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Kamimukai M, Rana BB, Bhattarai M, Murai M. Effects of dwarfing allele sd1-d originating from 'Dee-geo-woo-gen' and its tall alleles SD1-in and SD1-ja on morphological characteristics concerning dry-matter production and photosynthesis on the genetic background of indica-rice IR36. BREEDING SCIENCE 2022; 72:316-325. [PMID: 36699822 PMCID: PMC9868333 DOI: 10.1270/jsbbs.22016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/26/2022] [Indexed: 06/17/2023]
Abstract
sd1-d has been utilized to develop short-culmed indica varieties adaptable to higher fertilizer-applications. Its tall alleles SD1-in and SD1-ja are harbored in indica and japonica subspecies, respectively. SD1-in possesses a higher effect on elongating culm than SD1-ja. The sd1-d of indica IR36 was substituted with SD1-in or SD1-ja through recurrent backcrossing with IR36, and two tall isogenic lines ("5867-36" and "Koshi-36") were developed. IR36, 5867-36 and Koshi-36 were grown in a paddy field, and the effects of sd1-d, SD1-in and SD1-ja on morphological characteristics concerning dry-matter production and photosynthesis were compared mutually. sd1-d diminished dry weight of total brown rice/m2 and total dry matter weights, but enhanced harvest indexes, compared with SD1-in. In IR36, shorter lengths of the first (flag) to third leaves, and more panicle-bearing stems, caused by sd1-d, compared with SD1-in-carrying 5867-36, and erect first leaves, not caused by sd1-d, could construct the canopy structure appropriate for obtaining a high rate of photosynthesis at an optimum LAI. Koshi-36 could be used for a mid-mother line to develop indica varieties adaptable to middle and low fertilizer-applications, due to higher effect of SD1-ja on yielding ability, compared with that of sd1-d, no breaking-type lodging, and resistances to diseases and pests.
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Affiliation(s)
- Misa Kamimukai
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan
| | | | - Mukunda Bhattarai
- National Agricultural Genetic Resource Center (Genebank), Nepal Agriculture Research Council (NARC), Khumltar, Lalitpur, Kathmandu, Nepal
| | - Masayuki Murai
- Emeritus Professor of Kochi University, 201 Higashino, Noichi-cho, Konan, Kochi 781-5213, Japan
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Rana BB, Kamimukai M, Bhattarai M, Rana L, Matsumoto A, Nagano H, Oue H, Murai M. Effects of tall alleles SD1-in and SD1-ja to the dwarfing allele sd1-d originating from 'Dee-geo-woo-gen' on yield and related traits on the genetic background of indica IR36 in rice. BREEDING SCIENCE 2021; 71:334-343. [PMID: 34776740 PMCID: PMC8573555 DOI: 10.1270/jsbbs.21001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/09/2021] [Indexed: 06/13/2023]
Abstract
sd1-d originating from 'Dee-geo-woo-gen' has been utilized to develop short-culmed indica varieties adaptable to higher fertilizer-application. Its tall alleles SD1-in and SD1-ja are harbored in indica and japonica subspecies, respectively. The sd1-d of indica IR36 was substituted with SD1-in or SD1-ja by recurrent backcrossing with IR36, and two tall isogenic lines ("5867-36" and "Koshi-36") were developed. IR36, 5867-36 and Koshi-36 were grown in a paddy field in three years, and yield and related traits were measured, the effects of SD1-in and SD1-ja on yielding ability and related characteristics were examined on the genetic background of IR 36. SD1-in decreased panicle number per m2 but increased spikelet number per panicle, ripened-grain percentage and 1000-grain weight, compared with sd1-d, resulting in the increase of yield. The increase of 1000-grain weight by SD1-in, caused by the increases of length, width and thickness of grain, was due to the increases of the length and width of lemma. SD1-ja did not significantly affect yield, mainly because the decrease of panicle number per m2 was compensated by the enlarged 1000-grain weight owing to the increase of lemma length. Serious lodging was observed in long-culmed 5867-36, suggesting that sd1-d is indispensable for indica breeding programs.
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Affiliation(s)
| | - Misa Kamimukai
- The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Mukunda Bhattarai
- Nepal Agriculture Research Council (NARC), Khumaltar, Lalitpur, Kathmandu, Nepal
- The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Lokendra Rana
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Ayaka Matsumoto
- Faculty of Agriculture and Marine Science, Kochi University, 200 Otsu, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Hironori Nagano
- Field Science Center for Northern Biosphere, Hokkaido University, Kita 11, Nishi 10, Kita-ku, Sapporo, Hokkaido 060-0810, Japan
| | - Hiroki Oue
- The United Graduate School of Agricultural Sciences, Ehime University, 3-5-7 Tarumi, Matsuyama, Ehime 790-8566, Japan
| | - Masayuki Murai
- Emeritus Professor of Kochi University, Faculty of Agriculture and Marine Science, Kochi University, Nankoku, Kochi 783-8502, Japan
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Khlestkina EK, Shvachko NA, Zavarzin AA, Börner A. Vavilov’s Series of the “Green Revolution” Genes. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420110046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bhuvaneswari S, Gopala Krishnan S, Ellur RK, Vinod KK, Bollinedi H, Bhowmick PK, Bansal VP, Nagarajan M, Singh AK. Discovery of a Novel Induced Polymorphism in SD1 Gene Governing Semi-Dwarfism in Rice and Development of a Functional Marker for Marker-Assisted Selection. PLANTS 2020; 9:plants9091198. [PMID: 32937792 PMCID: PMC7570060 DOI: 10.3390/plants9091198] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/31/2020] [Accepted: 09/07/2020] [Indexed: 11/16/2022]
Abstract
The semi-dwarfing allele, sd1-d, has been widely utilized in developing high-yielding rice cultivars across the world. Originally identified from the rice cultivar Dee-Geo-Woo-Gen (DGWG), sd1-d, derived from a spontaneous mutation, has a 383-bp deletion in the SD1 gene. To date, as many as seven alleles of the SD1 gene have been identified and used in rice improvement, either with a functional single-nucleotide polymorphism (SNP), with insertion–deletions (InDels), or both. Here, we report discovery of a novel SNP in the SD1 gene from the rice genotype, Pusa 1652. Genetic analysis revealed that the inheritance of the semi-dwarfism in Pusa 1652 is monogenic and recessive, but it did not carry the sd1-d allele. However, response to exogenous gibberellic acid (GA3) application and the subsequent bulked segregant and linkage analyses confirmed that the SD1 gene is involved in the plant height reduction in Pusa 1652. Sequencing of the SD1 gene from Pusa 1652 revealed a novel transition in exon 3 (T/A) causing a nonsense mutation at the 300th codon. The stop codon leads to premature termination, resulting in a truncated protein of OsGA20ox2 obstructing the GA3 biosynthesis pathway. This novel recessive allele, named sd1-bm, is derived from Bindli Mutant 34 (BM34), a γ-ray induced mutant of a short-grain aromatic landrace, Bindli. BM34 is the parent of an aromatic semi-dwarf cultivar, Pusa 1176, from which Pusa 1652 is derived. The semi-dwarfing allele, sd1-bm, was further validated by developing a derived cleaved amplified polymorphic sequence (dCAPS) marker, AKS-sd1. This allele provides an alternative to the most widely used sd1-d in rice improvement programs and the functional dCAPS marker will facilitate marker-assisted introgression of the semi-dwarf trait into tall genotypes.
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Affiliation(s)
- Shivashankar Bhuvaneswari
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
- Division of Plant Breeding, ICAR RC NEH Region, Manipur Centre, Imphal 795004, Manipur, India
| | - Subbaiyan Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Ranjith Kumar Ellur
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Kunnummal Kurungara Vinod
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Haritha Bollinedi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Prolay Kumar Bhowmick
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Vijay Prakash Bansal
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
| | - Mariappan Nagarajan
- Rice Breeding and Genetics Research Centre, ICAR- Indian Agricultural Research Institute, Aduthurai 612101, Tamil Nadu, India;
| | - Ashok Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, Delhi, India; (S.B.); (S.G.K.); (R.K.E.); (K.K.V.); (H.B.); (P.K.B.); (V.P.B.)
- Correspondence: ; Tel.: +91-11-2584-3375
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Jia X, Yu L, Tang M, Tian D, Yang S, Zhang X, Traw MB. Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice. JOURNAL OF PLANT PHYSIOLOGY 2020; 248:153141. [PMID: 32143117 DOI: 10.1016/j.jplph.2020.153141] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 02/10/2020] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
The "Green Revolution" that dramatically reduced cultivar heights and sharply boosted rice production mid-century was achieved in large part through introgression of defective alleles of Semi-Dwarf 1 (SD1), which encodes a GA20ox oxidase involved in the final steps of the synthesis of bioactive gibberellin in rice. Here, we ask whether converting the defective sd1 version in a modern semi-dwarf cultivar back to wild-type SD1 in situ recovers ancestral plant traits, and more broadly, what it reveals about pleiotropic effects of this gene. We assess these effects of SD1 restoration in three independent recombinant lines recovered from F2 progeny of a cross between 93-11 and PA64s. We then used RNA-seq to dissect gene network changes that accompanied SD1 restoration. We report that this in situ restoration of wild-type SD1 nearly doubles plant height, increases total grain yield per panicle, and elongates the second-leaf length. Comparison of expression profiles reveals changes in key nodes of the gibberellin pathway, such as OsKO1 and OsGA2ox3, and more broadly in genes related to metabolic networks, defense response, and catabolic processes. Two JA-induced genes, RIR1b and OsPR1b, are extremely down-regulated after SD1 restoration, suggesting that SD1 restoration alters the balance between GA and JA to plant growth, at the cost of degrading the defense response. This in situ approach at the SD1 locus also provides a model example that is applicable to other systems and will further understanding of gene networks underlying high-yield traits in crops.
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Affiliation(s)
- Xianqing Jia
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Luyao Yu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Menglu Tang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Dacheng Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - M Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Genomics and expression analysis of DHHC-cysteine-rich domain S-acyl transferase protein family in apple. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0393-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Dockter C, Hansson M. Improving barley culm robustness for secured crop yield in a changing climate. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:3499-509. [PMID: 25614659 DOI: 10.1093/jxb/eru521] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The Green Revolution combined advancements in breeding and agricultural practice, and provided food security to millions of people. Daily food supply is still a major issue in many parts of the world and is further challenged by future climate change. Fortunately, life science research is currently making huge progress, and the development of future crop plants will be explored. Today, plant breeding typically follows one gene per trait. However, new scientific achievements have revealed that many of these traits depend on different genes and complex interactions of proteins reacting to various external stimuli. These findings open up new possibilities for breeding where variations in several genes can be combined to enhance productivity and quality. In this review we present an overview of genes determining plant architecture in barley, with a special focus on culm length. Many genes are currently known only through their mutant phenotypes, but emerging genomic sequence information will accelerate their identification. More than 1000 different short-culm barley mutants have been isolated and classified in different phenotypic groups according to culm length and additional pleiotropic characters. Some mutants have been connected to deficiencies in biosynthesis and reception of brassinosteroids and gibberellic acids. Still other mutants are unlikely to be connected to these hormones. The genes and corresponding mutations are of potential interest for development of stiff-straw crop plants tolerant to lodging, which occurs in extreme weather conditions with strong winds and heavy precipitation.
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Affiliation(s)
- Christoph Dockter
- Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK- Copenhagen V, Denmark.
| | - Mats Hansson
- Department of Biology, Lund University, Sölvegatan 35, SE-22362 Lund, Sweden
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