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Ashton M, Czado N, Harrel M, Hughes S. Genotyping strategies for tissues fixed with various embalming fluids for human identification, databasing, and traceability. J Forensic Sci 2023. [PMID: 37904606 DOI: 10.1111/1556-4029.15414] [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: 08/31/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 11/01/2023]
Abstract
Within anatomical willed body programs and skeletal collections, whole bodies and their disassociated limbs and organs are identified and tracked. However, if these tracking mechanisms fail, DNA recovered from the formalin-fixed tissues/organs could provide an additional layer of quality assurance. Embalming fluids preserve biological tissues; however, they also damage, fragment, and cross-link DNA and protein molecules. This project investigated the success of STR-typing from various soft tissue and bone samples that were fixed with embalming solutions with a range of formaldehyde concentrations. Formalin-fixed samples dissected from five cadavers, including skin, muscle, bone, heart, and kidney were used in Phase 1 of this study. In Phase 2, an additional 57 tissue samples from various embalmed organs and body parts were collected to demonstrate long-term fixation and direct applicability within a body donor program. DNA was extracted from the samples using the QIAamp® FFPE Tissue Kit (QIAGEN), quantified with the Investigator® QuantiPlex® Pro RGQ qPCR Kit (QIAGEN), and amplified using the Investigator® 24plex and 26plex QS Kits and the Investigator® DIPplex Kit (QIAGEN). The results show the DNA was severely damaged, degraded, and often in low amounts (after one year post-embalming). Sampling from skin and muscle tissues embalmed with ~2.5%-5% formaldehyde solutions appears to be the best strategy for identification, while also maintaining the preservation of the tissues. The results of this project can provide informative data when determining which genotyping strategy may be best suited for the identification, re-association, and establishment of a database for the provenance of formalin-fixed human remains.
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Affiliation(s)
- Madeline Ashton
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
| | - Natalia Czado
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Michelle Harrel
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Sheree Hughes
- School of Biomedical Sciences, The University of Queensland, Brisbane, Queensland, Australia
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
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Plavskin Y, de Biase MS, Schwarz RF, Siegal ML. The rate of spontaneous mutations in yeast deficient for MutSβ function. G3 (Bethesda) 2023; 13:6931805. [PMID: 36529906 PMCID: PMC9997558 DOI: 10.1093/g3journal/jkac330] [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: 08/25/2022] [Revised: 08/25/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022]
Abstract
Mutations in simple sequence repeat loci underlie many inherited disorders in humans, and are increasingly recognized as important determinants of natural phenotypic variation. In eukaryotes, mutations in these sequences are primarily repaired by the MutSβ mismatch repair complex. To better understand the role of this complex in mismatch repair and the determinants of simple sequence repeat mutation predisposition, we performed mutation accumulation in yeast strains with abrogated MutSβ function. We demonstrate that mutations in simple sequence repeat loci in the absence of mismatch repair are primarily deletions. We also show that mutations accumulate at drastically different rates in short (<8 bp) and longer repeat loci. These data lend support to a model in which the mismatch repair complex is responsible for repair primarily in longer simple sequence repeats.
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Affiliation(s)
- Yevgeniy Plavskin
- Center for Genomics and Systems Biology, New York University, New York 10003, USA.,Department of Biology, New York University, New York 10003, USA
| | - Maria Stella de Biase
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany.,Department of Biology, Humboldt-Universität zu Berlin, Berlin 10099, Germany
| | - Roland F Schwarz
- Berlin Institute for Medical Systems Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin 10115, Germany.,Institute for Computational Cancer Biology, Center for Integrated Oncology (CIO), Cancer Research Center Cologne Essen (CCCE), Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne 50937, Germany.,Berlin Institute for the Foundations of Learning and Data (BIFOLD), Berlin 10623, Germany
| | - Mark L Siegal
- Center for Genomics and Systems Biology, New York University, New York 10003, USA.,Department of Biology, New York University, New York 10003, USA
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Czado N, LaRue B, Wheeler A, Houston R, Holmes A, Grisedale K, Hughes S. The effectiveness of various strategies to improve DNA analysis of formaldehyde-damaged tissues from embalmed cadavers for human identification purposes. J Forensic Sci 2023; 68:596-607. [PMID: 36725687 DOI: 10.1111/1556-4029.15200] [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: 08/20/2022] [Revised: 12/06/2022] [Accepted: 01/03/2023] [Indexed: 02/03/2023]
Abstract
Formalin-fixed tissues provide the medical and forensic communities with alternative and often last resort sources of DNA for identification or diagnostic purposes. The DNA in these samples can be highly degraded and chemically damaged, making downstream genotyping using short tandem repeats (STRs) challenging. Therefore, the use of alternative genetic markers, methods that pre-amplify the low amount of good quality DNA present, or methods that repair the damaged DNA template may provide more probative genetic information. This study investigated whether whole genome amplification (WGA) and DNA repair could improve STR typing of formaldehyde-damaged (FD) tissues from embalmed cadavers. Additionally, comparative genotyping success using bi-allelic markers, including INDELs and SNPs, was explored. Calculated random match probabilities (RMPs) using traditional STRs, INDEL markers, and two next generation sequencing (NGS) panels were compared across all samples. Overall, results showed that neither WGA nor DNA repair substantially improved STR success rates from formalin-fixed tissue samples. However, when DNA from FD samples was genotyped using INDEL and SNP-based panels, the RMP of each sample was markedly lower than the RMPs calculated from partial STR profiles. Therefore, the results of this study suggest that rather than attempting to improve the quantity and quality of severely damaged and degraded DNA prior to STR typing, a more productive approach may be to target smaller amplicons to provide more discriminatory DNA identifications. Furthermore, an NGS panel with less loci may yield better results when examining FD samples, due to more optimized chemistries that result in greater allelic balance and amplicon coverage.
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Affiliation(s)
- Natalia Czado
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Bobby LaRue
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA.,Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Amanda Wheeler
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Rachel Houston
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Amy Holmes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
| | - Kelly Grisedale
- Chemistry and Physics Department, Western Carolina University,1 University Drive, Cullowhee, North Carolina, USA
| | - Sheree Hughes
- Department of Forensic Science, College of Criminal Justice, Sam Houston State University, Huntsville, Texas, USA
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Akaishi T, Fujiwara K, Ishii T. Variable number tandem repeats of a 9-base insertion in the N-terminal domain of severe acute respiratory syndrome coronavirus 2 spike gene. Front Microbiol 2023; 13:1089399. [PMID: 36687631 PMCID: PMC9846035 DOI: 10.3389/fmicb.2022.1089399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 12/12/2022] [Indexed: 01/06/2023] Open
Abstract
Introduction The world is still struggling against the pandemic of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), in 2022. The pandemic has been facilitated by the intermittent emergence of variant strains, which has been explained and classified mainly by the patterns of point mutations of the spike (S) gene. However, the profiles of insertions/deletions (indels) in SARS-CoV-2 genomes during the pandemic remain largely unevaluated yet. Methods In this study, we first screened for the genome regions of polymorphic indel sites by performing multiple sequence alignment; then, NCBI BLAST search and GISAID database search were performed to comprehensively investigate the indel profiles at the polymorphic indel hotspot and elucidate the emergence and spread of the indels in time and geographical distribution. Results A polymorphic indel hotspot was identified in the N-terminal domain of the S gene at approximately 22,200 nucleotide position, corresponding to 210-215 amino acid positions of SARS-CoV-2 S protein. This polymorphic hotspot was comprised of adjacent 3-base deletion (5'-ATT-3'; Spike_N211del) and 9-base insertion (5'-AGCCAGAAG-3'; Spike_ins214EPE). By performing NCBI BLAST search and GISAID database search, we identified several types of tandem repeats of the 9-base insertion, creating an 18-base insertion (Spike_ins214EPEEPE, Spike_ins214EPDEPE). The results of the searches suggested that the two-cycle tandem repeats of the 9-base insertion were created in November 2021 in Central Europe, whereas the emergence of the original one-cycle 9-base insertion (Spike_ins214EPE) would date back to the middle of 2020 and was away from the Central Europe. The identified 18-base insertions based on 2-cycle tandem repeat of the 9-base insertion were collected between November 2021 and April 2022, suggesting that these mutations could not survive and have been already eliminated. Discussion The GISAID database search implied that this polymorphic indel hotspot to be with one of the highest tolerability for incorporating indels in SARS-CoV-2 S gene. In summary, the present study identified a variable number of tandem repeat of 9-base insertion in the N-terminal domain of SARS-CoV-2 S gene, and the repeat could have occurred at different time from the insertion of the original 9-base insertion.
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Affiliation(s)
- Tetsuya Akaishi
- Department of Education and Support for Regional Medicine, Tohoku University, Sendai, Japan,COVID-19 Testing Center, Tohoku University, Sendai, Japan,*Correspondence: Tetsuya Akaishi, ✉
| | - Kei Fujiwara
- Department of Gastroenterology and Metabolism, Nagoya City University, Nagoya, Japan
| | - Tadashi Ishii
- Department of Education and Support for Regional Medicine, Tohoku University, Sendai, Japan,COVID-19 Testing Center, Tohoku University, Sendai, Japan
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Gardner EJ, Sifrim A, Lindsay SJ, Prigmore E, Rajan D, Danecek P, Gallone G, Eberhardt RY, Martin HC, Wright CF, FitzPatrick DR, Firth HV, Hurles ME. Detecting cryptic clinically relevant structural variation in exome-sequencing data increases diagnostic yield for developmental disorders. Am J Hum Genet 2021; 108:2186-2194. [PMID: 34626536 PMCID: PMC8595893 DOI: 10.1016/j.ajhg.2021.09.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 10/08/2020] [Accepted: 09/15/2021] [Indexed: 11/29/2022] Open
Abstract
Structural variation (SV) describes a broad class of genetic variation greater than 50 bp in size. SVs can cause a wide range of genetic diseases and are prevalent in rare developmental disorders (DDs). Individuals presenting with DDs are often referred for diagnostic testing with chromosomal microarrays (CMAs) to identify large copy-number variants (CNVs) and/or with single-gene, gene-panel, or exome sequencing (ES) to identify single-nucleotide variants, small insertions/deletions, and CNVs. However, individuals with pathogenic SVs undetectable by conventional analysis often remain undiagnosed. Consequently, we have developed the tool InDelible, which interrogates short-read sequencing data for split-read clusters characteristic of SV breakpoints. We applied InDelible to 13,438 probands with severe DDs recruited as part of the Deciphering Developmental Disorders (DDD) study and discovered 63 rare, damaging variants in genes previously associated with DDs missed by standard SNV, indel, or CNV discovery approaches. Clinical review of these 63 variants determined that about half (30/63) were plausibly pathogenic. InDelible was particularly effective at ascertaining variants between 21 and 500 bp in size and increased the total number of potentially pathogenic variants identified by DDD in this size range by 42.9%. Of particular interest were seven confirmed de novo variants in MECP2, which represent 35.0% of all de novo protein-truncating variants in MECP2 among DDD study participants. InDelible provides a framework for the discovery of pathogenic SVs that are most likely missed by standard analytical workflows and has the potential to improve the diagnostic yield of ES across a broad range of genetic diseases.
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Affiliation(s)
- Eugene J Gardner
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Alejandro Sifrim
- Department of Human Genetics, KU Leuven, Herestraat 49, Box 602, Leuven 3000, Belgium
| | - Sarah J Lindsay
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Diana Rajan
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Petr Danecek
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Giuseppe Gallone
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Ruth Y Eberhardt
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK
| | - Caroline F Wright
- University of Exeter Medical School, Institute of Biomedical and Clinical Science, Royal Devon and Exeter Hospital, Exeter EX2 5DW, UK
| | - David R FitzPatrick
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, WGH, Edinburgh EH4 2SP, UK
| | - Helen V Firth
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK; East Anglian Medical Genetics Service, Box 134, Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Matthew E Hurles
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge, Hinxton CB10 1SA, UK.
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Pan F, Zhang H, Dong X, Ye W, He P, Zhang S, Zhu JX, Zhong N. Comparative genomic analysis of multidrug-resistant Streptococcus pneumoniae isolates. Infect Drug Resist 2018; 11:659-670. [PMID: 29765237 PMCID: PMC5939923 DOI: 10.2147/idr.s147858] [Citation(s) in RCA: 7] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Introduction Multidrug resistance in Streptococcus pneumoniae has emerged as a serious problem to public health. A further understanding of the genetic diversity in antibiotic-resistant S. pneumoniae isolates is needed. Methods We conducted whole-genome resequencing for 25 pneumococcal strains isolated from children with different antimicrobial resistance profiles. Comparative analysis focus on detection of single-nucleotide polymorphisms (SNPs) and insertions and deletions (indels) was conducted. Moreover, phylogenetic analysis was applied to investigate the genetic relationship among these strains. Results The genome size of the isolates was ~2.1 Mbp, covering >90% of the total estimated size of the reference genome. The overall G+C% content was ~39.5%, and there were 2,200–2,400 open reading frames. All isolates with different drug resistance profiles harbored many indels (range 131–171) and SNPs (range 16,103–28,128). Genetic diversity analysis showed that the variation of different genes were associated with specific antibiotic resistance. Known antibiotic resistance genes (pbps, murMN, ciaH, rplD, sulA, and dpr) were identified, and new genes (regR, argH, trkH, and PTS-EII) closely related with antibiotic resistance were found, although these genes were primarily annotated with functions in virulence as well as carbohydrate and amino acid transport and metabolism. Phylogenetic analysis unambiguously indicated that isolates with different antibiotic resistance profiles harbored similar genetic backgrounds. One isolate, 14-LC.ER1025, showed a much weaker phylogenetic relationship with the other isolates, possibly caused by genomic variation. Conclusion In this study, although pneumococcal isolates had similar genetic backgrounds, strains were diverse at the genomic level. These strains exhibited distinct variations in their indel and SNP compositions associated with drug resistance.
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Affiliation(s)
- Fen Pan
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Hong Zhang
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Xiaoyan Dong
- Department of Respiratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Weixing Ye
- Shanghai Personal Biotechnology Co., Ltd, Shanghai, China
| | - Ping He
- Department of Medical Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shulin Zhang
- Department of Medical Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | - Nanbert Zhong
- Department of Clinical Laboratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China.,Department of Respiratory, Shanghai Children's Hospital, Shanghai Jiaotong University, Shanghai, China.,New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, USA
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Abstract
H1 is involved in chromatin higher-order structure and gene regulation. H1 has a tripartite structure. The central domain is stably folded in solution, while the N- and C-terminal domains are intrinsically disordered. The terminal domains are encoded by DNA of low sequence complexity, and are thus prone to short insertions/deletions (indels). We have examined the evolution of the H1.1-H1.5 gene family from 27 mammalian species. Multiple sequence alignment has revealed a strong preferential conservation of the number and position of basic residues among paralogs, suggesting that overall H1 basicity is under a strong purifying selection. The presence of a conserved pattern of indels, ancestral to the splitting of mammalian orders, in the N- and C-terminal domains of the paralogs, suggests that slippage may have favored the rapid divergence of the subtypes and that purifying selection has maintained this pattern because it is associated with function. Evolutionary analyses have found evidences of positive selection events in H1.1, both before and after the radiation of mammalian orders. Positive selection ancestral to mammalian radiation involved changes at specific sites that may have contributed to the low relative affinity of H1.1 for chromatin. More recent episodes of positive selection were detected at codon positions encoding amino acids of the C-terminal domain of H1.1, which may modulate the folding of the CTD. The detection of putative recombination points in H1.1-H1.5 subtypes suggests that this process may has been involved in the acquisition of the tripartite H1 structure.
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Affiliation(s)
- Inma Ponte
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Devani Romero
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Daniel Yero
- Instituto de Biotecnología y de Biomedicina (IBB) y Departamento de Genética y Microbiología, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Pedro Suau
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
| | - Alicia Roque
- Departamento de Bioquímica y Biología Molecular, Facultad de Biociencias, Universidad Autónoma de Barcelona, Barcelona, Spain
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Jain M, Moharana KC, Shankar R, Kumari R, Garg R. Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance. Plant Biotechnol J 2014; 12:253-64. [PMID: 24460890 DOI: 10.1111/pbi.12133] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2013] [Revised: 09/10/2013] [Accepted: 09/12/2013] [Indexed: 05/04/2023]
Abstract
Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole-genome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice.
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Affiliation(s)
- Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
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