profiles for different developmental processes and in response to various types of stresses. The HvC3H1, HvC3H2 and HvC3H13 of arginine-rich tandem CCCH zinc finger (RR-TZF) genes were significantly induced by multiple types of abiotic stress and/or phytohormone treatment, which might make them as excellent targets for the molecular breeding of barley. CONCLUSIONS Overall, our study provides a comprehensive characterization of barley CCCH transcription factors, their diversity, and their biological functions.
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Affiliation(s)
- Qi Ai
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Wenqiu Pan
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yan Zeng
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Yihan Li
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
| | - Licao Cui
- College of Bioscience and Engineering, Jiangxi Agricultural University, Nanchang, 330045 Jiangxi China
- Key Laboratory for Crop Gene Resources and Germplasm Enhancement, MOA, National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
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23
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Veena KV, Siddamalla S, Deenadayal M, Shivaji S, Bhanoori M. DNMT1 and DNMT3B gene variants and their association with endometriosis in South Indian women. Mol Biol Rep 2022; 49:321-329. [PMID: 34697715 DOI: 10.1007/s11033-021-06877-x] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 09/23/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Endometriosis is a multifactorial estrogen dependent gynecological disease characterized by implantation of functional endometrial tissue at ectopic positions. Though this disease is benign, it is associated with an increased risk of malignant transformation. Epigenetic disruptions like aberrant DNA methylation, resulting changes in gene expression capacity, are important in tumor progression and malignant cellular transformation. Therefore, variation in genes involved in DNA methylation might lead to disease susceptibility. PURPOSE To investigate the association between DNA methyl transferases (DNMT1 and DNMT3B) single nucleotide polymorphisms (SNPs) and the risk of endometriosis in South Indian women. METHODS In the present study, we examined the genotypic and allele distribution of DNMT1 (rs10423341C/A, rs2228611G/Aandrs4804490C/A) and DNMT3B (rs1569686G/T) among the endometriosis patients (n = 150) and controls (n = 150). The genotypes were analyzed by polymerase chain reaction (PCR) and sequencing methods. Haplotype frequencies for multiple loci and the standardized disequilibrium coefficient (D') for pairwise linkage disequilibrium (LD) were surveyed by Haploview Software. RESULT Significant increase in the frequencies of DNMT1 rs10423341 (P = 0.04601), rs2228611 (P = 0.00175) and DNMT3B rs1569686 (P = 0.033) genotypes and alleles was observed in patients compared to controls. In addition, the frequency of A/A/C (P = 0.0065) haplotype was significantly high in patients. But the DNMT1 (rs4804490) SNP did not show significant association with the disease. CONCLUSION The DNMT1 and DNMT3B polymorphism may constitute an inheritable risk factor for endometriosis in South Indian women. To the best of our knowledge there is no reported study on the association of polymorphisms in DNMT1 and DNMT3B with endometriosis risk.
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Affiliation(s)
- K V Veena
- Department of Biochemistry, Osmania University, Hyderabad, 500 007, India
| | - Swapna Siddamalla
- Department of Biochemistry, Osmania University, Hyderabad, 500 007, India
| | - Mamata Deenadayal
- Infertility Institute and Research Centre (IIRC), Secunderabad, India
| | - Sisinthy Shivaji
- Centre for Cellular and Molecular Biology (CCMB), Hyderabad, India
- Brien Holden Eye Research Centre, L V Prasad Eye Institute, Hyderabad, India
| | - Manjula Bhanoori
- Department of Biochemistry, Osmania University, Hyderabad, 500 007, India.
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24
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Li Y, Liu C, Wang N, Zhang Z, Hou L, Xin D, Qi Z, Li C, Yu Y, Jiang H, Chen Q. Fine mapping of a QTL locus ( QNFSP07-1) and analysis of candidate genes for four-seeded pods in soybean. Mol Breed 2021; 41:71. [PMID: 37309363 PMCID: PMC10236057 DOI: 10.1007/s11032-021-01265-6] [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: 07/07/2021] [Accepted: 11/06/2021] [Indexed: 06/14/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is an important grain and oil crop in the world, and it is the main source of high-quality protein. The number of four-seeded pods is a quantitative trait in soybean and is closely related to yield in terms of breeding. Therefore, it is of great significance to study the inheritance of four-seed pods and to excavate related genes for improving soybean yield. In this study, individuals with high ratio of four-seed pods which from chromosome segment substitution lines (CSSLs) that can be stably inherited were selected as the parent, and Suinong 14 (SN14) was used as recurrent parent to construct secondary mapping population via marker-assisted selection. From 2006 to 2017, QTL analysis was performed using secondary mapping populations, and the initial QTL mapping interval was 0.67 Mb and was located on Gm07. Based on the initial QTL mapping results, individuals that were heterozygous at the interval (36,116,118-37,399,738 bp) were screened in 2018, and the heterozygous individuals were subjected to inbreeding to obtain 13 F3 populations, with a target interval of 321 kb. Gene annotation was performed on the fine mapping interval, and 27 genes were obtained. Among 27 genes, Glyma.07G200900 and Glyma.07G201200 were identified as candidate genes. qRT-PCR was used to measure the expression of the 2 candidate genes at different developmental stages of soybean, and the expression levels of the 2 candidate genes in terms of cell division (axillary buds, COTs, EMs) were higher than those in terms of cell expansion (MM, LM), and these genes play a positive regulatory role in the formation of four-seeded pods. Haplotype analysis of 2 candidate genes which shows that Glyma.07G201200 has two excellent haplotypes, and the significance level between the two excellent haplotypes at p < 0.05. Those results provide the information for gene map-based cloning and molecular marker-assisted breeding of the number of four-seeded pod in soybean. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01265-6.
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Affiliation(s)
- Yingying Li
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
- Key Laboratory of Molecular Epigenetics of MOE, Institute of Genetics and Cytology, Northeast Normal University, Changchun, 130024 China
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Nannan Wang
- HeiLongJiang Academy of Agricultural Sciences JiaMuSi Branch Institute, Jiamusi, 154000 China
| | - Zhanguo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Lilong Hou
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Zhaoming Qi
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
| | - Candong Li
- HeiLongJiang Academy of Agricultural Sciences JiaMuSi Branch Institute, Jiamusi, 154000 China
| | - Yan Yu
- Changchun Sci-Tech University, Changchun, 130600 China
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun, 130033 China
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin, 150030 China
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25
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Fu Y, Ren X, Bai W, Yu Q, Sun Y, Yu Y, Zhou N. Association between C-Maf-inducing protein gene rs2287112 polymorphism and schizophrenia. PeerJ 2021; 9:e11907. [PMID: 34484985 PMCID: PMC8381876 DOI: 10.7717/peerj.11907] [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: 07/14/2021] [Indexed: 12/18/2022] Open
Abstract
Background Schizophrenia is a severely multifactorial neuropsychiatric disorder, and the majority of cases are due to genetic variations. In this study, we evaluated the genetic association between the C-Maf-inducing protein (CMIP) gene and schizophrenia in the Han Chinese population. Methods In this case-control study, 761 schizophrenia patients and 775 healthy controls were recruited. Tag single-nucleotide polymorphisms (SNPs; rs12925980, rs2287112, rs3751859 and rs77700579) from the CMIP gene were genotyped via matrix-assisted laser desorption/ionization time of flight mass spectrometry. We used logistic regression to estimate the associations between the genotypes/alleles of each SNP and schizophrenia in males and females, respectively. The in-depth link between CMIP and schizophrenia was explored through linkage disequilibrium (LD) and further haplotype analyses. False discovery rate correction was utilized to control for Type I errors caused by multiple comparisons. Results There was a significant difference in rs287112 allele frequencies between female schizophrenia patients and healthy controls after adjusting for multiple comparisons (χ2 = 12.296, Padj = 0.008). Females carrying minor allele G had 4.445 times higher risk of schizophrenia compared with people who carried the T allele (OR = 4.445, 95% CI [1.788–11.046]). Linkage-disequilibrium was not observed in the subjects, and people with haplotype TTGT of rs12925980–rs2287112–rs3751859–rs77700579 had a lower risk of schizophrenia (OR = 0.42, 95% CI [0.19–0.94]) when compared with CTGA haplotypes. However, the association did not survive false discovery rate correction. Conclusion This study identified a potential CMIP variant that may confer schizophrenia risk in the female Han Chinese population.
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Affiliation(s)
- Yingli Fu
- Division of Clinical Research, First Hospital of Jilin University, Changchun, Jilin, China.,Department of Epidemiology and Biostatistics, Jilin University, School of Public Health, Changchun, Jilin, China
| | - Xiaojun Ren
- Department of Radiation Oncology, The Second Hospital of Jilin University, Changchun, Jilin, China
| | - Wei Bai
- Center for Cognition and Brain Sciences, University of Macau, Macao SAR, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, Jilin University, School of Public Health, Changchun, Jilin, China
| | - Yaoyao Sun
- Department of Epidemiology and Biostatistics, Jilin University, School of Public Health, Changchun, Jilin, China
| | - Yaqin Yu
- Department of Epidemiology and Biostatistics, Jilin University, School of Public Health, Changchun, Jilin, China
| | - Na Zhou
- State Key Laboratory of Quality Research in Chinese Medicine and School of Pharmacy, Macau University of Science and Technology, Macao SAR, China
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Hu X, Zuo J. The CCCH zinc finger family of soybean (Glycine max L.): genome-wide identification, expression, domestication, GWAS and haplotype analysis. BMC Genomics 2021; 22:511. [PMID: 34233625 PMCID: PMC8261996 DOI: 10.1186/s12864-021-07787-9] [Citation(s) in RCA: 1] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 06/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The CCCH zinc finger (zf_CCCH) is a unique subfamily featured one or more zinc finger motif(s) comprising of three Cys and one His residues. The zf_CCCH family have been reported involving in various processes of plant development and adaptation. RESULTS In this study, the zf_CCCH genes were identified via a genome-wide search and were systematically analyzed. 116 Gmzf_CCCHs were obtained and classified into seventeen subfamilies. Gene duplication and expansion analysis showed that tandem and segmental duplications contributed to the expansion of the Gmzf_CCCH gene family, and that segmental duplication play the main role. The expression patterns of Gmzf_CCCH genes were tissue-specific. Eleven domesticated genes were detected involved in the regulation of seed oil and protein synthesis as well as growth and development of soybean through GWAS and haplotype analysis for Gmzf_CCCH genes among the 164 of 302 soybeans resequencing data. Among which, 8 genes play an important role in the synthesis of seed oil or fatty acid, and the frequency of their elite haplotypes changes significantly among wild, landrace and improved cultivars, indicating that they have been strongly selected in the process of soybean domestication. CONCLUSIONS This study provides a scientific foundation for the comprehensive understanding, future cloning and functional studies of Gmzf_CCCH genes in soybean, meanwhile, it was also helpful for the improvement of soybean with high oil content.
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Affiliation(s)
- Xin Hu
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Linan, Hangzhou, 311300, Zhejiang, China.
| | - Jianfang Zuo
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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27
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Wang Y, Zhai F, Guan S, Yan Z, Zhu X, Kuo Y, Wang N, Zhi X, Lian Y, Huang J, Jia J, Liu P, Li R, Qiao J, Yan L. A comprehensive PGT-M strategy for ADPKD patients with de novo PKD1 mutations using affected embryo or gametes as proband. J Assist Reprod Genet 2021; 38:2425-2434. [PMID: 33939064 DOI: 10.1007/s10815-021-02188-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [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: 01/31/2021] [Accepted: 04/04/2021] [Indexed: 10/21/2022] Open
Abstract
Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disease characterized by the development of renal cysts and progression to renal failure. Preimplantation genetic testing-monogenic disease (PGT-M) is an alternative option to obtain healthy babies. However, de novo PKD1 mutation of one of the spouses or the absence of a positive family history poses a serious challenge to PGT-M. Here, we described a comprehensive strategy which includes preimplantation genetic testing for aneuploidies (PGT-A) study and monogenic diagnosis study for ADPKD patients bearing de novo mutations. The innovation of our strategy is to use the gamete (polar body or single sperm) as proband for single-nucleotide polymorphism (SNP) linkage analysis to detect an embryo's carrier status. Nine ADPKD couples with either de novo mutation or without a positive family history were recruited and a total of 34 embryos from 13 PGT-M cycles were examined. Within these nine couples, two successfully delivered healthy babies had their genetic status confirmed by amniocentesis. This study provides a creative approach for embryo diagnosis of patients with de novo mutations or patients who lack essential family members for linkage analysis.
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Affiliation(s)
- Yuqian Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China
| | - Fan Zhai
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Shuo Guan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Zhiqiang Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xiaohui Zhu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Kuo
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Nan Wang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Xu Zhi
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ying Lian
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jin Huang
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jialin Jia
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Ping Liu
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Rong Li
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China
| | - Jie Qiao
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China.,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China.,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China.,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100191, China.,Beijing Advanced Innovation Center for Genomics, Beijing, 100191, China
| | - Liying Yan
- Center for Reproductive Medicine, Department of Obstetrics and Gynecology, Peking University Third Hospital, No. 49, North Garden Road, Haidian District, Beijing, 100191, People's Republic of China. .,National Clinical Research Center for Obstetrics and Gynecology (Peking University Third Hospital), Beijing, 100191, China. .,Key Laboratory of Assisted Reproduction (Peking University), Ministry of Education, Beijing, 100191, China. .,Beijing Key Laboratory of Reproductive Endocrinology and Assisted Reproductive Technology, Beijing, 100191, China.
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Li Y, Qiu S, Zhong W, Li Y, Liu Y, Cheng Y, Liu Y. Association Between DCC Polymorphisms and Susceptibility to Autism Spectrum Disorder. J Autism Dev Disord 2020; 50:3800-3809. [PMID: 32144606 DOI: 10.1007/s10803-020-04417-3] [Citation(s) in RCA: 4] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Autism spectrum disorder (ASD) represents a group of childhood-onset lifelong neuro-developmental disorders. However, the association between single nucleotide polymorphisms (SNPs) in the deleted in colorectal carcinoma (DCC) gene and ASD susceptibility remains unclear. We investigated the association between ASD susceptibility and seven SNPs in DCC on the basis of a case-control study (231 ASD cases and 242 controls) in Chinese Han. We found that there was no association between ASD susceptibility and the seven SNPs in DCC; however, T-A haplotype (rs2229082-rs2270954), T-A-T-C haplotype (rs2229082-rs2270954-rs2292043-rs2292044), C-G-T-C-T haplotype (rs934345-rs17753970-rs2229082-rs2270954-rs2292043), C-G-T-C-T-G haplotype (rs934345-rs17753970-rs2229082-rs2270954-rs2292043-rs2292044), and G-G-T-C-C-C-C haplotype (rs934345-rs17753970-rs2229082-rs2270954-rs2292043-rs2292044-rs16956878) were associated with ASD susceptibility. Our results indicate that the haplotypes formed on the basis of the seven SNPs in DCC may be implicated in ASD.
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Affiliation(s)
- Yan Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Shuang Qiu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Weijing Zhong
- Chunguang Rehabilitation Hospital, Changchun, 130021, China
| | - Yong Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Yunkai Liu
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, 130021, China
| | - Yi Cheng
- Institute of Translational Medicine, The First Hospital of Jilin University, Changchun, 130021, China.
| | - Yawen Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
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29
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Geng Y, Jian C, Xu W, Liu H, Hao C, Hou J, Liu H, Zhang X, Li T. miR164-targeted TaPSK5 encodes a phytosulfokine precursor that regulates root growth and yield traits in common wheat (Triticum aestivum L.). Plant Mol Biol 2020; 104:615-628. [PMID: 32968950 DOI: 10.1007/s11103-020-01064-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [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: 03/04/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
TaPSK5 is a less conserved target of miR164 in wheat encoding a positive regulator of root growth and yield traits that could be used for crop improvement. MicroRNAs (miRNAs) play key roles in regulating plant growth and development by targeting the mRNAs of conserved genes. However, little is known about the roles of less conserved miRNA-targeted genes in plants. In the current study, we identified TaPSK5, encoding a phytosulfokine precursor, as a novel target of miR164. Compared with miR164-targeted NAC transcription factor genes, TaPSK5 is less conserved between monocots and dicots. Expression analysis indicated that TaPSK5 homoeologs were constitutively expressed in wheat tissues, especially young spikes. Overexpression of TaPSK5-D and miR164-resistant TaPSK5-D (r-TaPSK5-D) led to increased primary root growth and grain yield in rice, with the latter having more significant effects. Comparison of the transcriptome between wild-type and r-TaPSK5-D overexpression plants revealed multiple differentially expressed genes involved in hormone signaling, transcription regulation, and reactive oxygen species (ROS) homeostasis. Moreover, we identified three TaPSK5-A haplotypes (TaPSK5-A-Hap1/2/3) and two TaPSK5-B haplotypes (TaPSK5-B-Hap1/2) in core collections of Chinese wheat. Both TaPSK5-A-Hap1 and TaPSK5-B-Hap2 are favorable haplotypes associated with superior yield traits that were under positive selection during wheat breeding. Together, our findings identify miR164-targeted TaPSK5 as a regulator of root growth and yield traits in common wheat with potential applications for the genetic improvement of crops.
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Affiliation(s)
- Yuke Geng
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- College of Life and Environmental Science, Minzu University of China, Beijing, 10081, China
| | - Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wu Xu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hong Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongxia Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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30
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Diao G, Lin DY. Statistically efficient association analysis of quantitative traits with haplotypes and untyped SNPs in family studies. BMC Genet 2020; 21:99. [PMID: 32894040 DOI: 10.1186/s12863-020-00902-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 08/17/2020] [Indexed: 11/23/2022] Open
Abstract
Background Associations between haplotypes and quantitative traits provide valuable information about the genetic basis of complex human diseases. Haplotypes also provide an effective way to deal with untyped SNPs. Two major challenges arise in haplotype-based association analysis of family data. First, haplotypes may not be inferred with certainty from genotype data. Second, the trait values within a family tend to be correlated because of common genetic and environmental factors. Results To address these challenges, we present an efficient likelihood-based approach to analyzing associations of quantitative traits with haplotypes or untyped SNPs. This approach properly accounts for within-family trait correlations and can handle general pedigrees with arbitrary patterns of missing genotypes. We characterize the genetic effects on the quantitative trait by a linear regression model with random effects and develop efficient likelihood-based inference procedures. Extensive simulation studies are conducted to examine the performance of the proposed methods. An application to family data from the Childhood Asthma Management Program Ancillary Genetic Study is provided. A computer program is freely available. Conclusions Results from extensive simulation studies show that the proposed methods for testing the haplotype effects on quantitative traits have correct type I error rates and are more powerful than some existing methods.
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31
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Guerrero Camacho JL, Corona Vázquez T, Flores Rivera JJ, Ochoa Morales A, Martínez Ruano L, Torres Ramírez de Arellano I, Dávila Ortiz de Montellano DJ, Jara Prado A. ABCB1 gene variants as risk factors and modulators of age of onset of demyelinating disease in Mexican patients. Neurologia 2020; 38:S0213-4853(20)30216-4. [PMID: 32912743 DOI: 10.1016/j.nrl.2020.05.013] [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: 01/30/2020] [Revised: 04/28/2020] [Accepted: 05/05/2020] [Indexed: 11/26/2022] Open
Abstract
INTRODUCTION The C1236T, G2677T/A, and C3435T variants of the ABCB1 gene alter the functioning of P-glycoprotein and the transport of endogenous and exogenous substances across the blood-brain barrier, and act as risk factors for some neurodegenerative diseases. This study aimed to determine the association between demyelinating disease and the C1236T, G2677T/A, and C3435T variants of ABCB1 and its haplotypes and combinations of genotypes. METHODS Polymerase chain reaction with restriction fragment length polymorphism analysis (PCR-RFLP) and Sanger sequencing were used to genotype 199 patients with demyelinating disease and 200 controls, all Mexicans of mixed race; frequencies of alleles, genotypes, haplotypes, and genotype combinations were compared between patients and controls. We conducted a logistic regression analysis and calculated chi-square values and 95% confidence intervals (CI); odds ratios (OR) were calculated to evaluate the association with demyelinating disease. RESULTS The TTT and CGC haplotypes were most frequent in both patients and controls. The G2677 allele was associated with demyelinating disease (OR: 1.79; 95% CI: 1.12-2.86; P=.015), as were the genotypes GG2677 (OR: 2.72; 95% CI: 1.11-6.68; P=.025) and CC3435 (OR: 1.82; 95% CI: 1.15-2.90; P=.010), the combination GG2677/CC3435 (OR: 2.02; 95% CI, 1.17-3.48; P=.010), and the CAT haplotype (OR: 0.21; 95% CI: 0.05-0.66; P=.001). TTTTTT carriers presented the earliest age of onset (23.0±7.7 years, vs. 31.6±10.7; P=.0001). CONCLUSIONS The GG2677/CC3435 genotype combination is associated with demyelinating disease in this sample, particularly among men, who may present toxic accumulation of P-glycoprotein substrates. In our study, the G2677 allele of ABCB1 may differentially modulate age of onset of demyelinating disease in men and women.
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Affiliation(s)
- J L Guerrero Camacho
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México
| | - T Corona Vázquez
- Laboratorio Clínico de Enfermedades Neurodegenerativas, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México
| | - J J Flores Rivera
- Laboratorio Clínico de Enfermedades Neurodegenerativas, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México
| | - A Ochoa Morales
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México
| | - L Martínez Ruano
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México
| | - I Torres Ramírez de Arellano
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México
| | - D J Dávila Ortiz de Montellano
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México
| | - A Jara Prado
- Departamento de Genética, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Ciudad de México, México.
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32
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Zhu Y, Yang L, Ma T, Lu Y, Tao D, Liu Y, Ma Y. Identification of two rare mutations c.1318G>A and c.6438+2T>G in a Chinese DMD family as genetic markers. Genes Genomics 2020; 42:1067-1074. [PMID: 32725577 DOI: 10.1007/s13258-020-00975-z] [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: 03/03/2020] [Accepted: 07/15/2020] [Indexed: 02/05/2023]
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive disorder with no effective treatment, which underscores the importance of avoiding the birth of children with DMD by identifying pathogenic mutations and obtaining an accurate prenatal diagnosis. OBJECTIVE The objective of this study was to analyze the genetic defect of a Chinese family where all male patients have died of DMD. METHODS Multiplex ligation dependent probe analysis (MLPA) and next-generation sequencing (NGS) were employed to detect DMD mutations. The candidate mutations were then validated by Sanger sequencing. In vitro splicing assay was further conducted to examine the potential effect of the novel DMD splice site mutation on splicing. RESULTS We found that two rare DMD mutations c.1318G>A and c.6438+2T>G passed from generation to generation among female carriers and they may be used as genetic markers in the Chinese DMD family. In vitro splicing assay further revealed that the novel classical splice site mutation c.6438+2T>G gave rise to a new donor splice site, which resulted in a frame shift of the transcripts and a premature termination at position 2159 in exon 45 (p.Y2144Nfs*16). CONCLUSION We found that two co-inherited mutations passed from generation to generation in female carriers and they may be used as genetic markers in the Chinese DMD family. Our findings not only expanded the DMD mutation spectrum, but also provided an important basis for identifying of female carriers and avoiding the birth of affected male children in this DMD family.
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Affiliation(s)
- Yingchuan Zhu
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, High-Tech Zone, Chengdu, 610041, Sichuan, China
| | - Lijun Yang
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, High-Tech Zone, Chengdu, 610041, Sichuan, China
| | - Tengjiao Ma
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, High-Tech Zone, Chengdu, 610041, Sichuan, China
| | - Yilu Lu
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, High-Tech Zone, Chengdu, 610041, Sichuan, China
| | - Dachang Tao
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, High-Tech Zone, Chengdu, 610041, Sichuan, China
| | - Yunqiang Liu
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, High-Tech Zone, Chengdu, 610041, Sichuan, China
| | - Yongxin Ma
- Department of Medical Genetics, West China Medical School, West China Hospital, Sichuan University, 1st Keyuan 4 Lu, High-Tech Zone, Chengdu, 610041, Sichuan, China.
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Addison CK, Angira B, Kongchum M, Harrell DL, Baisakh N, Linscombe SD, Famoso AN. Characterization of Haplotype Diversity in the BADH2 Aroma Gene and Development of a KASP SNP Assay for Predicting Aroma in U.S. Rice. Rice (N Y) 2020; 13:47. [PMID: 32666222 PMCID: PMC7360007 DOI: 10.1186/s12284-020-00410-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 07/06/2020] [Indexed: 05/27/2023]
Abstract
BACKGROUND Aroma is an important grain quality trait in rice, controlled by mutations within the BADH2 gene. The trait is simply inherited, and its importance in variety development makes it a practical target for marker-assisted selection in applied breeding programs. The predominant functional mutation within BADH2, an 8-bp indel, can be reliably detected using a PCR-based assay, but the available assays and associated genotyping platforms are insufficient for large-scale applied molecular breeding applications and are not compatible with outsourcing genotyping services. RESULTS We first characterized SNP diversity across the BADH2 gene in a collection of 2932 rice varieties to determine the number of gene haplotypes in O. sativa. Using 297 gene-based SNPs, 11 haplotype groups were detected, and subsequently identified a minimal set of nine informative SNPs that uniquely identified the BADH2 haplotypes. These nine SNPs were developed into KASP assays and used to examine a panel of 369 U.S. rice accessions. The panel represented modern breeding germplasm and included all known aroma pedigree sources in U.S. rice. Six haplotypes were detected within the U.S. panel, of which two were found in majority (85%) of varieties. A representative set of 39 varieties from all haplotype groups was evaluated phenotypically to distinguish aromatic from non-aromatic lines. CONCLUSION One haplotype (Hap 6) was found to be perfectly associated with the aromatic phenotype. A single KASP SNP unique to Hap 6 was demonstrated to reliably differentiate aromatic from non-aromatic rice varieties across U.S. germplasm.
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Affiliation(s)
- Christopher K. Addison
- School of Plant, Environmental and Soil Science, Louisiana State University, 104 Sturgis Hall, Baton Rouge, LA 70803 USA
| | - Brijesh Angira
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, 1373 Caffey Rd, Rayne, LA 70578 USA
| | - Manoch Kongchum
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, 1373 Caffey Rd, Rayne, LA 70578 USA
| | - Dustin L. Harrell
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, 1373 Caffey Rd, Rayne, LA 70578 USA
| | - Niranjan Baisakh
- School of Plant, Environmental and Soil Science, Louisiana State University, 104 Sturgis Hall, Baton Rouge, LA 70803 USA
| | - Steven D. Linscombe
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, 1373 Caffey Rd, Rayne, LA 70578 USA
| | - Adam N. Famoso
- H. Rouse Caffey Rice Research Station, Louisiana State University Agricultural Center, 1373 Caffey Rd, Rayne, LA 70578 USA
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Siddamalla S, Govatati S, Venu VK, Erram N, Deenadayal M, Shivaji S, Bhanoori M. Association of genetic variations in phosphatase and tensin homolog (PTEN) gene with polycystic ovary syndrome in South Indian women: a case control study. Arch Gynecol Obstet 2020; 302:1033-40. [PMID: 32583210 DOI: 10.1007/s00404-020-05658-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 06/18/2020] [Indexed: 10/24/2022]
Abstract
PURPOSE The purpose of the study was to investigate the association between gene phosphate and tensin homolog (PTEN) single nucleotide polymorphisms (SNPs) and risk of developing polycystic ovary syndrome (PCOS) in South Indian women. PTEN is one of the most important tumor suppressor genes that regulate cell proliferation, migration, and death. It is also involved in the maintenance of genome stability. PCOS is one of the most common endocrine disorders among women of reproductive age. It is a heterogeneous syndrome characterized by abnormal reproductive cycles, irregular ovulation, hormonal imbalance, hyperandrogenism, acne and hirsutism. RESEARCH QUESTION What is the association status of PTEN SNPs with PCOS? METHODS A total of 240 subjects were recruited in this case-control study comprising 110 patients with PCOS and 130 individuals without PCOS. All the subjects were of South Indian origin. The genotyping of PTEN SNPs (rs1903858 A/G, rs185262832G/A and rs10490920T/C) was carried out on DNA from subjects by polymerase chain reaction (PCR) and sequencing analysis. Haplotype frequencies for multiple loci and the standardized disequilibrium coefficient (D') for pairwise linkage disequilibrium (LD) were surveyed by Haploview Software. RESULTS Our results showed significant increase in the frequencies of rs1903858 A/G (P = 0.0016), rs185262832 G/A (P = 0.0122) and rs10490920 T/C (P = 0.0234) genotypes and alleles in cases compared to controls. CONCLUSION The PTEN (rs1903858A/G, rs185262832G/A and rs10490920T/C) gene polymorphisms may constitute an inheritable risk factor for PCOS in South Indian women.
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Cengiz G, Gonenc B. Comparison of molecular and morphological characterization and haplotype analysis of cattle and sheep isolates of cystic echinococcosis. Vet Parasitol 2020; 282:109132. [PMID: 32417601 DOI: 10.1016/j.vetpar.2020.109132] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [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: 01/02/2020] [Revised: 05/05/2020] [Accepted: 05/06/2020] [Indexed: 11/29/2022]
Abstract
Cystic echinococcosis is a zoonotic disease and the second most common foodborne parasitic infection worldwide. The aim of the present study was to investigate genetic variations in G1 and G3 genotypes of Echinococcus granulosus sensu stricto and determine the morphological differences between two genotypes. In total, 119 cystic samples were collected from 48 cattle and 71 sheep in slaughterhouses in four cities in three geographical regions of Turkey regions (Ankara, Central Anatolio region; Ordu, Black Sea region; and Adana, Mersin, Mediterranean region). For molecular characterization of the G1 and G3 genotypes, two gene regions (the complete mt-cox1 gene sequence and partial mt-nad5 gene sequence) were amplified. Haplotype analysis was conducted to determine the nucleotide differences between the complete sequences of the mt-cox1 gene for 47 samples. In addition, morphological parameters in protoscoleces of fertile cysts were measured to determine the relationship between the genotypes and morphometry. According to the obtained genotype and morphometry results, there were no statistically significant differences between the genotypes in terms of the number of hooks, total lengths of large and small hooks, blade lengths of large and small hooks, and widths of small hooks, although there was a statistically significant difference in large hook width (p > 0.05).
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Affiliation(s)
- Gorkem Cengiz
- Department of Parasitology, Faculty of Veterinary Medicine, Ankara University, Diskapi, 06110 Ankara, Turkey.
| | - Bahadır Gonenc
- Department of Parasitology, Faculty of Veterinary Medicine, Ankara University, Diskapi, 06110 Ankara, Turkey
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Shamim U, Ambawat S, Singh J, Thomas A, Pradeep-Chandra-Reddy C, Suroliya V, Uppilli B, Parveen S, Sharma P, Chanchal S, Nashi S, Preethish-Kumar V, Vengalil S, Polavarapu K, Keerthipriya M, Mahajan NP, Reddy N, Thomas PT, Sadasivan A, Warrier M, Seth M, Zahra S, Mathur A, Vibha D, Srivastava AK, Nalini A, Faruq M. C9orf72 hexanucleotide repeat expansion in Indian patients with ALS: a common founder and its geographical predilection. Neurobiol Aging 2020; 88:156.e1-156.e9. [PMID: 32035847 DOI: 10.1016/j.neurobiolaging.2019.12.024] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 12/27/2019] [Indexed: 12/16/2022]
Abstract
Hexanucleotide repeat expansion in C9orf72 is defined as a major causative factor for familial amyotrophic lateral sclerosis (ALS). The mutation frequency varies dramatically among populations of different ethnicity; however, in most cases, C9orf72 mutant has been described on a common founder haplotype. We assessed its frequency in a study cohort involving 593 clinically and electrophysiologically defined ALS cases. We also investigated the presence of reported Finnish haplotype among the mutation carriers. The identified common haplotype region was further screened in 192 (carrying 2-6 G4C2 repeats) and 96 (≥7 repeats) control chromosomes. The G4C2 expansion was observed in 3.2% (19/593) of total cases where 9/19 (47.4%) positive cases belonged to the eastern region of India. Haplotype analysis revealed 11 G4C2-Ex carriers shared the common haplotype (haplo-A) background spanning a region of ∼90 kbp (rs895021-rs11789520) including rs3849942 (a well-known global at-risk loci with T allele for G4C2 expansion). The other 3 G4C2-Ex cases had a different haplotype (haplo-B) with core difference from haplo-A at G4C2-Ex flanking 31 kbp region between rs3849942 and rs11789520 SNPs (allele 'C' of rs3849942 which is a nonrisk allele). Out of other five G4C2-cases, four carried the risk allele T of rs3849942 while one harbored the non-risk allele. This study establishes the prevalence of C9orf72 expansion in Indian ALS cases providing further evidence for geographical predilection. The global core risk haplotype predominated C9orf72 expansion-positive ALS cases, yet the existence of a different haplotype suggests a second lineage (haplo B), which may have been derived from the Finnish core haplotype or may imply a unique haplotype among Asians. The association of risk haplotype with normal intermediate C9orf72 alleles reinforced its role in conferring instability to the C9orf72-G4C2 region. We thus present an effective support to interpret future burden of ALS cases in India.
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Affiliation(s)
- Uzma Shamim
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Sakshi Ambawat
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Jyotsna Singh
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Aneesa Thomas
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences, New Delhi, India
| | | | - Varun Suroliya
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Bharathram Uppilli
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shaista Parveen
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Pooja Sharma
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Shankar Chanchal
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Saraswati Nashi
- Neurology Department, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Seena Vengalil
- Neurology Department, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Kiran Polavarapu
- Neurology Department, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Muddasu Keerthipriya
- Neurology Department, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | | | - Neeraja Reddy
- Neurology Department, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Priya Treesa Thomas
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Arun Sadasivan
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Manjusha Warrier
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Malika Seth
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Sana Zahra
- Department of Psychiatric Social Work, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Aradhana Mathur
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India
| | - Deepti Vibha
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Achal K Srivastava
- Department of Neurology, Neuroscience Centre, All India Institute of Medical Sciences, New Delhi, India
| | - Atchayaram Nalini
- Neurology Department, National Institute of Mental Health and Neurosciences, Bengaluru, India
| | - Mohammed Faruq
- Genomics and Molecular Medicine Division, CSIR - Institute of Genomics and Integrative Biology, New Delhi, India.
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Wang H, Sang W. Association of NM23 polymorphisms and clinicopathological features and recurrence of invasive pituitary adenomas. Pituitary 2020; 23:113-119. [PMID: 31734851 DOI: 10.1007/s11102-019-01006-1] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Pituitary adenomas (PAs) are intracranial tumors, deriving from anterior pituitary cells. Previously, expression of non-metastasis-23 (NM23) gene has been shown to correlate with the progression of PAs. In this study, we aim to determine whether there is association between specific NM23 polymorphisms and invasive pituitary adenoma (IPA). METHODS Genotypes of rs2302254 and rs16949649 of NM23 were identified in the peripheral venous blood of patients by PCR-RLFP. Next, the correlation between specific genotypes of rs2302254 and rs16949649 and risk of IPA was investigated. Finally, the correlations between NM23 polymorphisms and tumor size, Ki67 LI and recurrence of IPA were analyzed with 3 to 24 months follow-up for the enrolled patients. RESULTS We observed that the TT genotype at rs16949649 correlated closely with a high risk of IPA, while CC and CT genotypes reduced the risk of IPA. CC genotype at rs2302254 increased the risk of IPA, while CT and TT genotypes reduced the risk of IPA. Trs16949649Crs2302254 haplotype of NM23 was found to be a high-risk haplotype for IPA. TT genotype at rs16949649 and CC genotype at rs2302254 were associated with higher rates of tumors larger than 20 mm, Ki67 LI and tumor recurrence. CONCLUSION Taken together, the present study provides evidence that NM23 polymorphisms are closely associated with the incidence and recurrence of IPA. Specifically, TT genotype at rs16949649 and CC genotype at rs2302254 are risk factors of IPA. NM23 polymorphisms could therefore be used as a reference for clinical diagnosis and prognosis of IPA.
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Affiliation(s)
- Hua Wang
- 1st Ward of Department of Neurosurgery, Chifeng Municipal Hospital, No. 1, Zhaowuda Road, Chifeng, 024000, Inner Mongolia Autonomous Region, People's Republic of China
| | - Wenyuan Sang
- 1st Ward of Department of Neurosurgery, Chifeng Municipal Hospital, No. 1, Zhaowuda Road, Chifeng, 024000, Inner Mongolia Autonomous Region, People's Republic of China.
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Li P, Zhou H, Yang H, Xia D, Liu R, Sun P, Wang Q, Gao G, Zhang Q, Wang G, He Y. Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.). Rice (N Y) 2020; 13:11. [PMID: 32040640 PMCID: PMC7010892 DOI: 10.1186/s12284-020-0372-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/28/2020] [Indexed: 05/22/2023]
Abstract
BACKGROUND Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations. RESULTS In this study, two F1 populations with CMS-WA and CMS-HL background respectively were developed using 337 XI and aus accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with Rf4, and that for fertility restoration of CMS-HL was co-located with Rf5, which are cloned major restorer of fertility (Rf) genes. Furthermore, haplotype analysis of Rf4, Rf5 and Rf6, the three cloned major Rf genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for Rf4, and displayed different subgroup preferences. Two main haplotypes were identified for Rf5, and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for Rf6. CONCLUSIONS Haplotype analysis of three Rf genes, Rf4, Rf5 and Rf6, could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.
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Affiliation(s)
- Pingbo Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hao Zhou
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hanyuan Yang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Duo Xia
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rongjia Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Sun
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Quanxiu Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guanjun Gao
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qinglu Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Gongwei Wang
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuqing He
- National Key Laboratory of Crop Genetic Improvement and National Center of Crop Molecular Breeding, Huazhong Agricultural University, Wuhan, 430070, China.
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Rodrigues JAL, Ferrari GD, Trapé ÁA, de Moraes VN, Gonçalves TCP, Tavares SS, Tjønna AE, de Souza HCD, Júnior CRB. β 2 adrenergic interaction and cardiac autonomic function: effects of aerobic training in overweight/obese individuals. Eur J Appl Physiol 2020; 120:613-624. [PMID: 31915906 DOI: 10.1007/s00421-020-04301-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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] [Received: 05/02/2019] [Accepted: 01/03/2020] [Indexed: 12/20/2022]
Abstract
PURPOSE To verify the influence of different volumes and intensities of aerobic exercise on cardiac autonomic function (CAF) through heart rate variability (HRV) analysis as well the influence of β2 adrenergic receptor (ADRB2) variants in overweight/obese individuals. METHODS 70 physically inactive adults were randomly allocated into the following 16-week training: 1-high-intensity interval training (HIIT) (n = 25, 1 × 4 min bout at 85-95%HR peak, 3×/week), 4-HIIT (n = 26, 4 × 4 min bouts at 85-95%HR peak, interspersed with 3 min of recovery at 50-70%HR peak, 3×/week), and moderate continuous training (MCT) (n = 19, 30 min at 60-70%HR peak, 5×/week). Before and after the exercise training, anthropometric, BP, cardiorespiratory fitness, and HRV measures were evaluated. R-R intervals recorded for 10 min in a supine position at pre- and post-intervention were used to analyze HRV in the plot-Poincare indexes (SD1, SD2), and frequency-domain (LF, HF, LF/HF). Full blood samples were used for genotyping. RESULTS 4-HIIT and MCT showed positive outcomes for almost all variables while 1-HIIT had a positive influence only on SBP and SD2 index. No associations were observed between isolated ADRB2 variants and changes in HRV. In the analysis of the interaction genotypes, all groups responded positively for the SD1 index of HRV and only the H1 (GG and CC) and H2 (GG and CG + GG) groups presented increases in the RMSSD index. Furthermore, there was an increase in the LF index only in the H3 (CC and AA + AG) and H4 (AA + AG and CG + GG) groups. CONCLUSIONS ADRB2 variants and aerobic exercise training are important interacting variables to improve autonomic function and other health variables outcomes in overweight or obese individuals.
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Affiliation(s)
- Jhennyfer Aline Lima Rodrigues
- School of Nursing of Ribeirão Preto, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-907, Brazil.
- Laboratory of Physiology and Metabolism, School of Physical Education and Sport of Ribeirão Preto, University of São Paulo, Bandeirantes AvenueCEP 14.040-907, Ribeirão Preto, SP, 3900, Brazil.
| | - Gustavo Duarte Ferrari
- Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-903, Brazil
| | - Átila Alexandre Trapé
- School of Nursing of Ribeirão Preto, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-907, Brazil
| | - Vitor Nolasco de Moraes
- Ribeirão Preto Medical School, Department of Medical Clinic, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-907, Brazil
| | - Thiago Correa Porto Gonçalves
- Ribeirão Preto Medical School, Department of Medical Clinic, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-907, Brazil
| | - Simone Sakagute Tavares
- Department of Physics and Chemistry, Faculty of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-903, Brazil
| | - Arnt Erik Tjønna
- K.G. Jebsen Center of Exercise in Medicine at Department of Circulation and Medical Imaging, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hugo Celso Dutra de Souza
- Ribeirão Preto Medical School, Exercise Physiology Laboratory, Department of Health Science, University of São Paulo (USP), Bandeirantes Avenue, 3900Vila Monte Alegre, Ribeirão Preto, SP, 14049-900, Brazil
| | - Carlos Roberto Bueno Júnior
- School of Nursing of Ribeirão Preto, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-907, Brazil
- Ribeirão Preto Medical School, Department of Medical Clinic, University of São Paulo (USP), Bandeirantes Avenue 3900, Ribeirão Preto, SP, 14040-907, Brazil
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Tang L, Zhang F, Liu A, Sun J, Mei S, Wang X, Liu Z, Liu W, Lu Q, Chen S. Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice. Rice (N Y) 2019; 12:101. [PMID: 31889226 PMCID: PMC6937365 DOI: 10.1186/s12284-019-0362-2] [Citation(s) in RCA: 5] [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: 10/31/2019] [Accepted: 12/20/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Carbon (C) and nitrogen (N) are two fundamental components of starch and protein, which are important determinants of grain yield and quality. The food preferences of consumers and the expected end-use of grains in different rice-growing regions require diverse varieties that differ in terms of the grain N content (GNC) and grain C content (GCC) of milled rice. Thus, it is important that quantitative trait loci (QTLs)/genes with large effects on the variation of GNC and GCC are identified in breeding programs. RESULTS To dissect the genetic basis of the variation of GNC and GCC in rice, the Dumas combustion method was used to analyze 751 diverse accessions regarding the GNC, GCC, and C/N ratio of the milled grains. The GCC and GNC differed significantly among the rice subgroups, especially between Xian/Indica (XI) and Geng/Japonica (GJ). Interestingly, in the GJ subgroup, the GNC was significantly lower in modern varieties (MV) than in landraces (LAN). In the XI subgroup, the GCC was significantly higher in MV than in LAN. One, six, and nine QTLs, with 55 suggestively associated single nucleotide polymorphisms, were detected for the GNC, GCC, and C/N ratio in three panels during a single-locus genome-wide association study (GWAS). Three of these QTLs were also identified in a multi-locus GWAS. We screened 113 candidate genes in the 16 QTLs in gene-based haplotype analyses. Among these candidate genes, LOC_Os01g06240 at qNC-1.1, LOC_Os05g33300 at qCC-5.1, LOC_Os01g04360 at qCN-1.1, and LOC_Os05g43880 at qCN-5.2 may partially explain the significant differences between the LAN and MV. These candidate genes should be cloned and may be useful for molecular breeding to rapidly improve the GNC, GCC, and C/N ratio of rice. CONCLUSIONS Our findings represent valuable information regarding the genetic basis of the GNC and GCC and may be relevant for enhancing the application of favorable haplotypes of candidate genes for the molecular breeding of new rice varieties with specific grain N and C contents.
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Affiliation(s)
- Liang Tang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China.
| | - Fan Zhang
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing, 100081, China.
| | - Anjin Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jian Sun
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Song Mei
- Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, 12 South Zhong-Guan-Cun Street, Haidian District, Beijing, 100081, China
| | - Xin Wang
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhongyuan Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wanying Liu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Qing Lu
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
| | - Shuangjie Chen
- Rice Research Institute, Shenyang Agricultural University, Shenyang, 110866, China
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Xiao H, Deng S, Deng X, Gu S, Yang Z, Yin H, Deng H. Mutation Analysis of the ATP7B Gene in Seven Chinese Families with Wilson's Disease. Digestion 2019; 99:319-326. [PMID: 30384382 DOI: 10.1159/000493314] [Citation(s) in RCA: 5] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/27/2018] [Indexed: 02/04/2023]
Abstract
BACKGROUND Wilson's disease (WD) is an autosomal recessive disease, which is characterized by an excessive copper accumulation in the liver and brain, leading to subsequent hepatic and/or neurological disorders. The causative gene for WD has been identified as the ATPase Cu2+ transporting beta polypeptide gene (ATP7B), which encodes a protein called copper-transporting ATPase 2. ATP7B mutations may lead to reduced biliary excretion of excess copper and disrupted copper homeostasis, resulting in various clinical symptoms of WD. METHODS Direct sequencing of the ATP7B gene was performed in 7 Han Chinese families with WD, and haplotype analysis was conducted in families having the same mutation. RESULTS Nine ATP7B gene mutations were identified, including 7 missense mutations (p.Asp765Gly, p.Arg778Leu, p.Thr888Pro, p.Pro992Leu, p.Asp1047Val, p.Ile1148Thr and p.Ala1295Val), 1 duplication mutation (c.525dupA), and 1 nonsense mutation (p.Gly837*). Combined with our previous data, haplotype analysis revealed that the founder effect accounted for 48% of alleles in Han Chinese, constituted by high allele frequency mutations p.Arg778Leu, p.Pro992Leu and p.Ala1295Val. CONCLUSION This study revealed genetic defects of 7 Han Chinese families with WD, and has implications for their genetic counseling and clinical management.
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Affiliation(s)
- Heng Xiao
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Pathology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Sheng Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, China
| | - Xiong Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Shaojuan Gu
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China.,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhijian Yang
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hang Yin
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China
| | - Hao Deng
- Center for Experimental Medicine, The Third Xiangya Hospital, Central South University, Changsha, China, .,Department of Neurology, The Third Xiangya Hospital, Central South University, Changsha, China,
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Maldonado dos Santos JV, Ferreira EGC, Passianotto ALDL, Brumer BB, Santos ABD, Soares RM, Torkamaneh D, Arias CAA, Belzile F, Abdelnoor RV, Marcelino-Guimarães FC. Association mapping of a locus that confers southern stem canker resistance in soybean and SNP marker development. BMC Genomics 2019; 20:798. [PMID: 31672122 PMCID: PMC6824049 DOI: 10.1186/s12864-019-6139-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 09/25/2019] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Southern stem canker (SSC), caused by Diaporthe aspalathi (E. Jansen, Castl. & Crous), is an important soybean disease that has been responsible for severe losses in the past. The main strategy for controlling this fungus involves the introgression of resistance genes. Thus far, five main loci have been associated with resistance to SSC. However, there is a lack of information about useful allelic variation at these loci. In this work, a genome-wide association study (GWAS) was performed to identify allelic variation associated with resistance against Diaporthe aspalathi and to provide molecular markers that will be useful in breeding programs. RESULTS We characterized the response to SSC infection in a panel of 295 accessions from different regions of the world, including important Brazilian elite cultivars. Using a GBS approach, the panel was genotyped, and we identified marker loci associated with Diaporthe aspalathi resistance through GWAS. We identified 19 SNPs associated with southern stem canker resistance, all on chromosome 14. The peak SNP showed an extremely high degree of association (p-value = 6.35E-27) and explained a large amount of the observed phenotypic variance (R2 = 70%). This strongly suggests that a single major gene is responsible for resistance to D. aspalathi in most of the lines constituting this panel. In resequenced soybean materials, we identified other SNPs in the region identified through GWAS in the same LD block that clearly differentiate resistant and susceptible accessions. The peak SNP was selected and used to develop a cost-effective molecular marker assay, which was validated in a subset of the initial panel. In an accuracy test, this SNP assay demonstrated 98% selection efficiency. CONCLUSIONS Our results suggest relevance of this locus to SSC resistance in soybean cultivars and accessions from different countries, and the SNP marker assay developed in this study can be directly applied in MAS studies in breeding programs to select materials that are resistant against this pathogen and support its introgression.
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Affiliation(s)
- João Vitor Maldonado dos Santos
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
| | | | - André Luiz de Lima Passianotto
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
- Present address: Department of Plant Agriculture, University of Guelph, Guelph, Ontario N1G 2V7 Canada
| | - Bruna Bley Brumer
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
| | - Adriana Brombini Dos Santos
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
| | - Rafael Moreira Soares
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
| | - Davoud Torkamaneh
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, G1V 0A6 Canada
| | - Carlos Alberto Arrabal Arias
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
| | - François Belzile
- Department of Plant Sciences and Institute of Integrative Biology and Systems (IBIS), Université Laval, Quebec City, G1V 0A6 Canada
| | - Ricardo Vilela Abdelnoor
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
| | - Francismar Corrêa Marcelino-Guimarães
- Brazilian Agricultural Research Corporation, National Soybean Research Center (Embrapa Soja), Carlos João Strass Road, Warta County, PR Brazil
- Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR Brazil
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Al Bkhetan Z, Zobel J, Kowalczyk A, Verspoor K, Goudey B. Exploring effective approaches for haplotype block phasing. BMC Bioinformatics 2019; 20:540. [PMID: 31666002 PMCID: PMC6822470 DOI: 10.1186/s12859-019-3095-8] [Citation(s) in RCA: 14] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 09/10/2019] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Knowledge of phase, the specific allele sequence on each copy of homologous chromosomes, is increasingly recognized as critical for detecting certain classes of disease-associated mutations. One approach for detecting such mutations is through phased haplotype association analysis. While the accuracy of methods for phasing genotype data has been widely explored, there has been little attention given to phasing accuracy at haplotype block scale. Understanding the combined impact of the accuracy of phasing tool and the method used to determine haplotype blocks on the error rate within the determined blocks is essential to conduct accurate haplotype analyses. RESULTS We present a systematic study exploring the relationship between seven widely used phasing methods and two common methods for determining haplotype blocks. The evaluation focuses on the number of haplotype blocks that are incorrectly phased. Insights from these results are used to develop a haplotype estimator based on a consensus of three tools. The consensus estimator achieved the most accurate phasing in all applied tests. Individually, EAGLE2, BEAGLE and SHAPEIT2 alternate in being the best performing tool in different scenarios. Determining haplotype blocks based on linkage disequilibrium leads to more correctly phased blocks compared to a sliding window approach. We find that there is little difference between phasing sections of a genome (e.g. a gene) compared to phasing entire chromosomes. Finally, we show that the location of phasing error varies when the tools are applied to the same data several times, a finding that could be important for downstream analyses. CONCLUSIONS The choice of phasing and block determination algorithms and their interaction impacts the accuracy of phased haplotype blocks. This work provides guidance and evidence for the different design choices needed for analyses using haplotype blocks. The study highlights a number of issues that may have limited the replicability of previous haplotype analysis.
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Affiliation(s)
- Ziad Al Bkhetan
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Justin Zobel
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia
| | - Adam Kowalczyk
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.,Centre for Neural Engineering, University of Melbourne, Carlton, 3053, Australia.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, 00-662, Poland.,Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia
| | - Karin Verspoor
- School of Computing & Information Systems, University of Melbourne, Parkville, 3010, Australia.
| | - Benjamin Goudey
- Centre for Epidemiology and Biostatistics, The University of Melbourne, Parkville, 3010, Australia.,IBM Australia - Research, Southgate, 3006, Australia
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Passan S, Goyal S, Bhat MA, Singh D, Vanita V. Association of TNF-α gene alterations (c.-238G>A, c.-308G>A, c.-857C>T, c.-863C>A) with primary glaucoma in north Indian cohort. Gene 2019; 709:25-35. [PMID: 31132515 DOI: 10.1016/j.gene.2019.05.035] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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] [Received: 01/08/2019] [Revised: 04/27/2019] [Accepted: 05/17/2019] [Indexed: 01/08/2023]
Abstract
BACKGROUND Tumor Necrosis Factor-alpha (TNF-α) a pleuripotent pro-inflammatory cytokine, is involved in retinal ganglion cells apoptosis in glaucoma. Thus present study aimed to analyze the association of TNF-α promoter region alterations (c.-238G>A (rs361525), c.-308G>A (rs1800629), c.-857C>T (rs1799724) and c.-863C>A (rs1800630)) with glaucoma in north Indian cohort. METHODS Present hospital based case control study involved 286 glaucoma patients (Primary Open Angle Glaucoma [POAG], Primary Angle Closure Glaucoma [PACG], Primary Congenital Glaucoma [PCG]) and 300 controls. TNF-α gene alteration (c.-238G>A (also referred as c.-418G>A; NM_000594.3)), c.-308G>A (c.-488G>A; NM_000594.3), c.-857C>T (c.-1037C>T; NM_000594.3) and c.-863C>A (c.-1043C>A; NM_000594.3) harboring regions were PCR amplified and sequenced by Sanger sequencing. Allele frequency and genotype distribution in glaucoma cases and controls were compared using chi-square test and genetic association tested using different genetic models. RESULTS Statistically significant genotype and allelic association was observed between glaucoma cases and controls for c.-308G>A and c.-863C>A alterations (p = 0.001, p = 0.001; p = 0.001, p = 0.001 respectively). AA genotype of c.-308G>A conferred ~7 fold increased risk towards glaucoma (OR = 6.82, 95% CI = 2.82-16.53, p = 0.001). c.-863C>A alteration under dominant, recessive and co-dominant genetic models conferred ~2 fold increased risk for glaucoma. However, no association for c.-238G>A and c.-857C>T variants with glaucoma was observed. Further, three haplotypes (GGCA, GACC and GACA) (OR = 0.48, 95% CI = 0.35-0.67, p = 0.001; OR = 0.58, 95% CI = 0.36-0.91, p = 0.019 and OR = 0.16, 95% CI = 0.05-0.51, p = 0.002, respectively) conferred protective role towards glaucoma. CONCLUSIONS Present study is the first to indicate significant association of c.-308G>A and c.-863C>A alterations with glaucoma in cases from north Indian cohort. Also it is the first study from India to analyze the association and interaction of four promoter region alterations (c.-238G>A, c.-308G>A, c.-857C>T and c.-863C>A) in TNF-α resulting in three protective haplotypes.
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Affiliation(s)
- Shruti Passan
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Shiwali Goyal
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India
| | - Mohd Akbar Bhat
- Multidisciplinary Research Unit, Government Medical College, Amritsar, Punjab, India
| | - Daljit Singh
- Dr. Daljit Singh Eye Hospital, Amritsar, Punjab, India
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, India.
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Nave M, Avni R, Çakır E, Portnoy V, Sela H, Pourkheirandish M, Ozkan H, Hale I, Komatsuda T, Dvorak J, Distelfeld A. Wheat domestication in light of haplotype analyses of the Brittle rachis 1 genes (BTR1-A and BTR1-B). Plant Sci 2019; 285:193-199. [PMID: 31203884 DOI: 10.1016/j.plantsci.2019.05.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [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: 03/12/2019] [Revised: 05/08/2019] [Accepted: 05/15/2019] [Indexed: 06/09/2023]
Abstract
Wheat domestication was a milestone in the rise of agrarian societies in the Fertile Crescent. As opposed to the freely dispersing seeds of its tetraploid progenitor wild emmer, the hallmark trait of domesticated wheat is intact, harvestable spikes. During domestication, wheat acquired recessive loss-of-function mutations in the Brittle Rachis 1 genes, both in the A genome (BTR1-A) and B genome (BTR1-B). In this study, we probe the geographical provenances of these mutations via haplotype analyses of a collection of wild and domesticated accessions. Our results show that the precursor of the domesticated haplotype of BTR1-A was detected in 32% of the wild accessions gathered throughout the Levant, from central Israel to central Turkey. In contrast, the precursor of the domesticated haplotype of BTR1-B, which carries a distinct 11 bp deletion in the promoter region, was found in only 10% of the tested wild accessions, all from the Southern Levant. Moreover, we identified of a single wild emmer accession in Southern Levant that carries the progenitor haplotypes for both BTR1-A and BTR1-B genes. These observations suggest that at least part of the emmer domestication process occurred in Southern Levant, contrary to the widely held view that the northern part of the Fertile Crescent was the center of wheat domestication.
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Affiliation(s)
- Moran Nave
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Raz Avni
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Esra Çakır
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Vitaly Portnoy
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Hanan Sela
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel
| | - Mohammad Pourkheirandish
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Victoria, Australia
| | - Hakan Ozkan
- Department of Field Crops, Faculty of Agriculture, Cukurova University, Adana, Turkey
| | - Iago Hale
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH, USA
| | - Takao Komatsuda
- National Institute of Agrobiological Sciences, Tsukuba, Japan; Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | - Jan Dvorak
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Assaf Distelfeld
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv, Israel.
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Soltani S, Nasiri M. Association of ERAP2 gene variants with risk of pre-eclampsia among Iranian women. Int J Gynaecol Obstet 2019; 145:337-342. [PMID: 30933316 DOI: 10.1002/ijgo.12816] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 06/12/2018] [Revised: 10/21/2018] [Accepted: 03/29/2019] [Indexed: 11/09/2022]
Abstract
OBJECTIVES To determine the association between ERAP2 rs2549782 and rs17408150 polymorphisms and pre-eclampsia among Iranian women. METHODS A retrospective case-control study comparing 319 women with pre-eclampsia and 291 normotensive pregnant Iranian women between January and August 2016. Pre-eclampsia was diagnosed by the International Society for the Study of Hypertension in Pregnancy's criteria. Demographic data were collected by oral interview. Genotyping was done by allele-specific PCR. Data were analyzed using SPSS v. 16. RESULTS The frequency of the rs2549782TT genotype was 31.0% and 27.5% among cases and controls, respectively (P=0.006). There was no difference in the frequency of the T allele between groups (P>0.05). Regarding the rs17408150 polymorphism, a high portion of women with pre-eclampsia was homozygous for the AA genotype (P<0.001). The frequency of the A allele was 32.5% and 25.05% among cases and controls, respectively (P=0.004). The combined haplotype of the rs2549782A and rs17408150G alleles was associated with increased risk of pre-eclampsia (P=0.031). CONCLUSION ERAP2 gene polymorphisms were associated with the risk of pre-eclampsia in an Iranian population. The results provide further evidence of the role of ERAP2 in the pathophysiology of this disease.
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Affiliation(s)
- Sareh Soltani
- Department of Biology, Islamic Azad University, Arsanjan Branch, Arsanjan, Iran
| | - Mahboobeh Nasiri
- Department of Biology, Islamic Azad University, Arsanjan Branch, Arsanjan, Iran
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Hamdi Y, Ben Rekaya M, Jingxuan S, Nagara M, Messaoud O, Benammar Elgaaied A, Mrad R, Chouchane L, Boubaker MS, Abdelhak S, Boussen H, Romdhane L. A genome wide SNP genotyping study in the Tunisian population: specific reporting on a subset of common breast cancer risk loci. BMC Cancer 2018; 18:1295. [PMID: 30594178 PMCID: PMC6310952 DOI: 10.1186/s12885-018-5133-8] [Citation(s) in RCA: 11] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 11/26/2018] [Indexed: 01/06/2023] Open
Abstract
Background Breast cancer is the most common cancer in women worldwide. Around 50% of breast cancer familial risk has been so far explained by known susceptibility alleles with variable levels of risk and prevalence. The vast majority of these breast cancer associated variations reported to date are from populations of European ancestry. In spite of its heterogeneity and genetic wealth, North-African populations have not been studied by the HapMap and the 1000Genomes projects. Thus, very little is known about the genetic architecture of these populations. Methods This study aimed to investigate a subset of common breast cancer loci in the general Tunisian population and to compare their genetic composition to those of other ethnic groups. We undertook a genome-wide haplotype study by genotyping 135 Tunisian subjects using the Affymetrix 6.0-Array. We compared Tunisian allele frequencies and linkage disequilibrium patterns to those of HapMap populations and we performed a comprehensive assessment of the functional effects of several selected variants. Results Haplotype analyses showed that at risk haplotypes on 2p24, 4q21, 6q25, 9q31, 10q26, 11p15, 11q13 and 14q32 loci are considerably frequent in the Tunisian population (> 20%). Allele frequency comparison showed that the frequency of rs13329835 is significantly different between Tunisian and all other HapMap populations. LD-blocks and Principle Component Analysis revealed that the genetic characteristics of breast cancer variants in the Tunisian, and so probably the North-African populations, are more similar to those of Europeans than Africans. Using eQTl analysis, we characterized rs9911630 as the most strongly expression-associated SNP that seems to affect the expression levels of BRCA1 and two long non coding RNAs (NBR2 and LINC008854). Additional in-silico analysis also suggested a potential functional significance of this variant. Conclusions We illustrated the utility of combining haplotype analysis in diverse ethnic groups with functional analysis to explore breast cancer genetic architecture in Tunisia. Results presented in this study provide the first report on a large number of common breast cancer genetic polymorphisms in the Tunisian population which may establish a baseline database to guide future association studies in North Africa. Electronic supplementary material The online version of this article (10.1186/s12885-018-5133-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yosr Hamdi
- Laboratory of biomedical genomics and oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002, Tunis, Belvédère, Tunisie.
| | - Mariem Ben Rekaya
- Laboratory of biomedical genomics and oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002, Tunis, Belvédère, Tunisie
| | - Shan Jingxuan
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Majdi Nagara
- Laboratory of biomedical genomics and oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002, Tunis, Belvédère, Tunisie
| | - Olfa Messaoud
- Laboratory of biomedical genomics and oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002, Tunis, Belvédère, Tunisie
| | - Amel Benammar Elgaaied
- Laboratory of Genetics, Immunology and Human Pathology, Department of Biology, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | - Ridha Mrad
- Department of Human Genetics, Charles Nicolle Hospital, Tunis, Tunisia
| | - Lotfi Chouchane
- Department of Genetic Medicine, Weill Cornell Medical College-Qatar, Doha, Qatar
| | - Mohamed Samir Boubaker
- Laboratory of biomedical genomics and oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002, Tunis, Belvédère, Tunisie
| | - Sonia Abdelhak
- Laboratory of biomedical genomics and oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002, Tunis, Belvédère, Tunisie
| | - Hamouda Boussen
- Medical Oncology Department, Abderrahmen Mami Hospital, Ariana, Tunisia
| | - Lilia Romdhane
- Laboratory of biomedical genomics and oncogenetics, Institut Pasteur de Tunis, Université Tunis El Manar, 13, Place Pasteur BP 74, 1002, Tunis, Belvédère, Tunisie.,Department of Biology, Faculty of Science of Bizerte, Université Tunis Carthage, Tunis, Tunisia
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Lin HA, Chen SY, Chang FY, Tung CW, Chen YC, Shen WC, Chen RS, Wu CW, Chung CL. Genome-wide association study of rice genes and loci conferring resistance to Magnaporthe oryzae isolates from Taiwan. Bot Stud 2018; 59:32. [PMID: 30578469 PMCID: PMC6303224 DOI: 10.1186/s40529-018-0248-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 12/12/2018] [Indexed: 05/10/2023]
Abstract
BACKGROUND Rice blast, caused by Magnaporthe oryzae, is an important rice disease occurring in all rice-growing areas. To manage blast disease effectively and in an environmentally friendly way, it is important to continually discover diverse resistant resources for breeding. In this study, genome-wide association study (GWAS) was used to map genes/loci resistant to rice blast in the open-access rice diversity panel 1 (RDP1), previously genotyped with a 44K single-nucleotide polymorphism array. Two geographically and genetically different M. oryzae isolates from Taiwan, D41-2 and 12YL-DL3-2, were used to challenge RDP1. Infected leaves were visually rated for lesion type (LT) and evaluated for proportion of diseased leaf area (%DLA) by image analysis software. RESULTS A total of 32 quantitative trait loci (QTLs) were identified, including 6 from LT, 30 from DLA, and 4 from both LT and DLA. In all, 22 regions co-localized with previously reported resistance (R) genes and/or QTLs, including two cloned R genes, Pita and Ptr; 19 mapped R loci, and 20 QTLs. We identified 100 candidate genes encoding leucine-rich repeat-containing proteins, transcription factors, ubiquitination-related proteins, and peroxidases, among others, in the QTL intervals. Putative resistance and susceptibility haplotypes of the 32 QTL regions for each tested rice accessions were also determined. CONCLUSIONS By using Taiwanese M. oryzae isolates and image-based phenotyping for detailed GWAS, this study offers insights into the genetics underlying the natural variation of blast resistance in RDP1. The results can help facilitate the selection of desirable donors for gene/QTL validation and blast resistance breeding.
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Affiliation(s)
- Heng-An Lin
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Szu-Yu Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Fang-Yu Chang
- Kaohsiung District Agricultural Research and Extension Station, No. 2-6, Dehe Rd., Pingtung County, 90846 Taiwan
| | - Chih-Wei Tung
- Department of Agronomy, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Yi-Chia Chen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Wei-Chiang Shen
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
| | - Ruey-Shyang Chen
- Department of Biochemical Science and Technology, National Chiayi University, No. 300, Syuefu Rd., Chiayi City, 60004 Taiwan
| | - Chih-Wen Wu
- Kaohsiung District Agricultural Research and Extension Station, No. 2-6, Dehe Rd., Pingtung County, 90846 Taiwan
| | - Chia-Lin Chung
- Department of Plant Pathology and Microbiology, National Taiwan University, No. 1, Sec. 4, Roosevelt Rd., Taipei, 10617 Taiwan
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Tambets K, Yunusbayev B, Hudjashov G, Ilumäe AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q, Skoglund P, Kushniarevich A, Litvinov S, Reidla M, Metspalu E, Saag L, Rantanen T, Karmin M, Parik J, Zhadanov SI, Gubina M, Damba LD, Bermisheva M, Reisberg T, Dibirova K, Evseeva I, Nelis M, Klovins J, Metspalu A, Esko T, Balanovsky O, Balanovska E, Khusnutdinova EK, Osipova LP, Voevoda M, Villems R, Kivisild T, Metspalu M. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 2018; 19:139. [PMID: 30241495 PMCID: PMC6151024 DOI: 10.1186/s13059-018-1522-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively. RESULTS Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours. CONCLUSIONS We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.
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Affiliation(s)
- Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
| | - Bayazit Yunusbayev
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Anne-Mai Ilumäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Terhi Honkola
- Department of Biology, University of Turku, 20014, Turku, Finland
- Institute of Estonian and General Linguistics, University of Tartu, 51014, Tartu, Estonia
| | - Outi Vesakoski
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Quentin Atkinson
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - Sergey Litvinov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Timo Rantanen
- Department of Geography and Geology, University of Turku, 20014, Turku, Finland
| | - Monika Karmin
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Sergey I Zhadanov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Radiology, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Marina Gubina
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Larisa D Damba
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Institute of Medical and Social Problems and Control of the Healthcare Department of Tuva Republic, Kyzyl, 667003, Russia
| | - Marina Bermisheva
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Tuuli Reisberg
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Khadizhat Dibirova
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia
- Anthony Nolan, London, NW3 2NU, UK
| | - Mari Nelis
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Andres Metspalu
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Tõnu Esko
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
- Vavilov Institute for General Genetics, RAS, Moscow, 119991, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450054, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Mikhail Voevoda
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, 630090, Russia
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Department of Archaeology, University of Cambridge, Cambridge, CB2 1QH, UK
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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Arsenault-Labrecque G, Sonah H, Lebreton A, Labbé C, Marchand G, Xue A, Belzile F, Knaus BJ, Grünwald NJ, Bélanger RR. Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates. BMC Biol 2018; 16:80. [PMID: 30049268 PMCID: PMC6060493 DOI: 10.1186/s12915-018-0549-9] [Citation(s) in RCA: 18] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/19/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid diversification of P. sojae Avr genes in soybean fields and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines. RESULTS We sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions. CONCLUSIONS This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.
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Affiliation(s)
| | - Humira Sonah
- Département de Phytologie, Université Laval, Québec, QC Canada
| | | | - Caroline Labbé
- Département de Phytologie, Université Laval, Québec, QC Canada
| | | | - Allen Xue
- Agriculture and Agri-Food Canada, Ontario, ON Canada
| | | | - Brian J. Knaus
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR USA
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR USA
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