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Ezeah CSA, Shimazu J, Kawanabe T, Shimizu M, Kawashima S, Kaji M, Ezinma CO, Nuruzzaman M, Minato N, Fukai E, Okazaki K. Quantitative trait locus (QTL) analysis and fine-mapping for Fusarium oxysporum disease resistance in Raphanus sativus using GRAS-Di technology. BREEDING SCIENCE 2023; 73:421-434. [PMID: 38737918 PMCID: PMC11082455 DOI: 10.1270/jsbbs.23032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/16/2023] [Indexed: 05/14/2024]
Abstract
Fusarium wilt is a significant disease in radish, but the genetic mechanisms controlling yellows resistance (YR) are not well understood. This study aimed to identify YR-QTLs and to fine-map one of them using F2:3 populations developed from resistant and susceptible radish parents. In this study, two high-density genetic maps each containing shared co-dominant markers and either female or male dominant markers that spanned 988.6 and 1127.5 cM with average marker densities of 1.40 and 1.53 cM, respectively, were generated using Genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) technology. We identified two YR-QTLs on chromosome R2 and R7, and designated the latter as ForRs1 as the major QTL. Fine mapping narrowed down the ForRs1 locus to a 195 kb region. Among the 16 predicted genes in the delimited region, 4 genes including two receptor-like protein and -kinase genes (RLP/RLK) were identified as prime candidates for ForRs1 based on the nucleotide sequence comparisons between the parents and their predicted functions. This study is the first to use a GRAS-Di for genetic map construction of cruciferous crops and fine map the YR-QTL on the R7 chromosome of radish. These findings will provide groundbreaking insights into radish YR breeding and understanding the genetics of YR mechanism.
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Affiliation(s)
- Chukwunonso Sylvanus Austin Ezeah
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
- Federal Department of Agriculture, Federal Ministry of Agriculture and Rural Development, Abuja, FCT, Nigeria
| | | | | | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate 024-0003, Japan
| | | | - Makoto Kaji
- Watanabe Seed Co., Ltd., Miyagi 987-0003, Japan
| | - Charles Onyemaechi Ezinma
- Federal Department of Agriculture, Federal Ministry of Agriculture and Rural Development, Abuja, FCT, Nigeria
| | - Md Nuruzzaman
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
- Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Nami Minato
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
| | - Eigo Fukai
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
| | - Keiichi Okazaki
- Laboratory of Plant breeding, Graduate School of Science and Technology, Niigata University, 2-8050 Ikarashi, Nishi-ku, Niigata 950-2181, Japan
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Liu Z, Zheng WJ, Allen GI, Liu Y, Ruan J, Zhao Z. The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: from big data to big analytical tools. BMC Bioinformatics 2017; 18:405. [PMID: 28984189 PMCID: PMC5629550 DOI: 10.1186/s12859-017-1797-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
The 2016 International Conference on Intelligent Biology and Medicine (ICIBM 2016) was held on December 8-10, 2016 in Houston, Texas, USA. ICIBM included eight scientific sessions, four tutorials, one poster session, four highlighted talks and four keynotes that covered topics on 3D genomics structural analysis, next generation sequencing (NGS) analysis, computational drug discovery, medical informatics, cancer genomics, and systems biology. Here, we present a summary of the nine research articles selected from ICIBM 2016 program for publishing in BMC Bioinformatics.
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Affiliation(s)
- Zhandong Liu
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA. .,Department of Pediatrics-Neurology, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - W Jim Zheng
- School of Biomedical Informatics, The University of Texas Health Science Center, Houston, TX, 77030, USA
| | - Genevera I Allen
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, 77030, USA.,Department of Statistics, Rice University, Houston, TX, 77030, USA.,Department of Electrical and Computer Engineering, Rice University, Houston, TX, 77030, USA
| | - Yin Liu
- Department of Neurobiology and Anatomy, The University of Texas Medical School at Houston, Houston, TX, 77030, USA
| | - Jianhua Ruan
- Department of Computer Science, The University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Zhongming Zhao
- Center for Precision Health, School of Biomedical Informatics, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA. .,Human Genetics Center, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, 77030, USA.
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