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Ishikawa C, Date Y, Umeda M, Tarumoto Y, Okubo M, Morimitsu Y, Tamura Y, Nishiba Y, Ono H. A Data-Driven Approach to Sugarcane Breeding Programs with Agronomic Characteristics and Amino Acid Constituent Profiling. Metabolites 2024; 14:243. [PMID: 38668371 PMCID: PMC11052186 DOI: 10.3390/metabo14040243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 04/28/2024] Open
Abstract
Sugarcane (Saccharum spp. hybrids) and its processed products have supported local industries such as those in the Nansei Islands, Japan. To improve the sugarcane quality and productivity, breeders select better clones by evaluating agronomic characteristics, such as commercially recoverable sugar and cane yield. However, other constituents in sugarcane remain largely unutilized in sugarcane breeding programs. This study aims to establish a data-driven approach to analyze agronomic characteristics from breeding programs. This approach also determines a correlation between agronomic characteristics and free amino acid composition to make breeding programs more efficient. Sugarcane was sampled in clones in the later stage of breeding selection and cultivars from experimental fields on Tanegashima Island. Principal component analysis and hierarchical cluster analysis using agronomic characteristics revealed the diversity and variability of each sample, and the data-driven approach classified cultivars and clones into three groups based on yield type. A comparison of free amino acid constituents between these groups revealed significant differences in amino acids such as asparagine and glutamine. This approach dealing with a large volume of data on agronomic characteristics will be useful for assessing the characteristics of potential clones under selection and accelerating breeding programs.
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Affiliation(s)
- Chiaki Ishikawa
- Institute of Food Research, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Ibaraki, Japan
- Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan
| | - Yasuhiro Date
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Ibaraki, Japan; (Y.D.); (H.O.)
| | - Makoto Umeda
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Annou 1742-1, Nishinoomote, Kagoshima 891-3102, Japan; (M.U.); (Y.T.); (M.O.)
| | - Yusuke Tarumoto
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Annou 1742-1, Nishinoomote, Kagoshima 891-3102, Japan; (M.U.); (Y.T.); (M.O.)
| | - Megumi Okubo
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Annou 1742-1, Nishinoomote, Kagoshima 891-3102, Japan; (M.U.); (Y.T.); (M.O.)
| | - Yasujiro Morimitsu
- Institute for Human Life Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan;
| | - Yasuaki Tamura
- Western Region Agricultural Research Center (Kinki, Chugoku and Shikoku Regions), National Agriculture and Food Research Organization, 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan;
| | - Yoichi Nishiba
- Kyushu-Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, 2421 Suya, Koshi, Kumamoto 861-1192, Japan;
| | - Hiroshi Ono
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, 2-1-12 Kannondai, Tsukuba 305-8642, Ibaraki, Japan; (Y.D.); (H.O.)
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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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Reyes VP, Kitony JK, Nishiuchi S, Makihara D, Doi K. Utilization of Genotyping-by-Sequencing (GBS) for Rice Pre-Breeding and Improvement: A Review. Life (Basel) 2022; 12:1752. [PMID: 36362909 PMCID: PMC9694628 DOI: 10.3390/life12111752] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 09/29/2023] Open
Abstract
Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify the differences at a specific position in the genome of individuals. The advances in sequencing technologies have led to the development of different genotyping techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled the parallel sequencing and genotyping of hundreds of samples in a single run, making it more cost-effective. Currently, GBS is being used in several pre-breeding programs of rice to identify beneficial genes and QTL from different rice genetic resources. In this review, we present the current advances in the utilization of genotyping-by-sequencing for the development of rice pre-breeding materials and the improvement of existing rice cultivars. The challenges and perspectives of using this approach are also highlighted.
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Affiliation(s)
- Vincent Pamugas Reyes
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | | | - Shunsaku Nishiuchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Daigo Makihara
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya 464-8601, Japan
| | - Kazuyuki Doi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
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