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Tanaka R, Kawai T, Kawakatsu T, Tanaka N, Shenton M, Yabe S, Uga Y. Transcriptome-based prediction for polygenic traits in rice using different gene subsets. BMC Genomics 2024; 25:915. [PMID: 39354337 PMCID: PMC11443665 DOI: 10.1186/s12864-024-10803-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 09/13/2024] [Indexed: 10/03/2024] Open
Abstract
BACKGROUND Transcriptome-based prediction of complex phenotypes is a relatively new statistical method that links genetic variation to phenotypic variation. The selection of large-effect genes based on a priori biological knowledge is beneficial for predicting oligogenic traits; however, such a simple gene selection method is not applicable to polygenic traits because causal genes or large-effect loci are often unknown. Here, we used several gene-level features and tested whether it was possible to select a gene subset that resulted in better predictive ability than using all genes for predicting a polygenic trait. RESULTS Using the phenotypic values of shoot and root traits and transcript abundances in leaves and roots of 57 rice accessions, we evaluated the predictive abilities of the transcriptome-based prediction models. Leaf transcripts predicted shoot phenotypes, such as plant height, more accurately than root transcripts, whereas root transcripts predicted root phenotypes, such as crown root length, more accurately than leaf transcripts. Furthermore, we used the following three features to train the prediction model: (1) tissue specificity of the transcripts, (2) ontology annotations, and (3) co-expression modules for selecting gene subsets. Although models trained by a gene subset often resulted in lower predictive abilities than the model trained by all genes, some gene subsets showed improved predictive ability. For example, using genes expressed in roots but not in leaves, the predictive ability for crown root diameter was improved by more than 10% (R2 = 0.59 when using all genes; R2 = 0.66, using 1,554 root-specifically expressed genes). Similarly, genes annotated as "gibberellic acid sensitivity" showed higher predictive ability than using all genes for root dry weight. CONCLUSIONS Our results highlight both the possibility and difficulty of selecting an appropriate gene subset to predict polygenic traits from transcript abundance, given the current biological knowledge and information. Further integration of multiple sources of information, as well as improvements in gene characterization, may enable the selection of an optimal gene set for the prediction of polygenic phenotypes.
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Affiliation(s)
- Ryokei Tanaka
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Tsubasa Kawai
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8518, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Nobuhiro Tanaka
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8518, Japan
| | - Matthew Shenton
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8518, Japan
| | - Shiori Yabe
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8518, Japan
| | - Yusaku Uga
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8518, Japan
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2
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Toriyama K, Iwai Y, Takeda S, Takatsuka A, Igarashi K, Furuta T, Chen S, Kanaoka Y, Kishima Y, Arimura SI, Kazama T. Cryptic cytoplasmic male sterility-causing gene in the mitochondrial genome of common japonica rice. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39250703 DOI: 10.1111/tpj.17028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 08/20/2024] [Accepted: 08/22/2024] [Indexed: 09/11/2024]
Abstract
Cytoplasmic male sterility (CMS) is an agronomically significant trait that causes dysfunction in pollen and anther development. It is often observed during successive backcrossing between distantly related species. Here, we show that Asian japonica cultivars (Oryza sativa) exhibit CMS when the nucleus is replaced with that of the African rice Oryza glaberrima. The CMS line produced stunted anthers and did not set any seeds. Mitochondrial orf288 RNA was detected in the anthers of CMS lines but not in fertility restorer lines. The mitochondrial genome-edited japonica rice that was depleted of orf288 did not exhibit male sterility when backcrossed with O. glaberrima. These results demonstrate that orf288 is a CMS-causing gene. As orf288 commonly occurs in the mitochondrial genomes of japonica rice, these results indicate that common japonica rice cultivars possess a cryptic CMS-causing gene hidden in their mitochondrial genomes.
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Affiliation(s)
- Kinya Toriyama
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan
| | - Yuko Iwai
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan
| | - Shinya Takeda
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan
| | - Ayumu Takatsuka
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan
| | - Keisuke Igarashi
- Laboratory of Environmental Biotechnology, Graduate School of Agricultural Science, Tohoku University, Sendai, 980-8572, Japan
| | - Tomoyuki Furuta
- Laboratory of Integrated Genomic Breeding, Institute of Plant Science and Resources, Okayama University, Kurashiki, 710-0046, Japan
| | - Sunlu Chen
- Laboratory of Plant Breeding, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yoshitaka Kanaoka
- Laboratory of Plant Breeding, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Yuji Kishima
- Laboratory of Plant Breeding, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Shin-Ichi Arimura
- Laboratory of Plant Molecular Genetics, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-0012, Japan
| | - Tomohiko Kazama
- Genome Chemistry and Engineering Laboratory, Faculty of Agriculture, Kyushu University, Fukuoka, 819-0395, Japan
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3
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Sugimura Y, Oikawa K, Sugihara Y, Utsushi H, Kanzaki E, Ito K, Ogasawara Y, Fujioka T, Takagi H, Shimizu M, Shimono H, Terauchi R, Abe A. Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding. PLoS Genet 2024; 20:e1011369. [PMID: 39110723 PMCID: PMC11343456 DOI: 10.1371/journal.pgen.1011369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Revised: 08/23/2024] [Accepted: 07/12/2024] [Indexed: 08/25/2024] Open
Abstract
Direct seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL) qLTG11 from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containing GENERAL REGULATORY FACTOR14h (GF14h) gene, which is expressed during seed germination. The Arroz da Terra GF14h allele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functional GF14h in a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functional GF14h in Hitomebore increased LTG, indicating that GF14h is the causal gene behind qLTG11. Analysis of numerous Japanese rice accessions revealed that the functional GF14h allele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra including GF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functional GF14h allele from Arroz da Terra represents a valuable resource for direct seeding in cold regions.
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Affiliation(s)
| | - Kaori Oikawa
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Yu Sugihara
- Crop Evolution Laboratory, Kyoto University, Muko, Kyoto, Japan
| | - Hiroe Utsushi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Eiko Kanzaki
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Kazue Ito
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | | | | | - Hiroki Takagi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Motoki Shimizu
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroyuki Shimono
- Faculty of Agriculture, Iwate University, Morioka, Iwate, Japan
- Agri-Innovation Center, Iwate University, Morioka, Iwate, Japan
| | - Ryohei Terauchi
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
- Crop Evolution Laboratory, Kyoto University, Muko, Kyoto, Japan
| | - Akira Abe
- Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
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4
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Nishimura K, Kokaji H, Motoki K, Yamazaki A, Nagasaka K, Mori T, Takisawa R, Yasui Y, Kawai T, Ushijima K, Yamasaki M, Saito H, Nakano R, Nakazaki T. Degenerate oligonucleotide primer MIG-seq: an effective PCR-based method for high-throughput genotyping. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2296-2317. [PMID: 38459738 DOI: 10.1111/tpj.16708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 01/14/2024] [Accepted: 02/14/2024] [Indexed: 03/10/2024]
Abstract
Next-generation sequencing (NGS) library construction often involves using restriction enzymes to decrease genome complexity, enabling versatile polymorphism detection in plants. However, plant leaves frequently contain impurities, such as polyphenols, necessitating DNA purification before enzymatic reactions. To overcome this problem, we developed a PCR-based method for expeditious NGS library preparation, offering flexibility in number of detected polymorphisms. By substituting a segment of the simple sequence repeat sequence in the MIG-seq primer set (MIG-seq being a PCR method enabling library construction with low-quality DNA) with degenerate oligonucleotides, we introduced variability in detectable polymorphisms across various crops. This innovation, named degenerate oligonucleotide primer MIG-seq (dpMIG-seq), enabled a streamlined protocol for constructing dpMIG-seq libraries from unpurified DNA, which was implemented stably in several crop species, including fruit trees. Furthermore, dpMIG-seq facilitated efficient lineage selection in wheat and enabled linkage map construction and quantitative trait loci analysis in tomato, rice, and soybean without necessitating DNA concentration adjustments. These findings underscore the potential of the dpMIG-seq protocol for advancing genetic analyses across diverse plant species.
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Affiliation(s)
- Kazusa Nishimura
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Hiroyuki Kokaji
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Ko Motoki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Akira Yamazaki
- Faculty of Agriculture, Kindai University, 3327-204, Nakamachi, Nara City, Nara, 631-8505, Japan
| | - Kyoka Nagasaka
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Mori
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Rihito Takisawa
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu City, Shiga, 520-2194, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Takashi Kawai
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Koichiro Ushijima
- Graduate School of Environmental, Life, Natural Science and Technology, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama City, 700-8530, Okayama, Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2 no-cho, Nishi-ku, Niigata City, Niigata, 950-2181, Japan
| | - Hiroki Saito
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, 1091-1 Maezato-Kawarabaru, Ishigaki, Okinawa, 907-0002, Japan
| | - Ryohei Nakano
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
| | - Tetsuya Nakazaki
- Graduate School of Agriculture, Kyoto University, 4-2-1, Shiroyamadai, Kizugawa City, Kyoto, 619-0218, Japan
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5
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Kariya K, Mori H, Ueno M, Yoshikawa T, Teraishi M, Yabuta Y, Ueno K, Ishihara A. Identification and evolution of a diterpenoid phytoalexin oryzalactone biosynthetic gene in the genus Oryza. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:358-372. [PMID: 38194491 DOI: 10.1111/tpj.16608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 11/11/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
The natural variation of plant-specialized metabolites represents the evolutionary adaptation of plants to their environments. However, the molecular mechanisms that account for the diversification of the metabolic pathways have not been fully clarified. Rice plants resist attacks from pathogens by accumulating diterpenoid phytoalexins. It has been confirmed that the composition of rice phytoalexins exhibits numerous natural variations. Major rice phytoalexins (momilactones and phytocassanes) are accumulated in most cultivars, although oryzalactone is a cultivar-specific compound. Here, we attempted to reveal the evolutionary trajectory of the diversification of phytoalexins by analyzing the oryzalactone biosynthetic gene in Oryza species. The candidate gene, KSLX-OL, which accounts for oryzalactone biosynthesis, was found around the single-nucleotide polymorphisms specific to the oryzalactone-accumulating cultivars in the long arm of chromosome 11. The metabolite analyses in Nicotiana benthamiana and rice plants overexpressing KSLX-OL indicated that KSLX-OL is responsible for the oryzalactone biosynthesis. KSLX-OL is an allele of KSL8 that is involved in the biosynthesis of another diterpenoid phytoalexin, oryzalexin S and is specifically distributed in the AA genome species. KSLX-NOL and KSLX-bar, which encode similar enzymes but are not involved in oryzalactone biosynthesis, were also found in AA genome species. The phylogenetic analyses of KSLXs, KSL8s, and related pseudogenes (KSL9s) indicated that KSLX-OL was generated from a common ancestor with KSL8 and KSL9 via gene duplication, functional differentiation, and gene fusion. The wide distributions of KSLX-OL and KSL8 in AA genome species demonstrate their long-term coexistence beyond species differentiation, suggesting a balancing selection between the genes.
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Affiliation(s)
- Keisuke Kariya
- The United Graduate School of Agricultural Sciences, Tottori University, 4-110 Koyama Minami, Tottori, 680-8553, Japan
| | - Haruka Mori
- Faculty of Agriculture, Tottori University, 4-110 Koyama Minami, Tottori, 680-8553, Japan
| | - Makoto Ueno
- Faculty of Life and Environmental Sciences, Shimane University, Nishikawatsu 1060, Matsue, 690-8504, Japan
| | - Takanori Yoshikawa
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan
| | - Masayoshi Teraishi
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-Cho, Kyoto, 606-8502, Japan
| | - Yukinori Yabuta
- Faculty of Agriculture, Tottori University, 4-110 Koyama Minami, Tottori, 680-8553, Japan
| | - Kotomi Ueno
- Faculty of Agriculture, Tottori University, 4-110 Koyama Minami, Tottori, 680-8553, Japan
| | - Atsushi Ishihara
- Faculty of Agriculture, Tottori University, 4-110 Koyama Minami, Tottori, 680-8553, Japan
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6
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Baruah AR, Bannai H, Meija Y, Kimura A, Ueno H, Koide Y, Kishima Y, Palta J, Kasuga J, Yamamoto MP, Onishi K. Genetics of chilling response at early growth stage in rice: a recessive gene for tolerance and importance of acclimation. AOB PLANTS 2023; 15:plad075. [PMID: 38028749 PMCID: PMC10676198 DOI: 10.1093/aobpla/plad075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023]
Abstract
Low-temperature adaptation in rice is mediated by the ability of a genotype to tolerate chilling temperatures. A genetic locus on chromosome 11 was analysed for chilling tolerance at the plumule stage in rice. The tolerant allele of A58, a japonica landrace in Japan, was inherited as a recessive gene (ctp-1A58), whereas the susceptible alleles from wild rice (Ctp-1W107) and modern variety (Ctp-1HY) were the dominant genes. Another recessive tolerant allele (ctp-1Silewah) was found in a tropical japonica variety (Silewah). Fine-mapping revealed that a candidate gene for the ctp-1 locus encoded a protein similar to the nucleotide-binding domain and leucine-rich repeat (NLR) protein, in which frameshift mutation by a 73 bp-deletion might confer chilling tolerance in ctp-1A58. Analysis of near-isogenic lines demonstrated that ctp-1A58 imparted tolerance effects only at severe chilling temperatures of 0.5 °C and 2 °C, both at plumule and seedling stages. Chilling acclimation treatments at a wide range of temperatures (8 °C-16 °C) for 72 h concealed the susceptible phenotype of Ctp-1W107 and Ctp-1HY. Furthermore, short-term acclimation treatment of 12 h at 8 °C was enough to be fully acclimated. These results suggest that the NLR gene induces a susceptible response upon exposure to severe chilling stress, however, another interacting gene(s) for acclimation response could suppress the maladaptive phenotype caused by the Ctp-1 allele. This study provides new insights for the adaptation and breeding of rice in a low-temperature environment.
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Affiliation(s)
- Akhil Ranjan Baruah
- Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat-13, Assam, India
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Hiroaki Bannai
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yan Meija
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Ayumi Kimura
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Haruka Ueno
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Yohei Koide
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Yuji Kishima
- Research Faculty of Agriculture, Hokkaido University, Sapporo, Hokkaido 060-8589, Japan
| | - Jiwan Palta
- Department of Horticulture, University of Wisconsin-Madison, 490 Moore Hall, 1575 Linden Drive, Madison, WI 53706, USA
| | - Jun Kasuga
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
| | - Masayuki P Yamamoto
- Faculty of Science, Academic Assembly, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Kazumitsu Onishi
- Department of Agro-Environmental Science, Obihiro University of Agriculture and Veterinary Medicine, Obihiro, Hokkaido 080-8555, Japan
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Shigita G, Dung TP, Pervin MN, Duong TT, Imoh ON, Monden Y, Nishida H, Tanaka K, Sugiyama M, Kawazu Y, Tomooka N, Kato K. Elucidation of genetic variation and population structure of melon genetic resources in the NARO Genebank, and construction of the World Melon Core Collection. BREEDING SCIENCE 2023; 73:269-277. [PMID: 37840980 PMCID: PMC10570884 DOI: 10.1270/jsbbs.22071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/25/2023] [Indexed: 10/17/2023]
Abstract
Numerous genetic resources of major crops have been introduced from around the world and deposited in Japanese National Agriculture and Food Research Organization (NARO) Genebank. Understanding their genetic variation and selecting a representative subset ("core collection") are essential for optimal management and efficient use of genetic resources. In this study, we conducted genotyping-by-sequencing (GBS) to characterize the genetic relationships and population structure in 755 accessions of melon genetic resources. The GBS identified 39,324 single-nucleotide polymorphisms (SNPs) that are distributed throughout the melon genome with high density (one SNP/10.6 kb). The phylogenetic relationships and population structure inferred using this SNP dataset are highly associated with the cytoplasm type and geographical origin. Our results strongly support the recent hypothesis that cultivated melon was established in Africa and India through multiple independent domestication events. Finally, we constructed a World Melon Core Collection that covers at least 82% of the genetic diversity and has a wide range of geographical origins and fruit morphology. The genome-wide SNP dataset, phylogenetic relationships, population structure, and the core collection provided in this study should largely contribute to genetic research, breeding, and genetic resource preservation in melon.
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Affiliation(s)
- Gentaro Shigita
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Department of Life Science Systems, Technical University of Munich, Emil-Ramann Strasse 2, Freising 85354, Germany
| | - Tran Phuong Dung
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Mst. Naznin Pervin
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Thanh-Thuy Duong
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
- Faculty of Agronomy, University of Agriculture and Forestry, Hue University, 102 Phung Hung Street, Hue City, Vietnam
| | - Odirich Nnennaya Imoh
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Yuki Monden
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Hidetaka Nishida
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo, Hirosaki, Aomori 036-8561, Japan
| | - Mitsuhiro Sugiyama
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Yoichi Kawazu
- Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), 360 Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Norihiko Tomooka
- Research Center of Genetic Resources, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Kenji Kato
- Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-Naka, Kita-ku, Okayama 700-8530, Japan
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8
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Nagata K, Nonoue Y, Matsubara K, Mizobuchi R, Ono N, Shibaya T, Ebana K, Ogiso-Tanaka E, Tanabata T, Sugimoto K, Taguchi-Shiobara F, Yonemaru JI, Uga Y, Fukuda A, Ueda T, Yamamoto SI, Yamanouchi U, Takai T, Ikka T, Kondo K, Hoshino T, Yamamoto E, Adachi S, Sun J, Kuya N, Kitomi Y, Iijima K, Nagasaki H, Shomura A, Mizubayashi T, Kitazawa N, Hori K, Ando T, Yamamoto T, Fukuoka S, Yano M. Development of 12 sets of chromosome segment substitution lines that enhance allele mining in Asian cultivated rice. BREEDING SCIENCE 2023; 73:332-342. [PMID: 37840983 PMCID: PMC10570878 DOI: 10.1270/jsbbs.23006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 04/12/2023] [Indexed: 10/17/2023]
Abstract
Many agronomic traits that are important in rice breeding are controlled by multiple genes. The extensive time and effort devoted so far to identifying and selecting such genes are still not enough to target multiple agronomic traits in practical breeding in Japan because of a lack of suitable plant materials in which to efficiently detect and validate beneficial alleles from diverse genetic resources. To facilitate the comprehensive analysis of genetic variation in agronomic traits among Asian cultivated rice, we developed 12 sets of chromosome segment substitution lines (CSSLs) with the japonica background, 11 of them in the same genetic background, using donors representing the genetic diversity of Asian cultivated rice. Using these materials, we overviewed the chromosomal locations of 1079 putative QTLs for seven agronomic traits and their allelic distribution in Asian cultivated rice through multiple linear regression analysis. The CSSLs will allow the effects of putative QTLs in the highly homogeneous japonica background to be validated.
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Affiliation(s)
- Kazufumi Nagata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yasunori Nonoue
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuki Matsubara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ritsuko Mizobuchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Nozomi Ono
- Institute of the Society for Techno-innovation of Agriculture, Forestry and Fisheries, 446-1 Ippaizuka, Kamiyokoba, Tsukuba, Ibaraki 305-0854, Japan
| | - Taeko Shibaya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kaworu Ebana
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eri Ogiso-Tanaka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takanari Tanabata
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kazuhiko Sugimoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Fumio Taguchi-Shiobara
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jun-ichi Yonemaru
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Atsunori Fukuda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tadamasa Ueda
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shin-ichi Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Utako Yamanouchi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshiyuki Takai
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Takashi Ikka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Katsuhiko Kondo
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tomoki Hoshino
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Eiji Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shunsuke Adachi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Jian Sun
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kuya
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Yuka Kitomi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ken Iijima
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Hideki Nagasaki
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Ayahiko Shomura
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tatsumi Mizubayashi
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Noriyuki Kitazawa
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Kiyosumi Hori
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Tsuyu Ando
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Toshio Yamamoto
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
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9
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Ta KN, Shimizu-Sato S, Agata A, Yoshida Y, Taoka KI, Tsuji H, Akagi T, Tanizawa Y, Sano R, Nosaka-Takahashi M, Suzuki T, Demura T, Toyoda A, Nakamura Y, Sato Y. A leaf-emanated signal orchestrates grain size and number in response to maternal resources. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36994645 DOI: 10.1111/tpj.16219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 03/25/2023] [Indexed: 05/13/2023]
Abstract
In plants, variations in seed size and number are outcomes of different reproductive strategies. Both traits are often environmentally influenced, suggesting that a mechanism exists to coordinate these phenotypes in response to available maternal resources. Yet, how maternal resources are sensed and influence seed size and number is largely unknown. Here, we report a mechanism that senses maternal resources and coordinates grain size and number in the wild rice Oryza rufipogon, a wild progenitor of Asian cultivated rice. We showed that FT-like 9 (FTL9) regulates both grain size and number and that maternal photosynthetic assimilates induce FTL9 expression in leaves to act as a long-range signal that increases grain number and reduces size. Our findings highlight a strategy that benefits wild plants to survive in a fluctuating environment. In this strategy, when maternal resources are sufficient, wild plants increase their offspring number while preventing an increase in offspring size by the action of FTL9, which helps expand their habitats. In addition, we found that a loss-of-function allele (ftl9) is prevalent among wild and cultivated populations, offering a new scenario in the history of rice domestication.
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Affiliation(s)
- Kim Nhung Ta
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Vietnam Japan University, Vietnam National University, Hanoi, Vietnam
| | - Sae Shimizu-Sato
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Ayumi Agata
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Yuri Yoshida
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Ken-Ichiro Taoka
- Kihara Institute for Biological Research, Yokohama City University, 244-0813, Yokohama, 641-12 Maioka, Totsuka, Japan
| | - Hiroyuki Tsuji
- Kihara Institute for Biological Research, Yokohama City University, 244-0813, Yokohama, 641-12 Maioka, Totsuka, Japan
| | - Takashi Akagi
- Graduate School of Environmental and Life Science, Okayama University, 700-8530, Okayama, Japan
| | - Yasuhiro Tanizawa
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Misuzu Nosaka-Takahashi
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Toshiya Suzuki
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, 630-0192, Ikoma, Japan
| | - Atsushi Toyoda
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Yasukazu Nakamura
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
| | - Yutaka Sato
- National Institute of Genetics, 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
- Department of Genetics, School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), 411-8540, Shizuoka, 1111 Yata, Mishima, Japan
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10
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Fukai C, Tanabata T, Nishizawa T, Koizumi M, Kutsuwada K, Kusano M. A developed system to extract specific responses of increment length in rice shoots under gradient changes in nitrogen concentration regimes. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:1-8. [PMID: 38213927 PMCID: PMC10777135 DOI: 10.5511/plantbiotechnology.22.1107a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 11/07/2022] [Indexed: 01/13/2024]
Abstract
Nitrogen (N) fertilization is one of the most crucial factors that contribute to increasing food production requiring the generation of rice cultivars with improved N use efficiency (NUE) to maintain yield during low N fertilizer application. To assay NUE extent, we developed a screening system to evaluate shoot growth of each rice cultivar under gradient changes in N concentrations. This system comprises a gradient hydroponic culture and growth visualization systems. The former allows gradient changes in ammonium concentrations, while the latter records the increment in shoot length of individual rice seedlings at given time periods using a fixed-point camera. We chose 69 cultivars including two controls (Oryza sativa L. cv. Nipponbare [WRC01] and Kasalath [WRC02]) from the World Rice Core Collection to investigate shoot growth responses under ammonium-sufficient, ammonium-limited, and low ammonium concentration gradients without transplanting stress. We observed three growth patterns in response to different ammonium concentrations. Subsequently, we selected three representative cultivars (Kasalath, WRC03, and WRC05) for the characteristic responses under the different ammonium environments. Distinct expression patterns of glutamine synthetase 1;2 (OsGS1;2) but OsGS1;1 were observed in response to varying ammonium concentration regimes, indicating that the expression patterns of OsGS1;2 may be a growth marker in terms of shoot growth when transitioning from ammonium-limited to low ammonium concentrations. This system with the level of OsGS1;2 allows us to screen for candidate cultivars that return high NUE in low N environments.
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Affiliation(s)
- Chihaya Fukai
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | | | - Tomoko Nishizawa
- Riken Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Mikiko Koizumi
- Riken Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Keisuke Kutsuwada
- Graduate School of Life and Environmental Science, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Miyako Kusano
- Riken Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
- Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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11
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Shankar R, Dwivedi AK, Singh V, Jain M. Genome-wide discovery of genetic variations between rice cultivars with contrasting drought stress response and their potential functional relevance. PHYSIOLOGIA PLANTARUM 2023; 175:e13879. [PMID: 36805564 DOI: 10.1111/ppl.13879] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 02/14/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
Drought stress is a serious threat to rice productivity. Investigating genetic variations between drought-tolerant (DT) and drought-sensitive (DS) rice cultivars may decipher the candidate genes/regulatory regions involved in drought stress tolerance/response. In this study, whole-genome resequencing data of four DS and five DT rice cultivars were analyzed. We identified a total of approximately 4.8 million single nucleotide polymorphisms (SNPs) and 0.54 million insertions/deletions (InDels). The genetic variations (162,638 SNPs and 17,217 InDels) differentiating DS and DT rice cultivars were found to be unevenly distributed throughout the rice genome; however, they were more frequent near the transcription start and stop sites than in the genic regions. The cis-regulatory motifs representing the binding sites of stress-related transcription factors (MYB, HB, bZIP, ERF, ARR, and AREB) harboring the SNPs/InDels in the promoter regions of a few differentially expressed genes (DEGs) were identified. Importantly, many of these DEGs were located within the drought-associated quantitative trait loci. Overall, this study provides a valuable large-scale genotyping resource and facilitates the discovery of candidate genes associated with drought stress tolerance in rice.
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Affiliation(s)
- Rama Shankar
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Anuj Kumar Dwivedi
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Vikram Singh
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Mukesh Jain
- School of Computational & Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
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12
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Quach T, Nguyen H, Meyer O, Sato SJ, Clemente TE, Guo M. Introduction of Genome Editing Reagents and Genotyping of Derived Edited Alleles in Soybean (Glycine max (L.) Merr.). Methods Mol Biol 2023; 2653:273-285. [PMID: 36995632 DOI: 10.1007/978-1-0716-3131-7_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Cas9-based genome editing is a powerful genetic tool for loci specifically targeted for genome modification. This chapter describes up-to-date protocols using Cas9-based genome editing technology, including vector construction with GoldenBraid assembly, Agrobacterium-mediated soybean transformation, and identification of editing in the genome.
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Affiliation(s)
- Truyen Quach
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Hanh Nguyen
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Olivia Meyer
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Shirley J Sato
- Center for Plant Science Innovation, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Tom Elmo Clemente
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Ming Guo
- Department of Agronomy & Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.
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13
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Samejima H, Sugimoto Y. Phenotypic Diversity in Pre- and Post-Attachment Resistance to Striga hermonthica in a Core Collection of Rice Germplasms. PLANTS (BASEL, SWITZERLAND) 2022; 12:19. [PMID: 36616148 PMCID: PMC9824375 DOI: 10.3390/plants12010019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/17/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
In sub-Saharan Africa, upland rice cultivation is expanding into rainfed areas endemic to the root parasitic weed Striga hermonthica. We evaluated the Striga resistance of 69 accessions from the World Rice Core Collection (WRC) to estimate the phenotypic diversity within the Oryza sativa species. Pre-attachment resistance was screened based on the germination-inducing activities of the root exudates, while post-attachment resistance was screened through rhizotron evaluation. The 69 WRC accessions showed a wide variation in both pre- and post-attachment resistance. Root exudates of one accession induced 0.04% germination, and those of some accessions displayed >80% germination. In the evaluation of post-attachment resistance, the successful parasitism percentages ranged from 1.3% to 60.7%. The results of these resistance evaluations were subjected to cluster analysis, which recognized five groups: group I of 27 accessions, with high pre- and post-attachment resistance; group II of 12 accessions, with high post-attachment resistance but moderate pre-attachment resistance; group III of 4 accessions, with low pre-attachment resistance; group IV of 13 accessions, with low post-attachment resistance; and group V of 13 accessions, with low pre- and post-attachment resistance. The wide variation found in the WRC accessions will help to elucidate the genetic factors underpinning pre- and post-attachment resistance.
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14
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Yoshida Y, Nosaka-T M, Yoshikawa T, Sato Y. Measurements of Antibacterial Activity of Seed Crude Extracts in Cultivated Rice and Wild Oryza Species. RICE (NEW YORK, N.Y.) 2022; 15:63. [PMID: 36513947 PMCID: PMC9748026 DOI: 10.1186/s12284-022-00610-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Seeds are continuously exposed to a wide variety of microorganisms in the soil. In addition, seeds contain large amounts of carbon and nitrogen sources that support initial growth after germination. Thus, seeds in the soil can easily promote microbial growth, and seeds are susceptible to decay. Therefore, seed defense against microorganisms is important for plant survival. Seed-microbe interactions are also important issues from the perspective of food production, in seed quality and shelf life. However, seed-microbe interactions remain largely unexplored. In this study, we established a simple and rapid assay system for the antibacterial activity of rice seed crude extracts by colorimetric quantification methods by the reduction of tetrazolium compound. Using this experimental system, the diversity of effects of rice seed extracts on microbial growth was analyzed using Escherichia coli as a bacterial model. We used collections of cultivated rice, comprising 50 accessions of Japanese landraces, 52 accessions of world rice core collections, and of 30 wild Oryza accessions. Furthermore, we attempted to find genetic factors responsible for the diversity by genome-wide association analysis. Our results demonstrate that this experimental system can easily analyze the effects of seed extracts on bacterial growth. It also suggests that there are various compounds in rice seeds that affect microbial growth. Overall, this experimental system can be used to clarify the chemical entities and genetic control of seed-microbe interactions and will open the door for understanding the diverse seed-microbe interactions through metabolites.
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Affiliation(s)
| | - Misuzu Nosaka-T
- National Institute of Genetics, Shizuoka, Japan
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Shizuoka, Japan
| | - Takanori Yoshikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Yutaka Sato
- National Institute of Genetics, Shizuoka, Japan.
- Department of Genetics, School of Life Science, Sokendai (Graduate University for Advanced Studies), Shizuoka, Japan.
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15
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Imaizumi T, Kawahara Y, Auge G. Hybrid-derived weedy rice maintains adaptive combinations of alleles associated with seed dormancy. Mol Ecol 2022; 31:6556-6569. [PMID: 36178060 DOI: 10.1111/mec.16709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 01/13/2023]
Abstract
Plant hybridization is a pathway for the evolution of adaptive traits. However, hybridization between adapted and nonadapted populations may affect the persistence of combinations of adaptive alleles evolved through natural selection. Seed dormancy is an adaptive trait for weedy rice because it regulates the timing of seed germination and the persistence of the soil seed bank. Hybridization between weedy and cultivated rice has been confirmed with an adaptive introgression of deep seed dormancy alleles from cultivated rice. Here, we explored the influence of hybridization on the conservation of adaptive allele combinations by evaluating natural variation and genetic structure in seed dormancy-associated genomic regions. Based on sequence variation in the genomic regions associated with seed dormancy, hybrid-derived weedy rice strains maintained most of the adaptive combinations for this trait observed in the parental weedy rice, despite equal representation of the parental weedy and cultivated rice in the whole genome sequence. Moreover, hybrid-derived weedy rice strains were more dormant than their parental weedy rice strains, and this trait was strongly influenced by the environment. This study suggests that hybridization between weedy rice (adaptive allelic combinations for seed dormancy) and cultivated rice (nonadaptive combinations) generates weedy rice strains expressing deep seed dormancy caused by genome stabilization through the removal of alleles derived from cultivated rice, in addition to the adaptive introgression of deep seed dormancy alleles derived from cultivated rice. Thus, hybridization between adapted and nonadapted populations appears to be reinforcing the trajectory towards the evolution of adaptive traits.
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Affiliation(s)
- Toshiyuki Imaizumi
- Institute for Plant Protection, National Agriculture and Food Research Organization (NARO), Tsukuba, Japan
| | | | - Gabriela Auge
- Consejo Nacional de Investigaciones Científicas y Tecnológicas (CONICET) - Instituto de Biociencias, Biotecnología y Biología Traslacional, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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16
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Zhang J, Pan D, Fan Z, Yu H, Jiang L, Lv S, Sun B, Chen W, Mao X, Liu Q, Li C. Genetic diversity of wild rice accessions ( Oryza rufipogon Griff.) in Guangdong and Hainan Provinces, China, and construction of a wild rice core collection. FRONTIERS IN PLANT SCIENCE 2022; 13:999454. [PMID: 36262660 PMCID: PMC9576158 DOI: 10.3389/fpls.2022.999454] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 09/02/2022] [Indexed: 05/28/2023]
Abstract
Oryza rufipogon Griff. is a valuable germplasm resource for rice genetic improvement. However, natural habitat loss has led to the erosion of the genetic diversity of wild rice populations. Genetic diversity analysis of O. rufipogon accessions and development of the core collection are crucial for conserving natural genetic diversity and providing novel traits for rice breeding. In the present study, we developed 1,592 SNPs by multiplex PCR and next-generation sequencing (NGS) technology and used them to genotype 998 O. rufipogon accessions from 14 agroclimatic zones in Guangdong and Hainan Provinces, China. These SNPs were mapped onto 12 chromosomes, and the average MAF value was 0.128 with a minimum of 0.01 and a maximum of 0.499. The O. rufipogon accessions were classified into ten groups. The mean Nei's diversity index and Shannon-Wiener index (I) were 0.187 and 0.308, respectively, in all populations, indicating that O. rufipogon accessions had rich genetic diversity. There were also differences in the genetic diversity of O. rufipogon resources in the 14 regions. Hainan populations possessed higher levels of genetic diversity, whereas the Guangzhou population had lower levels of genetic diversity than did the other populations. Phylogenetic analysis revealed that the genetic relationship among the distribution sites of O. rufipogon was closely related to geographical location. Based on genetic distance, a core collection of 299 accessions captured more than 99% of the genetic variation in the germplasm. This study provides insights into O. rufipogon conservation, and the constructed core collection provides valuable resources for future research and genomics-assisted breeding of rice.
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Affiliation(s)
- Jing Zhang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Dajian Pan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Zhilan Fan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Hang Yu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Liqun Jiang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Shuwei Lv
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Bingrui Sun
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Wenfeng Chen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Xingxue Mao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, China
| | - Qing Liu
- *Correspondence: Qing Liu, ; Chen Li,
| | - Chen Li
- *Correspondence: Qing Liu, ; Chen Li,
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17
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A stepwise route to domesticate rice by controlling seed shattering and panicle shape. Proc Natl Acad Sci U S A 2022; 119:e2121692119. [PMID: 35733263 PMCID: PMC9245615 DOI: 10.1073/pnas.2121692119] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Asian rice (Oryza sativa L.) is consumed by more than half of the world's population. Despite its global importance, the process of early rice domestication remains unclear. During domestication, wild rice (Oryza rufipogon Griff.) acquired non-seed-shattering behavior, allowing humans to increase grain yield. Previous studies argued that a reduction in seed shattering triggered by the sh4 mutation led to increased yield during rice domestication, but our experiments using wild introgression lines show that the domesticated sh4 allele alone is insufficient for shattering loss in O. rufipogon. The interruption of abscission layer formation requires both sh4 and qSH3 mutations, demonstrating that the selection of shattering loss in wild rice was not as simple as previously suggested. Here we identified a causal single-nucleotide polymorphism at qSH3 within the seed-shattering gene OsSh1, which is conserved in indica and japonica subspecies but absent in the circum-aus group of rice. Through harvest experiments, we further demonstrated that seed shattering alone did not significantly impact yield; rather, yield increases were observed with closed panicle formation controlled by SPR3 and further augmented by nonshattering, conferred by integration of sh4 and qSH3 alleles. Complementary manipulation of panicle shape and seed shattering results in a mechanically stable panicle structure. We propose a stepwise route for the earliest phase of rice domestication, wherein selection of visible SPR3-controlled closed panicle morphology was instrumental in the sequential recruitment of sh4 and qSH3, which together led to the loss of shattering.
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18
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Teramoto S, Yamasaki M, Uga Y. Identification of a unique allele in the quantitative trait locus for crown root number in japonica rice from Japan using genome-wide association studies. BREEDING SCIENCE 2022; 72:222-231. [PMID: 36408322 PMCID: PMC9653191 DOI: 10.1270/jsbbs.22010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/10/2022] [Indexed: 06/16/2023]
Abstract
To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo 675-2103, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
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Ereful NC, Jones H, Fradgley N, Boyd L, Cherie HA, Milner MJ. Nutritional and genetic variation in a core set of Ethiopian Tef (Eragrostis tef) varieties. BMC PLANT BIOLOGY 2022; 22:220. [PMID: 35484480 PMCID: PMC9047342 DOI: 10.1186/s12870-022-03595-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Tef (Eragrostis tef) is a tropical cereal domesticated and grown in the Ethiopian highlands, where it has been a staple food of Ethiopians for many centuries. Food insecurity and nutrient deficiencies are major problems in the country, so breeding for enhanced nutritional traits, such as Zn content, could help to alleviate problems with malnutrition. RESULTS To understand the breeding potential of nutritional traits in tef a core set of 24 varieties were sequenced and their mineral content, levels of phytate and protein, as well as a number of nutritionally valuable phenolic compounds measured in grain. Significant variation in all these traits was found between varieties. Genome wide sequencing of the 24 tef varieties revealed 3,193,582 unique SNPs and 897,272 unique INDELs relative to the tef reference var. Dabbi. Sequence analysis of two key transporter families involved in the uptake and transport of Zn by the plant led to the identification of 32 Zinc Iron Permease (ZIP) transporters and 14 Heavy Metal Associated (HMA) transporters in tef. Further analysis identified numerous variants, of which 14.6% of EtZIP and 12.4% of EtHMA variants were non-synonymous changes. Analysis of a key enzyme in flavanol synthesis, flavonoid 3'-hydroxylase (F3'H), identified a T-G variant in the tef homologue Et_s3159-0.29-1.mrna1 that was associated with the differences observed in kaempferol glycoside and quercetin glycoside levels. CONCLUSION Wide genetic and phenotypic variation was found in 24 Ethiopian tef varieties which would allow for breeding gains in many nutritional traits of importance to human health.
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Affiliation(s)
- Nelzo C Ereful
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Philippine Genome Centre, University of the Philippines Los Baňos, Laguna, Philippines
| | - Huw Jones
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Nick Fradgley
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Lesley Boyd
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Hirut Assaye Cherie
- Faculty of Chemical and Food Engineering, Bahir Dar Institute of Technology, P.O.Box 26, Bahir Dar, Ethiopia
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20
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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21
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Tay Fernandez CG, Nestor BJ, Danilevicz MF, Gill M, Petereit J, Bayer PE, Finnegan PM, Batley J, Edwards D. Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species. Int J Mol Sci 2022; 23:2671. [PMID: 35269811 PMCID: PMC8910360 DOI: 10.3390/ijms23052671] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/21/2022] [Accepted: 02/21/2022] [Indexed: 02/01/2023] Open
Abstract
Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
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Affiliation(s)
| | | | | | | | | | | | | | | | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia; (C.G.T.F.); (B.J.N.); (M.F.D.); (M.G.); (J.P.); (P.E.B.); (P.M.F.); (J.B.)
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22
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Mekbib Y, Tesfaye K, Dong X, Saina JK, Hu GW, Wang QF. Whole-genome resequencing of Coffea arabica L. (Rubiaceae) genotypes identify SNP and unravels distinct groups showing a strong geographical pattern. BMC PLANT BIOLOGY 2022; 22:69. [PMID: 35164709 PMCID: PMC8842891 DOI: 10.1186/s12870-022-03449-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/27/2022] [Indexed: 06/04/2023]
Abstract
BACKGROUND Coffea arabica L. is an economically important agricultural crop and the most popular beverage worldwide. As a perennial crop with recalcitrant seed, conservation of the genetic resources of coffee can be achieved through the complementary approach of in-situ and ex-situ field genebank. In Ethiopia, a large collection of C. arabica L. germplasm is preserved in field gene banks. Here, we report the whole-genome resequencing of 90 accessions from Choche germplasm bank representing garden and forest-based coffee production systems using Illumina sequencing technology. RESULTS The genome sequencing generated 6.41 billion paired-end reads, with a mean of 71.19 million reads per sample. More than 93% of the clean reads were mapped onto the C. arabica L. reference genome. A total of 11.08 million variants were identified, among which 9.74 million (87.9%) were SNPs (Single nucleotide polymorphisms) and 1.34 million (12.1%) were InDels. In all accessions, genomic variants were unevenly distributed across the coffee genome. The phylogenetic analysis using the SNP markers displayed distinct groups. CONCLUSIONS Resequencing of the coffee accessions has allowed identification of genetic markers, such as SNPs and InDels. The SNPs discovered in this study might contribute to the variation in important pathways of genes for important agronomic traits such as caffeine content, yield, disease, and pest in coffee. Moreover, the genome resequencing data and the genetic markers identified from 90 accessions provide insight into the genetic variation of the coffee germplasm and facilitate a broad range of genetic studies.
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Affiliation(s)
- Yeshitila Mekbib
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Ethiopian Biodiversity Institute, P.O. Box 30726, Addis Ababa, Ethiopia
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Innovation and Technology, Addis Ababa, Ethiopia
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Josphat K Saina
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, 666303, China
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China.
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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Ishihara A. Defense mechanisms involving secondary metabolism in the grass family. JOURNAL OF PESTICIDE SCIENCE 2021; 46:382-392. [PMID: 34908899 PMCID: PMC8640679 DOI: 10.1584/jpestics.j21-05] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 08/10/2021] [Indexed: 05/13/2023]
Abstract
Plants synthesize and accumulate a wide variety of compounds called secondary metabolites. Secondary metabolites serve as chemical barriers to protect plants from pathogens and herbivores. Antimicrobial secondary metabolites are accumulated to prevent pathogen infection. These metabolites are classified into phytoalexins (induced in response to pathogen attack) and phytoanticipins (present prior to pathogen infection). The antimicrobial compounds in the grass family (Poaceae) were studied from the viewpoint of evolution. The studies were performed at three hierarchies, families, genera, and species and include the following: 1) the distribution of benzoxazinoids (Bxs) in the grass family, 2) evolutionary replacement of phytoanticipins from Bxs to hydroxycinnamic acid amide dimers in the genus Hordeum, and 3) chemodiversity of flavonoid and diterpenoid phytoalexins in rice. These studies demonstrated dynamic changes in secondary metabolism during evolution, indicating the adaptation of plants to their environment by repeating scrap-and-build cycles.
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Affiliation(s)
- Atsushi Ishihara
- Department of Agricultural, Life and Environmental Sciences, Faculty of Agriculture, Tottori University, Tottori 680–8553, Japan
- To whom correspondence should be addressed. E-mail:
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24
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Kawakatsu T, Teramoto S, Takayasu S, Maruyama N, Nishijima R, Kitomi Y, Uga Y. The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1177-1190. [PMID: 33751672 DOI: 10.1101/2020.12.11.421685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 05/26/2023]
Abstract
Root system architecture affects plant drought resistance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, particularly for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field. We found that four principal components explained the phenotypic variation and that accessions could be classified into four subpopulations (indica, aus, japonica and admixed) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific subpopulations were enriched with stress response-related genes, suggesting that subpopulations have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and upland field conditions. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under upland field conditions.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Shota Teramoto
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satoko Takayasu
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Natsuko Maruyama
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- Department of Anatomy and Structural Biology, Faculty of Medicine Graduate School, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuka Kitomi
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yusaku Uga
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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25
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Kawakatsu T, Teramoto S, Takayasu S, Maruyama N, Nishijima R, Kitomi Y, Uga Y. The transcriptomic landscapes of rice cultivars with diverse root system architectures grown in upland field conditions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 106:1177-1190. [PMID: 33751672 DOI: 10.1111/tpj.15226] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/02/2021] [Accepted: 03/05/2021] [Indexed: 06/12/2023]
Abstract
Root system architecture affects plant drought resistance and other key agronomic traits such as lodging. However, although phenotypic and genomic variation has been extensively analyzed, few field studies have integrated phenotypic and transcriptomic information, particularly for below-ground traits such as root system architecture. Here, we report the phenotypic and transcriptomic landscape of 61 rice (Oryza sativa) accessions with highly diverse below-ground traits grown in an upland field. We found that four principal components explained the phenotypic variation and that accessions could be classified into four subpopulations (indica, aus, japonica and admixed) based on their tiller numbers and crown root diameters. Transcriptome analysis revealed that differentially expressed genes associated with specific subpopulations were enriched with stress response-related genes, suggesting that subpopulations have distinct stress response mechanisms. Root growth was negatively correlated with auxin-inducible genes, suggesting an association between auxin signaling and upland field conditions. A negative correlation between crown root diameter and stress response-related genes suggested that thicker crown root diameter is associated with resistance to mild drought stress. Finally, co-expression network analysis implemented with DNA affinity purification followed by sequencing analysis identified phytohormone signaling networks and key transcription factors negatively regulating crown root diameter. Our datasets provide a useful resource for understanding the genomic and transcriptomic basis of phenotypic variation under upland field conditions.
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Affiliation(s)
- Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Shota Teramoto
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Satoko Takayasu
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Natsuko Maruyama
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
- Department of Anatomy and Structural Biology, Faculty of Medicine Graduate School, University of Yamanashi, Chuo, Yamanashi, 409-3898, Japan
| | - Ryo Nishijima
- Institute of Agrobiological Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8604, Japan
| | - Yuka Kitomi
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
| | - Yusaku Uga
- Institute of Crop Sciences, National Agriculture & Food Research Organization, Tsukuba, Ibaraki, 305-8602, Japan
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26
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Guo F, Endo M, Yamaguchi T, Uchino A, Sunohara Y, Matsumoto H, Iwakami S. Investigation of clomazone-tolerance mechanism in a long-grain cultivar of rice. PEST MANAGEMENT SCIENCE 2021; 77:2454-2461. [PMID: 33432689 DOI: 10.1002/ps.6274] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 01/03/2021] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Clomazone is a potent herbicide for controlling weeds that have evolved resistance to other herbicides due to its unique mode of action. Clomazone is used in rice cultivation, but is limited to long-grain cultivars because other cultivars are highly sensitive to it. In this study, we investigated the mechanism of clomazone tolerance in a long-grain cultivar. RESULTS The long-grain cultivar Kasalath tolerated approximately five-fold higher doses of clomazone compared to two short-grain cultivars, Nipponbare and Koshihikari. While Arabidopsis thaliana transformed with a rice cytochrome P450, CYP81A6, showed resistance to clomazone, the cyp81a6 knockout Kasalath was unchanged in its clomazone sensitivity. The inheritance of clomazone sensitivity in the F1 and F2 of Kasalath and Nipponbare indicated the involvement of multiple loci for clomazone tolerance. Four chromosome segment substitution lines of Nipponbare/Kasalath and Koshihikari/Kasalath exhibited partial tolerance to clomazone. The overlapping DNA region among the four lines is on chromosome 5 within 11.5 Mb. CONCLUSION Multiple loci are involved in clomazone tolerance in Kasalath, one of which is located on chromosome 5. This information will help develop short-grain cultivars tolerant to clomazone. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Feng Guo
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Masaki Endo
- Plant Genome Engineering Research Unit, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Takuya Yamaguchi
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akira Uchino
- Central Region Agricultural Research Center, National Agriculture and Food Research Organization, Tsu, Japan
| | - Yukari Sunohara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroshi Matsumoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Satoshi Iwakami
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-Oiwake-cho, Kyoto, Japan
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Tanaka N, Shenton M, Kawahara Y, Kumagai M, Sakai H, Kanamori H, Yonemaru JI, Fukuoka S, Sugimoto K, Ishimoto M, Wu J, Ebana K. Investigation of the Genetic Diversity of a Rice Core Collection of Japanese Landraces using Whole-Genome Sequencing. PLANT & CELL PHYSIOLOGY 2021; 61:2087-2096. [PMID: 33539537 PMCID: PMC7861467 DOI: 10.1093/pcp/pcaa125] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/22/2020] [Indexed: 06/12/2023]
Abstract
The Rice Core Collection of Japanese Landraces (JRC) consisting of 50 accessions was developed by the genebank at the National Agriculture and Food Research Organization (NARO) in 2008. As a Japanese landrace core collection, the JRC has been used for many research projects, including screening for different phenotypes and allele mining for target genes. To understand the genetic diversity of Japanese Landraces, we performed whole-genome resequencing of these 50 accessions and obtained a total of 2,145,095 single nucleotide polymorphism (SNPs) and 317,832 insertion-deletions (indels) by mapping against the Oryza sativa ssp. japonica Nipponbare genome. A JRC phylogenetic tree based on 1,394 representative SNPs showed that JRC accessions were divided into two major groups and one small group. We used the multiple genome browser, TASUKE+, to examine the haplotypes of flowering genes and detected new mutations in these genes. Finally, we performed genome-wide association studies (GWAS) for agronomical traits using the JRC and another core collection, the World Rice Core Collection (WRC), comprising 69 accessions also provided by the NARO genebank. In leaf blade width, a strong peak close to NAL1, a key gene for the regulation of leaf width, and, in heading date, a peak near HESO1 involved in flowering regulation were observed in GWAS using the JRC. They were also detected in GWAS using the combined JRC + WRC. Thus, JRC and JRC + WRC are suitable populations for GWAS of particular traits.
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Affiliation(s)
- Nobuhiro Tanaka
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Matthew Shenton
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Yoshihiro Kawahara
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Masahiko Kumagai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Hiroaki Sakai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Hiroyuki Kanamori
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Jun-ichi Yonemaru
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Shinichi Fukuoka
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Kazuhiko Sugimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Masao Ishimoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Jianzhong Wu
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
| | - Kaworu Ebana
- Genetic Resources Center, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, 305-8518 Japan
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28
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Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Kaila S, Nguyen H, Sivasankar S, Jackson SA, Close TJ, Shubo W, Varshney RK. Genomic resources in plant breeding for sustainable agriculture. JOURNAL OF PLANT PHYSIOLOGY 2021; 257:153351. [PMID: 33412425 PMCID: PMC7903322 DOI: 10.1016/j.jplph.2020.153351] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/14/2020] [Accepted: 12/14/2020] [Indexed: 05/19/2023]
Abstract
Climate change during the last 40 years has had a serious impact on agriculture and threatens global food and nutritional security. From over half a million plant species, cereals and legumes are the most important for food and nutritional security. Although systematic plant breeding has a relatively short history, conventional breeding coupled with advances in technology and crop management strategies has increased crop yields by 56 % globally between 1965-85, referred to as the Green Revolution. Nevertheless, increased demand for food, feed, fiber, and fuel necessitates the need to break existing yield barriers in many crop plants. In the first decade of the 21st century we witnessed rapid discovery, transformative technological development and declining costs of genomics technologies. In the second decade, the field turned towards making sense of the vast amount of genomic information and subsequently moved towards accurately predicting gene-to-phenotype associations and tailoring plants for climate resilience and global food security. In this review we focus on genomic resources, genome and germplasm sequencing, sequencing-based trait mapping, and genomics-assisted breeding approaches aimed at developing biotic stress resistant, abiotic stress tolerant and high nutrition varieties in six major cereals (rice, maize, wheat, barley, sorghum and pearl millet), and six major legumes (soybean, groundnut, cowpea, common bean, chickpea and pigeonpea). We further provide a perspective and way forward to use genomic breeding approaches including marker-assisted selection, marker-assisted backcrossing, haplotype based breeding and genomic prediction approaches coupled with machine learning and artificial intelligence, to speed breeding approaches. The overall goal is to accelerate genetic gains and deliver climate resilient and high nutrition crop varieties for sustainable agriculture.
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Affiliation(s)
- Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India; University of Southern Queensland, Toowoomba, Australia
| | - Ramesh Palakurthi
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Emma Mace
- Agri-Science Queensland, Department of Agriculture & Fisheries (DAF), Warwick, Australia
| | - Rakesh K Srivastava
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C Tara Satyavathi
- Indian Council of Agricultural Research (ICAR)- Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Damaris Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | | | - Hon-Ming Lam
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region
| | - Yan Bin Hong
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Vikas K Singh
- South Asia Hub, International Rice Research Institute (IRRI), Hyderabad, India
| | - Guowei Li
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Yunbi Xu
- International Maize and Wheat Improvement Center (CYMMIT), Mexico DF, Mexico; Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Sanjay Kaila
- Department of Biotechnology, Ministry of Science and Technology, Government of India, India
| | - Henry Nguyen
- National Centre for Soybean Research, University of Missouri, Columbia, USA
| | - Sobhana Sivasankar
- Joint FAO/IAEA Division of Nuclear Techniques in Food and Agriculture, Vienna, Austria
| | | | | | - Wan Shubo
- Shandong Academy of Agricultural Sciences, Jinan, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Mochida K, Lipka AE, Hirayama T. Exploration of Life-Course Factors Influencing Phenotypic Outcomes in Crops. PLANT & CELL PHYSIOLOGY 2020; 61:1381-1383. [PMID: 32603418 PMCID: PMC7434585 DOI: 10.1093/pcp/pcaa087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 06/22/2020] [Indexed: 05/06/2023]
Affiliation(s)
- Keiichi Mochida
- RIKEN Center for Sustainable Resource Science, Tsurumi-ku, Yokohama, Japan 230-0045
- Kihara Institute for Biological Research, Yokohama City University, Totsuka-ku, Yokohama, Japan 244-0813
- Yokohama City University, Kanazawa-ku, Yokohama, Japan 236-0027
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan 710-0046
- Corresponding author: Email, ; Fax, +81-45-503-9182
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Takashi Hirayama
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan 710-0046
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