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Bian Z, Cao D, Zou Y, Xie D, Zhuang W, Sun Z, Mou N, Sun Y, Zhang C, Li Q, Liu Q, Zhang L. Genetic Dissection of Major Rice QTLs for Strong Culms and Fine Mapping of qWS5 for Breeding Application in Transplanted System. RICE (NEW YORK, N.Y.) 2024; 17:43. [PMID: 38995403 PMCID: PMC11245457 DOI: 10.1186/s12284-024-00723-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Accepted: 06/30/2024] [Indexed: 07/13/2024]
Abstract
BACKGROUND Rice is one of the major staples that feeds about one half of the global populations, and it is important to identify the genetic loci for the traits related to yield improvement. Lodging will cause severe yield loss when it happens, and stem diameter has been characterized as an important trait for lodging resistance. However, most QTLs for stem diameter have not been finely dissected due to their sensitivity to environmental fluctuation. RESULT In this study, we performed QTL analysis for stem diameter using populations derived from Nipponbare (NIP) and strong culm variety YYP1, and confirmed the single and combined effect of three major QTLs by recombinant inbred lines (RILs). Based on the QTL location, we found that qWS5 is a novel QTL not well characterized before. To finely dissect the novel locus, several recombinant heterogeneous inbred families (HIFs) were selected from the RILs for linkage analysis and their derived nearly isogenic lines (NILs) were subjected to detailed trait investigation throughout different years. The HIF-NILs strategy confined the QTL to about 380 kb region supported by repeated genotype and phenotype data, and it lays the foundation for QTL cloning in the future. In addition, introgression of the QTL to an elite japonica variety SD785 was performed by successive backcrossing, and it confirmed the value of qWS5 in increasing stem diameter and other agronomic traits during rice breeding. CONCLUSIONS We prove that qWS5 is a novel QTL with relatively stable effect for stem diameter and the QTL can be finely mapped to small region by the HIF-NILs strategy. The result will facilitate the improvement of rice lodging resistance by molecular marker assisted selection breeding.
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Affiliation(s)
- Zhong Bian
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Dongping Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Yiting Zou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Dong Xie
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Wenshu Zhuang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Zixing Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Nana Mou
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Yangyang Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China
| | - Changquan Zhang
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
| | - Qianfeng Li
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops/Jiangsu Key Laboratory of Crop Genetics and Physiology, Yangzhou University, Yangzhou, China.
| | - Lin Zhang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education/Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, China.
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2
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Zhao J, Wang J, Liu J, Zhang P, Kudoyarova G, Liu CJ, Zhang K. Spatially distributed cytokinins: Metabolism, signaling, and transport. PLANT COMMUNICATIONS 2024; 5:100936. [PMID: 38689499 DOI: 10.1016/j.xplc.2024.100936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/25/2024] [Accepted: 04/28/2024] [Indexed: 05/02/2024]
Abstract
Cytokinins are mobile phytohormones that regulate plant growth, development, and environmental adaptability. The major cytokinin species include isopentenyl adenine (iP), trans-zeatin (tZ), cis-zeatin (cZ), and dihydrozeatin (DZ). The spatial distributions of different cytokinin species in different organelles, cells, tissues, and organs are primarily shaped by biosynthesis via isopentenyltransferases (IPT), cytochrome P450 monooxygenase, and 5'-ribonucleotide phosphohydrolase and by conjugation or catabolism via glycosyltransferase or cytokinin oxidase/dehydrogenase. Cytokinins bind to histidine receptor kinases in the endoplasmic reticulum or plasma membrane and relay signals to response regulators in the nucleus via shuttle proteins known as histidine phosphotransfer proteins. The movements of cytokinins from sites of biosynthesis to sites of signal perception usually require long-distance, intercellular, and intracellular transport. In the past decade, ATP-binding cassette (ABC) transporters, purine permeases (PUP), AZA-GUANINE RESISTANT (AZG) transporters, equilibrative nucleoside transporters (ENT), and Sugars Will Eventually Be Exported transporters (SWEET) have been characterized as involved in cytokinin transport processes. This review begins by introducing the spatial distributions of various cytokinins and the subcellular localizations of the proteins involved in their metabolism and signaling. Highlights focus on an inventory of the characterized transporters involved in cytokinin compartmentalization, including long-distance, intercellular, and intracellular transport, and the regulation of the spatial distributions of cytokinins by environmental cues. Future directions for cytokinin research are also discussed.
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Affiliation(s)
- Jiangzhe Zhao
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Jingqi Wang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Jie Liu
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Penghong Zhang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China
| | - Guzel Kudoyarova
- Ufa Institute of Biology, Ufa Federal Research Center, RAS, Prospekt Oktyabrya 69, Ufa 450054, Russia
| | - Chang-Jun Liu
- Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Kewei Zhang
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, College of Life Sciences, Zhejiang Normal University, Jinhua, Zhejiang 321004, P.R. China.
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3
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Yang H, Huang J, Ye Y, Xu Y, Xiao Y, Chen Z, Li X, Ma Y, Lu T, Rao Y. Research Progress on Mechanical Strength of Rice Stalks. PLANTS (BASEL, SWITZERLAND) 2024; 13:1726. [PMID: 38999566 PMCID: PMC11243543 DOI: 10.3390/plants13131726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 06/17/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
As one of the most important food crops in the world, rice yield is directly related to national food security. Lodging is one of the most important factors restricting rice production, and the cultivation of rice varieties with lodging resistance is of great significance in rice breeding. The lodging resistance of rice is directly related to the mechanical strength of the stalks. In this paper, we reviewed the cell wall structure, its components, and its genetic regulatory mechanism, which improved the regulatory network of rice stalk mechanical strength. Meanwhile, we analyzed the new progress in genetic breeding and put forward some scientific problems that need to be solved in this field in order to provide theoretical support for the improvement and application of rice breeding.
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Affiliation(s)
- Huimin Yang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jiahui Huang
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuhan Ye
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuqing Xu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yao Xiao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Ziying Chen
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Xinyu Li
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yingying Ma
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Tao Lu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Yuchun Rao
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China
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4
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Zhang X, Meng W, Liu D, Pan D, Yang Y, Chen Z, Ma X, Yin W, Niu M, Dong N, Liu J, Shen W, Liu Y, Lu Z, Chu C, Qian Q, Zhao M, Tong H. Enhancing rice panicle branching and grain yield through tissue-specific brassinosteroid inhibition. Science 2024; 383:eadk8838. [PMID: 38452087 DOI: 10.1126/science.adk8838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024]
Abstract
Crop yield potential is constrained by the inherent trade-offs among traits such as between grain size and number. Brassinosteroids (BRs) promote grain size, yet their role in regulating grain number is unclear. By deciphering the clustered-spikelet rice germplasm, we show that activation of the BR catabolic gene BRASSINOSTEROID-DEFICIENT DWARF3 (BRD3) markedly increases grain number. We establish a molecular pathway in which the BR signaling inhibitor GSK3/SHAGGY-LIKE KINASE2 phosphorylates and stabilizes OsMADS1 transcriptional factor, which targets TERMINAL FLOWER1-like gene RICE CENTRORADIALIS2. The tissue-specific activation of BRD3 in the secondary branch meristems enhances panicle branching, minimizing negative effects on grain size, and improves grain yield. Our study showcases the power of tissue-specific hormonal manipulation in dismantling the trade-offs among various traits and thus unleashing crop yield potential in rice.
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Affiliation(s)
- Xiaoxing Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenjing Meng
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dapu Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dezhuo Pan
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Yanzhao Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhuo Chen
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoding Ma
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenchao Yin
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mei Niu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Nana Dong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jihong Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weifeng Shen
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Yuqin Liu
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Zefu Lu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chengcai Chu
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Qian Qian
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Mingfu Zhao
- Rice Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou 350018, China
| | - Hongning Tong
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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Fan C, Xu D, Wang C, Chen Z, Dou T, Qin D, Guo A, Zhao M, Pei H, Zhao M, Zhang R, Wang K, Zhang J, Ni Z, Guo G. Natural variations of HvSRN1 modulate the spike rachis node number in barley. PLANT COMMUNICATIONS 2024; 5:100670. [PMID: 37563835 PMCID: PMC10811343 DOI: 10.1016/j.xplc.2023.100670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 07/13/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Grain number, one of the major determinants of yield in Triticeae crops, is largely determined by spikelet number and spike rachis node number (SRN). Here, we identified three quantitative trait loci (QTLs) for SRN using 145 recombinant inbred lines derived from a barley R90/1815D cross. qSRN1, the major-effect QTL, was mapped to chromosome 2H and explained up to 38.77% of SRN variation. Map-based cloning revealed that qSRN1 encodes the RAWUL domain-containing protein HvSRN1. Further analysis revealed that two key SNPs in the HvSRN1 promoter region (∼2 kb upstream of the transcription start site) affect the transcript level of HvSRN1 and contribute to variation in SRN. Similar to its orthologous proteins OsLAX2 and ZmBA2, HvSRN1 showed protein-protein interactions with HvLAX1, suggesting that the LAX2-LAX1 model for spike morphology regulation may be conserved in Poaceae crops. CRISPR-Cas9-induced HvSRN1 mutants showed reduced SRN but increased grain size and weight, demonstrating a trade-off effect. Our results shed light on the role of HvSRN1 variation in regulating the balance between grain number and weight in barley.
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Affiliation(s)
- Chaofeng Fan
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China
| | - Dongdong Xu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China; Institute of Industrial Crops, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunchao Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhaoyan Chen
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Tingyu Dou
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Dandan Qin
- Key Laboratory for Crop Molecular Breeding of Ministry of Agriculture and Rural Affairs, Institute of Food Crops, Hubei Academy of Agricultural Sciences, Wuhan 430064, China
| | - Aikui Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Meng Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Honghong Pei
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Mengwei Zhao
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Renxu Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Ke Wang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Jing Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China
| | - Zhongfu Ni
- Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China.
| | - Ganggang Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization (MARA), The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (ICS-CAAS), Beijing 100081, China.
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6
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Zhang Y, Shen C, Shi J, Shi J, Zhang D. Boosting Triticeae crop grain yield by manipulating molecular modules to regulate inflorescence architecture: insights and knowledge from other cereal crops. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:17-35. [PMID: 37935244 DOI: 10.1093/jxb/erad386] [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: 03/28/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
One of the challenges for global food security is to reliably and sustainably improve the grain yield of cereal crops. One solution is to modify the architecture of the grain-bearing inflorescence to optimize for grain number and size. Cereal inflorescences are complex structures, with determinacy, branching patterns, and spikelet/floret growth patterns that vary by species. Recent decades have witnessed rapid advancements in our understanding of the genetic regulation of inflorescence architecture in rice, maize, wheat, and barley. Here, we summarize current knowledge on key genetic factors underlying the different inflorescence morphologies of these crops and model plants (Arabidopsis and tomato), focusing particularly on the regulation of inflorescence meristem determinacy and spikelet meristem identity and determinacy. We also discuss strategies to identify and utilize these superior alleles to optimize inflorescence architecture and, ultimately, improve crop grain yield.
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Affiliation(s)
- Yueya Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Chaoqun Shen
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Shanghai 200240, China
- Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Sanya 572025, China
- School of Agriculture, Food, and Wine, University of Adelaide, Adelaide, South Australia 5064, Australia
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7
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Liu Z, Sun H, Zhang Y, Du M, Xiang J, Li X, Chang Y, Sun J, Cheng X, Xiong M, Zhao Z, Liu E. Mining the candidate genes of rice panicle traits via a genome-wide association study. Front Genet 2023; 14:1239550. [PMID: 37732315 PMCID: PMC10507276 DOI: 10.3389/fgene.2023.1239550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/16/2023] [Indexed: 09/22/2023] Open
Abstract
Panicle traits are important for improving the panicle architecture and grain yield of rice. Therefore, we performed a genome-wide association study (GWAS) to analyze and determine the genetic determinants of five panicle traits. A total of 1.29 million single nucleotide polymorphism (SNP) loci were detected in 162 rice materials. We carried out a GWAS of panicle length (PL), total grain number per panicle (TGP), filled grain number per panicle (FGP), seed setting rate (SSR) and grain weight per panicle (GWP) in 2019, 2020 and 2021. Four quantitative trait loci (QTLs) for PL were detected on chromosomes 1, 6, and 9; one QTL for TGP, FGP, and GWP was detected on chromosome 4; two QTLs for FGP were detected on chromosomes 4 and 7; and one QTL for SSR was detected on chromosome 1. These QTLs were detected via a general linear model (GLM) and mixed linear model (MLM) in both years of the study period. In this study, the genomic best linear unbiased prediction (BLUP) method was used to verify the accuracy of the GWAS results. There are nine QTLs were both detected by the multi-environment GWAS method and the BLUP method. Moreover, further analysis revealed that three candidate genes, LOC_Os01g43700, LOC_Os09g25784, and LOC_Os04g47890, may be significantly related to panicle traits of rice. Haplotype analysis indicated that LOC_Os01g43700 and LOC_Os09g25784 are highly associated with PL and that LOC_Os04g47890 is highly associated with TGP, FGP, and GWP. Our results offer essential genetic information for the molecular improvement of panicle traits. The identified candidate genes and elite haplotypes could be used in marker-assisted selection to improve rice yield through pyramid breeding.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Erbao Liu
- College of Agronomy, Anhui Agricultural University, Hefei, China
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8
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Wang S, Wu H, Lu Z, Liu W, Wang X, Fang Z, He X. Combining Ability Analysis of Yield-Related Traits of Two Elite Rice Restorer Lines in Chinese Hybrid Rice. Int J Mol Sci 2023; 24:12395. [PMID: 37569770 PMCID: PMC10418745 DOI: 10.3390/ijms241512395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023] Open
Abstract
Hybrid rice breeding is an important strategy for enhancing grain yield. Breeding high-performance parental lines and identifying combining abilities is a top priority for hybrid breeding. Yuenongsimiao (YNSM) and its derivative variety Yuehesimiao (YHSM) are elite restorer lines with a high ability of fertility restoration, from which 67 derived hybrid combinations have been authorized to different degrees in more than 110 instances in China. In this study, we found that YNSM and YHSM contained three candidate restorer-of-fertility (Rf) genes, Rf3, Rf4, and Rf5/Rf1a, that might confer their restoration ability. Subsequently, we investigated heterosis and combining ability of YNSM and YHSM using 50 F1 hybrids from a 5 × 10 incomplete diallelic mating design. Our results indicated that hybrid combinations exhibited significant genetic differences, and the additive effects of the parental genes played a preponderant role in the inheritance of observed traits. The metrics of plant height (PH), 1000-grain weight (TGW), panicle length (PL), and the number of spikelets per panicle (NSP) were mainly affected by genetic inheritance with higher heritability. Notably, the general combining ability (GCA) of YHSM exhibited the largest positive effect on the number of grains per panicle (NGP), NSP, PL, and TGW. Thus, YHSM had the largest GCA effect on yield per plant (YPP). In addition, the GCA of YNSM exhibited a positive impact on YPP, mainly due to the critical contribution of seed setting percentage (SSP). Moreover, YNSM and YHSM exhibited negative GCA effects on PH, implying that YNSM and YHSM could effectively enhance plant lodging resistance by reducing the plant height of the derived hybrids. Remarkably, among the hybrids, Yuanxiang A/YNSM (YXA/YNSM), Shen 08S/Yuemeizhan (S08S/YMZ), and Quan 9311A/YHSM (Q9311A/YHSM) represent promising new combinations with a higher specific combining ability (SCA) effect value on YPP with a value more than 3.50. Our research thus highlights the promising application for the rational utilization of YNSM and YHSM in hybrid rice breeding.
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Affiliation(s)
- Shiguang Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Haoxiang Wu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhanhua Lu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Wei Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiaofei Wang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Zhiqiang Fang
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
| | - Xiuying He
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China; (S.W.); (H.W.); (Z.L.); (W.L.); (X.W.); (Z.F.)
- Key Laboratory of Genetics and Breeding of High Quality Rice in Southern China (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangzhou 510640, China
- Guangdong Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, China
- Guangdong Rice Engineering Laboratory, Guangzhou 510640, China
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9
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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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10
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Li J, Zhang C, Luo X, Zhang T, Zhang X, Liu P, Yang W, Lei Y, Tang S, Kang L, Huang L, Li T, Wang Y, Chen W, Yuan H, Qin P, Li S, Ma B, Tu B. Fine mapping of the grain chalkiness quantitative trait locus qCGP6 reveals the involvement of Wx in grain chalkiness formation. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad112. [PMID: 36964899 DOI: 10.1093/jxb/erad112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Indexed: 06/18/2023]
Abstract
Grain chalkiness is an important index of rice appearance quality and is negatively associated with rice processing and eating qualities. However, the genetic mechanism underlying chalkiness formation is largely unknown. To identify the genetic basis of chalkiness, 410 recombinant inbred lines (RILs) derived from two representative indica rice varieties, Shuhui498 (R498) and Yihui3551 (R3551), were used to discover quantitative trait loci (QTL). The two parental lines and RILs were grown in three locations in China under three controlled fertilizer application level. Analyses indicated that chalkiness was significantly affected by genotype, the environment, and the interaction between the two, and that heritability was high. Several QTLs were isolated, including the two stable QTLs, i.e., qCGP6 and qCGP8. Fine mapping and candidate gene verification of qCGP6 showed that Wx may play a key role in chalkiness formation. Chromosomal segment substitution lines (CSSLs) and near-isogenic lines (NILs) carrying the Wxa or Wxin allele produced more chalky grain than the R498 parent. A similar result was also observed in the 3611 background. Notably, the effect of the Wx genotype on rice chalkiness was shown to be dependent on environmental conditions and Wx alleles exhibited different sensitivities to shading treatment. Using CRISPR/Cas9, the Wxa promoter region was successfully edited, down-regulating Wx alleviates chalkiness formation in NILR498-Wxa. This study developed a new strategy for synergistic improvement of eating and appearance qualities in rice, and created a novel Wx allele with great potential in breeding applications.
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Affiliation(s)
- Jialian Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Cheng Zhang
- Liaoning Rice Research Institute, Shenyang, Liaoning 110101, China
| | - Xia Luo
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoyu Zhang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Pin Liu
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Wen Yang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Yuekun Lei
- Chengdu Juannong Intelligent Agriculture Technology Development Co., Ltd
| | - Siwen Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Liangzhu Kang
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Lin Huang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Ting Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Yuping Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Weilan Chen
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Hua Yuan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
| | - Peng Qin
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Shigui Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Bingtian Ma
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
| | - Bin Tu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu 611130, China
- Rice Research Institute of Sichuan Agricultural University, Chengdu 611130, China
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11
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Tanaka W, Yamauchi T, Tsuda K. Genetic basis controlling rice plant architecture and its modification for breeding. BREEDING SCIENCE 2023; 73:3-45. [PMID: 37168811 PMCID: PMC10165344 DOI: 10.1270/jsbbs.22088] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/25/2022] [Indexed: 05/13/2023]
Abstract
The shoot and root system architectures are fundamental for crop productivity. During the history of artificial selection of domestication and post-domestication breeding, the architecture of rice has significantly changed from its wild ancestor to fulfil requirements in agriculture. We review the recent studies on developmental biology in rice by focusing on components determining rice plant architecture; shoot meristems, leaves, tillers, stems, inflorescences and roots. We also highlight natural variations that affected these structures and were utilized in cultivars. Importantly, many core regulators identified from developmental mutants have been utilized in breeding as weak alleles moderately affecting these architectures. Given a surge of functional genomics and genome editing, the genetic mechanisms underlying the rice plant architecture discussed here will provide a theoretical basis to push breeding further forward not only in rice but also in other crops and their wild relatives.
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Affiliation(s)
- Wakana Tanaka
- Graduate School of Integrated Sciences for Life, Hiroshima University, 1-4-4 Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8528, Japan
| | - Takaki Yamauchi
- Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan
| | - Katsutoshi Tsuda
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
- Corresponding author (e-mail: )
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12
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Zheng X, Zhang S, Liang Y, Zhang R, Liu L, Qin P, Zhang Z, Wang Y, Zhou J, Tang X, Zhang Y. Loss-function mutants of OsCKX gene family based on CRISPR-Cas systems revealed their diversified roles in rice. THE PLANT GENOME 2023:e20283. [PMID: 36660867 DOI: 10.1002/tpg2.20283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/08/2022] [Indexed: 06/17/2023]
Abstract
Cytokinin (CTK) is an important plant hormone that promotes cell division, controls cell differentiation, and regulates a variety of plant growth and development processes. Cytokinin oxidase/dehydrogenase (CKX) is an irreversible cytokinin-degrading enzyme that affects plant growth and development by regulating the dynamic balance of CTKs synthesis and degradation. There are presumed 11 members of the CKX gene family in rice (Oryza sativa L.), but limited members have been reported. In this study, based on CRISPR-Cas9 and CRISPR-Cas12a genome-editing technology, we established a complete set of OsCKX1-OsCKX11 single-gene mutants, as well as double-gene and triple-gene mutants of different OsCKXs gene combinations with high similarity. The results revealed that CRISPR-Cas12a outperformed Cas9 to generate biallelic mutations, multi-gene mutants, and more diverse genotypes. And then, we found, except the reported OsCKX2, OsCKX4, OsCKX9 and OsCKX11, OsCKX5, OsCKX6, OsCKX7, and OsCKX8 also had significant effects on agronomic traits such as plant height, panicle size, grain size, and grain number per panicle in rice. In addition, the different loss-of-function of the OsCKX genes also changed the seed appearance quality and starch composition. Interestingly, by comparing different combinations of multi-gene mutants, we found significant functional redundancy among OsCKX gene members in the same phylogenetic clade. These data collectively reveal the diversified regulating capabilities of OsCKX genes in rice, and also provide the valuable reference for further rice molecular breeding.
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Affiliation(s)
- Xuelian Zheng
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Shuting Zhang
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Yanling Liang
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Rui Zhang
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Li Liu
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Pengchen Qin
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Zhe Zhang
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Yan Wang
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Jianping Zhou
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Xu Tang
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
| | - Yong Zhang
- Dep. of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, Univ. of Electronic Science and Technology of China, Chengdu, 610054, China
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13
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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: 5] [Impact Index Per Article: 5.0] [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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14
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Huang P, Zhao J, Hong J, Zhu B, Xia S, Zhu E, Han P, Zhang K. Cytokinins regulate rice lamina joint development and leaf angle. PLANT PHYSIOLOGY 2023; 191:56-69. [PMID: 36031806 PMCID: PMC9806582 DOI: 10.1093/plphys/kiac401] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Leaf angle is determined by lamina joint inclination and is an important agronomic trait that determines plant architecture, photosynthetic efficiency, and crop yield. Cytokinins (CKs) are phytohormones involved in shaping rice (Oryza sativa L.) architecture, but their role in leaf angle remains unknown. Here, we report that CK accumulation mediated by rice CK OXIDASE/DEHYDROGENASE3 (OsCKX3) controls lamina joint development and negatively regulates leaf angle. Phenotypic analysis showed that rice osckx3 mutants had smaller leaf angles, while the overexpression lines (OsCKX3-OE) had larger leaf angles. Histological sections indicated that the leaf inclination changes in the osckx3 and OsCKX3-OE lines resulted from asymmetric proliferation of the cells and vascular bundles in the lamina joint. Reverse transcription quantitative PCR, promoter-fused β-glucuronidase expression, and subcellular localization assays indicated that OsCKX3 was highly expressed in the lamina joint, and OsCKX3-GFP fusion protein localized to the endoplasmic reticulum. The enzyme assays using recombinant protein OsCKX3 revealed that OsCKX3 prefers trans-zeatin (tZ) and isopentenyladenine (iP). Consistently, tZ and iP levels increased in the osckx3 mutants but decreased in the OsCKX3 overexpression lines. Interestingly, agronomic trait analysis of the rice grown in the paddy field indicated that osckx3 displayed a smaller leaf angle and enhanced primary branch number, grain size, 1,000-grain weight, and flag leaf size. Collectively, our results revealed that enhancing CK levels in the lamina joint by disrupting OsCKX3 negatively regulates leaf angle, highlighting that the CK pathway can be engineered to reduce leaf angle in rice and possibly in other cereals.
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Affiliation(s)
- Peng Huang
- Institute of Plant Stress Adaptation and Genetic Enhancement, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jiangzhe Zhao
- Institute of Plant Stress Adaptation and Genetic Enhancement, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Jiale Hong
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Bao Zhu
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Shuai Xia
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Engao Zhu
- Institute of Plant Stress Adaptation and Genetic Enhancement, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Pingfei Han
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
| | - Kewei Zhang
- Institute of Plant Stress Adaptation and Genetic Enhancement, Zhejiang Normal University, Jinhua 321004, China
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Department of Biology, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, China
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15
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Zhao H, Liu X, Wang J, Qian Q, Zhang G. The coordinated regulation mechanism of rice plant architecture and its tolerance to stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1087378. [PMID: 36600918 PMCID: PMC9807110 DOI: 10.3389/fpls.2022.1087378] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
Rice plant architecture and stress tolerance have historically been primary concerns for rice breeders. The "Green Revolution" and super-rice breeding practices have demonstrated that ideal plant architecture can effectively improve both stress tolerance and yield. The synergistic selection and breeding of rice varieties with ideal architecture and stress tolerance can increase and stabilize yield. While rice plant plant architecture and stress tolerance are separately regulated by complicated genetic networks, the molecular mechanisms underlying their relationships and synergism have not yet been explored. In this paper, we review the regulatory mechanism between plant architecture, stress tolerance, and biological defense at the different level to provide a theoretical basis for the genetic network of the synergistic regulation and improvement of multiple traits.
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Affiliation(s)
- Huibo Zhao
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Xiong Liu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Jiajia Wang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Guangheng Zhang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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16
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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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Lu Y, Chuan M, Wang H, Chen R, Tao T, Zhou Y, Xu Y, Li P, Yao Y, Xu C, Yang Z. Genetic and molecular factors in determining grain number per panicle of rice. FRONTIERS IN PLANT SCIENCE 2022; 13:964246. [PMID: 35991390 PMCID: PMC9386260 DOI: 10.3389/fpls.2022.964246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
It was suggested that the most effective way to improve rice grain yield is to increase the grain number per panicle (GN) through the breeding practice in recent decades. GN is a representative quantitative trait affected by multiple genetic and environmental factors. Understanding the mechanisms controlling GN has become an important research field in rice biotechnology and breeding. The regulation of rice GN is coordinately controlled by panicle architecture and branch differentiation, and many GN-associated genes showed pleiotropic effect in regulating tillering, grain size, flowering time, and other domestication-related traits. It is also revealed that GN determination is closely related to vascular development and the metabolism of some phytohormones. In this review, we summarize the recent findings in rice GN determination and discuss the genetic and molecular mechanisms of GN regulators.
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Affiliation(s)
- Yue Lu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Mingli Chuan
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Hanyao Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Rujia Chen
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Tianyun Tao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Yong Zhou
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Yang Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Pengcheng Li
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
| | - Youli Yao
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Chenwu Xu
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
| | - Zefeng Yang
- Key Laboratory of Plant Functional Genomics of the Ministry of Education, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, College of Agriculture, Yangzhou University, Yangzhou, China
- Jiangsu Key Laboratory of Crop Genetics and Physiology, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of the Ministry of Education, Yangzhou University, Yangzhou, China
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19
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Yang Y, Dong S, Miao H, Liu X, Dai Z, Li X, Gu X, Zhang S. Genome-Wide Association Studies Reveal Candidate Genes Related to Stem Diameter in Cucumber ( Cucumis sativus L.). Genes (Basel) 2022; 13:genes13061095. [PMID: 35741858 PMCID: PMC9222855 DOI: 10.3390/genes13061095] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 06/10/2022] [Accepted: 06/16/2022] [Indexed: 02/04/2023] Open
Abstract
The stem diameter, an important agronomic trait, affects cucumber growth and yield. However, no genes responsible for cucumber stem diameter have been identified yet. In this study, the stem diameter of 88 cucumber core germplasms were measured in spring 2020, autumn 2020 and autumn 2021, and a genome-wide association study (GWAS) was carried out based on the gene sequence and stem diameter of core germplasms. A total of eight loci (gSD1.1, gSD2.1, gSD3.1, gSD3.2, gSD4.1, gSD5.1, gSD5.2, and gSD6.1) significantly associated with cucumber stem diameter were detected. Of these, five loci (gSD1.1, gSD2.1, gSD3.1, gSD5.2, and gSD6.1) were repeatedly detected in two or more seasons and were considered as robust and reliable loci. Based on the linkage disequilibrium sequences of the associated SNP loci, 37 genes were selected. By further investigating the five loci via analyzing Arabidopsis homologous genes and gene haplotypes, five genes (CsaV3_1G028310, CsaV3_2G006960, CsaV3_3G009560, CsaV3_5G031320, and CsaV3_6G031260) showed variations in amino acid sequence between thick stem lines and thin stem lines. Expression pattern analyses of these genes also showed a significant difference between thick stem and thin stem lines. This study laid the foundation for gene cloning and molecular mechanism study of cucumber stem development.
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Liu P, He L, Mei L, Zhai W, Chen X, Ma B. Rapid and Directional Improvement of Elite Rice Variety via Combination of Genomics and Multiplex Genome Editing. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6156-6167. [PMID: 35575308 DOI: 10.1021/acs.jafc.1c08028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
High yield and superior quality are the main goals pursued by breeders for crop improvement. However, both of them are complex agronomic traits controlled by multiple genes, so the simultaneous improvement of these traits via sexual recombination is time-consuming and direction-uncontrolled. In this study, to solve this dilemma, we introduced the comparative genomic analysis based multiplex genome editing system (CG-MGE), a method for rapid and directional improvement of multiple traits. Application of this method, association analysis between genotypes and phenotypes was carried out to mine excellent alleles; subsequently, the rare excellent alleles of Gn1a, GW2, TGW3, and Chalk5 were simultaneously created by multiplex genome editing and successfully improved the plant architecture, grain yield, and quality of a widely cultivated elite rice variety. Overall, this study provides a method for rapid and directional improvement of crops, and the application of the CG-MGE will be helpful to accelerate rational design breeding.
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Affiliation(s)
- Pengcheng Liu
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Lumei He
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Le Mei
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xifeng Chen
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
| | - Bojun Ma
- College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, Zhejiang, China
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