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Badri J, Padmashree R, Anilkumar C, Mamidi A, Isetty SR, Swamy AVSR, Sundaram RM. Genome-wide association studies for a comprehensive understanding of the genetic architecture of culm strength and yield traits in rice. FRONTIERS IN PLANT SCIENCE 2024; 14:1298083. [PMID: 38317832 PMCID: PMC10839031 DOI: 10.3389/fpls.2023.1298083] [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: 09/21/2023] [Accepted: 12/14/2023] [Indexed: 02/07/2024]
Abstract
Lodging resistance in rice is a complex trait determined by culm morphological and culm physical strength traits, and these traits are a major determinant of yield. We made a detailed analysis of various component traits with the aim of deriving optimized parameters for measuring culm strength. Genotyping by sequencing (GBS)-based genome-wide association study (GWAS) was employed among 181 genotypes for dissecting the genetic control of culm strength traits. The VanRaden kinship algorithm using 6,822 filtered single-nucleotide polymorphisms (SNPs) revealed the presence of two sub-groups within the association panel with kinship values concentrated at<0.5 level, indicating greater diversity among the genotypes. A wide range of phenotypic variation and high heritability for culm strength and yield traits were observed over two seasons, as reflected in best linear unbiased prediction (BLUP) estimates. The multi-locus model for GWAS resulted in the identification of 15 highly significant associations (p< 0.0001) for culm strength traits. Two novel major effect marker-trait associations (MTAs) for section modulus and bending stress were identified on chromosomes 2 and 12 with a phenotypic variance of 21.87% and 10.14%, respectively. Other MTAs were also noted in the vicinity of previously reported putative candidate genes for lodging resistance, providing an opportunity for further research on the biochemical basis of culm strength. The quantitative trait locus (QTL) hotspot identified on chromosome 12 with the synergistic association for culm strength trait (section modulus, bending stress, and internode breaking weight) and grain number can be considered a novel genomic region that can serve a dual purpose of enhancing culm strength and grain yield. Elite donors in the indica background with beneficial alleles of the identified major QTLs could be a valuable resource with greater significance in practical plant breeding programs focusing on improving lodging resistance in rice.
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Affiliation(s)
- Jyothi Badri
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Revadi Padmashree
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Chandrappa Anilkumar
- Crop Improvement Section, ICAR-National Rice Research Institute (ICAR-NRRI), Cuttack, India
| | - Akshay Mamidi
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
- Department of Genetics and Plant Breeding, College of Agriculture, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Subhakara Rao Isetty
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - AVSR Swamy
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
| | - Raman Menakshi Sundaram
- Crop Improvement Section, ICAR-Indian Institute of Rice Research (ICAR-IIRR), Hyderabad, India
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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: 0] [Impact Index Per Article: 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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Wang C, Feng X, Yuan Q, Lin K, Zhang X, Yan L, Nan J, Zhang W, Wang R, Wang L, Xue Q, Yang X, Liu Z, Lin S. Upgrading the genome of an elite japonica rice variety Kongyu 131 for lodging resistance improvement. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:419-432. [PMID: 36382925 PMCID: PMC9884016 DOI: 10.1111/pbi.13963] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 10/08/2022] [Accepted: 11/10/2022] [Indexed: 06/16/2023]
Abstract
Developing a new rice variety requires tremendous efforts and years of input. To improve the defect traits of the excellent varieties becomes more cost and time efficient than breeding a completely new variety. Kongyu 131 is a high-performing japonica variety with early maturity, high yield, wide adaptability and cold resistance, but the poor-lodging resistance hinders the industrial production of Kongyu 131 in the Northeastern China. In this study, we attempted to improve the lodging resistance of Kongyu 131 from perspectives of both gene and trait. On the one hand, by QTL analysis and fine mapping we discovered the candidate gene loci. The following CRISPR/Cas9 and transgenic complementation study confirmed that Sd1 dominated the lodging resistance and favourable allele was mined for precise introduction and improvement. On the other hand, the Sd1 allelic variant was identified in Kongyu 131 by sequence alignment, then introduced another excellent allelic variation by backcrossing. Then, the two new resulting Kongyu 131 went through the field evaluation under different environments, planting densities and nitrogen fertilizer conditions. The results showed that the plant height of upgraded Kongyu 131 was 17%-26% lower than Kongyu 131 without penalty in yield. This study demonstrated a precise and targeted way to update the rice genome and upgrade the elite rice varieties by improving only a few gene defects from the perspective of breeding.
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Affiliation(s)
- Chen Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Xiaomin Feng
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhouChina
| | - Qingbo Yuan
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Kangxue Lin
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Xiaohui Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Li Yan
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Jianzong Nan
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Wenqi Zhang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Rongsheng Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Lihong Wang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Qian Xue
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Xiaowen Yang
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
| | - Zhixia Liu
- Rice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhouChina
- Guangdong Key Laboratory of New Technology in Rice BreedingGuangzhouChina
| | - Shaoyang Lin
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental Biology, Chinese Academy of SciencesBeijingChina
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Chigira K, Yamasaki M, Adachi S, Nagano AJ, Ookawa T. Identification of Novel Quantitative Trait Loci for Culm Thickness of Rice Derived from Strong-Culm Landrace in Japan, Omachi. RICE (NEW YORK, N.Y.) 2023; 16:4. [PMID: 36705856 PMCID: PMC9883377 DOI: 10.1186/s12284-023-00621-8] [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: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Increasing the lodging resistance of rice through genetic improvement has been an important target in breeding. To further enhance the lodging resistance of high-yielding rice varieties amidst climate change, it is necessary to not only shorten culms but strengthen them as well. A landrace rice variety, Omachi, which was established more than 100 years ago, has the largest culm diameter and bending moment at breaking in the basal internodes among 135 temperate japonica accessions. Using unused alleles in such a landrace is an effective way to strengthen the culm. In this study, we performed quantitative trait locus (QTL) analysis to identify the genetic factors of culm strength of Omachi using recombinant inbred lines (RILs) derived from a cross between Omachi and Koshihikari, a standard variety in Japan. We identified three QTLs for the culm diameter of the 5th internode on chromosomes 3 (qCD3) and 7 (qCD7-1, qCD7-2). Among them, qCD7-2 was verified by QTL analysis using the F2 population derived from a cross between one of the RILs and Koshihikari. RNA-seq analysis of shoot apex raised 10 candidate genes underlying the region of qCD7-2. The increase in culm strength by accumulating Omachi alleles of qCD3, qCD7-1 and qCD7-2 was 25.0% in 2020. These QTLs for culm diameter pleiotropically increased spikelet number per panicle but did not affect days to heading or culm length. These results suggest that the Omachi alleles of qCD3, qCD7-1 and qCD7-2 are useful for breeding to increase lodging resistance and yield.
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Affiliation(s)
- Koki Chigira
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Masanori Yamasaki
- Graduate School of Science and Technology, Niigata University, 8050 Ikarashi 2-no-cho, Nishi-Ku, Niigata City, Niigata 950-2181 Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
| | - Atsushi J. Nagano
- Faculty of Agriculture, Ryukoku University, 1-5 Yokotani, Seta Oe-cho, Otsu, Shiga 520-2194 Japan
- Institute for Advanced Biosciences, Keio University, 403-1 Nipponkoku, Daihouji, Tsuruoka, Yamagata 997-0017 Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509 Japan
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Lodging resistance of rice plants studied from the perspective of culm mechanical properties, carbon framework, free volume, and chemical composition. Sci Rep 2022; 12:20026. [PMID: 36414706 PMCID: PMC9681888 DOI: 10.1038/s41598-022-24714-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 11/18/2022] [Indexed: 11/23/2022] Open
Abstract
In this study, four varieties of rice were cultivated on the same farmland under same conditions and for same duration. However, their lodging resistance was found to be obviously different from each other. Herein, three key factors that highly influenced the lodging resistance were identified. First, in terms of morphological trait, in contrast to the generally believed theory that the overall thickness of the fresh culm wall governs the strength, the thickness of the depressed region of the dried basal culm wall largely determined the mechanical properties by acting as the weak link. This depressed region represents the vulnerable part with high syneresis rate. Second, the culm and its carbon framework exhibited sufficient strength and rigidity for both support and stability of the rice stem. The constraint of high lodging resistance of rice plants is attributed to the culm flexibility. Furthermore, the results of the positron annihilation lifetime spectroscopy corroborate that the most amorphous part and the highest-fraction free volume in the culm carbon framework were found for samples that exhibited high lodging resistance. This result confirmed the significant influence of the culm flexibility on lodging resistance. Third, a higher level of nitrogen element content in the basal culm can benefit its growth and development, which may contribute to an increase in lodging resistance of rice plants.
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Miyagi A, Mori K, Ishikawa T, Ohkubo S, Adachi S, Yamaguchi M, Ookawa T, Kotake T, Kawai-Yamada M. Metabolomic analysis of rice brittle culm mutants reveals each mutant- specific metabolic pattern in each organ. Metabolomics 2022; 18:95. [PMID: 36409428 DOI: 10.1007/s11306-022-01958-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 11/11/2022] [Indexed: 11/22/2022]
Abstract
INTRODUCTION Plant cell walls play an important role in providing physical strength and defence against abiotic stress. Rice brittle culm (bc) mutants are a strength-decreased mutant because of abnormal cell walls, and it has been reported that the causative genes of bc mutants affect cell wall composition. However, the metabolic alterations in each organ of bc mutants have remained unknown. OBJECTIVES To evaluate the metabolic changes in rice bc mutants, comparative analysis of the primary metabolites was conducted. METHODS The primary metabolites in leaves, internodes, and nodes of rice bc mutants and wild-type control were measured using CE- and LC-MS/MS. Multivariate analyses using metabolomic data was performed. RESULTS We found that mutations in each bc mutant had different effects on metabolism. For example, higher oxalate content was observed in bc3 and bc1 bc3 mutants, suggesting that surplus carbon that was not used for cell wall components might be used for oxalate synthesis. In addition, common metabolic alterations such as a decrease of sugar nucleotides in nodes were found in bc1 and Bc6, in which the causative genes are involved in cellulose accumulation. CONCLUSION These results suggest that metabolic analysis of the bc mutants could elucidate the functions of causative gene and improve the cell wall components for livestock feed or bioethanol production.
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Affiliation(s)
- Atsuko Miyagi
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama, 338-8570, Japan.
- Faculty of Agriculture, Yamagata University, 1-23 Wakaba-Machi, Tsuruoka, Yamagata, 997-8555, Japan.
| | - Kazuhisa Mori
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama, 338-8570, Japan
| | - Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama, 338-8570, Japan
| | - Satoshi Ohkubo
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3‑5‑8 Saiwai‑cho, Fuchu-City, Tokyo, 183‑8509, Japan
- Graduate School of Life Sciences, Tohoku University, 2-1-1 Katahira, Aoba-Ku, Sendai-City, Miyagi, 980-8577, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3‑5‑8 Saiwai‑cho, Fuchu-City, Tokyo, 183‑8509, Japan
| | - Masatoshi Yamaguchi
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama, 338-8570, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3‑5‑8 Saiwai‑cho, Fuchu-City, Tokyo, 183‑8509, Japan
| | - Toshihisa Kotake
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama, 338-8570, Japan
| | - Maki Kawai-Yamada
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-Ku, Saitama-City, Saitama, 338-8570, Japan.
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Ookawa T, Nomura T, Kamahora E, Jiang M, Ochiai Y, Samadi AF, Yamaguchi T, Adachi S, Katsura K, Motobayashi T. Pyramiding of multiple strong-culm genes originating from indica and tropical japonica to the temperate japonica rice. Sci Rep 2022; 12:15400. [PMID: 36100633 PMCID: PMC9470567 DOI: 10.1038/s41598-022-19768-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 09/05/2022] [Indexed: 11/16/2022] Open
Abstract
Severe lodging has recurrently occurred at strong typhoon’s hitting in recent climate change. The identification of quantitative trait loci and their responsible genes associated with a strong culm and their pyramiding are important for developing high-yielding varieties with a superior lodging resistance. To evaluate the effects of four strong-culm genes on lodging resistance, the temperate japonica near isogenic line (NIL) with the introgressed SCM1 or SCM2 locus of the indica variety, Habataki and the other NIL with the introgeressed SCM3 or SCM4 locus of the tropical japonica variety, Chugoku 117 were developed. Then, we developed the pyramiding lines with double,triple and quadruple combinations derived from step-by-step crosses among NIL-SCM1–NIL-SCM4. Quadruple pyramiding line (NIL-SCM1 + 2 + 3 + 4) showed the largest culm diameter and the highest culm strength among the combinations and increased spikelet number due to the pleiotropic effects of these genes. Pyramiding of strong culm genes resulted in much increased culm thickness, culm strength and spikelet number due to their additive effect. SCM1 mainly contributed to enhance their pyramiding effect. These results in this study suggest the importance of identifying the combinations of superior alleles of strong culm genes among natural variation and pyramiding these genes for improving high-yielding varieties with a superior lodging resistance.
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Affiliation(s)
- Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan.
| | - Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Eri Kamahora
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Mingjin Jiang
- Rice Research Institute of Guizhou Academy of Agricultural Science, Guiyang, 550006, Guizhou, China
| | - Yusuke Ochiai
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Ahmad Fahim Samadi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takuya Yamaguchi
- Toyama Prefectural Tonami Agriculture and Forestry Promotion Center, 1-7 Saiwai-cho, Tonami, Toyama, 939-1386, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Keisuke Katsura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
| | - Takashi Motobayashi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, 3-5-8 Saiwai-cho, Fuchu, Tokyo, 183-8509, Japan
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Rashid MAR, Zhao Y, Azeem F, Zhao Y, Ahmed HGMD, Atif RM, Pan Y, Zhu X, Liang Y, Zhang H, Li D, Zhang Z, Li Z. Unveiling the genetic architecture for lodging resistance in rice ( Oryza sativa. L) by genome-wide association analyses. Front Genet 2022; 13:960007. [PMID: 36147492 PMCID: PMC9486067 DOI: 10.3389/fgene.2022.960007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 07/06/2022] [Indexed: 11/13/2022] Open
Abstract
Lodging is one of the major abiotic stresses, affecting the total crop yield and quality. The improved lodging resistance and its component traits potentially reduce the yield losses. The section modulus (SM), bending moment at breaking (M), pushing resistance (PR), and coefficient of lodging resistance (cLr) are the key elements to estimate the lodging resistance. Understanding the genetic architecture of lodging resistance-related traits will help to improve the culm strength and overall yield potential. In this study, a natural population of 795 globally diverse genotypes was further divided into two (indica and japonica) subpopulations and was used to evaluate the lodging resistance and culm strength-related traits. Significant diversity was observed among the studied traits. We carried out the genome-wide association evaluation of four lodging resistance traits with 3.3 million deep resolution single-nucleotide polymorphic (SNP) markers. The general linear model (GLM) and compressed mixed linear model (MLM) were used for the whole population and two subpopulation genome-wide association studies (GWAS), and a 1000-time permutation test was performed to remove the false positives. A total of 375 nonredundant QTLs were observed for four culm strength traits on 12 chromosomes of the rice genome. Then, 33 pleiotropic loci governing more than one trait were mined. A total of 4031 annotated genes were detected within the candidate genomic region of 33 pleiotropic loci. The functional annotations and metabolic pathway enrichment analysis showed cellular localization and transmembrane transport as the top gene ontological terms. The in silico and in vitro expression analyses were conducted to validate the three candidate genes in a pleiotropic QTL on chromosome 7. It validated OsFBA2 as a candidate gene to contribute to lodging resistance in rice. The haplotype analysis for the candidate gene revealed a significant functional variation in the promoter region. Validation and introgression of alleles that are beneficial to induce culm strength may be used in rice breeding for lodging resistance.
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Affiliation(s)
- Muhammad Abdul Rehman Rashid
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Yong Zhao
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Farrukh Azeem
- Department of Bioinformatics and Biotechnology, Government College University Faisalabad, Faisalabad, Pakistan
| | - Yan Zhao
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- College of Agronomy, Shandong Agricultural University, Tai’an, China
| | | | - Rana Muhammad Atif
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad, Pakistan
- Precision Agriculture and Analytics Lab, National Centre in Big Data and Cloud Computing, Centre for Advanced Studies in Agriculture and Food Security, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Yinghua Pan
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Xiaoyang Zhu
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yuntao Liang
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Hongliang Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Danting Li
- Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning, China
| | - Zhanying Zhang
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zichao Li
- State Key Laboratory of Agrobiotechnology/Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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9
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Dreccer MF, Macdonald B, Farnsworth CA, Paccapelo MV, Awasi MA, Condon AG, Forrest K, Lee Long I, McIntyre CL. Multi-donor × elite-based populations reveal QTL for low-lodging wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1685-1703. [PMID: 35312799 PMCID: PMC9110543 DOI: 10.1007/s00122-022-04063-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 02/12/2022] [Indexed: 05/15/2023]
Abstract
Low-lodging high-yielding wheat germplasm and SNP-tagged novel alleles for lodging were identified in a process that involved selecting donors through functional phenotyping for underlying traits with a designed phenotypic screen, and a crossing strategy involving multiple-donor × elite populations. Lodging is a barrier to achieving high yield in wheat. As part of a study investigating the potential to breed low-lodging high-yielding wheat, populations were developed crossing four low-lodging high-yielding donors selected based on lodging related traits, with three cultivars. Lodging was evaluated in single rows in an early generation and subsequently in plots in 2 years with contrasting lodging environment. A large number of lines lodged less than their recurrent parents, and some were also higher yielding. Heritability for lodging was high, but the genetic correlation between contrasting environments was intermediate-low. Lodging genotypic rankings in single rows did not correlate well with plots. Populations from the highest lodging background were genotyped (90 K iSelect BeadChip array). Fourteen markers on nine chromosomes were associated with lodging, differing under high- versus low-lodging conditions. Of the fourteen markers, ten were found to co-locate with previously identified QTL for lodging-related traits or at homoeologous locations for previously identified lodging-related QTL, while the remaining four markers (in chromosomes 2D, 4D, 7B and 7D) appear to map to novel QTL for lodging. Lines with more favourable markers lodged less, suggesting value in these markers as a selection tool. This study demonstrates that the combination of donor functional phenotyping, screen design and crossing strategy can help identify novel alleles in germplasm without requiring extensive bi-parental populations.
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Affiliation(s)
- M Fernanda Dreccer
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia.
| | - Bethany Macdonald
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Claire A Farnsworth
- CSIRO Cooper Laboratory, University of Queensland Gatton Campus, Gatton, QLD, 4343, Australia
| | - M Valeria Paccapelo
- Department of Agriculture and Fisheries, Leslie Research Facility, Toowoomba, QLD, 4350, Australia
| | - Mary Anne Awasi
- CSIRO Cooper Laboratory, University of Queensland Gatton Campus, Gatton, QLD, 4343, Australia
| | - Anthony G Condon
- CSIRO Agriculture and Food, Building 101, Clunies Ross Street, Black Mountain, ACT, 2600, Australia
| | - Kerrie Forrest
- Agriculture Victoria Research, Department of Jobs, Precincts and Regions, Agribio, 5 Ring Rd., Bundoora, VIC, 3083, Australia
| | - Ian Lee Long
- CSIRO Cooper Laboratory, University of Queensland Gatton Campus, Gatton, QLD, 4343, Australia
| | - C Lynne McIntyre
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, Saint Lucia, QLD, 4067, Australia
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10
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Zhang B, Ma L, Wu B, Xing Y, Qiu X. Introgression Lines: Valuable Resources for Functional Genomics Research and Breeding in Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2022; 13:863789. [PMID: 35557720 PMCID: PMC9087921 DOI: 10.3389/fpls.2022.863789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/01/2022] [Indexed: 05/14/2023]
Abstract
The narrow base of genetic diversity of modern rice varieties is mainly attributed to the overuse of the common backbone parents that leads to the lack of varied favorable alleles in the process of breeding new varieties. Introgression lines (ILs) developed by a backcross strategy combined with marker-assisted selection (MAS) are powerful prebreeding tools for broadening the genetic base of existing cultivars. They have high power for mapping quantitative trait loci (QTLs) either with major or minor effects, and are used for precisely evaluating the genetic effects of QTLs and detecting the gene-by-gene or gene-by-environment interactions due to their low genetic background noise. ILs developed from multiple donors in a fixed background can be used as an IL platform to identify the best alleles or allele combinations for breeding by design. In the present paper, we reviewed the recent achievements from ILs in rice functional genomics research and breeding, including the genetic dissection of complex traits, identification of elite alleles and background-independent and epistatic QTLs, analysis of genetic interaction, and genetic improvement of single and multiple target traits. We also discussed how to develop ILs for further identification of new elite alleles, and how to utilize IL platforms for rice genetic improvement.
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Affiliation(s)
- Bo Zhang
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Bi Wu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xianjin Qiu
- College of Agriculture, Yangtze University, Jingzhou, China
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11
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Muszynska A, Guendel A, Melzer M, Tandron Moya YA, Röder MS, Rolletschek H, Rutten T, Munz E, Melz G, Ortleb S, Borisjuk L, Börner A. A mechanistic view on lodging resistance in rye and wheat: a multiscale comparative study. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:2646-2661. [PMID: 34449959 PMCID: PMC8633492 DOI: 10.1111/pbi.13689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 07/10/2021] [Accepted: 08/22/2021] [Indexed: 05/12/2023]
Abstract
The development of crop varieties that are resistant to lodging is a top priority for breeding programmes. Herein, we characterize the rye mutant ´Stabilstroh' ('stable straw') possessing an exceptional combination of high lodging resistance, tall posture and high biomass production. Nuclear magnetic resonance imaging displayed the 3-dimensional assembly of vascular bundles in stem. A higher number of vascular bundles and a higher degree of their incline were the features of lodging-resistant versus lodging-prone lines. Histology and electron microscopy revealed that stems are fortified by a higher proportion of sclerenchyma and thickened cell walls, as well as some epidermal invaginations. Biochemical analysis using Fourier-transform infrared spectroscopy and inductively coupled plasma-optical emission spectrometry further identified elevated levels of lignin, xylan, zinc and silicon as features associated with high lodging resistance. Combined effects of above features caused superior culm stability. A simplistic mathematical model showed how mechanical forces distribute within the stem under stress. Main traits of the lodging-resistant parental line were heritable and could be traced back to the genetic structure of the mutant. Evaluation of lodging-resistant wheat 'Babax' ('Baviacora') versus contrasting, lodging-prone, genotype ´Pastor´ agreed with above findings on rye. Our findings on mechanical stability and extraordinary culm properties may be important for breeders for the improvement of lodging resistance of tall posture cereal crops.
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Affiliation(s)
- Aleksandra Muszynska
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Andre Guendel
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Michael Melzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | | | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Hardy Rolletschek
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Twan Rutten
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Eberhard Munz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
- Institute of Experimental Physics 5University of WürzburgWürzburgGermany
| | | | - Stefan Ortleb
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Ljudmilla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Stadt SeelandGermany
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12
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Kashima M, Sakamoto RL, Saito H, Ohkubo S, Tezuka A, Deguchi A, Hashida Y, Kurita Y, Iwayama K, Adachi S, Nagano AJ. Genomic Basis of Transcriptome Dynamics in Rice under Field Conditions. PLANT & CELL PHYSIOLOGY 2021; 62:1436-1445. [PMID: 34131748 PMCID: PMC8600290 DOI: 10.1093/pcp/pcab088] [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: 02/15/2021] [Revised: 05/09/2021] [Accepted: 06/15/2021] [Indexed: 05/07/2023]
Abstract
How genetic variations affect gene expression dynamics of field-grown plants remains unclear. Expression quantitative trait loci (eQTL) analysis is frequently used to find genomic regions underlying gene expression polymorphisms. This approach requires transcriptome data for the complete set of the QTL mapping population under the given conditions. Therefore, only a limited range of environmental conditions is covered by a conventional eQTL analysis. We sampled sparse time series of field-grown rice from chromosome segment substitution lines (CSSLs) and conducted RNA sequencing (RNA-Seq). Then, by using statistical analysis integrating meteorological data and the RNA-Seq data, we identified 1,675 eQTLs leading to polymorphisms in expression dynamics under field conditions. A genomic region on chromosome 11 influences the expression of several defense-related genes in a time-of-day- and scaled-age-dependent manner. This includes the eQTLs that possibly influence the time-of-day- and scaled-age-dependent differences in the innate immunity between Koshihikari and Takanari. Based on the eQTL and meteorological data, we successfully predicted gene expression under environments different from training environments and in rice cultivars with more complex genotypes than the CSSLs. Our novel approach of eQTL identification facilitated the understanding of the genetic architecture of expression dynamics under field conditions, which is difficult to assess by conventional eQTL studies. The prediction of expression based on eQTLs and environmental information could contribute to the understanding of plant traits under diverse field conditions.
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Affiliation(s)
- Makoto Kashima
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | | | - Hiroki Saito
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyo-ku, Kyoto 606-8317, Japan
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Maezato 1091-1, Ishigaki, Okinawa 907-0002, Japan
| | - Satoshi Ohkubo
- Graduate School of Agriculture, Kyoto University, Kitashirakawa-oiwake, Sakyo-ku, Kyoto 606-8317, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo 183-8509, Japan
| | - Ayumi Tezuka
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Ayumi Deguchi
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Yoichi Hashida
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Yuko Kurita
- Research Institute for Food and Agriculture, Ryukoku University, Yokotani 1-5, Seta Oe-cho, Otsu, Shiga 520-2194, Japan
| | - Koji Iwayama
- Faculty of Data Science, Shiga University, Bamba 1-1-1, Hikone, Shiga 522-0069, Japan
| | - Shunsuke Adachi
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Saiwaicho 3-5-8, Fuchu, Tokyo 183-8509, Japan
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13
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Potupureddi G, Balija V, Ballichatla S, C. G. G, Awalellu K, Lekkala S, Jallipalli K, M. G. G, Mohammad E, M M, Arutla S, Burka R, Gouri Shankar L, Ayyangari Phani P, Lella Venkata S, Raman Meenakshi S, B. C. V, Vemuri RB, Brahma K, Madnala R, Patel HK, Sonti RV, Madhav MS. Mutation resource of Samba Mahsuri revealed the presence of high extent of variations among key traits for rice improvement. PLoS One 2021; 16:e0258816. [PMID: 34669755 PMCID: PMC8528289 DOI: 10.1371/journal.pone.0258816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 10/05/2021] [Indexed: 11/18/2022] Open
Abstract
To create novel variants for morphological, physiological, and biotic stress tolerance traits, induced mutations were created using Ethyl Methane Sulphonate (EMS) in the background of Samba Mahsuri (BPT 5204), a popular and mega rice variety of India. A population derived from 10, 500 M1 plants and their descendants were phenotyped for a wide range of traits leading to the identification of 124 mutants having variations in key agro-morphological traits, and 106 mutants exhibiting variation for physiological traits. Higher yield is the ultimate goal of crop improvement and we identified 574 mutants having higher yield compared to wild type by having better yield attributing traits. Further, a total of 50 mutants showed better panicle exertion phenotypes as compared to Samba Mahsuri leading to enhancement of yield. Upon rigorous screening for three major biotic stresses, 8 mutants showed enhanced tolerance for yellow stem borer (YSB), and 13 different mutants each showed enhanced tolerance for sheath blight (ShB) and bacterial leaf blight (BLB), respectively. In addition, screening at multiple locations that have diverse field isolates identified 3, 3, and 5 lines for tolerance to ShB, YSB and BLB, respectively. On the whole, 1231 desired mutant lines identified at M2 were forwarded to an advanced generation (M5). PCR based allele mining indicated that the BLB tolerant mutants have a different allele than the reported alleles for well-known genes affecting bacterial blight resistance. Whole genome re-sequencing revealed substantial variation in comparison to Samba Mahsuri. The lines showing enhanced tolerance to important biotic stresses (YSB, ShB and BLB) as well as several economically important traits are unique genetic resources which can be utilized for the identification of novel genes/alleles for different traits. The lines which have better agronomic features can be used as pre-breeding lines. The entire mutant population is maintained as a national resource for genetic improvement of the rice crop.
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Affiliation(s)
- Gopi Potupureddi
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Vishalakshi Balija
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Suneel Ballichatla
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Gokulan C. G.
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Komal Awalellu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Swathi Lekkala
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Karteek Jallipalli
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Gayathri M. G.
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Ershad Mohammad
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Milton M
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Srikanth Arutla
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Rajender Burka
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Laha Gouri Shankar
- Crop Protection, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | | | | | | | - Viraktamath B. C.
- Crop Improvement, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | | | - Kranthi Brahma
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Raju Madnala
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
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14
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Potential of rice landraces with strong culms as genetic resources for improving lodging resistance against super typhoons. Sci Rep 2021; 11:15780. [PMID: 34349177 PMCID: PMC8339031 DOI: 10.1038/s41598-021-95268-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/16/2021] [Indexed: 11/08/2022] Open
Abstract
It is generally believed that rice landraces with long culms are susceptible to lodging, and have not been utilized for breeding to improve lodging resistance. However, little is known about the structural culm strength of landraces and their beneficial genetic loci. Therefore, in this study, genome-wide association studies (GWAS) were performed using a rice population panel including Japanese rice landraces to identify beneficial loci associated with strong culms. As a result, the landraces were found to have higher structural culm strength and greater diversity than the breeding varieties. Genetic loci associated with strong culms were identified, and it was demonstrated that haplotypes with positive effects of those loci were present in a high proportion of these landraces. These results indicated that the utilization of the strong culm-associated loci present in Japanese rice landraces may further improve the lodging resistance of modern breeding varieties that have relied on semi-dwarfism.
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15
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Landraces of temperate japonica rice have superior alleles for improving culm strength associated with lodging resistance. Sci Rep 2020; 10:19855. [PMID: 33199753 PMCID: PMC7670413 DOI: 10.1038/s41598-020-76949-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 10/22/2020] [Indexed: 11/26/2022] Open
Abstract
Lodging can reduce grain yield and quality in cereal crops including rice (Oryza sativa L.). To achieve both high biomass production and lodging resistance, the breeding of new cultivars with strong culms is a promising strategy. However, little is known about the diversity of culm strength in temperate japonica rice and underlying genetic factors. Here, we report a wide variation of culm strength among 135 temperate japonica cultivars, and some landraces having the strongest culms among these cultivars. The genome-wide association study (GWAS) identified 55 quantitative trait loci for culm strength and morphological traits, and revealed several candidate genes. The superior allele of candidate gene for culm thickness, OsRLCK191, was found in many landraces but had not inherited to the modern improved cultivars. Our results suggest that landraces of temperate japonica rice have unutilized superior alleles for contributing future improvements of culm strength and lodging resistance.
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16
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Gaur VS, Channappa G, Chakraborti M, Sharma TR, Mondal TK. ‘Green revolution’ dwarf genesd1of rice has gigantic impact. Brief Funct Genomics 2020. [DOI: 10.1093/bfgp/elaa019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
AbstractRice (Oryza sativa L.) is one of the most important cereal that has fed the world over a longer period. Before green revolution, cultivated rice is believed to have consisted of thousands of landraces each adapted to its specific climatic conditions by surviving against different abiotic and biotic selection pressure. However, owing to the low yield, photo-period sensitivity, late maturity and sensitivity to lodging of these landraces grown world-wide, serious concerns of impending global food crisis was felt during the 1960s because of (i) unprecedented increase of the population and (ii) concomitant decline in the cultivable land. Fortunately, high-yielding varieties developed through the introgression of the semi-dwarf1 gene (popularly known as sd1) during the 1960s led to significant increments in the food grain production that averted the apprehensions of nearing famine. This historical achievement having deep impact in the global agriculture is popularly referred as ‘Green Revolution.’ In this paper, we reviewed, its genetics as well as molecular regulations, evolutionary relationship with orthologous genes from other cereals as well as pseudo-cereals and attempted to provide an up-to-date information about its introgression to different rice cultivars of the world.
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Affiliation(s)
- Vikram Singh Gaur
- College of Agriculture, Balaghat, JNKVV, Jabalpur, Madhya Pradesh, India
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17
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Ohkubo S, Tanaka Y, Yamori W, Adachi S. Rice Cultivar Takanari Has Higher Photosynthetic Performance Under Fluctuating Light Than Koshihikari, Especially Under Limited Nitrogen Supply and Elevated CO 2. FRONTIERS IN PLANT SCIENCE 2020; 11:1308. [PMID: 32983198 PMCID: PMC7490297 DOI: 10.3389/fpls.2020.01308] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/11/2020] [Indexed: 05/31/2023]
Abstract
Plants in the field experience dynamic changes of sunlight rather than steady-state irradiation. Therefore, increasing the photosynthetic rate of an individual leaf under fluctuating light is essential for improving crop productivity. The high-yielding indica rice (Oryza sativa L.) cultivar Takanari is considered a potential donor of photosynthesis genes because of its higher steady-state photosynthesis at both atmospheric and elevated CO2 concentrations than those of several Japanese commercial cultivars, including Koshihikari. Photosynthetic induction after a sudden increase in light intensity is faster in Takanari than in Koshihikari, but whether the daily carbon gain of Takanari outperforms that of Koshihikari under fluctuating light in the field is unclear. Here we report that Takanari has higher non-steady-state photosynthesis, especially under low nitrogen (N) supply, than Koshihikari. In a pot experiment, Takanari had greater leaf carbon gain during the initial 10 min after a sudden increase in irradiation and higher daily CO2 assimilation under simulated natural fluctuating light, at both atmospheric (400 ppm) and elevated (800 ppm) CO2 concentrations. The electron transport rate during a day under field conditions with low N supply was also higher in Takanari than in Koshihikari. Although the advantages of Takanari were diminished under high N supply, photosynthetic N use efficiency was consistently higher in Takanari than in Koshihikari, under both low and high N supply. This study demonstrates that Takanari is a promising donor parent to use in breeding programs aimed at increasing CO2 assimilation in a wide range of environments, including future higher CO2 concentrations.
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Affiliation(s)
- Satoshi Ohkubo
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Japan
| | - Yu Tanaka
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Wataru Yamori
- Graduate School of Agricultural and Life Sciences, Institute for Sustainable Agro-Ecosystem Services, The University of Tokyo, Nishitokyo, Japan
| | - Shunsuke Adachi
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Fuchu, Japan
- College of Agriculture, Ibaraki University, Inashiki, Japan
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18
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Yuan R, Zhao N, Usman B, Luo L, Liao S, Qin Y, Nawaz G, Li R. Development of Chromosome Segment Substitution Lines (CSSLs) Derived from Guangxi Wild Rice ( Oryza rufipogon Griff.) under Rice ( Oryza sativa L.) Background and the Identification of QTLs for Plant Architecture, Agronomic Traits and Cold Tolerance. Genes (Basel) 2020; 11:E980. [PMID: 32842674 PMCID: PMC7564255 DOI: 10.3390/genes11090980] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 11/16/2022] Open
Abstract
Common wild rice contains valuable resources of novel alleles for rice improvement. It is well known that genetic populations provide the basis for a wide range of genetic and genomic studies. In particular, chromosome segment substitution lines (CSSLs) ais a powerful tool for fine mapping of quantitative traits, new gene discovery and marker-assisted breeding. In this study, 132 CSSLs were developed from a cultivated rice (Oryza sativa) cultivar (93-11) and common wild rice (Oryza rufipogon Griff. DP30) by selfing-crossing, backcrossing and marker-assisted selection (MAS). Based on the high-throughput sequencing of the 93-11 and DP30, 285 pairs of Insertion-deletions (InDel) markers were selected with an average distance of 1.23 Mb. The length of this DP30-CSSLs library was 536.4 cM. The coverage rate of substitution lines cumulatively overlapping the whole genome of DP30 was about 91.55%. DP30-CSSLs were used to analyze the variation for 17 traits leading to the detection of 36 quantitative trait loci (QTLs) with significant phenotypic effects. A cold-tolerant line (RZ) was selected to construct a secondary mapping F2 population, which revealed that qCT2.1 is in the 1.7 Mb region of chromosome 2. These CSSLs may, therefore, provide powerful tools for genome wide large-scale gene discovery in wild rice. This research will also facilitate fine mapping and cloning of QTLs and genome-wide study of wild rice. Moreover, these CSSLs will provide a foundation for rice variety improvement.
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Affiliation(s)
| | | | | | | | | | | | | | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China; (R.Y.); (N.Z.); (B.U.); (L.L.); (S.L.); (Y.Q.); (G.N.)
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19
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Long W, Dan D, Yuan Z, Chen Y, Jin J, Yang W, Zhang Z, Li N, Li S. Deciphering the Genetic Basis of Lodging Resistance in Wild Rice Oryza longistaminata. FRONTIERS IN PLANT SCIENCE 2020; 11:628. [PMID: 32547576 PMCID: PMC7274161 DOI: 10.3389/fpls.2020.00628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/23/2020] [Indexed: 05/27/2023]
Abstract
The abuse of fertilizer results in tall rice plants that are susceptible to lodging and reduced plant yield. Hence, it is important to identify and utilize the quantitative trait loci (QTLs)/genes for lodging resistance breeding. Oryza longistaminata exhibits a strong stem and high biomass productivity, which could be a candidate gene pool for cultivars lodging resistance improvement. Here, a set of 152 BC2F20 lines derived from a cross between a cultivated line 93-11 and O. longistaminata was evaluated for lodging resistance. QTL mapping analysis combined with single-nucleotide polymorphism (SNP) marker derived from high-throughput sequencing identified 12 QTLs for stem diameter (SD), 11 QTLs for stem length (SL), and 3 QTLs for breaking strength (BS). Of which, 14 QTLs were first identified from O. longistaminata. A major QTL, qLR1, which was delimited to a region ∼80 kb on chromosome 1, increased stem diameter, stem length, and breaking strength. Another major QTL, qLR8, that was delimited in an interval ∼120 kb on chromosome 8, significantly enhanced the breaking strength. These results provide evidence that O. longistaminata can be exploited to develop lodging-resistant rice lines.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Shaoqing Li
- State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan, China
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20
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Kato Y, Collard BCY, Septiningsih EM, Ismail AM. Increasing flooding tolerance in rice: combining tolerance of submergence and of stagnant flooding. ANNALS OF BOTANY 2020; 124:1199-1210. [PMID: 31306479 PMCID: PMC6944782 DOI: 10.1093/aob/mcz118] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 07/11/2019] [Indexed: 05/25/2023]
Abstract
BACKGROUND AND AIMS Rice ecosystems in the tropical coastal areas are subject to two types of flooding stress: transient complete submergence and long-term water stagnation (stagnant flooding). Here, we aimed to dissect the mechanisms for stagnant flooding tolerance of rice genotypes carrying SUB1, a quantitative trait locus for submergence tolerance. METHODS We screened 80 elite genotypes under stagnant flooding stress in the lowland rice fields in the wet and dry seasons, and examined the tolerance mechanisms of promising genotypes for the two following seasons. KEY RESULTS Yield reduction under stagnant flooding averaged 48 % in the dry season and 89 % in the wet season. Elite genotypes carrying SUB1 showed 49 % lower yield than those without SUB1 under stagnant flooding, with no differences under shallow water conditions. However, we identified a few high-yielding Sub1 genotypes that were as tolerant of stagnant flooding as a reference genotype that lacked SUB1. These genotypes had intermediate stature with more shoot elongation in response to rising water than a moderately tolerant Sub1 reference variety, resulting in greater canopy expansion and higher yield. It was important to increase lodging resistance, since plant height >140 cm increased lodging under stagnant flooding. The culm diameter was closely associated with culm strength; reduced aerenchyma formation and increased lignin accumulation in the culm should increase lodging resistance. CONCLUSIONS The study demonstrated a successful combination of submergence and stagnant flooding tolerance in a rice breeding programme, and identified elite Sub1 genotypes that also tolerate stagnant flooding. Our results will support genetic improvement of Sub1 varieties for stagnant flooding tolerance.
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Affiliation(s)
- Yoichiro Kato
- International Rice Research Institute, Metro Manila, Philippines
- Institute for Sustainable Agro-ecosystem Services, University of Tokyo, Tokyo, Japan
| | - Bertrand C Y Collard
- International Rice Research Institute, Metro Manila, Philippines
- Yanco Agricultural Institute, Department of Primary Industries, New South Wales, Australia
| | - Endang M Septiningsih
- International Rice Research Institute, Metro Manila, Philippines
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, USA
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21
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Li R, Jiang H, Zhang Z, Zhao Y, Xie J, Wang Q, Zheng H, Hou L, Xiong X, Xin D, Hu Z, Liu C, Wu X, Chen Q. Combined Linkage Mapping and BSA to Identify QTL and Candidate Genes for Plant Height and the Number of Nodes on the Main Stem in Soybean. Int J Mol Sci 2019; 21:E42. [PMID: 31861685 PMCID: PMC6981803 DOI: 10.3390/ijms21010042] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/12/2019] [Accepted: 12/17/2019] [Indexed: 11/16/2022] Open
Abstract
Soybean is one of the most important food and oil crops in the world. Plant height (PH) and the number of nodes on the main stem (NNMS) are quantitative traits closely related to soybean yield. In this study, we used 208 chromosome segment substitution lines (CSSL) populations constructed using "SN14" and "ZYD00006" for quantitative trait locus (QTL) mapping of PH and NNMS. Combined with bulked segregant analysis (BSA) by extreme materials, 8 consistent QTLs were identified. According to the gene annotation of the QTL interval, a total of 335 genes were obtained. Five of which were associated with PH and NNMS, potentially representing candidate genes. RT-qPCR of these 5 candidate genes revealed two genes with differential relative expression levels in the stems of different materials. Haplotype analysis showed that different single nucleotide polymorphisms (SNPs) between the excellent haplotypes in Glyma.04G251900 and Glyma.16G156700 may be the cause of changes in these traits. These results provide the basis for research on candidate genes and marker-assisted selection (MAS) in soybean breeding.
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Affiliation(s)
- Ruichao Li
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Hongwei Jiang
- Jilin Academy of Agricultural Sciences, Soybean Research Institute, Changchun 130033, China;
| | - Zhanguo Zhang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Yuanyuan Zhao
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Jianguo Xie
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Qiao Wang
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Haiyang Zheng
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Lilong Hou
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Xin Xiong
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Dawei Xin
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Zhenbang Hu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Chunyan Liu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Xiaoxia Wu
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
| | - Qingshan Chen
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China; (R.L.); (Z.Z.); (Y.Z.); (J.X.); (Q.W.); (H.Z.); (L.H.); (X.X.); (D.X.); (Z.H.); (C.L.)
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22
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Nakano H, Takai T, Kondo M. Identification of Quantitative Trait Loci for the Concentrations of Phenylpropanoid Glycosides in Brown Rice. ACS OMEGA 2019; 4:17317-17325. [PMID: 31656905 PMCID: PMC6811851 DOI: 10.1021/acsomega.9b02030] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/26/2019] [Indexed: 06/10/2023]
Abstract
Rice (Oryza sativa L.) is a staple food for most of the world's population, as it is eaten by nearly half of its inhabitants. Phenylpropanoid glycosides derived from plants have various biomedical effects. The comparison of the concentrations of the four major phenylpropanoid glycosides in brown rice, i.e., 6-O-feruloylsucrose (1), 3',6-di-O-sinapoylsucrose (2), 3'-O-sinapoyl-6-O-feruloylsucrose (3), and 3',6-di-O-feruloylsucrose (4), between a conventional japonica-type cultivar Koshihikari and a high-yielding indica-type cultivar Takanari revealed that they were 57-162% higher in Koshihikari than in Takanari. To identify quantitative trait loci (QTLs) for the concentrations of these compounds (1-4), reciprocal chromosome segment substitution lines derived from a cross between Koshihikari and Takanari were analyzed. We identified QTLs for the concentrations of compound 1 on chromosome 2 and of compound 2 on chromosome 4 in the reciprocal genetic background. The concentrations of these compounds were increased by the Koshihikari alleles and decreased by the Takanari alleles. Therefore, the favorable alleles of Koshihikari are available to ameliorate the lower concentrations of compounds 1 and 2 in Takanari. The combinations of QTLs identified in the present study together with those of other biologically active compounds make it possible to breed health beneficial cultivars.
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Affiliation(s)
- Hiroshi Nakano
- Institute
of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Kyushu
Okinawa Agricultural Research Center, NARO, 496 Izumi, Chikugo, Fukuoka 833-0041, Japan
| | - Toshiyuki Takai
- Institute
of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Japan
International Research Center for Agricultural Sciences, 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
| | - Motohiko Kondo
- Institute
of Crop Science, NARO, 2-1-18 Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Graduate
School of Bioagricultural Sciences, Nagoya
University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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23
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Shah L, Yahya M, Shah SMA, Nadeem M, Ali A, Ali A, Wang J, Riaz MW, Rehman S, Wu W, Khan RM, Abbas A, Riaz A, Anis GB, Si H, Jiang H, Ma C. Improving Lodging Resistance: Using Wheat and Rice as Classical Examples. Int J Mol Sci 2019; 20:E4211. [PMID: 31466256 PMCID: PMC6747267 DOI: 10.3390/ijms20174211] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/04/2019] [Accepted: 08/19/2019] [Indexed: 01/07/2023] Open
Abstract
One of the most chronic constraints to crop production is the grain yield reduction near the crop harvest stage by lodging worldwide. This is more prevalent in cereal crops, particularly in wheat and rice. Major factors associated with lodging involve morphological and anatomical traits along with the chemical composition of the stem. These traits have built up the remarkable relationship in wheat and rice genotypes either prone to lodging or displaying lodging resistance. In this review, we have made a comparison of our conceptual perceptions with foregoing published reports and proposed the fundamental controlling techniques that could be practiced to control the devastating effects of lodging stress. The management of lodging stress is, however, reliant on chemical, agronomical, and genetic factors that are reducing the risk of lodging threat in wheat and rice. But, still, there are many questions remain to be answered to elucidate the complex lodging phenomenon, so agronomists, breeders, physiologists, and molecular biologists require further investigation to address this challenging problem.
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Affiliation(s)
- Liaqat Shah
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Muhammad Yahya
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Syed Mehar Ali Shah
- Department of Plant Breeding and Genetics, University of Agriculture Peshawar, Peshawar 57000, Pakistan
| | - Muhammad Nadeem
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Ahmad Ali
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Asif Ali
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Jing Wang
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Muhammad Waheed Riaz
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
| | - Shamsur Rehman
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China
| | - Weixun Wu
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Riaz Muhammad Khan
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Adil Abbas
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Aamir Riaz
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
| | - Galal Bakr Anis
- State Key Laboratory for Rice Biology, China National Rice Research Institute, 359#, Tiyuchang Road, Hangzhou 310006, China
- Rice Research and Training Center, Field Crops Research Institute, Agriculture Research Center, Kafrelsheikh 33717, Egypt
| | - Hongqi Si
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China.
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China.
| | - Haiyang Jiang
- National Engineering Laboratory of Crop Stress Resistance Breeding, Anhui Agricultural University, Hefei 230036, China
| | - Chuanxi Ma
- School of Agronomy, Anhui Agricultural University, Hefei 230036, China
- Key Laboratory of Wheat Biology and Genetic Improvement on South Yellow & Huai River Valley, Ministry of Agriculture, Anhui Agricultural University, Hefei 230036, China
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24
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Nomura T, Arakawa N, Yamamoto T, Ueda T, Adachi S, Yonemaru JI, Abe A, Takagi H, Yokoyama T, Ookawa T. Next generation long-culm rice with superior lodging resistance and high grain yield, Monster Rice 1. PLoS One 2019; 14:e0221424. [PMID: 31437205 PMCID: PMC6705783 DOI: 10.1371/journal.pone.0221424] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/06/2019] [Indexed: 12/30/2022] Open
Abstract
During late 1960s Green Revolution, researchers utilized semidwarf 1 (sd1) to improve the yield and lodging resistance in rice (Oryza sativa L.). However, sd1 has a negative effect to culm strength and biomass production. To increase yield dramatically in 21th century, development of next generation long-culm rice for non-lodging and high grain yield independent of sd1 has been needed. The present study developed Monster Rice 1, a long-culm and heavy-panicle type of rice line and compared it with Takanari, a high-yielding semidwarf rice variety about yield and lodging resistance associated traits. Brown rice yield and bending moment at breaking of the basal elongated internode were higher in Monster Rice 1 than those in Takanari due to a large number of spikelets per panicle and thicker culm. Furthermore, to identify QTLs with superior alleles for these traits, QTL and haplotype analyses were performed using F2 population and recombinant inbred lines derived from a cross between Monster Rice 1 and Takanari. The results from this study suggest that long-culm and heavy-panicle type of rice with a superior lodging resistance by culm strength can perform its high yield potential by using these identified QTLs contributing yield and lodging resistance.
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Affiliation(s)
- Tomohiro Nomura
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Naoya Arakawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Toshio Yamamoto
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Okayama, Japan
| | - Tadamasa Ueda
- Institute of Crop Science, NARO, Tsukuba, Ibaraki, Japan
| | - Shunsuke Adachi
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | | | - Akira Abe
- Department of Genomics and Breeding, Iwate Biotechnology Research Center, Kitakami, Iwate, Japan
| | - Hiroki Takagi
- Faculty of Bioresources and Environmental Sciences, Ishikawa Prefectural University, Nonoichi, Ishikawa, Japan
| | - Tadashi Yokoyama
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
| | - Taiichiro Ookawa
- Graduate School of Agriculture, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, Japan
- * E-mail:
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25
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Balakrishnan D, Surapaneni M, Mesapogu S, Neelamraju S. Development and use of chromosome segment substitution lines as a genetic resource for crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1-25. [PMID: 30483819 DOI: 10.1007/s00122-018-3219-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 10/24/2018] [Indexed: 05/27/2023]
Abstract
CSSLs are a complete library of introgression lines with chromosomal segments of usually a distant genotype in an adapted background and are valuable genetic resources for basic and applied research on improvement of complex traits. Chromosome segment substitution lines (CSSLs) are genetic stocks representing the complete genome of any genotype in the background of a cultivar as overlapping segments. Ideally, each CSSL has a single chromosome segment from the donor with a maximum recurrent parent genome recovered in the background. CSSL development program requires population-wide backcross breeding and genome-wide marker-assisted selection followed by selfing. Each line in a CSSL library has a specific marker-defined large donor segment. CSSLs are evaluated for any target phenotype to identify lines significantly different from the parental line. These CSSLs are then used to map quantitative trait loci (QTLs) or causal genes. CSSLs are valuable prebreeding tools for broadening the genetic base of existing cultivars and harnessing the genetic diversity from the wild- and distant-related species. These are resources for genetic map construction, mapping QTLs, genes or gene interactions and their functional analysis for crop improvement. In the last two decades, the utility of CSSLs in identification of novel genomic regions and QTL hot spots influencing a wide range of traits has been well demonstrated in food and commercial crops. This review presents an overview of how CSSLs are developed, their status in major crops and their use in genomic studies and gene discovery.
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Affiliation(s)
- Divya Balakrishnan
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Malathi Surapaneni
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sukumar Mesapogu
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India
| | - Sarla Neelamraju
- ICAR- National Professor Project, ICAR- Indian Institute of Rice Research, Hyderabad, India.
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26
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Mulsanti IW, Yamamoto T, Ueda T, Samadi AF, Kamahora E, Rumanti IA, Thanh VC, Adachi S, Suzuki S, Kanekatsu M, Hirasawa T, Ookawa T. Finding the superior allele of japonica-type for increasing stem lodging resistance in indica rice varieties using chromosome segment substitution lines. RICE 2018; 11:25. [PMID: 29671092 PMCID: PMC5906422 DOI: 10.1186/s12284-018-0216-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 04/04/2018] [Indexed: 05/04/2023]
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27
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Nakano H, Takai T, Kondo M. Quantitative trait loci regulate the concentrations of steryl ferulates in brown rice. Cereal Chem 2018. [DOI: 10.1002/cche.10099] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Hiroshi Nakano
- NARO Institute of Crop Science; Tsukuba Japan
- NARO Kyushu Okinawa Agricultural Research Center; Chikugo Japan
| | - Toshiyuki Takai
- NARO Institute of Crop Science; Tsukuba Japan
- Japan International Research Center for Agricultural Sciences; Ibaraki Japan
| | - Motohiko Kondo
- NARO Institute of Crop Science; Tsukuba Japan
- Graduate School of Bioagricultural Sciences; Nagoya University; Nagoya Japan
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28
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Gomez FE, Carvalho G, Shi F, Muliana AH, Rooney WL. High throughput phenotyping of morpho-anatomical stem properties using X-ray computed tomography in sorghum. PLANT METHODS 2018; 14:59. [PMID: 30008795 PMCID: PMC6043981 DOI: 10.1186/s13007-018-0326-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Accepted: 07/04/2018] [Indexed: 05/24/2023]
Abstract
BACKGROUND In bioenergy/forage sorghum, morpho-anatomical stem properties are major components affecting standability and juice yield. However, phenotyping these traits is low-throughput, and has been restricted by the lack of a high-throughput phenotyping platforms that can collect both morphological and anatomical stem properties. X-ray computed tomography (CT) offers a potential solution, but studies using this technology in plants have evaluated limited numbers of genotypes with limited throughput. Here we suggest that using a medical CT might overcome sample size limitations when higher resolution is not needed. Thus, the aim of this study was to develop a practical high-throughput phenotyping and image data processing pipeline that extracts stem morpho-anatomical traits faster, more efficiently and on a larger number of samples. RESULTS A medical CT was used to image morpho-anatomical stem properties in sorghum. The platform and image analysis pipeline revealed extensive phenotypic variation for important morpho-anatomical traits in well-characterized sorghum genotypes at suitable repeatability rates. CT estimates were highly predictive of morphological traits and moderately predictive of anatomical traits. The image analysis pipeline also identified genotypes with superior morpho-anatomical traits that were consistent with ground-truth based classification in previous studies. In addition, stem cross section intensity measured by the CT was highly correlated with stem dry-weight density, and can potentially serve as a high-throughput approach to measure stem density in grass stems. CONCLUSIONS The use of CT on a diverse set of sorghum genotypes with a defined platform and image analysis pipeline was effective at predicting traits such as stem length, diameter, and pithiness ratio at the internode level. High-throughput phenotyping of stem traits using CT appears to be useful and feasible for use in an applied breeding program.
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Affiliation(s)
- Francisco E. Gomez
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695 USA
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843 USA
| | - Geraldo Carvalho
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843 USA
| | - Fuhao Shi
- Department of Computer Science and Engineering, Texas A&M University, 3112 TAMU, 710 Ross St, College Station, TX 77843 USA
| | - Anastasia H. Muliana
- Department of Mechanical Engineering, Texas A& M University, 401 Joe Routt Blvd, College Station, TX 77843 USA
| | - William L. Rooney
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843 USA
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29
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Gomez FE, Carvalho G, Shi F, Muliana AH, Rooney WL. High throughput phenotyping of morpho-anatomical stem properties using X-ray computed tomography in sorghum. PLANT METHODS 2018. [PMID: 30008795 DOI: 10.1186/s13007-018-0326-323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
BACKGROUND In bioenergy/forage sorghum, morpho-anatomical stem properties are major components affecting standability and juice yield. However, phenotyping these traits is low-throughput, and has been restricted by the lack of a high-throughput phenotyping platforms that can collect both morphological and anatomical stem properties. X-ray computed tomography (CT) offers a potential solution, but studies using this technology in plants have evaluated limited numbers of genotypes with limited throughput. Here we suggest that using a medical CT might overcome sample size limitations when higher resolution is not needed. Thus, the aim of this study was to develop a practical high-throughput phenotyping and image data processing pipeline that extracts stem morpho-anatomical traits faster, more efficiently and on a larger number of samples. RESULTS A medical CT was used to image morpho-anatomical stem properties in sorghum. The platform and image analysis pipeline revealed extensive phenotypic variation for important morpho-anatomical traits in well-characterized sorghum genotypes at suitable repeatability rates. CT estimates were highly predictive of morphological traits and moderately predictive of anatomical traits. The image analysis pipeline also identified genotypes with superior morpho-anatomical traits that were consistent with ground-truth based classification in previous studies. In addition, stem cross section intensity measured by the CT was highly correlated with stem dry-weight density, and can potentially serve as a high-throughput approach to measure stem density in grass stems. CONCLUSIONS The use of CT on a diverse set of sorghum genotypes with a defined platform and image analysis pipeline was effective at predicting traits such as stem length, diameter, and pithiness ratio at the internode level. High-throughput phenotyping of stem traits using CT appears to be useful and feasible for use in an applied breeding program.
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Affiliation(s)
- Francisco E Gomez
- 1Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695 USA
- 2Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843 USA
| | - Geraldo Carvalho
- 2Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843 USA
| | - Fuhao Shi
- 3Department of Computer Science and Engineering, Texas A&M University, 3112 TAMU, 710 Ross St, College Station, TX 77843 USA
| | - Anastasia H Muliana
- 4Department of Mechanical Engineering, Texas A& M University, 401 Joe Routt Blvd, College Station, TX 77843 USA
| | - William L Rooney
- 2Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843 USA
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Surapaneni M, Balakrishnan D, Mesapogu S, Addanki KR, Yadavalli VR, Tripura Venkata VGN, Neelamraju S. Identification of Major Effect QTLs for Agronomic Traits and CSSLs in Rice from Swarna/ Oryza nivara Derived Backcross Inbred Lines. FRONTIERS IN PLANT SCIENCE 2017; 8:1027. [PMID: 28690618 PMCID: PMC5480306 DOI: 10.3389/fpls.2017.01027] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 05/29/2017] [Indexed: 05/04/2023]
Abstract
Backcross inbred lines (BILs) derived from elite x wild crosses are very useful for basic studies and breeding. The aim of this study was to map quantitative trait loci (QTLs) associated with yield and related traits and to identify chromosomal segment substitution lines (CSSLs) from unselected BC2F8 BILs of Swarna/Oryza nivara IRGC81848. In all, 94 BILs were field evaluated in 2 years (wet seasons, 2014 and 2015) for nine traits; days to 50% flowering, days to maturity (DM), plant height (PH), number of tillers, number of productive tillers, panicle weight, yield per plant, bulk yield, and biomass. BILs were genotyped using 111 polymorphic simple sequence repeats distributed across the genome. Fifteen QTLs including 10 novel QTLs were identified using composite interval mapping, Inclusive composite interval mapping and multiple interval mapping (MIM). O. nivara alleles were trait-enhancing in 26% of QTLs. Only 3 of 15 QTLs were also reported previously in BC2F2 of the same cross. These three included the two major effect QTLs for DM and PH detected in both years with 13 and 20% phenotypic variance. Further, a set of 74 CSSLs was identified using CSSL Finder and 22 of these showed significantly higher values than Swarna for five yield traits. CSSLs, 220S for panicle weight and 10-2S with consistent high yield in both years are worthy of large scale field evaluation. The major QTLs and 22 significantly different CSSLs are a useful resource for rice improvement and dissecting yield related traits.
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Yadav S, Singh UM, Naik SM, Venkateshwarlu C, Ramayya PJ, Raman KA, Sandhu N, Kumar A. Molecular Mapping of QTLs Associated with Lodging Resistance in Dry Direct-Seeded Rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1431. [PMID: 28871266 PMCID: PMC5567065 DOI: 10.3389/fpls.2017.01431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/03/2017] [Indexed: 05/04/2023]
Abstract
Dry direct-seeded rice (DSR) is an alternative crop establishment method with less water and labor requirement through mechanization. It provides better opportunities for a second crop during the cropping season and therefore, a feasible alternative system to transplanted lowland rice. However, lodging is one of the major constraints in attaining high yield in DSR. Identification of QTLs for lodging resistance and their subsequent use in improving varieties under DSR will be an efficient breeding strategy to address the problem. In order to map the QTLs associated with lodging resistance, a set of 253 BC3F4 lines derived from a backcross between Swarna and Moroberekan were evaluated in two consecutive years. A total of 12 QTLs associated with lodging resistance traits [culm length (qCL), culm diameter (qCD), and culm strength (qCS)] were mapped on chromosomes 1, 2, 6, and 7 using 193 polymorphic SNP markers. Two major and consistent effect QTLs, namely qCD1.1 (with R2 of 10%) and qCS1.1 (with R2 of 14%) on chromosome 1 with id1003559 being the peak SNP marker (flanking markers; id1001973-id1006772) were identified as a common genomic region associated with important lodging resistance traits. In silico analysis revealed the presence of Gibberellic Acid 3 beta-hydroxylase along with 34 other putative candidate genes in the marker interval region of id1001973-id1006772. The positive alleles for culm length, culm diameter, and culm strength were contributed by the upland adaptive parent Moroberekan. Our results identified significant positive correlation between lodging related traits (culm length diameter and strength) and grain yield under DSR, indicating the role of lodging resistant traits in grain yield improvement under DSR. Deployment of the identified alleles influencing the culm strength and culm diameter in marker assisted introgression program may facilitate the lodging resistance under DSR.
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Affiliation(s)
- Shailesh Yadav
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- International Rice Research InstituteMetro Manila, Philippines
| | - Uma M Singh
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Shilpa M Naik
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Perumalla J Ramayya
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - K Anitha Raman
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Nitika Sandhu
- International Rice Research InstituteMetro Manila, Philippines
| | - Arvind Kumar
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- International Rice Research InstituteMetro Manila, Philippines
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HIRANO K, ORDONIO RL, MATSUOKA M. Engineering the lodging resistance mechanism of post-Green Revolution rice to meet future demands. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2017; 93:220-233. [PMID: 28413198 PMCID: PMC5489430 DOI: 10.2183/pjab.93.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 02/14/2017] [Indexed: 05/20/2023]
Abstract
Traditional breeding for high-yielding rice has been dependent on the widespread cultivation of gibberellin (GA)-deficient semi-dwarf varieties. Dwarfism lowers the "center of gravity" of the plant body, which increases resistance against lodging and enables plants to support high grain yield. Although this approach was successful in latter half of the 20th century in rice and wheat breeding, this may no longer be enough to sustain rice with even higher yields. This is because relying solely on the semi-dwarf trait is subject to certain limitations, making it necessary to use other important traits to reinforce it. In this review, we present an alternative approach to increase lodging resistance by improving the quality of the culm by identifying genes related to culm quality and introducing these genes into high-yielding rice cultivars through molecular breeding technique.
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Affiliation(s)
- Ko HIRANO
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | | | - Makoto MATSUOKA
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
- Correspondence should be addressed: M. Matsuoka, Bioscience and Biotechnology Center, Nagoya University, Nagoya 464-8601, Japan (e-mail: )
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