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Guha PK, Magar ND, Kommana M, Barbadikar KM, Suneel B, Gokulan C, Lakshmi DV, Patel HK, Sonti RV, Sundaram RM, Madhav MS. Strong culm: a crucial trait for developing next-generation climate-resilient rice lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:665-686. [PMID: 38737321 PMCID: PMC11087419 DOI: 10.1007/s12298-024-01445-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 05/14/2024]
Abstract
Lodging, a phenomenon characterized by the bending or breaking of rice plants, poses substantial constraints on productivity, particularly during the harvesting phase in regions susceptible to strong winds. The rice strong culm trait is influenced by the intricate interplay of genetic, physiological, epigenetic, and environmental factors. Stem architecture, encompassing morphological and anatomical attributes, alongside the composition of both structural and non-structural carbohydrates, emerges as a critical determinant of lodging resistance. The adaptive response of the rice culm to various biotic and abiotic environmental factors further modulates the propensity for lodging. Advancements in next-generation sequencing technologies have expedited the genetic dissection of lodging resistance, enabling the identification of pertinent genes, quantitative trait loci, and novel alleles. Concurrently, contemporary breeding strategies, ranging from biparental approaches to more sophisticated methods such as multi-parent-based breeding, gene pyramiding, genomic selection, genome-wide association studies, and haplotype-based breeding, offer perspectives on the genetic underpinnings of culm strength. This review comprehensively delves into physiological attributes, culm histology, epigenetic determinants, and gene expression profiles associated with lodging resistance, with a specialized focus on leveraging next-generation sequencing for candidate gene discovery.
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Affiliation(s)
- Pritam Kanti Guha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Nakul D. Magar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Madhavilatha Kommana
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Kalyani M. Barbadikar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - B. Suneel
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - C. Gokulan
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - D. Vijay Lakshmi
- Department of Microbiology, Yogi Vemana University., Y.S.R Kadapa, India
| | - Hitendra Kumar Patel
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh V. Sonti
- Department of Biotechnology, CSIR-Center for Cellular and Molecular Biology, Hyderabad, India
- International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - R. M. Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Maganti Sheshu Madhav
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Hyderabad, India
- ICAR-Central Tobacco Research Institute, Rajahmundry, India
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Li X, Dong J, Zhu W, Zhao J, Zhou L. Progress in the study of functional genes related to direct seeding of rice. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:46. [PMID: 37309311 PMCID: PMC10248684 DOI: 10.1007/s11032-023-01388-y] [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: 09/22/2022] [Accepted: 04/20/2023] [Indexed: 06/14/2023]
Abstract
Rice is a major food crop in the world. Owing to the shortage of rural labor and the development of agricultural mechanization, direct seeding has become the main method of rice cultivation. At present, the main problems faced by direct seeding of rice are low whole seedling rate, serious weeds, and easy lodging of rice in the middle and late stages of growth. Along with the rapid development of functional genomics, the functions of a large number of genes have been confirmed, including seed vigor, low-temperature tolerance germination, low oxygen tolerance growth, early seedling vigor, early root vigor, resistance to lodging, and other functional genes related to the direct seeding of rice. A review of the related functional genes has not yet been reported. In this study, the genes related to direct seeding of rice are summarized to comprehensively understand the genetic basis and mechanism of action in direct seeding of rice and to lay the foundation for further basic theoretical research and breeding application research in direct seeding of rice.
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Affiliation(s)
- Xuezhong Li
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Jingfang Dong
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Wen Zhu
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Junliang Zhao
- Rice Research Institute, Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of New Technology in Rice Breeding/Guangdong Rice Engineering Laboratory, Guangzhou, 510640 China
| | - Lingyan Zhou
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou, 510225 Guangdong China
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Wang C, Chen Y, Cui C, Shan F, Zhang R, Lyu X, Lyu L, Chang H, Yan C, Ma C. Blue Light Regulates Cell Wall Structure and Carbohydrate Metabolism of Soybean Hypocotyl. Int J Mol Sci 2023; 24:1017. [PMID: 36674538 PMCID: PMC9864885 DOI: 10.3390/ijms24021017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/06/2023] Open
Abstract
Soybean stem elongation and thickening are related to cell wall composition. Plant morphogenesis can be influenced by blue light, which can regulate cell wall structure and composition, and affect stem growth and development. Here, using proteomics and metabolomics, differentially expressed proteins and metabolites of hypocotyls grown in the dark and under blue light were studied to clarify the effects of blue light on the cell wall structure and carbohydrate metabolism pathway of soybean hypocotyls. Results showed that 1120 differential proteins were upregulated and 797 differential proteins were downregulated under blue light treatment, while 63 differential metabolites were upregulated and 36 differential metabolites were downregulated. Blue light promoted the establishment of cell wall structure and composition by regulating the expression of both the enzymes and metabolites related to cell wall structural composition and nonstructural carbohydrates. Thus, under blue light, the cross-sectional area of the hypocotyl and xylem were larger, the longitudinal length of pith cells was smaller, elongation of the soybean hypocotyl was inhibited, and diameter was increased.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Chao Yan
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Chunmei Ma
- College of Agriculture, Northeast Agricultural University, Harbin 150030, China
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Yang X, Lai Y, Wang L, Zhao M, Wang J, Li M, Chi L, Lv G, Liu Y, Cui Z, Li R, Wu L, Sun B, Zhang X, Jiang S. Isolation of a Novel QTL, qSCM4, Associated with Strong Culm Affects Lodging Resistance and Panicle Branch Number in Rice. Int J Mol Sci 2023; 24:ijms24010812. [PMID: 36614255 PMCID: PMC9821088 DOI: 10.3390/ijms24010812] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/26/2022] [Accepted: 12/28/2022] [Indexed: 01/04/2023] Open
Abstract
Rice breeders are now developing new varieties with semi-high or even high plant height to further increase the grain yield, and the problem of lodging has re-appeared. We identified a major quantitative trait locus (QTL), qSCM4, for resistance to lodging by using an F2 segregant population and a recombinant self-incompatible line population from the cross between Shennong265 (SN265) and Lijiangxintuanheigu (LTH) after multiple years and multiple environments. Then, the residual heterozygous derived segregant population which consisted of 1781 individual plants, and the BC3F2 segregant population which consisted of 3216 individual plants, were used to shorten the physical interval of qSCM4 to 58.5 kb including 11 genes. DNA sequencing revealed the most likely candidate gene for qSCM4 was Os04g0615000, which encoded a functional protein with structural domains of serine and cysteine. There were 13 DNA sequence changes in LTH compared to SN265 in this gene, including a fragment deletion, two base changes in the 3' UTR region, six base changes in the exons, and four base changes in the introns. A near-isogenic line carrying qSCM4 showed that it improved the lodging resistance through increasing stem thickness by 25.3% and increasing stem folding resistance by 20.3%. Furthermore, it was also discovered that qSCM4 enhanced the primary branch per panicle by 16.7%, secondary branch by per panicle 9.9%, and grain number per panicle by 14.7%. All the above results will give us a valuable genetic resource for concurrently boosting culm strength and lodging resistance, and they will also provide a basis for further research on the lodging resistance mechanism of rice.
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Affiliation(s)
- Xianli Yang
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Yongcai Lai
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Lizhi Wang
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Minghui Zhao
- Rice Research Institute, Shenyang Agricultural University, Collaborative Innovation Center Co-Sponsored by Liaoning Provincial Government and Ministry of Education for Northeast Japonica Rice Genetic Improvement and High Efficiency Production, Shenyang 110161, China; (M.Z.); (J.W.); (Z.C.)
| | - Jiayu Wang
- Rice Research Institute, Shenyang Agricultural University, Collaborative Innovation Center Co-Sponsored by Liaoning Provincial Government and Ministry of Education for Northeast Japonica Rice Genetic Improvement and High Efficiency Production, Shenyang 110161, China; (M.Z.); (J.W.); (Z.C.)
| | - Mingxian Li
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Liyong Chi
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Guoyi Lv
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
| | - Youhong Liu
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
| | - Zhibo Cui
- Rice Research Institute, Shenyang Agricultural University, Collaborative Innovation Center Co-Sponsored by Liaoning Provincial Government and Ministry of Education for Northeast Japonica Rice Genetic Improvement and High Efficiency Production, Shenyang 110161, China; (M.Z.); (J.W.); (Z.C.)
| | - Rui Li
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
| | - Liren Wu
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
| | - Bing Sun
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
| | - Xijuan Zhang
- Crop Cultivation and Tillage Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (X.Y.); (Y.L.); (L.W.); (M.L.); (L.C.); (G.L.); (Y.L.); (R.L.); (L.W.); (B.S.)
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
- Correspondence: (X.Z.); (S.J.)
| | - Shukun Jiang
- Heilongjiang Provincial Key Laboratory, Crop Physiology and Ecology in Cold Region, Heilongjiang Provincial Engineering Technology Research Center of Crop Cold Damage, Harbin 150086, China
- Northeast Center of National Salt-Alkali Tolerant Rice Technology Innovation Center, Harbin 150086, China
- Qiqihar Branch, Heilongjiang Academy of Agricultural Sciences, Qiqihar 161006, China
- Correspondence: (X.Z.); (S.J.)
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Gao H, Dou Z, Chen L, Lu Y, Sun D, Xu Q, Sun R, Chen X. Effects of semi-deep water irrigation on hybrid indica rice lodging resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:1038129. [PMID: 36589088 PMCID: PMC9798435 DOI: 10.3389/fpls.2022.1038129] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/04/2022] [Indexed: 06/17/2023]
Abstract
Recently, rice-aquatic animal integrated farming (RAAIF) has grown rapidly in China due to its favorable benefits and the lower application of pesticides and fertilizers. However, rice lodging occurs frequently under RAAIF, which restricts rice yield. We assumed that semi-deep water irrigation may cause weaker rice-lodging resistance since it is the most significant environmental factor for RAAIF that distinguishes it from rice monoculture. To investigate the response of rice stem lodging resistance to semi-deep water irrigation and its mechanism, three irrigation management modes, namely the typical high-yield irrigation model that is mainly based on swallow and wetting (CK), semi-deep water irrigation from the late tillering stage to the jointing stage (SDI1), and semi-deep water irrigation from the jointing stage to the middle grain-filling stage (SDI2), were conducted using three hybrid indica rice varieties: Shenliangyou136 (SLY136), Huiliangyousimiao (HLYSM), and Wanxiangyou982 (WXY982). Mechanics analysis indicated that the bending moment by the whole plant (WP) and the breaking strength (M) were both decreased by semi-deep water irrigation when compared with CK, while M presented a larger decreasing amplitude than WP, which induced the increased lodging index (LI) of rice, for all the tested varieties. SLY136 and HLYSM were affected more strongly by SDI1, whereas WXY982 was affected more strongly by SDI2. Significant weaker breaking force under two semi-deep water irrigation modes contributed to the decreased M relative to CK. Morphology results showed that semi-deep water irrigation reduced the thickness of mechanical tissues, sclerenchyma cells, and parenchyma cells; reduced the number of vascular bundles; and caused a looser arrangement, inducing the lower fullness of the rice basal internode. Decreased accumulation of lignin and cellulose was also linked to the weaker breaking force of the basal internode under semi-deep water irrigation, which was verified by correlation analysis. WXY982 had obvious lower structural carbohydrates content under semi-deep water irrigation than the other two varieties and thus showed worse breaking force and LI. In conclusion, the worse mechanical strength of the rice basal internode under semi-deep water irrigation was closely associated with weaker vascular bundle development and suppressed structural carbohydrate accumulation, and the decreasing degree of lodging resistance varied between rice varieties and semi-deep water irrigation periods.
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Affiliation(s)
- Hui Gao
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Jiangsu Provincial Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
- Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, China
| | - Zhi Dou
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, China
| | - Linrong Chen
- Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, China
| | - Yao Lu
- Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, China
| | - Dong Sun
- Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, China
| | - Qiang Xu
- Research Institute of Rice Industrial Engineering Technology, Yangzhou University, Yangzhou, China
| | - Ruyin Sun
- Tianchang Modern Agricultural Industrial Park Management Service Center, Chuzhou, China
| | - Xueying Chen
- Tianchang Agriculture Science and Technology Extension Centre, Chuzhou, China
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Bretani G, Shaaf S, Tondelli A, Cattivelli L, Delbono S, Waugh R, Thomas W, Russell J, Bull H, Igartua E, Casas AM, Gracia P, Rossi R, Schulman AH, Rossini L. Multi-environment genome -wide association mapping of culm morphology traits in barley. FRONTIERS IN PLANT SCIENCE 2022; 13:926277. [PMID: 36212331 PMCID: PMC9539552 DOI: 10.3389/fpls.2022.926277] [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: 04/22/2022] [Accepted: 07/28/2022] [Indexed: 06/16/2023]
Abstract
In cereals with hollow internodes, lodging resistance is influenced by morphological characteristics such as internode diameter and culm wall thickness. Despite their relevance, knowledge of the genetic control of these traits and their relationship with lodging is lacking in temperate cereals such as barley. To fill this gap, we developed an image analysis-based protocol to accurately phenotype culm diameters and culm wall thickness across 261 barley accessions. Analysis of culm trait data collected from field trials in seven different environments revealed high heritability values (>50%) for most traits except thickness and stiffness, as well as genotype-by-environment interactions. The collection was structured mainly according to row-type, which had a confounding effect on culm traits as evidenced by phenotypic correlations. Within both row-type subsets, outer diameter and section modulus showed significant negative correlations with lodging (<-0.52 and <-0.45, respectively), but no correlation with plant height, indicating the possibility of improving lodging resistance independent of plant height. Using 50k iSelect SNP genotyping data, we conducted multi-environment genome-wide association studies using mixed model approach across the whole panel and row-type subsets: we identified a total of 192 quantitative trait loci (QTLs) for the studied traits, including subpopulation-specific QTLs and 21 main effect loci for culm diameter and/or section modulus showing effects on lodging without impacting plant height. Providing insights into the genetic architecture of culm morphology in barley and the possible role of candidate genes involved in hormone and cell wall-related pathways, this work supports the potential of loci underpinning culm features to improve lodging resistance and increase barley yield stability under changing environments.
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Affiliation(s)
- Gianluca Bretani
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Salar Shaaf
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Tondelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Luigi Cattivelli
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Stefano Delbono
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Fiorenzuola d’Arda, Italy
| | - Robbie Waugh
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - William Thomas
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Joanne Russell
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Hazel Bull
- Cell and Molecular Sciences, The James Hutton Institute, Dundee, United Kingdom
| | - Ernesto Igartua
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Ana M. Casas
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Pilar Gracia
- Aula Dei Experimental Station (EEAD-CSIC), Spanish Research Council, Zaragoza, Spain
| | - Roberta Rossi
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
| | - Alan H. Schulman
- Viikki Plant Sciences Centre, Natural Resources Institue (LUKE), HiLIFE Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Laura Rossini
- Department of Agricultural and Environmental Sciences - Production, Landscape, Agroenergy, Università degli Studi di Milano, Milan, Italy
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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: 5] [Impact Index Per Article: 2.5] [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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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: 6] [Impact Index Per Article: 2.0] [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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Guo Z, Liu X, Zhang B, Yuan X, Xing Y, Liu H, Luo L, Chen G, Xiong L. Genetic analyses of lodging resistance and yield provide insights into post-Green-Revolution breeding in rice. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:814-829. [PMID: 33159401 PMCID: PMC8051602 DOI: 10.1111/pbi.13509] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 10/22/2020] [Accepted: 11/01/2020] [Indexed: 05/10/2023]
Abstract
Lodging reduces grain yield in cereal crops. Understanding the genetic basis of lodging resistance (LR) benefits LR breeding. In the study, 524 accessions from a rice germplasm collection and 193 recombinant inbred lines were phenotyped for 17 LR-related traits. Height and culm strength (the magnitude of applied force necessary to break the culm) were two major factors affecting LR. We conducted genome-wide association study (GWAS) and identified 127 LR-associated loci. Significant phenotypic correlations between culm-strength traits and yield-related traits were observed. To reveal the genetic relationship between them, we conducted GWAS of culm-strength traits with adding yield-related trait as a covariate and detected 63 loci linking culm strength and yield. As a proof, a near-isogenic line for an association locus on chromosome 7 showed enhanced LR and yield. Strikingly, 58 additional loci were identified in the covariate-added GWAS. Several LR-associated loci had undergone divergent selection. Linkage analysis supported the GWAS results. We propose that introgression of alleles beneficial for both culm strength and panicle weight without negative effects on panicle number or pyramiding high-yielding alleles and lodging-resistant alleles without effects on yield can be employed for the post-Green-Revolution breeding.
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Affiliation(s)
- Zilong Guo
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
- Fujian Agriculture and Forestry UniversityFuzhouChina
| | - Xiao Liu
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverHuazhong Agricultural UniversityWuhanChina
| | - Bo Zhang
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Xinjie Yuan
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverHuazhong Agricultural UniversityWuhanChina
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
| | - Hongyan Liu
- Shanghai Agrobiological Gene CenterShanghaiChina
| | - Lijun Luo
- Shanghai Agrobiological Gene CenterShanghaiChina
| | - Guoxing Chen
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze RiverHuazhong Agricultural UniversityWuhanChina
| | - Lizhong Xiong
- National Key Laboratory of Crop Genetic ImprovementNational Center of Plant Gene ResearchHuazhong Agricultural UniversityWuhanChina
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10
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Identification of a novel QTL and candidate gene associated with grain size using chromosome segment substitution lines in rice. Sci Rep 2021; 11:189. [PMID: 33420305 PMCID: PMC7794494 DOI: 10.1038/s41598-020-80667-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/24/2020] [Indexed: 12/18/2022] Open
Abstract
Rice is one of the staple crops in the world. Grain size is an important determinant of rice grain yield, but the genetic basis of the grain size remains unclear. Here, we report a set of chromosome segment substitution lines (CSSL) developed in the genetic background of the genome-sequenced indica cultivar Zhenshan 97. Genotyping of the CSSLs by single nucleotide polymorphism array shows that most carry only one or two segments introduced from the genome-sequenced japonica cultivar Nipponbare. Using this population and the high-density markers, a total of 43 quantitative trait loci were identified for seven panicle- and grain-related traits. Among these loci, the novel locus qGL11 for grain length and thousand-grain weight was validated in a CSSL-derived segregating population and finely mapped to a 25-kb region that contains an IAA-amido synthetase gene OsGH3.13, This gene exhibited a significant expression difference in the young panicle between the near-isogenic lines that carry the contrasting Zhenshan 97 and Nipponbare alleles at qGL11. Expression and sequence analyses suggest that this gene is the most likely candidate for qGL11. Furthermore, several OsGH3.13 mutants induced by a CRISPR/Cas9 approach in either japonica or indica exhibit an increased grain length and thousand-grain weight, thus enhancing the final grain yield per plant. These findings provide insights into the genetic basis of grain size for the improvement of yield potential in rice breeding programs.
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11
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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: 11] [Impact Index Per Article: 2.8] [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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12
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Cui Y, Hu X, Liang G, Feng A, Wang F, Ruan S, Dong G, Shen L, Zhang B, Chen D, Zhu L, Hu J, Lin Y, Guo L, Matsuoka M, Qian Q. Production of novel beneficial alleles of a rice yield-related QTL by CRISPR/Cas9. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:1987-1989. [PMID: 32115804 PMCID: PMC7540660 DOI: 10.1111/pbi.13370] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/06/2020] [Accepted: 02/17/2020] [Indexed: 05/04/2023]
Affiliation(s)
- Yongtao Cui
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Xingming Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Guohua Liang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Key Laboratory of Plant Functional Genomics of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Anhui Feng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Fanmiao Wang
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Shuang Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guojun Dong
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Lan Shen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dongdong Chen
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Zhu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Yongjun Lin
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research, Huazhong Agricultural University, Wuhan, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Makoto Matsuoka
- Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
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13
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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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14
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Balakrishnan D, Surapaneni M, Yadavalli VR, Addanki KR, Mesapogu S, Beerelli K, Neelamraju S. Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross. Sci Rep 2020; 10:7766. [PMID: 32385410 PMCID: PMC7210974 DOI: 10.1038/s41598-020-64300-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 04/10/2020] [Indexed: 12/25/2022] Open
Abstract
Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC2F8 generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.
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15
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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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16
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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: 45] [Impact Index Per Article: 9.0] [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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17
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Zhang B, Shang L, Ruan B, Zhang A, Yang S, Jiang H, Liu C, Hong K, Lin H, Gao Z, Hu J, Zeng D, Guo L, Qian Q. Development of Three Sets of High-Throughput Genotyped Rice Chromosome Segment Substitution Lines and QTL Mapping for Eleven Traits. RICE (NEW YORK, N.Y.) 2019; 12:33. [PMID: 31076960 PMCID: PMC6510774 DOI: 10.1186/s12284-019-0293-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 04/22/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Detecting and mapping chromosomal regions that are related to quantitative phenotypic variation in chromosome segment substitution lines (CSSLs) provides an effective means to characterize the genetic basis of complex agronomic trait. CSSLs are also powerful tools for studying the effects of quantitative trait loci (QTLs) pyramiding and interaction on phenotypic variation. RESULTS Here, we developed three sets of CSSLs consisting of 81, 55, and 61 lines, which were derived from PA64s × 9311, Nipponbare × 9311 and PA64s × Nipponbare crosses, respectively. All of the 197 CSSLs were subjected to high-throughput genotyping by whole-genome resequencing to obtain accurate physical maps for the 3 sets of CSSLs. The 3 sets of CSSLs were used to analyze variation for 11 major agronomic traits in Hangzhou and Shenzhen and led to the detection of 71 QTLs with phenotypic effect that ranged from 7.6% to 44.8%. Eight QTLs were commonly detected under two environments for the same phenotype, and there were also 8 QTL clusters that were found. Combined with GWAS on grain length and expression profiles on young panicle tissues, qGL1 detected in CSSLs was fine mapped within a 119 kb region on chromosome 1 and LOC_Os01g53140 and LOC_Os01g53250 were the two most likely candidate genes. CONCLUSIONS Our results indicate that developing CSSLs genotyped by whole-genome resequencing are powerful tools for basic genetic research and provide a platform for the rational design of rice breeding. Meanwhile, the conjoint analysis of different CSSLs, natural population and expression profiles can facilitate QTL fine mapping.
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Affiliation(s)
- Bin Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Lianguang Shang
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Banpu Ruan
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Anpeng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Shenglong Yang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Hongzhen Jiang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Chaolei Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Kai Hong
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Hai Lin
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Zhenyu Gao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Dali Zeng
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, 310006, China.
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
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18
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Khobra R, Sareen S, Meena BK, Kumar A, Tiwari V, Singh GP. Exploring the traits for lodging tolerance in wheat genotypes: a review. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2019; 25:589-600. [PMID: 31168225 PMCID: PMC6522606 DOI: 10.1007/s12298-018-0629-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 11/02/2018] [Accepted: 11/20/2018] [Indexed: 05/23/2023]
Abstract
The rising population entails enhancement in wheat productivity to ensure substantial food supply which often get hindered by various biotic and abiotic stresses. Lodging, due to rain and high velocity wind causes significant economic and yield losses in cereals. Hence, lodging is emerging as a major hurdle to achieve the required yield targets. Various morphological, biochemical, anatomical and genetic traits contribute to produce a plant competent enough to bear lodging stress. Hence, in this review, we intend to elaborate the cause and impact relationship of lodging and tried to link lodging tolerance traits to field practices to minimize the losses. Because of the complex nature of lodging phenomenon, it is still obscure to identify best correlated traits to screen genotype in breeding programmes. However, the genotypes with best correlated traits like plant height, culm wall thickness should be introduced/selected in breeding programmes to inculcate lodging tolerance in a high yielding variety as in recent era lodging tolerance is a key factor to enhance productivity and farmer's income as well.
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Affiliation(s)
- Rinki Khobra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - Braj Kishor Meena
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - Arvind Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - Vinod Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
| | - G. P. Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana 132001 India
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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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