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Li X, Lowey D, Lessard J, Caicedo AL. Comparative histology of abscission zones reveals the extent of convergence and divergence in seed shattering in weedy and cultivated rice. JOURNAL OF EXPERIMENTAL BOTANY 2024:erae221. [PMID: 38972665 DOI: 10.1093/jxb/erae221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 05/29/2024] [Indexed: 07/09/2024]
Abstract
The modification of seed shattering has been a recurring theme in rice evolution. The wild ancestor of cultivated rice disperses its seeds, but reduced shattering was selected during multiple domestication events to facilitate harvesting. Conversely, selection for increased shattering occurred during the evolution of weedy rice, a weed invading cultivated rice fields that has originated multiple times from domesticated ancestors. Shattering requires formation of a tissue known as the abscission zone (AZ), but how the AZ has been modified throughout rice evolution is unclear. We quantitatively characterized the AZ characteristics of relative length, discontinuity, and intensity in 86 cultivated and weedy rice accessions. We reconstructed AZ evolutionary trajectories and determined the degree of convergence among different cultivated varieties and among independent weedy rice populations. AZ relative length emerged as the best feature to distinguish high and low shattering rice. Cultivated varieties differed in average AZ morphology, revealing lack of convergence in how shattering reduction was achieved during domestication. In contrast, weedy rice populations typically converged on complete AZs, irrespective of origin. By examining AZ population-level morphology, our study reveals its evolutionary plasticity, and suggests that the genetic potential to modify the ecologically and agronomically important trait of shattering is plentiful in rice lineages.
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Affiliation(s)
- Xiang Li
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Daniel Lowey
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Jessica Lessard
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
| | - Ana L Caicedo
- Plant Biology Graduate Program and Department of Biology, University of Massachusetts Amherst, Amherst, MA 01003, USA
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2
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Presotto A, Hernández F, Vercellino RB, Kruger RD, Fontana ML, Ureta MS, Crepy M, Auge G, Caicedo A. Introgression from local cultivars is a driver of agricultural adaptation in Argentinian weedy rice. Mol Ecol 2024; 33:e17368. [PMID: 38676602 DOI: 10.1111/mec.17368] [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: 09/30/2023] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 04/29/2024]
Abstract
Weedy rice, a pervasive and troublesome weed found across the globe, has often evolved through fertilization of rice cultivars with little importance of crop-weed gene flow. In Argentina, weedy rice has been reported as an important constraint since the early 1970s, and, in the last few years, strains with herbicide-resistance are suspected to evolve. Despite their importance, the origin and genetic composition of Argentinian weedy rice as well its adaptation to agricultural environments has not been explored so far. To study this, we conducted genotyping-by-sequencing on samples of Argentinian weedy and cultivated rice and compared them with published data from weedy, cultivated and wild rice accessions distributed worldwide. In addition, we conducted a phenotypic characterization for weedy-related traits, a herbicide resistance screening and genotyped accessions for known mutations in the acetolactate synthase (ALS) gene, which confers herbicide resistance. Our results revealed large phenotypic variability in Argentinian weedy rice. Most strains were resistant to ALS-inhibiting herbicides with a high frequency of the ALS mutation (A122T) present in Argentinian rice cultivars. Argentinian cultivars belonged to the three major genetic groups of rice: japonica, indica and aus while weeds were mostly aus or aus-indica admixed, resembling weedy rice strains from the Southern Cone region. Phylogenetic analysis supports a single origin for aus-like South American weeds, likely as seed contaminants from the United States, and then admixture with local indica cultivars. Our findings demonstrate that crop to weed introgression can facilitate rapid adaptation to agriculture environments.
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Affiliation(s)
- Alejandro Presotto
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - Fernando Hernández
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Román Boris Vercellino
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | | | | | - María Soledad Ureta
- Departamento de Agronomía, CERZOS, Universidad Nacional del Sur (UNS)-CONICET, Bahía Blanca, Argentina
| | - María Crepy
- EEA INTA Concepción del Uruguay-CONICET, Concepción del Uruguay, Entre Ríos, Argentina
| | - Gabriela Auge
- Centro de Investigaciones en Ciencias Agronómicas y Veterinarias (CICVyA), Instituto de Agrobiotecnología y Biología Molecular (IABIMO) - (INTA-CONICET), Instituto de Biotecnología, Hurlingham, Buenos Aires, Argentina
| | - Ana Caicedo
- Deparment of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Roy N, Kabir AH, Zahan N, Mouna ST, Chakravarty S, Rahman AH, Bayzid MS. Genome wide association studies on seven yield-related traits of 183 rice varieties in Bangladesh. PLANT DIRECT 2024; 8:e593. [PMID: 38887667 PMCID: PMC11182691 DOI: 10.1002/pld3.593] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 03/26/2024] [Accepted: 05/02/2024] [Indexed: 06/20/2024]
Abstract
Rice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. We performed genome wide association studies (GWASs) on seven rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width, and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWASs reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain-shape-related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. This is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh-the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.
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Affiliation(s)
- Nilanjan Roy
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
- Molecular, Cellular, and Developmental BiologyUniversity of KansasLawrenceKansasUSA
| | - Acramul Haque Kabir
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
- Department of Biomedical EngineeringUniversity of UtahSalt Lake CityUtahUSA
| | - Nourin Zahan
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
| | - Shahba Tasmiya Mouna
- Department of Biomedical EngineeringMilitary Institute of Science and TechnologyDhakaBangladesh
| | - Sakshar Chakravarty
- Department of Computer Science and EngineeringUniversity of CaliforniaRiversideCaliforniaUSA
- Department of Computer Science and EngineeringBangladesh University of Engineering and TechnologyDhakaBangladesh
| | - Atif Hasan Rahman
- Department of Computer Science and EngineeringBangladesh University of Engineering and TechnologyDhakaBangladesh
| | - Md. Shamsuzzoha Bayzid
- Department of Computer Science and EngineeringBangladesh University of Engineering and TechnologyDhakaBangladesh
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4
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Wu J, Liu H, Zhang Y, Zhang Y, Li D, Liu S, Lu S, Wei L, Hua J, Zou B. A major gene for chilling tolerance variation in Indica rice codes for a kinase OsCTK1 that phosphorylates multiple substrates under cold. THE NEW PHYTOLOGIST 2024; 242:2077-2092. [PMID: 38494697 DOI: 10.1111/nph.19696] [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: 11/20/2023] [Accepted: 02/28/2024] [Indexed: 03/19/2024]
Abstract
Rice is susceptible to chilling stress. Identifying chilling tolerance genes and their mechanisms are key to improve rice performance. Here, we performed a genome-wide association study to identify regulatory genes for chilling tolerance in rice. One major gene for chilling tolerance variation in Indica rice was identified as a casein kinase gene OsCTK1. Its function and natural variation are investigated at the physiological and molecular level by its mutants and transgenic plants. Potential substrates of OsCTK1 were identified by phosphoproteomic analysis, protein-protein interaction assay, in vitro kinase assay, and mutant characterization. OsCTK1 positively regulates rice chilling tolerance. Three of its putative substrates, acidic ribosomal protein OsP3B, cyclic nucleotide-gated ion channel OsCNGC9, and dual-specific mitogen-activated protein kinase phosphatase OsMKP1, are each involved in chilling tolerance. In addition, a natural OsCTK1 chilling-tolerant (CT) variant exhibited a higher kinase activity and conferred greater chilling tolerance compared with a chilling-sensitive (CS) variant. The CT variant is more prevalent in CT accessions and is distributed more frequently in higher latitude compared with the CS variant. This study thus enables a better understanding of chilling tolerance mechanisms and provides gene variants for genetic improvement of chilling tolerance in rice.
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Affiliation(s)
- Jiawen Wu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Huimin Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Yan Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
- China National Rice Research Institute, 359 Tiyuchang Road, Hangzhou, 310006, China
| | - Yingdong Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Dongling Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shiyan Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shan Lu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lihui Wei
- Institute of Plant Protection, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Jian Hua
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Baohong Zou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Cyrus Tang Innovation Center for Crop Seed Industry, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
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5
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Siddiqui MN, Jahiu M, Kamruzzaman M, Sanchez-Garcia M, Mason AS, Léon J, Ballvora A. Genetic control of root architectural traits under drought stress in spring barley (Hordeum vulgare L.). THE PLANT GENOME 2024; 17:e20463. [PMID: 38764204 DOI: 10.1002/tpg2.20463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 03/22/2024] [Accepted: 04/12/2024] [Indexed: 05/21/2024]
Abstract
Root architectural traits play pivotal roles in plant adaptation to drought stress, and hence they are considered promising targets in breeding programs. Here, we phenotyped eight root architecture traits in response to well-watered and drought stress conditions in 200 spring barley (Hordeum vulgare L.) inbred lines over two consecutive field seasons. Root architecture traits were less developed under drought in both seasons when compared with control treatments. Genetic variation in root architectural traits was dissected employing a genome-wide association study (GWAS) coupled with linkage disequilibrium mapping. GWAS uncovered a total of 186 significant single nucleotide polymorphism-trait associations for eight root traits under control, drought, and drought-related indices. Of these, a few loci for root traits were detected on chromosomes 3 and 5, which co-located with QTL identified in previous studies. Interestingly, 13 loci showed simultaneou associations with multiple root traits under drought and drought-related indices. These loci harbored candidate genes, which included a wide range of drought-responsive components such as transcription factors, binding proteins, protein kinases, nutrient and ion transporters, and stress signaling factors. For instance, two candidate genes, HORVU7Hr3G0713160 and HORVU6H r3G0626550, are orthologous to AtACX3 and AtVAMPs, which have reported functions in root length-mediated drought tolerance and as a key protein in abiotic stress tolerance, respectively. Interestingly, one of these loci underlying a high-confidence candidate gene NEW ENHANCER OF ROOT DWARFISM1 (NERD1) showed involvement with root development. An allelic variation of this locus in non-coding region was significantly associated with increased root length under drought. Collectively, these results offer promising multi-trait affecting loci and candidate genes underlying root phenotypic responses to drought stress, which may provide valuable resources for genetic improvement of drought tolerance in barley.
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Affiliation(s)
- Md Nurealam Siddiqui
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Department of Biochemistry and Molecular Biology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, Bangladesh
| | - Melisa Jahiu
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Mohammad Kamruzzaman
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Miguel Sanchez-Garcia
- Department of Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Annaliese S Mason
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
| | - Jens Léon
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
- Field Lab Campus Klein-Altendorf, University of Bonn, Rheinbach, Germany
| | - Agim Ballvora
- Plant Breeding Department, Institute of Crop Science and Resource Conservation (INRES), University of Bonn, Bonn, Germany
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6
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Xie Z, Xu X, Li L, Wu C, Ma Y, He J, Wei S, Wang J, Feng X. Residual networks without pooling layers improve the accuracy of genomic predictions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:138. [PMID: 38771334 DOI: 10.1007/s00122-024-04649-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 05/10/2024] [Indexed: 05/22/2024]
Abstract
KEY MESSAGE Residual neural network genomic selection is the first GS algorithm to reach 35 layers, and its prediction accuracy surpasses previous algorithms. With the decrease in DNA sequencing costs and the development of deep learning, phenotype prediction accuracy by genomic selection (GS) continues to improve. Residual networks, a widely validated deep learning technique, are introduced to deep learning for GS. Since each locus has a different weighted impact on the phenotype, strided convolutions are more suitable for GS problems than pooling layers. Through the above technological innovations, we propose a GS deep learning algorithm, residual neural network for genomic selection (ResGS). ResGS is the first neural network to reach 35 layers in GS. In 15 cases from four public data, the prediction accuracy of ResGS is higher than that of ridge-regression best linear unbiased prediction, support vector regression, random forest, gradient boosting regressor, and deep neural network genomic prediction in most cases. ResGS performs well in dealing with gene-environment interaction. Phenotypes from other environments are imported into ResGS along with genetic data. The prediction results are much better than just providing genetic data as input, which demonstrates the effectiveness of GS multi-modal learning. Standard deviation is recommended as an auxiliary GS evaluation metric, which could improve the distribution of predicted results. Deep learning for GS, such as ResGS, is becoming more accurate in phenotype prediction.
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Affiliation(s)
| | - Xiaogang Xu
- School of Computer Science and Technology, Zhejiang Gongshang University, Hangzhou, 310012, China.
| | - Ling Li
- Zhejiang Laboratory, Hangzhou, 311100, China
| | - Cuiling Wu
- Zhejiang Laboratory, Hangzhou, 311100, China
| | - Yinxing Ma
- Zhejiang Laboratory, Hangzhou, 311100, China
| | - Jingjing He
- Zhejiang Laboratory, Hangzhou, 311100, China
| | - Sidi Wei
- Zhejiang Laboratory, Hangzhou, 311100, China
| | - Jun Wang
- Zhejiang Laboratory, Hangzhou, 311100, China
| | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, China
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7
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Lee SY, Lee G, Han J, Ha SK, Lee CM, Kang K, Jin M, Suh JP, Jeung JU, Mo Y, Lee HS. GWAS analysis reveals the genetic basis of blast resistance associated with heading date in rice. FRONTIERS IN PLANT SCIENCE 2024; 15:1412614. [PMID: 38835858 PMCID: PMC11148375 DOI: 10.3389/fpls.2024.1412614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/06/2024] [Indexed: 06/06/2024]
Abstract
Rice blast is a destructive fungal disease affecting rice plants at various growth stages, significantly threatening global yield stability. Development of resistant rice cultivars stands as a practical means of disease control. Generally, association mapping with a diversity panel powerfully identifies new alleles controlling trait of interest. On the other hand, utilization of a breeding panel has its advantage that can be directly applied in a breeding program. In this study, we conducted a genome-wide association study (GWAS) for blast resistance using 296 commercial rice cultivars with low population structure but large phenotypic diversity. We attempt to answer the genetic basis behind rice blast resistance among early maturing cultivars by subdividing the population based on its Heading date 1 (Hd1) functionality. Subpopulation-specific GWAS using the mixed linear model (MLM) based on blast nursery screening conducted in three years revealed a total of 26 significant signals, including three nucleotide-binding site leucine-rich repeat (NBS-LRR) genes (Os06g0286500, Os06g0286700, and Os06g0287500) located at Piz locus on chromosome 6, and one at the Pi-ta locus (Os12g0281300) on chromosome 12. Haplotype analysis revealed blast resistance associated with Piz locus was exclusively specific to Type 14 hd1 among japonica rice. Our findings provide valuable insights for breeding blast resistant rice and highlight the applicability of our elite cultivar panel to detect superior alleles associated with important agronomic traits.
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Affiliation(s)
- Seung Young Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Gileung Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jiheon Han
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Su-Kyung Ha
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Chang-Min Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Kyeongmin Kang
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Mina Jin
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Jung-Pil Suh
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
| | - Ji-Ung Jeung
- Department of Southern Area Crop Science, National Institute of Crop Science, Rural Development Administration, Miryang, Republic of Korea
| | - Youngjun Mo
- Department of Crop Science and Biotechnology, Jeonbuk National University, Jeonju, Republic of Korea
- Institute of Agricultural Science and Technology, Jeonbuk National University, Jeonju, Republic of Korea
| | - Hyun-Sook Lee
- Crop Breeding Division, National Institute of Crop Science, Rural Development Administration, Wanju, Republic of Korea
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8
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Sivabharathi RC, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M. Haplotype-based breeding: A new insight in crop improvement. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112129. [PMID: 38763472 DOI: 10.1016/j.plantsci.2024.112129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 05/09/2024] [Accepted: 05/15/2024] [Indexed: 05/21/2024]
Abstract
Haplotype-based breeding (HBB) is one of the cutting-edge technologies in the realm of crop improvement due to the increasing availability of Single Nucleotide Polymorphisms identified by Next Generation Sequencing technologies. The complexity of the data can be decreased with fewer statistical tests and a lower probability of spurious associations by combining thousands of SNPs into a few hundred haplotype blocks. The presence of strong genomic regions in breeding lines of most crop species facilitates the use of haplotypes to improve the efficiency of genomic and marker-assisted selection. Haplotype-based breeding as a Genomic Assisted Breeding (GAB) approach harnesses the genome sequence data to pinpoint the allelic variation used to hasten the breeding cycle and circumvent the challenges associated with linkage drag. This review article demonstrates ways to identify candidate genes, superior haplotype identification, haplo-pheno analysis, and haplotype-based marker-assisted selection. The crop improvement strategies that utilize superior haplotypes will hasten the breeding progress to safeguard global food security.
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Affiliation(s)
- R C Sivabharathi
- Department of Genetics and Plant breeding, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Veera Ranjani Rajagopalan
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India
| | - R Suresh
- Department of Rice, CPBG, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Sudha
- Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, 641003, India.
| | - G Karthikeyan
- Department of Plant Pathology, CPPS, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Jayakanthan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M Raveendran
- Directorate of research, Tamil Nadu Agricultural University, Coimbatore 641003, India.
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9
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Han D, Zhao X, Zhang D, Wang Z, Zhu Z, Sun H, Qu Z, Wang L, Liu Z, Zhu X, Yuan M. Genome-wide association studies reveal novel QTLs for agronomic traits in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1375646. [PMID: 38807775 PMCID: PMC11132100 DOI: 10.3389/fpls.2024.1375646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
Introduction Soybean, as a globally significant crop, has garnered substantial attention due to its agricultural importance. The utilization of molecular approaches to enhance grain yield in soybean has gained popularity. Methods In this study, we conducted a genome-wide association study (GWAS) using 156 Chinese soybean accessions over a two-year period. We employed the general linear model (GLM) and the mixed linear model (MLM) to analyze three agronomic traits: pod number, grain number, and grain weight. Results Our findings revealed significant associations between qgPNpP-98, qgGNpP-89 and qgHGW-85 QTLs and pod number, grain number, and grain weight, respectively. These QTLs were identified on chromosome 16, a region spanning 413171bp exhibited associations with all three traits. Discussion These QTL markers identified in this study hold potential for improving yield and agronomic traits through marker-assisted selection and genomic selection in breeding programs.
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Affiliation(s)
- Dongwei Han
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
- Heilongjiang Chinese Academy of Sciences Qiuying Zhang Soybean Scientist Studio, Qiqihar, Heilongjiang, China
| | - Xi Zhao
- Biotechnology Institute, Heilongjiang Academy of Agricultural Science, Harbin, Heilongjiang, China
| | - Di Zhang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhen Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhijia Zhu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Haoyue Sun
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhongcheng Qu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Lianxia Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhangxiong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu Zhu
- Department of Research and Development, Ruibiotech Co., Ltd, Beijing, China
| | - Ming Yuan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
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10
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Sahu TK, Verma SK, Gayacharan, Singh NP, Joshi DC, Wankhede DP, Singh M, Bhardwaj R, Singh B, Parida SK, Chattopadhyay D, Singh GP, Singh AK. Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata). BMC PLANT BIOLOGY 2024; 24:379. [PMID: 38720284 PMCID: PMC11077894 DOI: 10.1186/s12870-024-04976-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. RESULTS The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo-keto-reductase with flowering and maturity were revealed. CONCLUSION This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.
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Affiliation(s)
- Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, Uttar Pradesh, India
| | - Sachin Kumar Verma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | | | - Dinesh Chandra Joshi
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - D P Wankhede
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Mohar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Badal Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | | | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India.
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11
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Ghazy MI, El-Naem SA, Hefeina AG, Sallam A, Eltaher S. Genome-Wide Association Study of Rice Diversity Panel Reveals New QTLs for Tolerance to Water Deficit Under the Egyptian Conditions. RICE (NEW YORK, N.Y.) 2024; 17:29. [PMID: 38649523 PMCID: PMC11035518 DOI: 10.1186/s12284-024-00703-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
Drought has a significant impact on rice yield by restricting the crop's ability to grow and develop. Producing rice cultivars adapted to water deficit conditions is still the main interest of rice breeders and geneticists. To address this challenge, a set of 413 highly diverse rice populations were evaluated under normal and water deficit conditions for two growing seasons of 2021 and 2022. High genetic variation was found among genotypes for all studied traits. The heritability estimates ranged from 0.82 (panicle length) to 0.95 (plant height). Sterility percentage (SET%) was the most trait affected by water deficit in two growing seasons. 22 Rice genotypes were classified as drought tolerant in both years. Genome-wide association mapping was performed for all traits in the two growing seasons under both conditions using a total of 700,000 SNPs. The GWAS results revealed important and major SNPs associated with all traits. 26 Significant SNPs with stable allele effects were found to be associated with yield traits under water deficit conditions in both years. The results of this study provided rice genotypes that can be adapted under water deficit conditions and important stable SNP markers that can be used for marker-assisted selection after validation in different genetic backgrounds.
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Affiliation(s)
- Mohamed I Ghazy
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt
| | - Sabry A El-Naem
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt
| | - Ahmed G Hefeina
- Rice Research and Training Department, Field Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt
| | - Ahmed Sallam
- Department of Plant Biotechnology, Genetic Engineering and Biotechnology Research Institute (GEBRI), University of Sadat City (USC), Sadat City, 32897, Egypt.
| | - Shamseldeen Eltaher
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
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12
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Zeng P, Xie T, Shen J, Liang T, Yin L, Liu K, He Y, Chen M, Tang H, Chen S, Shabala S, Zhang H, Cheng J. Potassium transporter OsHAK9 regulates seed germination under salt stress by preventing gibberellin degradation through mediating OsGA2ox7 in rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:731-748. [PMID: 38482956 DOI: 10.1111/jipb.13642] [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: 10/22/2023] [Accepted: 02/27/2024] [Indexed: 04/11/2024]
Abstract
Soil salinity has a major impact on rice seed germination, severely limiting rice production. Herein, a rice germination defective mutant under salt stress (gdss) was identified by using chemical mutagenesis. The GDSS gene was detected via MutMap and shown to encode potassium transporter OsHAK9. Phenotypic analysis of complementation and mutant lines demonstrated that OsHAK9 was an essential regulator responsible for seed germination under salt stress. OsHAK9 is highly expressed in germinating seed embryos. Ion contents and non-invasive micro-test technology results showed that OsHAK9 restricted K+ efflux in salt-exposed germinating seeds for the balance of K+/Na+. Disruption of OsHAK9 significantly reduced gibberellin 4 (GA4) levels, and the germination defective phenotype of oshak9a was partly rescued by exogenous GA3 treatment under salt stress. RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction analysis demonstrated that the disruption of OsHAK9 improved the GA-deactivated gene OsGA2ox7 expression in germinating seeds under salt stress, and the expression of OsGA2ox7 was significantly inhibited by salt stress. Null mutants of OsGA2ox7 created using clustered, regularly interspaced, short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 approach displayed a dramatically increased seed germination ability under salt stress. Overall, our results highlight that OsHAK9 regulates seed germination performance under salt stress involving preventing GA degradation by mediating OsGA2ox7, which provides a novel clue about the relationship between GA and OsHAKs in rice.
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Affiliation(s)
- Peng Zeng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Ting Xie
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jiaxin Shen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Taokai Liang
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
| | - Lu Yin
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kexin Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ying He
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingming Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Haijuan Tang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sunlu Chen
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sergey Shabala
- International Research Center for Environmental Membrane Biology, Foshan University, Foshan, 528000, China
- School of Biological Sciences, University of Western Australia, Crawley, WA 6009, Australia
| | - Hongsheng Zhang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinping Cheng
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Center for Modern Crop Production, Hainan Yazhou Bay Seed Lab, Jiangsu Province Engineering Research Center of Seed Industry Science and Technology, Nanjing Agricultural University, Nanjing, 210095, China
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13
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Sar P, Gupta S, Behera M, Chakraborty K, Ngangkham U, Verma BC, Banerjee A, Hanjagi PS, Bhaduri D, Shil S, Kumar J, Mandal NP, Kole PC, Purugganan MD, Roy S. Exploring Genetic Diversity within aus Rice Germplasm: Insights into the Variations in Agro-morphological Traits. RICE (NEW YORK, N.Y.) 2024; 17:20. [PMID: 38526679 DOI: 10.1186/s12284-024-00700-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/12/2024] [Indexed: 03/27/2024]
Abstract
The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowledge gap, we investigated the genetic structure of 181 aus accessions using 399,115 SNP markers and evaluated them for 11 morpho-agronomic traits. Through genome-wide association studies (GWAS), we aimed to identify key loci controlling yield and plant architectural traits.Our population genetic analysis unveiled six subpopulations with strong geographical patterns. Subpopulation-specific differences were observed in most phenotypic traits. Principal component analysis (PCA) of agronomic traits showed that principal component 1 (PC1) was primarily associated with panicle traits, plant height, and heading date, while PC2 and PC3 were linked to primary grain yield traits. GWAS using PC1 identified OsSAC1 on Chromosome 7 as a significant gene influencing multiple agronomic traits. PC2-based GWAS highlighted the importance of OsGLT1 and OsPUP4/ Big Grain 3 in determining grain yield. Haplotype analysis of these genes in the 3,000 Rice Genome Panel revealed distinct genetic variations in aus rice.In summary, this study offers valuable insights into the genetic structure and phenotypic diversity of aus rice accessions. We have identified significant loci associated with essential agronomic traits, with GLT1, PUP4, and SAC1 genes emerging as key players in yield determination.
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Affiliation(s)
- Puranjoy Sar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Sonal Gupta
- Center for Genomics and Systems Biology, New York University, New York, NY, USA
| | - Motilal Behera
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Koushik Chakraborty
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Umakanta Ngangkham
- Manipur Center, ICAR Research Complex for NEH Region, Imphal, Manipur, 795 004, India
| | - Bibhash Chandra Verma
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Amrita Banerjee
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Prashantkumar S Hanjagi
- Crop Physiology and Biochemistry Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Debarati Bhaduri
- Crop Production Division, ICAR-National Rice Research Institute, Cuttack, Odisha, 753 006, India
| | - Sandip Shil
- Research Centre - Mohitnagar, ICAR-Central Plantation Crops Research Institute, Jalpaiguri, West Bengal, 735 101, India
| | - Jitendra Kumar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Nimai Prasad Mandal
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India
| | - Paresh Chandra Kole
- Palli Siksha Bhavana (Institute of Agriculture), Visva-Bharati, Sriniketan, West Bengal, 731236, India
| | | | - Somnath Roy
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, Jharkhand, 825 301, India.
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14
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Abdelraheem A, Zhu Y, Zeng L, Stetina S, Zhang J. A genome-wide association study for resistance to Fusarium wilt (Fusarium oxysporum f. sp. vasinfectum) race 4 in diploid cotton (Gossypium arboreum) and resistance transfer to tetraploid Gossypium hirsutum. Mol Genet Genomics 2024; 299:30. [PMID: 38472439 DOI: 10.1007/s00438-024-02130-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/21/2024] [Indexed: 03/14/2024]
Abstract
Fusarium wilt, caused by the soilborne fungus Fusarium oxysporum f. sp. vasinfectum (FOV), is a devastating disease affecting cotton (Gossypium spp.) worldwide. Understanding the genetic basis of resistance in diploid cotton and successfully transferring the resistance to tetraploid Upland cotton (G. hirsutum) are crucial for developing resistant cotton cultivars. Although numerous studies have been conducted to investigate the genetic basis of Fusarium wilt in tetraploid cotton, little research has been conducted on diploid species. In this study, an association mapping panel consisting of 246 accessions of G. arboreum, was used to identify chromosomal regions for FOV race 4 (FOV4) resistance based on foliar disease severity ratings in four greenhouse tests. Through a genome-wide association study (GWAS) based on 7,009 single nucleotide polymorphic (SNP) markers, 24 FOV4 resistance QTLs, including three major QTLs on chromosomes A04, A06, and A11, were detected. A validation panel consisting of 97 diploid cotton accessions was employed, confirming the presence of several QTLs. Evaluation of an introgressed BC2F7 population derived from G. hirsutum/G. aridum/G. arboreum showed significant differences in disease incidence and mortality rate, as compared to susceptible and resistant controls, suggesting that the resistance in G. arboreum and/or G. aridum was transferred into Upland cotton for the first time. The identification of novel major resistance QTLs, along with the transfer of resistance from the diploid species, expands our understanding of the genomic regions involved in conferring resistance to FOV4 and contributes to the development of resilient Upland cotton cultivars.
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Affiliation(s)
- Abdelraheem Abdelraheem
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Yi Zhu
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA
| | - Linghe Zeng
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Salliana Stetina
- USDA Agricultural Research Service Crop Genetics Research Unit, Stoneville, MS, 38776, USA
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, 88003, USA.
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15
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Yin M, Tong X, Yang J, Cheng Y, Zhou P, Li G, Wang Y, Ying J. Dissecting the Genetic Basis of Yield Traits and Validation of a Novel Quantitative Trait Locus for Grain Width and Weight in Rice. PLANTS (BASEL, SWITZERLAND) 2024; 13:770. [PMID: 38592774 PMCID: PMC10975080 DOI: 10.3390/plants13060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 04/11/2024]
Abstract
Grain yield in rice is a complex trait and it is controlled by a number of quantitative trait loci (QTL). To dissect the genetic basis of rice yield, QTL analysis for nine yield traits was performed using an F2 population containing 190 plants, which was developed from a cross between Youyidao (YYD) and Sanfenhe (SFH), and each plant in the population evaluated with respect to nine yield traits. In this study, the correlations among the nine yield traits were analyzed. The grain yield per plant positively correlated with six yield traits, except for grain length and grain width, and showed the highest correlation coefficient of 0.98 with the number of filled grains per plant. A genetic map containing 133 DNA markers was constructed and it spanned 1831.7 cM throughout 12 chromosomes. A total of 36 QTLs for the yield traits were detected on nine chromosomes, except for the remaining chromosomes 5, 8, and 9. The phenotypic variation was explained by a single QTL that ranged from 6.19% to 36.01%. Furthermore, a major QTL for grain width and weight, qGW2-1, was confirmed to be newly identified and was narrowed down to a relatively smaller interval of about ~2.94-Mb. Collectively, we detected a total of 36 QTLs for yield traits and a major QTL, qGW2-1, was confirmed to control grain weight and width, which laid the foundation for further map-based cloning and molecular design breeding in rice.
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Affiliation(s)
| | | | | | | | | | | | | | - Jiezheng Ying
- State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou 311400, China; (M.Y.); (J.Y.); (Y.C.); (P.Z.); (G.L.); (Y.W.)
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16
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Tang W, Chen H, Zhang S, Tang J, Lin J, Fang X, Chen G, Zhang Y. A Novel Allele in the Promoter of Wx Decreases Gene Expression and Confers Lower Apparent Amylose Contents in Japonica Rice ( Oryza sativa L.). PLANTS (BASEL, SWITZERLAND) 2024; 13:745. [PMID: 38475591 DOI: 10.3390/plants13050745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Wx is the key gene that controls amylose content (AC), and various alleles have been found in rice populations. Wxb is the major allele in japonica and produces moderate AC (15~18%). It was recently found that editing the promoter of Wx could produce a series of alleles that have different Wx activities. Although some studies have edited the promoter, few studies have focused on the natural variations in Wx. Here, we used the Rice3K database to investigate variations in the Wx promoter and found that the allele Wx1764178 (A/G) has a higher LD (linkage disequilibrium) with the two key SNPs (1765751, T/G; 1768006, A/C), which could produce different Wx alleles and influence AC, as reported previously. Further study showed that the Wx1764178 allele (A/G) is functional and influences the expression of Wx positively. Editing the A allele using CRISPR‒Cas9 produced 36 and 3 bp deletions and caused a decrease in the expression of Wx. The apparent amylose content (AAC) in the edited lines was decreased by 7.09% and 11.50% compared with that of the wild type, which was the japonica variety Nipponbare with Wxb and the A allele at 1764178, while a complementary line with the G allele showed a lower AAC than the A allele with no effect on other agronomic traits. The AAC of the edited lines showed a higher increase than that of the wild type (Nipponbare, Wxb) in low-nitrogen conditions relative to high-nitrogen conditions. We also developed a dCAPS marker to identify the allele and found that the G allele has widely been used (82.95%) in japonica-bred varieties from Jiangsu Province, China. Overall, we found a functional allele (Wx1764178, A/G) in the Wx promoter that could affect AAC in japonica cultivars and be developed as markers for quality improvement in rice breeding programs.
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Affiliation(s)
- Weijie Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Haiyuan Chen
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Suobing Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jun Tang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Jing Lin
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Xianwen Fang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
| | - Gaoming Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Jiangsu Collaborative Innovation Centre for Modern Crop Production, Nanjing Agricultural University, Nanjing 210095, China
| | - Yunhui Zhang
- Provincial Key Laboratory of Agrobiology, Institute of Germplasm Resources and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Zhongshan Biological Breeding Laboratory, Nanjing 210014, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
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17
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Thapa R, Tabien RE, Thomson MJ, Septiningsih EM. Genetic factors underlying anaerobic germination in rice: Genome-wide association study and transcriptomic analysis. THE PLANT GENOME 2024; 17:e20261. [PMID: 36169134 DOI: 10.1002/tpg2.20261] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/10/2022] [Indexed: 06/16/2023]
Abstract
The success of rice (Oryza sativa L.) germination and survival under submerged conditions is mainly determined by the rapid growth of the coleoptile to reach the water surface. Previous reports have shown the presence of genetic variability within rice accessions in the levels of flooding tolerance during germination or anaerobic germination (AG). Although many studies have focused on the physiological mechanisms of oxygen stress, few studies have explored the breadth of natural variation in AG tolerance-related traits in rice. In this study, we evaluated the coleoptile lengths of a geographically diverse rice panel of 241 accessions, including global accessions along with elite breeding lines and released cultivars from the United States, under the normal and flooded conditions in laboratory and greenhouse environments. A genome-wide association study (GWAS) was performed using a 7K single-nucleotide polymorphism (SNP) array and the phenotypic data of normal coleoptile length, flooded coleoptile length, flooding tolerance index, and survival at 14 d after seeding (DAS). Out of the 30 significant GWAS quantitative trait loci (QTL) regions identified, 14 colocalized with previously identified candidate genes of AG tolerance, whereas 16 were potentially novel. Two rice accessions showing contrasting phenotypic responses to AG stress were selected for the transcriptomics study. The combined approach of GWAS and transcriptomics analysis identified 77 potential candidate genes related to AG tolerance. The findings of our study may assist rice improvement programs in developing rice cultivars with robust tolerance under flooding stress during germination and the early seedling stage.
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Affiliation(s)
- Ranjita Thapa
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell Univ., Ithaca, NY, 14853, USA
| | | | - Michael J Thomson
- Dep. of Soil and Crop Sciences, Texas A&M Univ., College Station, TX, 77843, USA
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18
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Naik S, Sudan J, Urwat U, Pakhtoon MM, Bhat B, Sharma V, Sofi PA, Shikari AB, Bhat BA, Sofi NR, Prasad PVV, Zargar SM. Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat. THE PLANT GENOME 2024; 17:e20427. [PMID: 38239091 DOI: 10.1002/tpg2.20427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/07/2023] [Accepted: 12/22/2023] [Indexed: 03/22/2024]
Abstract
Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.
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Affiliation(s)
- Samiullah Naik
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jebi Sudan
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Varun Sharma
- Bioinformatics Division, NMC Genetics India Pvt. Ltd., Gurugram, India
| | - Parvaze A Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Asif B Shikari
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Bilal A Bhat
- Mountain Agriculture Research & Extension Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Najeebul Rehman Sofi
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, Kansas, USA
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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Gnanapragasam N, Prasanth VV, Sundaram KT, Kumar A, Pahi B, Gurjar A, Venkateshwarlu C, Kalia S, Kumar A, Dixit S, Kohli A, Singh UM, Singh VK, Sinha P. Extreme trait GWAS (Et-GWAS): Unraveling rare variants in the 3,000 rice genome. Life Sci Alliance 2024; 7:e202302352. [PMID: 38148113 PMCID: PMC10751245 DOI: 10.26508/lsa.202302352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/28/2023] Open
Abstract
Identifying high-impact, rare genetic variants associated with specific traits is crucial for crop improvement. The 3,010 rice genome (3K RG) dataset offers a valuable resource for discovering genomic regions with potential applications in crop breeding. We used Extreme Trait GWAS (Et-GWAS), employing bulk pooling and allele frequency measurement to efficiently extract rare variants from the 3K RG. This innovative approach facilitates the detection of associations between genetic variants and target traits, concentrating and quantifying rare alleles. In our study, on grain yield under drought stress, Et-GWAS successfully identified five key genes (OsPP2C11, OsK5.2, OsIRO2, OsPEX1, and OsPWA1) known for enhancing yield under drought. In addition, we examined the overlap of our results with previously reported qDTY-QTLs and observed that OsUCH1 and OsUCH2 genes were located within qDTY2.2 We compared Et-GWAS with conventional GWAS, finding it effectively capturing most candidate genes associated with the target trait. Validation with resistant starch showed similar results. To enhance user-friendliness, we developed a GUI for Et-GWAS; https://et-gwas.shinyapps.io/Et-GWAS/.
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Affiliation(s)
| | | | | | - Ajay Kumar
- International Rice Research Institute, South Asia Hub, Patancheru, India
| | - Bandana Pahi
- International Rice Research Institute, South Asia Hub, Patancheru, India
| | - Anoop Gurjar
- International Rice Research Institute, South-Asia Regional Centre, Varanasi, India
| | | | - Sanjay Kalia
- Department of Biotechnology, CGO Complex, New Delhi, India
| | - Arvind Kumar
- International Rice Research Institute, South-Asia Regional Centre, Varanasi, India
| | - Shalabh Dixit
- International Rice Research Institute, Los Banos, Philippines
| | - Ajay Kohli
- International Rice Research Institute, Los Banos, Philippines
| | - Uma Maheshwer Singh
- International Rice Research Institute, South-Asia Regional Centre, Varanasi, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, Patancheru, India
| | - Pallavi Sinha
- International Rice Research Institute, South Asia Hub, Patancheru, India
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20
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Hiraoka Y, Ferrante SP, Wu GA, Federici CT, Roose ML. Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives. PLANTS (BASEL, SWITZERLAND) 2024; 13:691. [PMID: 38475537 DOI: 10.3390/plants13050691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Rapid advancements in technologies provide various tools to analyze fruit crop genomes to better understand genetic diversity and relationships and aid in breeding. Genome-wide single nucleotide polymorphism (SNP) genotyping arrays offer highly multiplexed assays at a relatively low cost per data point. We report the development and validation of 1.4M SNP Axiom® Citrus HD Genotyping Array (Citrus 15AX 1 and Citrus 15AX 2) and 58K SNP Axiom® Citrus Genotyping Arrays for Citrus and close relatives. SNPs represented were chosen from a citrus variant discovery panel consisting of 41 diverse whole-genome re-sequenced accessions of Citrus and close relatives, including eight progenitor citrus species. SNPs chosen mainly target putative genic regions of the genome and are accurately called in both Citrus and its closely related genera while providing good coverage of the nuclear and chloroplast genomes. Reproducibility of the arrays was nearly 100%, with a large majority of the SNPs classified as the most stringent class of markers, "PolyHighResolution" (PHR) polymorphisms. Concordance between SNP calls in sequence data and array data average 98%. Phylogenies generated with array data were similar to those with comparable sequence data and little affected by 3 to 5% genotyping error. Both arrays are publicly available.
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Affiliation(s)
- Yoko Hiraoka
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Sergio Pietro Ferrante
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Guohong Albert Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA
| | - Claire T Federici
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
| | - Mikeal L Roose
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521, USA
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21
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Phosuwan S, Nounjan N, Theerakulpisut P, Siangliw M, Charoensawan V. Comparative quantitative trait loci analysis framework reveals relationships between salt stress responsive phenotypes and pathways. FRONTIERS IN PLANT SCIENCE 2024; 15:1264909. [PMID: 38463565 PMCID: PMC10920293 DOI: 10.3389/fpls.2024.1264909] [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: 07/21/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Soil salinity is a complex abiotic stress that involves several biological pathways. Hence, focusing on a specific or a few salt-tolerant phenotypes is unlikely to provide comprehensive insights into the intricate and interwinding mechanisms that regulate salt responsiveness. In this study, we develop a heuristic framework for systematically integrating and comprehensively evaluating quantitative trait loci (QTL) analyses from multiple stress-related traits obtained by different studies. Making use of a combined set of 46 salinity-related traits from three independent studies that were based on the same chromosome segment substitution line (CSSL) population of rice (Oryza sativa), we demonstrate how our approach can address technical biases and limitations from different QTL studies and calling methods. This allows us to compile a comprehensive list of trait-specific and multi-trait QTLs, as well as salinity-related candidate genes. In doing so, we discover several novel relationships between traits that demonstrate similar trends of phenotype scores across the CSSLs, as well as the similarities between genomic locations that the traits were mapped to. Finally, we experimentally validate our findings by expression analyses and functional validations of several selected candidate genes from multiple pathways in rice and Arabidopsis orthologous genes, including OsKS7 (ENT-KAURENE SYNTHASE 7), OsNUC1 (NUCLEOLIN 1) and OsFRO1 (FERRIC REDUCTASE OXIDASE 1) to name a few. This work not only introduces a novel approach for conducting comparative analyses of multiple QTLs, but also provides a list of candidate genes and testable hypotheses for salinity-related mechanisms across several biological pathways.
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Affiliation(s)
- Sunadda Phosuwan
- Doctor of Philosophy Program in Biochemistry (International Program), Faculty of Science, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Noppawan Nounjan
- Biodiversity and Environmental Management Division, International College, Khon Kaen University, Khon Kaen, Thailand
| | - Piyada Theerakulpisut
- Salt-tolerant Rice Research Group, Department of Biology, Faculty of Science, Khon Kaen University, Khon Kaen, Thailand
| | - Meechai Siangliw
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Thailand
| | - Varodom Charoensawan
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Integrative Computational BioScience (ICBS) Center, Mahidol University, Nakhon Pathom, Thailand
- Division of Medical Bioinformatics, Research Department, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Siriraj Genomics, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- School of Chemistry, Institute of Science, Suranaree University of Technology, Nakhon Ratchasima, Thailand
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22
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Wang L, Niu F, Wang J, Zhang H, Zhang D, Hu Z. Genome-Wide Association Studies Prioritize Genes Controlling Seed Size and Reproductive Period Length in Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:615. [PMID: 38475461 DOI: 10.3390/plants13050615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/14/2024]
Abstract
Hundred-seed weight (HSW) and reproductive period length (RPL) are two major agronomic traits critical for soybean production and adaptation. However, both traits are quantitatively controlled by multiple genes that have yet to be comprehensively elucidated due to the lack of major genes; thereby, the genetic basis is largely unknown. In the present study, we conducted comprehensive genome-wide association analyses (GWAS) of HSW and RPL with multiple sets of accessions that were phenotyped across different environments. The large-scale analysis led to the identification of sixty-one and seventy-four significant QTLs for HSW and RPL, respectively. An ortholog-based search analysis prioritized the most promising candidate genes for the QTLs, including nine genes (TTG2, BZR1, BRI1, ANT, KLU, EOD1/BB, GPA1, ABA2, and ABI5) for HSW QTLs and nine genes (such as AGL8, AGL9, TOC1, and COL4) and six known soybean flowering time genes (E2, E3, E4, Tof11, Tof12, and FT2b) for RPL QTLs. We also demonstrated that some QTLs were targeted during domestication to drive the artificial selection of both traits towards human-favored traits. Local adaptation likely contributes to the increased genomic diversity of the QTLs underlying RPL. The results provide additional insight into the genetic basis of HSW and RPL and prioritize a valuable resource of candidate genes that merits further investigation to reveal the complex molecular mechanism and facilitate soybean improvement.
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Affiliation(s)
- Le Wang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Fu'an Niu
- Institute of Crop Breeding and Cultivation, Shanghai Academy of Agricultural Sciences, Shanghai 201403, China
| | - Jinshe Wang
- National Innovation Centre for Bio-Breeding Industry, Institute of Crop Molecular Breeding, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Hengyou Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, China
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhenbin Hu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
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23
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Gao J, Li J, Zhang J, Sun Y, Ju X, Li W, Duan H, Xue Z, Sun L, Hussain Sahito J, Fu Z, Zhang X, Tang J. Identification of Novel QTL for Mercury Accumulation in Maize Using an Enlarged SNP Panel. Genes (Basel) 2024; 15:257. [PMID: 38397246 PMCID: PMC10888321 DOI: 10.3390/genes15020257] [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: 01/10/2024] [Revised: 02/14/2024] [Accepted: 02/17/2024] [Indexed: 02/25/2024] Open
Abstract
Mercury (Hg) pollution not only poses a threat to the environment but also adversely affects the growth and development of plants, with potential repercussions for animals and humans through bioaccumulation in the food chain. Maize, a crucial source of food, industrial materials, and livestock feed, requires special attention in understanding the genetic factors influencing mercury accumulation. Developing maize varieties with low mercury accumulation is vital for both maize production and human health. In this study, a comprehensive genome-wide association study (GWAS) was conducted using an enlarged SNP panel comprising 1.25 million single nucleotide polymorphisms (SNPs) in 230 maize inbred lines across three environments. The analysis identified 111 significant SNPs within 78 quantitative trait loci (QTL), involving 169 candidate genes under the Q model. Compared to the previous study, the increased marker density and optimized statistical model led to the discovery of 74 additional QTL, demonstrating improved statistical power. Gene ontology (GO) enrichment analysis revealed that most genes participate in arsenate reduction and stress responses. Notably, GRMZM2G440968, which has been reported in previous studies, is associated with the significant SNP chr6.S_155668107 in axis tissue. It encodes a cysteine proteinase inhibitor, implying its potential role in mitigating mercury toxicity by inhibiting cysteine. Haplotype analyses provided further insights, indicating that lines carrying hap3 exhibited the lowest mercury content compared to other haplotypes. In summary, our study significantly enhances the statistical power of GWAS, identifying additional genes related to mercury accumulation and metabolism. These findings offer valuable insights into unraveling the genetic basis of mercury content in maize and contribute to the development of maize varieties with low mercury accumulation.
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Affiliation(s)
- Jionghao Gao
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jianxin Li
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jihong Zhang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Yan Sun
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Xiaolong Ju
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Wenlong Li
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Haiyang Duan
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Zhengjie Xue
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Li Sun
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Javed Hussain Sahito
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Zhiyuan Fu
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Xuehai Zhang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
| | - Jihua Tang
- Key Laboratory of Wheat and Maize Crops Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China; (J.G.); (J.L.); (J.Z.); (Y.S.); (X.J.); (W.L.); (H.D.); (Z.X.); (L.S.); (J.H.S.); (Z.F.)
- The Shennong Laboratory, Zhengzhou 450002, China
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24
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Li S, Jiang F, Bi Y, Yin X, Li L, Zhang X, Li J, Liu M, Shaw RK, Fan X. Utilizing Two Populations Derived from Tropical Maize for Genome-Wide Association Analysis of Banded Leaf and Sheath Blight Resistance. PLANTS (BASEL, SWITZERLAND) 2024; 13:456. [PMID: 38337988 PMCID: PMC10856972 DOI: 10.3390/plants13030456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/01/2024] [Accepted: 02/02/2024] [Indexed: 02/12/2024]
Abstract
Banded leaf and sheath blight (BLSB) in maize is a soil-borne fungal disease caused by Rhizoctonia solani Kühn, resulting in significant yield losses. Investigating the genes responsible for regulating resistance to BLSB is crucial for yield enhancement. In this study, a multiparent maize population was developed, comprising two recombinant inbred line (RIL) populations totaling 442 F8RILs. The populations were generated by crossing two tropical inbred lines, CML444 and NK40-1, known for their BLSB resistance, as female parents, with the high-yielding but BLSB-susceptible inbred line Ye107 serving as the common male parent. Subsequently, we utilized 562,212 high-quality single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing (GBS) for a comprehensive genome-wide association study (GWAS) aimed at identifying genes responsible for BLSB resistance. The objectives of this study were to (1) identify SNPs associated with BLSB resistance through genome-wide association analyses, (2) explore candidate genes regulating BLSB resistance in maize, and (3) investigate pathways involved in BLSB resistance and discover key candidate genes through Gene Ontology (GO) analysis. The GWAS analysis revealed nineteen SNPs significantly associated with BLSB that were consistently identified across four environments in the GWAS, with phenotypic variation explained (PVE) ranging from 2.48% to 11.71%. Screening a 40 kb region upstream and downstream of the significant SNPs revealed several potential candidate genes. By integrating information from maize GDB and the NCBI, we identified five novel candidate genes, namely, Zm00001d009723, Zm00001d009975, Zm00001d009566, Zm00001d009567, located on chromosome 8, and Zm00001d026376, on chromosome 10, related to BLSB resistance. These candidate genes exhibit association with various aspects, including maize cell membrane proteins and cell immune proteins, as well as connections to cell metabolism, transport, transcriptional regulation, and structural proteins. These proteins and biochemical processes play crucial roles in maize defense against BLSB. When Rhizoctonia solani invades maize plants, it induces the expression of genes encoding specific proteins and regulates corresponding metabolic pathways to thwart the invasion of this fungus. The present study significantly contributes to our understanding of the genetic basis of BLSB resistance in maize, offering valuable insights into novel candidate genes that could be instrumental in future breeding efforts to develop maize varieties with enhanced BLSB resistance.
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Affiliation(s)
- Shaoxiong Li
- College of Agriculture, Yunnan University, Kunming 650500, China; (S.L.); (L.L.); (X.Z.); (J.L.); (M.L.)
| | - Fuyan Jiang
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (F.J.); (Y.B.); (X.Y.); (R.K.S.)
| | - Yaqi Bi
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (F.J.); (Y.B.); (X.Y.); (R.K.S.)
| | - Xingfu Yin
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (F.J.); (Y.B.); (X.Y.); (R.K.S.)
| | - Linzhuo Li
- College of Agriculture, Yunnan University, Kunming 650500, China; (S.L.); (L.L.); (X.Z.); (J.L.); (M.L.)
| | - Xingjie Zhang
- College of Agriculture, Yunnan University, Kunming 650500, China; (S.L.); (L.L.); (X.Z.); (J.L.); (M.L.)
| | - Jinfeng Li
- College of Agriculture, Yunnan University, Kunming 650500, China; (S.L.); (L.L.); (X.Z.); (J.L.); (M.L.)
| | - Meichen Liu
- College of Agriculture, Yunnan University, Kunming 650500, China; (S.L.); (L.L.); (X.Z.); (J.L.); (M.L.)
| | - Ranjan K. Shaw
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (F.J.); (Y.B.); (X.Y.); (R.K.S.)
| | - Xingming Fan
- Institute of Food Crops, Yunnan Academy of Agricultural Sciences, Kunming 650205, China; (F.J.); (Y.B.); (X.Y.); (R.K.S.)
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25
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Chen J, Tan C, Zhu M, Zhang C, Wang Z, Ni X, Liu Y, Wei T, Wei X, Fang X, Xu Y, Huang X, Qiu J, Liu H. CropGS-Hub: a comprehensive database of genotype and phenotype resources for genomic prediction in major crops. Nucleic Acids Res 2024; 52:D1519-D1529. [PMID: 38000385 PMCID: PMC10767954 DOI: 10.1093/nar/gkad1062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/15/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The explosive amount of multi-omics data has brought a paradigm shift both in academic research and further application in life science. However, managing and reusing the growing resources of genomic and phenotype data points presents considerable challenges for the research community. There is an urgent need for an integrated database that combines genome-wide association studies (GWAS) with genomic selection (GS). Here, we present CropGS-Hub, a comprehensive database comprising genotype, phenotype, and GWAS signals, as well as a one-stop platform with built-in algorithms for genomic prediction and crossing design. This database encompasses a comprehensive collection of over 224 billion genotype data and 434 thousand phenotype data generated from >30 000 individuals in 14 representative populations belonging to 7 major crop species. Moreover, the platform implemented three complete functional genomic selection related modules including phenotype prediction, user model training and crossing design, as well as a fast SNP genotyper plugin-in called SNPGT specifically built for CropGS-Hub, aiming to assist crop scientists and breeders without necessitating coding skills. CropGS-Hub can be accessed at https://iagr.genomics.cn/CropGS/.
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Affiliation(s)
- Jiaxin Chen
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Cong Tan
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - Min Zhu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Chenyang Zhang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
| | - Zhihan Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Xuemei Ni
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
| | - Yanlin Liu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Tong Wei
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Wuhan 430074, China
| | - XiaoFeng Wei
- China National GeneBank, BGI, Shenzhen 518120, China
| | - Xiaodong Fang
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Research, Sanya 572025, China
| | - Yang Xu
- Agricultural College, Yangzhou University, Yangzhou 225009, China
| | - Xuehui Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Collaborative Innovation Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, Key Laboratory of Genomics, Ministry of Agriculture, BGI Research, Shenzhen 518083, China
- BGI Bioverse, Shenzhen 518083, China
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Rahman MW, Deokar AA, Lindsay D, Tar’an B. Novel Alleles from Cicer reticulatum L. for Genetic Improvement of Cultivated Chickpeas Identified through Genome Wide Association Analysis. Int J Mol Sci 2024; 25:648. [PMID: 38203819 PMCID: PMC10779240 DOI: 10.3390/ijms25010648] [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: 11/14/2023] [Revised: 12/24/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
The availability of wild chickpea (Cicer reticulatum L.) accessions has the potential to be used for the improvement of important traits in cultivated chickpeas. The main objectives of this study were to evaluate the phenotypic and genetic variations of chickpea progeny derived from interspecific crosses between C. arietinum and C. reticulatum, and to establish the association between single nucleotide polymorphism (SNP) markers and a series of important agronomic traits in chickpea. A total of 486 lines derived from interspecific crosses between C. arietinum (CDC Leader) and 20 accessions of C. reticulatum were evaluated at different locations in Saskatchewan, Canada in 2017 and 2018. Significant variations were observed for seed weight per plant, number of seeds per plant, thousand seed weight, and plant biomass. Path coefficient analysis showed significant positive direct effects of the number of seeds per plant, thousand seed weight, and biomass on the total seed weight. Cluster analysis based on the agronomic traits generated six groups that allowed the identification of potential heterotic groups within the interspecific lines for yield improvement and resistance to ascochyta blight disease. Genotyping of the 381 interspecific lines using a modified genotyping by sequencing (tGBS) generated a total of 14,591 SNPs. Neighbour-joining cluster analysis using the SNP data grouped the lines into 20 clusters. The genome wide association analysis identified 51 SNPs that had significant associations with different traits. Several candidate genes associated with early flowering and yield components were identified. The candidate genes and the significant SNP markers associated with different traits have a potential to aid the trait introgression in the breeding program.
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Affiliation(s)
| | | | | | - Bunyamin Tar’an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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Ding X, Shi J, Gui J, Zhou H, Yan Y, Zhu X, Xie B, Liu X, He J. Rice Seed Protrusion Quantitative Trait Loci Mapping through Genome-Wide Association Study. PLANTS (BASEL, SWITZERLAND) 2024; 13:134. [PMID: 38202442 PMCID: PMC10780921 DOI: 10.3390/plants13010134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 12/19/2023] [Accepted: 12/23/2023] [Indexed: 01/12/2024]
Abstract
The germination of seeds is a prerequisite for crop production. Protrusion is important for seed germination, and visible radicle protrusion through seed covering layers is the second phase of the process of seed germination. Analyzing the mechanism of protrusion is important for the cultivation of rice varieties. In this study, 302 microcore germplasm populations were used for the GWAS of the protrusion percentage (PP). The frequency distribution of the PP at 48 h and 72 h is continuous, and six PP-associated QTLs were identified, but only qPP2 was detected repeatedly two times. The candidate gene analysis showed that LOC_Os02g57530 (ETR3), LOC_Os01g57610 (GH3.1) and LOC_Os04g0425 (CTB2) were the candidate genes for qPP2, qPP1 and qPP4, respectively. The haplotype (Hap) analysis revealed that Hap1 of ETR3, Hap1 and 3 of GH3.1 and Hap2 and 5 of CTB2 are elite alleles for the PP. Further validation of the germination phenotype of these candidate genes showed that Hap1 of ETR3 is a favorable allele for the germination percentage; Hap3 of GH3.1 is an elite allele for seed germination; and Hap5 of CTB2 is an elite allele for the PP, the germination percentage and the vigor index. The results of this study identified three putative candidate genes that provide valuable information for understanding the genetic control of seed protrusion in rice.
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Affiliation(s)
| | | | | | | | | | | | | | - Xionglun Liu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (X.D.); (J.S.); (J.G.); (Y.Y.); (X.Z.); (B.X.)
| | - Jiwai He
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China; (X.D.); (J.S.); (J.G.); (Y.Y.); (X.Z.); (B.X.)
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28
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Panahabadi R, Ahmadikhah A, Farrokhi N. Genetic dissection of monosaccharides contents in rice whole grain using genome-wide association study. THE PLANT GENOME 2023; 16:e20292. [PMID: 36691363 DOI: 10.1002/tpg2.20292] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
The simplest form of carbohydrates are monosaccharides which are the building blocks for the synthesis of polymers or complex carbohydrates. Monosaccharide contents of 197 rice accessions were quantified by HPAEC-PAD in rice (Oryza sativa L.) whole grain (RWG). A genome-wide association study (GWAS) was carried out using 33,812 single nucleotide polymorphisms (SNPs) to identify corresponding genomic regions influencing neutral monosaccharides contents. In total, 49 GWAS signals contained in 17 genomic regions (quantitative trait loci [QTLs]) on seven chromosomes of rice were determined to be associated with monosaccharides contents of whole grain. The QTLs were found for fucose (1), mannose (1), xylose (2), arabinose (2), galactose (4), and rhamnose (7) contents, all of which are novel. Based on co-location of annotated rice genes in the vicinity of GWAS signals, the constituents of the whole grain were associated with the following candidate genes: arabinose content with α-N-arabinofuranosidase, pectinesterase inhibitor, and glucosamine-fructose-6-phosphate aminotransferase 1; xylose content with ZOS1-10 (a C2H2 zinc finger transcription factor [TF]); mannose content with aldose 1-epimerase-like protein and a MYB family TF; galactose content with a GT8 family member (galacturonosyltransferase-like 3), a GRAS family TF, and a GH16 family member (xyloglucan endotransglucosylase/hydrolase xyloglucan 23); fucose content with gibberellin 20 oxidase and a lysine-rich arabinogalactan protein 19, and finally rhamnose content with myo-inositol-1-phosphate synthase, UDP-arabinopyranose mutase, and COBRA-like protein precursor. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in the biosynthesis, regulation, and turnover of monosaccharides in RWG, aiming to enhance the nutritional value of rice grain and impact the related industries.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
| | | | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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29
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Malik N, Basu U, Srivastava R, Daware A, Ranjan R, Sharma A, Thakro V, Mohanty JK, Jha UC, Tripathi S, Tyagi AK, Parida SK. Natural alleles of Mediator subunit genes modulate plant height in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1271-1292. [PMID: 37671896 DOI: 10.1111/tpj.16423] [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: 05/23/2023] [Accepted: 08/04/2023] [Indexed: 09/07/2023]
Abstract
SUMMARYPlant height (PH) is an important plant architectural trait targeted during Green Revolution to enhance crop yields. Identification of genes and natural alleles governing plant height without compromising agronomic performance can fill the lacuna of knowledge connecting ideal plant architecture with maximum achievable yield in chickpea. Through coherent strategy involving genome‐wide association study, QTL/fine mapping, map‐based cloning, molecular haplotyping, and downstream functional genomics, the current study identified two Mediator subunit genes namely, CaMED23 and CaMED5b and their derived natural alleles/haplotypes underlying the major QTLs and trans‐acting eQTLs regulating plant height in chickpea. Differential accumulation of haplotype‐specific transcripts of these two Mediator genes in corresponding haplotype‐introgressed near‐isogenic lines (NILs) correlates negatively with the plant height trait. Quantitative as well as qualitative estimation based on histology, scanning electron microscopy, and histochemical assay unraveled the reduced lengths and cell sizes of internodes along with compromised lignin levels in dwarf/semi‐dwarf chickpea NILs introgressed with superior CaMED23 and CaMED5b gene haplotypes. This observation, supported by global transcriptome profiling‐based diminished expression of various phenylpropanoid pathway genes upstream of lignin biosynthesis in dwarf/semi‐dwarf NILs, essentially links plant height with lignin accumulation. The identified molecular signatures in the Mediator subunit genes can be efficiently utilized to develop desirable dwarf/semi‐dwarf‐type chickpea cultivars without affecting their yield per plant via modulating lignin/phenylpropanoid biosynthesis.
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Affiliation(s)
- Naveen Malik
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303002, India
| | - Udita Basu
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rajeev Ranjan
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Akash Sharma
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Mohanty
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | | | - Akhilesh K Tyagi
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- Genomics-assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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30
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Vicentini G, Biancucci M, Mineri L, Chirivì D, Giaume F, Miao Y, Kyozuka J, Brambilla V, Betti C, Fornara F. Environmental control of rice flowering time. PLANT COMMUNICATIONS 2023; 4:100610. [PMID: 37147799 PMCID: PMC10504588 DOI: 10.1016/j.xplc.2023.100610] [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: 10/02/2022] [Revised: 04/14/2023] [Accepted: 04/30/2023] [Indexed: 05/07/2023]
Abstract
Correct measurement of environmental parameters is fundamental for plant fitness and survival, as well as for timing developmental transitions, including the switch from vegetative to reproductive growth. Important parameters that affect flowering time include day length (photoperiod) and temperature. Their response pathways have been best described in Arabidopsis, which currently offers a detailed conceptual framework and serves as a comparison for other species. Rice, the focus of this review, also possesses a photoperiodic flowering pathway, but 150 million years of divergent evolution in very different environments have diversified its molecular architecture. The ambient temperature perception pathway is strongly intertwined with the photoperiod pathway and essentially converges on the same genes to modify flowering time. When observing network topologies, it is evident that the rice flowering network is centered on EARLY HEADING DATE 1, a rice-specific transcriptional regulator. Here, we summarize the most important features of the rice photoperiodic flowering network, with an emphasis on its uniqueness, and discuss its connections with hormonal, temperature perception, and stress pathways.
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Affiliation(s)
- Giulio Vicentini
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Marco Biancucci
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Lorenzo Mineri
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Daniele Chirivì
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Francesca Giaume
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Yiling Miao
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Vittoria Brambilla
- Department of Agricultural and Environmental Sciences, University of Milan, via Celoria 2, 20133 Milan, Italy
| | - Camilla Betti
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy
| | - Fabio Fornara
- Department of Biosciences, University of Milan, via Celoria 26, 20133 Milan, Italy.
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31
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Zheng Y, Thi KM, Lin L, Xie X, Khine EE, Nyein EE, Lin MHW, New WW, Aye SS, Wu W. Genome-wide association study of cooking-caused grain expansion in rice ( Oryza sativa L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1250854. [PMID: 37711286 PMCID: PMC10498926 DOI: 10.3389/fpls.2023.1250854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023]
Abstract
Cooking-caused rice grain expansion (CCRGE) is a critical trait for evaluating the cooking quality of rice. Previous quantitative trait locus (QTL) mapping studies on CCRGE have been limited to bi-parental populations, which restrict the exploration of natural variation and mapping resolution. To comprehensively and precisely dissect the genetic basis of CCRGE, we performed a genome-wide association study (GWAS) on three related indices: grain breadth expansion index (GBEI), grain length expansion index (GLEI), and grain length-breadth ratio expansion index (GREI), using 345 rice accessions grown in two years (environments) and 193,582 SNP markers. By analyzing each environment separately using seven different methods (3VmrMLM, mrMLM, FASTmrMLM, FASTmrEMMA, pLARmEB, pKWmEB, ISIS EM-BLASSO), we identified a total of 32, 19 and 27 reliable quantitative trait nucleotides (QTNs) associated with GBEI, GLEI and GREI, respectively. Furthermore, by jointly analyzing the two environments using 3VmrMLM, we discovered 19, 22 and 25 QTNs, as well as 9, 5 and 7 QTN-by-environment interaction (QEIs) associated with GBEI, GLEI and GREI, respectively. Notably, 12, 9 and 15 QTNs for GBEI, GLEI and GREI were found within the intervals of previously reported QTLs. In the vicinity of these QTNs or QEIs, based on analyses of mutation type, gene ontology classification, haplotype, and expression pattern, we identified five candidate genes that are related to starch synthesis and endosperm development. The five candidate genes, namely, LOC_Os04g53310 (OsSSIIIb, near QTN qGREI-4.5s), LOC_Os05g02070 (OsMT2b, near QTN qGLEI-5.1s), LOC_Os06g04200 (wx, near QEI qGBEI-6.1i and QTNs qGREI-6.1s and qGLEI-6.1t), LOC_Os06g12450 (OsSSIIa, near QTN qGLEI-6.2t), and LOC_Os08g09230 (OsSSIIIa, near QTN qGBEI-8.1t), are predicted to be involved in the process of rice grain starch synthesis and to influence grain expansion after cooking. Our findings provide valuable insights and will facilitate genetic research and improvement of CCRGE.
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Affiliation(s)
- Yan Zheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Khin Mar Thi
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Lihui Lin
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Xiaofang Xie
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ei Ei Khine
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Ei Ei Nyein
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| | - Min Htay Wai Lin
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - Win Win New
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - San San Aye
- Department of Botany, Mawlamyine University, Mawlamyine, Myanmar
| | - Weiren Wu
- Fujian Provincial Key Laboratory of Crop Breeding by Design, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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32
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Hou M, Cao Y, Zhang X, Zhang S, Jia T, Yang J, Han S, Wang L, Li J, Wang H, Zhang L, Wu X, Duan C, Li H. Genome-wide association study of maize resistance to Pythium aristosporum stalk rot. FRONTIERS IN PLANT SCIENCE 2023; 14:1239635. [PMID: 37662167 PMCID: PMC10470045 DOI: 10.3389/fpls.2023.1239635] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 07/28/2023] [Indexed: 09/05/2023]
Abstract
Stalk rot, a severe and widespread soil-borne disease in maize, globally reduces yield and quality. Recent documentation reveals that Pythium aristosporum has emerged as one of the dominant causal agents of maize stalk rot. However, a previous study of maize stalk rot disease resistance mechanisms and breeding had mainly focused on other pathogens, neglecting P. aristosporum. To mitigate crop loss, resistance breeding is the most economical and effective strategy against this disease. This study involved characterizing resistance in 295 inbred lines using the drilling inoculation method and genotyping them via sequencing. By combining with population structure, disease resistance phenotype, and genome-wide association study (GWAS), we identified 39 significant single-nucleotide polymorphisms (SNPs) associated with P. aristosporum stalk rot resistance by utilizing six statistical methods. Bioinformatics analysis of these SNPs revealed 69 potential resistance genes, among which Zm00001d051313 was finally evaluated for its roles in host defense response to P. aristosporum infection. Through virus-induced gene silencing (VIGS) verification and physiological index determination, we found that transient silencing of Zm00001d051313 promoted P. aristosporum infection, indicating a positive regulatory role of this gene in maize's antifungal defense mechanism. Therefore, these findings will help advance our current understanding of the underlying mechanisms of maize defense to Pythium stalk rot.
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Affiliation(s)
- Mengwei Hou
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Yanyong Cao
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xingrui Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shulin Zhang
- College of Biology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Tengjiao Jia
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiwei Yang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Shengbo Han
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lifeng Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Jingjing Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Hao Wang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Lili Zhang
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Xiaolin Wu
- College of Life Science, Henan Agricultural University, Zhengzhou, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Huiyong Li
- Institute of Cereal Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
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33
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Khan N, Zhang J, Islam S, Appels R, Dell B. Wheat Water-Soluble Carbohydrate Remobilisation under Water Deficit by 1-FEH w3. Curr Issues Mol Biol 2023; 45:6634-6650. [PMID: 37623238 PMCID: PMC10453044 DOI: 10.3390/cimb45080419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/26/2023] Open
Abstract
Fructan 1-exohydrolase (1-FEH) is one of the major enzymes in water-soluble carbohydrate (WSC) remobilisation for grains in wheat. We investigated the functional role of 1-FEH w1, w2, and w3 isoforms in WSC remobilisation under post-anthesis water deficit using mutation lines derived from the Australian wheat variety Chara. F1 seeds, developed by backcrossing the 1-FEH w1, w2, and w3 mutation lines with Chara, were genotyped using the Infinium 90K SNP iSelect platform to characterise the mutated region. Putative deletions were identified in FEH mutation lines encompassing the FEH genomic regions. Mapping analysis demonstrated that mutations affected significantly longer regions than the target FEH gene regions. Functional roles of the non-target genes were carried out utilising bioinformatics and confirmed that the non-target genes were unlikely to confound the effects considered to be due to the influence of 1-FEH gene functions. Glasshouse experiments revealed that the 1-FEH w3 mutation line had a slower degradation and remobilisation of fructans than the 1-FEH w2 and w1 mutation lines and Chara, which reduced grain filling and grain yield. Thus, 1-FEH w3 plays a vital role in reducing yield loss under drought. This insight into the distinct role of the 1-FEH isoforms provides new gene targets for water-deficit-tolerant wheat breeding.
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Affiliation(s)
- Nusrat Khan
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Jingjuan Zhang
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
| | - Shahidul Islam
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58102, USA
| | - Rudi Appels
- Faculty of Science, University of Melbourne, Parkville, VIC 3010, Australia;
| | - Bernard Dell
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, 90 South Street, Murdoch, WA 6163, Australia; (N.K.); (J.Z.); (S.I.)
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34
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Rodríguez AA, Vilas JM, Sartore GD, Bezus R, Colazo J, Maiale SJ. Field and genetic evidence support the photosynthetic performance index (PI ABS) as an indicator of rice grain yield. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107897. [PMID: 37487369 DOI: 10.1016/j.plaphy.2023.107897] [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: 02/08/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/26/2023]
Abstract
The rice breeding process for grain yield could be effectively enhanced by developing efficient tools that accelerate plant selection through the rapid determination of reliable predictors. In this study, we have described various associations between grain yield and photosynthetic parameters, which can be easily and quickly obtained using a non-invasive technique on the flag leaf during the anthesis stage. Among the analyzed photosynthetic parameters, the photosynthetic performance index (PIABS) stood out due to its strong association with grain yield. A genome-wide association analysis conducted on plants from a rice diversity panel at the tillering stage revealed the presence of a quantitative trait locus on chromosome 9. This locus was characterized by a group of candidate chloroplastic genes that exhibited contrasting haplotypes for PIABS. An analysis of these haplotypes revealed a clear division into two groups. One group consisted of haplotypes linked to high values of PIABS, which were predominantly associated with Japonica spp. subpopulations. The other group consisted of haplotypes linked to low values of PIABS, which were exclusively associated with Indica spp. subpopulations. Japonica spp. genotypes exhibited higher values in the yield component panicle weight compared with the Indica spp. genotypes. The findings of this study indicate that PIABS could serve as an early predictor of yield parameters during the tillering stage in rice breeding processes.
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Affiliation(s)
- Andrés Alberto Rodríguez
- Laboratorio de Fisiología y Asistencia al Mejoramiento Vegetal, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Argentina.
| | - Juan Manuel Vilas
- Laboratorio de Fisiología y Asistencia al Mejoramiento Vegetal, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Argentina.
| | - Gustavo Daniel Sartore
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de la Plata, 60 y 119, La Plata, Pcia. Bs. As., Argentina.
| | - Rodolfo Bezus
- Facultad de Ciencias Agrarias y Forestales, Universidad Nacional de la Plata, 60 y 119, La Plata, Pcia. Bs. As., Argentina.
| | - José Colazo
- EEA INTA Concepción del Uruguay, Ruta 39 Km 143, Concepción del Uruguay, Pcia. de Entre Ríos, Argentina.
| | - Santiago Javier Maiale
- Laboratorio de Fisiología y Asistencia al Mejoramiento Vegetal, Instituto Tecnológico de Chascomús (CONICET-UNSAM), Escuela de Bio y Nanotecnologías (UNSAM), Argentina.
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Feng F, Ma X, Yan M, Zhang H, Mei D, Fan P, Xu X, Wei C, Lou Q, Li T, Liu H, Luo L, Mei H. Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations. PLANTS (BASEL, SWITZERLAND) 2023; 12:2743. [PMID: 37514357 PMCID: PMC10385686 DOI: 10.3390/plants12142743] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by -log10(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed.
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Affiliation(s)
- Fangjun Feng
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Xiaosong Ma
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Ming Yan
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Hong Zhang
- Anji Administrative Station of Water and Soil Conservation, Huzhou 313300, China
| | - Daoliang Mei
- Anji Administrative Station of Water and Soil Conservation, Huzhou 313300, China
| | - Peiqing Fan
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Xiaoyan Xu
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Chunlong Wei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
| | - Qiaojun Lou
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Tianfei Li
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Hongyan Liu
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
| | - Lijun Luo
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Hanwei Mei
- Shanghai Agrobiological Gene Center, Shanghai 201106, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai 201106, China
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36
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Peng S, Liu Y, Xu Y, Zhao J, Gao P, Liu Q, Yan S, Xiao Y, Zuo SM, Kang H. Genome-Wide Association Study Identifies a Plant-Height-Associated Gene OsPG3 in a Population of Commercial Rice Varieties. Int J Mol Sci 2023; 24:11454. [PMID: 37511211 PMCID: PMC10380248 DOI: 10.3390/ijms241411454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Plant height is one of the most crucial components of plant structure. However, due to its complexity, the genetic architecture of rice plant height has not been fully elucidated. In this study, we performed a genome-wide association study (GWAS) to determine rice plant height using 178 commercial rice varieties and identified 37 loci associated with rice plant height (LAPH). Among these loci, in LAPH2, we identified a polygalacturonase gene, OsPG3, which was genetically and functionally associated with rice plant height. The rice plant exhibits a super dwarf phenotype when the knockout of the OsPG3 gene occurs via CRISPR-Cas9 gene-editing technology. RNA-Seq analysis indicated that OsPG3 modulates the expression of genes involved in phytohormone metabolism and cell-wall-biosynthesis pathways. Our findings suggest that OsPG3 plays a vital role in controlling rice plant height by regulating cell wall biosynthesis. Given that rice architecture is one of the most critical phenotypes in rice breeding, OsPG3 has potential in rice's molecular design breeding toward an ideal plant height.
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Affiliation(s)
- Shasha Peng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yanchen Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yuchen Xu
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jianhua Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Peng Gao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Qi Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shuangyong Yan
- Tianjin Key Laboratory of Crop Genetic Breeding, Tianjin Crop Research Institute, Tianjin Academy of Agriculture Sciences, Tianjin 300112, China
| | - Yinghui Xiao
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Shi-Min Zuo
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/Key Laboratory of Plant Functional Genomics of the Ministry of Education, Agricultural College of Yangzhou University, Yangzhou 225009, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
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Oliveira GF, Nascimento ACC, Azevedo CF, de Oliveira Celeri M, Barroso LMA, de Castro Sant'Anna I, Viana JMS, de Resende MDV, Nascimento M. Population size in QTL detection using quantile regression in genome-wide association studies. Sci Rep 2023; 13:9585. [PMID: 37311810 DOI: 10.1038/s41598-023-36730-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/08/2023] [Indexed: 06/15/2023] Open
Abstract
The aim of this study was to evaluate the performance of Quantile Regression (QR) in Genome-Wide Association Studies (GWAS) regarding the ability to detect QTLs (Quantitative Trait Locus) associated with phenotypic traits of interest, considering different population sizes. For this, simulated data was used, with traits of different levels of heritability (0.30 and 0.50), and controlled by 3 and 100 QTLs. Populations of 1,000 to 200 individuals were defined, with a random reduction of 100 individuals for each population. The power of detection of QTLs and the false positive rate were obtained by means of QR considering three different quantiles (0.10, 0.50 and 0.90) and also by means of the General Linear Model (GLM). In general, it was observed that the QR models showed greater power of detection of QTLs in all scenarios evaluated and a relatively low false positive rate in scenarios with a greater number of individuals. The models with the highest detection power of true QTLs at the extreme quantils (0.10 and 0.90) were the ones with the highest detection power of true QTLs. In contrast, the analysis based on the GLM detected few (scenarios with larger population size) or no QTLs in the evaluated scenarios. In the scenarios with low heritability, QR obtained a high detection power. Thus, it was verified that the use of QR in GWAS is effective, allowing the detection of QTLs associated with traits of interest even in scenarios with few genotyped and phenotyped individuals.
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Affiliation(s)
- Gabriela França Oliveira
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil.
| | - Ana Carolina Campana Nascimento
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
| | - Camila Ferreira Azevedo
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
| | - Maurício de Oliveira Celeri
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
| | | | - Isabela de Castro Sant'Anna
- Rubber Tree and Agroforestry Systems Research Center, Campinas Agronomy Institute (IAC), Votuporanga, São Paulo, Brazil
| | | | | | - Moysés Nascimento
- Department of Statistics, Federal University of Viçosa, Av. Peter Henry Rolfs, S/N, Campus Universitário, 36570.900, Viçosa, Minas Gerais, Brazil
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Sakhale SA, Yadav S, Clark LV, Lipka AE, Kumar A, Sacks EJ. Genome-wide association analysis for emergence of deeply sown rice ( Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1172816. [PMID: 37377815 PMCID: PMC10291202 DOI: 10.3389/fpls.2023.1172816] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Dry direct-seeded rice (dry-DSR) is typically sown deeply to circumvent the need for irrigation, and thus seedling emergence is a crucial trait affecting plant stand and yield. To breed elite cultivars that use less water and are climate-resilient, an understanding of the genomic regions and underlying genes that confer emergence in deeply sown dry-DSR would be highly advantageous. A combined diversity panel of 470 rice accessions (RDP1 plus aus subset of 3K RGP) was evaluated with 2.9 million single nucleotide polymorphisms (SNPs) to identify associations with dry-DSR traits in the field and component traits in a controlled-environment experiment. Using genome-wide association study (GWAS) analyses, we identified 18 unique QTLs on chromosomes 1, 2, 4, 5, 6, 7, 9, 10, and 11, explaining phenotypic variance ranging from 2.6% to 17.8%. Three QTLs, namely, qSOE-1.1, qEMERG-AUS-1.2, and qEMERG-AUS-7.1, were co-located with previously reported QTLs for mesocotyl length. Among the identified QTLs, half were associated with the emergence of aus, and six were unique to the aus genetic group. Based on functional annotation, we identified eleven compelling candidate genes that primarily regulate phytohormone pathways such as cytokinin, auxin, gibberellic acid, and jasmonic acid. Prior studies indicated that these phytohormones play a critical role in mesocotyl length under deep sowing. This study provides new insight into the importance of aus and indica as desirable genetic resources to mine favorable alleles for deep-sowing tolerance in rice. The candidate genes and marker-tagged desirable alleles identified in this study should benefit rice breeding programs directly.
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Affiliation(s)
- Sandeep A. Sakhale
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Shailesh Yadav
- International Rice Research Institute (IRRI), Los Baños, Philippines
- Africa Rice Center (AfricaRice), Abidjan, Côte d’Ivoire
| | - Lindsay V. Clark
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
- Seattle Children’s Research Institute, Seattle, WA, United States
| | - Alexander E. Lipka
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
| | - Arvind Kumar
- International Rice Research Institute (IRRI), Los Baños, Philippines
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois Urbana-Champaign, Urbana, IL, United States
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39
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Han Z, Lei X, Sha H, Liu J, Zhang C, Wang J, Zheng H, Zou D, Fang J. Adaptation to high latitudes through a novel allele of Hd3a strongly promoting heading date in rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:141. [PMID: 37247094 DOI: 10.1007/s00122-023-04391-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/20/2023] [Indexed: 05/30/2023]
Abstract
KEY MESSAGE A novel Hd3a allele strongly promoting rice heading date was identified, and it functions through florigen activation complex (FAC) and was selected during the spread of rice cultivation to high-latitude areas. Heading date is a critical agronomic trait for rice that determines the utilization of light and temperature conditions and thereby affects grain yield. Rice is a short day (SD) plant, and its photoperiodic information is processed by complex pathways and integrated by florigens to control flowering. In this study, we identified a novel allele for the florigen gene Heading date 3a (Hd3a), characterized by a C435G substitution in its coding region, by a genome-wide association study (GWAS) approach in a panel of 199 high-latitude japonica rice varieties. The C435G substitution induces plants to flower 10 days earlier in high-latitude area (long day condition). Then, we mutated C435 to G in Hd3a by prime editing and found the point mutation plants flowered 12 days earlier. Further molecular experiments showed the novel Hd3a protein can interact with GF14b protein and increase the expression of OsMADS14, the output gene of florigen activation complex (FAC). Molecular signatures of selection indicated that the novel Hd3a allele was selected during the process of rice cultivation expansion into high-latitude areas. Collectively, these results provide new insights into heading date regulation in high-latitude areas and advance improvements to rice adaptability to enhance crop yield.
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Affiliation(s)
- Zhongmin Han
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Xiangliang Lei
- Jiangxi Agricultural University/Fuzhou Institute of Agricultural Science, Nanchang, China
| | - Hanjing Sha
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jia Liu
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Chuanzhong Zhang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Jingguo Wang
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Hongliang Zheng
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Detang Zou
- Key Laboratory of Germplasm Enhancement, Physiology and Ecology of Food Crops in Cold Region, Ministry of Education, Northeast Agricultural University, Harbin, 150030, China
| | - Jun Fang
- State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
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40
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Andreo-Jimenez B, Te Beest DE, Kruijer W, Vannier N, Kadam NN, Melandri G, Jagadish SVK, van der Linden G, Ruyter-Spira C, Vandenkoornhuyse P, Bouwmeester HJ. Genetic Mapping of the Root Mycobiota in Rice and its Role in Drought Tolerance. RICE (NEW YORK, N.Y.) 2023; 16:26. [PMID: 37212977 DOI: 10.1186/s12284-023-00641-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/11/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND Rice is the second most produced crop worldwide, but is highly susceptible to drought. Micro-organisms can potentially alleviate the effects of drought. The aim of the present study was to unravel the genetic factors involved in the rice-microbe interaction, and whether genetics play a role in rice drought tolerance. For this purpose, the composition of the root mycobiota was characterized in 296 rice accessions (Oryza sativa L. subsp. indica) under control and drought conditions. Genome wide association mapping (GWAS) resulted in the identification of ten significant (LOD > 4) single nucleotide polymorphisms (SNPs) associated with six root-associated fungi: Ceratosphaeria spp., Cladosporium spp., Boudiera spp., Chaetomium spp., and with a few fungi from the Rhizophydiales order. Four SNPs associated with fungi-mediated drought tolerance were also found. Genes located around those SNPs, such as a DEFENSIN-LIKE (DEFL) protein, EXOCYST TETHERING COMPLEX (EXO70), RAPID ALKALINIZATION FACTOR-LIKE (RALFL) protein, peroxidase and xylosyltransferase, have been shown to be involved in pathogen defense, abiotic stress responses and cell wall remodeling processes. Our study shows that rice genetics affects the recruitment of fungi, and that some fungi affect yield under drought. We identified candidate target genes for breeding to improve rice-fungal interactions and hence drought tolerance.
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Affiliation(s)
- Beatriz Andreo-Jimenez
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Biointeractions and Plant Health, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB, Wageningen, The Netherlands.
| | - Dennis E Te Beest
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | - Willem Kruijer
- Biometris, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Niteen N Kadam
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Centre for Crop Systems Analysis, Wageningen University and Research, Wageningen, The Netherlands
| | - Giovanni Melandri
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
- School of Plant Sciences, University of Arizona, Tucson, USA
| | - S V Krishna Jagadish
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Kansas State University, Manhattan, KS, 66506, USA
| | | | - Carolien Ruyter-Spira
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands
| | | | - Harro J Bouwmeester
- Laboratory of Plant Physiology, Wageningen University and Research, Wageningen, The Netherlands.
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands.
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Li J, Shi X, Wang C, Li Q, Lu J, Zeng D, Xie J, Shi Y, Zhai W, Zhou Y. Genome-Wide Association Study Identifies Resistance Loci for Bacterial Blight in a Collection of Asian Temperate Japonica Rice Germplasm. Int J Mol Sci 2023; 24:ijms24108810. [PMID: 37240156 DOI: 10.3390/ijms24108810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/29/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Growing resistant rice cultivars is the most effective strategy to control bacterial blight (BB), a devastating disease caused by Xanthomonas oryzae pv. oryzae (Xoo). Screening resistant germplasm and identifying resistance (R) genes are prerequisites for breeding resistant rice cultivars. We conducted a genome-wide association study (GWAS) to detect quantitative trait loci (QTL) associated with BB resistance using 359 East Asian temperate Japonica accessions inoculated with two Chinese Xoo strains (KS6-6 and GV) and one Philippine Xoo strain (PXO99A). Based on the 55K SNPs Array dataset of the 359 Japonica accessions, eight QTL were identified on rice chromosomes 1, 2, 4, 10, and 11. Four of the QTL coincided with previously reported QTL, and four were novel loci. Six R genes were localized in the qBBV-11.1, qBBV-11.2, and qBBV-11.3 loci on chromosome 11 in this Japonica collection. Haplotype analysis revealed candidate genes associated with BB resistance in each QTL. Notably, LOC_Os11g47290 in qBBV-11.3, encoding a leucine-rich repeat receptor-like kinase, was a candidate gene associated with resistance to the virulent strain GV. Knockout mutants of Nipponbare with the susceptible haplotype of LOC_Os11g47290 exhibited significantly improved BB resistance. These results will be useful for cloning BB resistance genes and breeding resistant rice cultivars.
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Affiliation(s)
- Jianmin Li
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Xiaorong Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Chunchao Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Quanlin Li
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Jialing Lu
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dan Zeng
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Junping Xie
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230036, China
| | - Wenxue Zhai
- Institute of Genetics and Developmental Biological, Chinese Academy of Sciences, No. 1 Beichen West Road, Chaoyang District, Beijing 100101, China
| | - Yongli Zhou
- National Key Facility for Crop Gene Resources and Genetic Improvement/Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
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42
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Yang SP, Zhu XX, Qu ZX, Chen CY, Wu YB, Wu Y, Luo ZD, Wang XY, He CY, Fang JW, Wang LQ, Hong GL, Zheng ST, Zeng JM, Yan AF, Feng J, Liu L, Zhang XL, Zhang LG, Miao K, Tang DS. Production of MSTN knockout porcine cells using adenine base-editing-mediated exon skipping. In Vitro Cell Dev Biol Anim 2023:10.1007/s11626-023-00763-5. [PMID: 37099179 DOI: 10.1007/s11626-023-00763-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/24/2023] [Indexed: 04/27/2023]
Abstract
Gene-knockout pigs have important applications in agriculture and medicine. Compared with CRISPR/Cas9 and cytosine base editing (CBE) technologies, adenine base editing (ABE) shows better safety and accuracy in gene modification. However, because of the characteristics of gene sequences, the ABE system cannot be widely used in gene knockout. Alternative splicing of mRNA is an important biological mechanism in eukaryotes for the formation of proteins with different functional activities. The splicing apparatus recognizes conserved sequences of the 5' end splice donor and 3' end splice acceptor motifs of introns in pre-mRNA that can trigger exon skipping, leading to the production of new functional proteins, or causing gene inactivation through frameshift mutations. This study aimed to construct a MSTN knockout pig by inducing exon skipping with the aid of the ABE system to expand the application of the ABE system for the preparation of knockout pigs. In this study, first, we constructed ABEmaxAW and ABE8eV106W plasmid vectors and found that their editing efficiencies at the targets were at least sixfold and even 260-fold higher than that of ABEmaxAW by contrasting the editing efficiencies at the gene targets of endogenous CD163, IGF2, and MSTN in pigs. Subsequently, we used the ABE8eV106W system to realize adenine base (the base of the antisense strand is thymine) editing of the conserved splice donor sequence (5'-GT) of intron 2 of the porcine MSTN gene. A porcine single-cell clone carrying a homozygous mutation (5'-GC) in the conserved sequence (5'-GT) of the intron 2 splice donor of the MSTN gene was successfully generated after drug selection. Unfortunately, the MSTN gene was not expressed and, therefore, could not be characterized at this level. No detectable genomic off-target edits were identified by Sanger sequencing. In this study, we verified that the ABE8eV106W vector had higher editing efficiency and could expand the editing scope of ABE. Additionally, we successfully achieved the precise modification of the alternative splice acceptor of intron 2 of the porcine MSTN gene, which may provide a new strategy for gene knockout in pigs.
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Affiliation(s)
- Shuai-Peng Yang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China
| | - Xiang-Xing Zhu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China.
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China.
| | - Zi-Xiao Qu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China
| | - Cai-Yue Chen
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Yao-Bing Wu
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Yue Wu
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Zi-Dan Luo
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Xin-Yi Wang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Chu-Yu He
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Jia-Wen Fang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Ling-Qi Wang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Guang-Long Hong
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Shu-Tao Zheng
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Jie-Mei Zeng
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Ai-Fen Yan
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Juan Feng
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Lian Liu
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Xiao-Li Zhang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Li-Gang Zhang
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China
| | - Kai Miao
- Centre for Precision Medicine Research and Training, Faculty of Health Sciences, University of Macau, Macau SAR, China.
| | - Dong-Sheng Tang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Sciences and Engineering, Foshan University, Foshan, 528225, China.
- Gene Editing Technology Center of Guangdong Province, School of Medicine, Foshan University, Foshan, 528225, China.
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He Y, Sun S, Zhao J, Huang Z, Peng L, Huang C, Tang Z, Huang Q, Wang Z. UDP-glucosyltransferase OsUGT75A promotes submergence tolerance during rice seed germination. Nat Commun 2023; 14:2296. [PMID: 37085517 PMCID: PMC10121563 DOI: 10.1038/s41467-023-38085-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/14/2023] [Indexed: 04/23/2023] Open
Abstract
Submergence stress represents a major obstacle limiting the application of direct seeding in rice cultivation. Under flooding conditions, coleoptile elongation can function as an escape strategy that contributes to submergence tolerance during seed germination in rice; however, the underlying molecular bases have yet to be fully determined. Herein, we report that natural variation of rice coleoptile length subjected to submergence is determined by the glucosyltransferase encoding gene OsUGT75A. OsUGT75A regulates coleoptile length via decreasing free abscisic acid (ABA) and jasmonic acid (JA) levels by promoting glycosylation of these two phytohormones under submergence. Moreover, we find that OsUGT75A accelerates coleoptile length through mediating the interactions between JASMONATE ZIMDOMAIN (OsJAZ) and ABSCISIC ACID-INSENSITIVE (OsABI) proteins. Last, we reveal the origin of the haplotype that contributes to coleoptile length in response to submergence and transferring this haplotype to indica rice can enhance coleoptile length in submergence conditions. Thus, we propose that OsUGT75A is a useful target in breeding of rice varieties suitable for direct seeding cultivation.
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Affiliation(s)
- Yongqi He
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Shan Sun
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Jia Zhao
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Zhibo Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Liling Peng
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Chengwei Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Zhengbin Tang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Qianqian Huang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China
| | - Zhoufei Wang
- The Laboratory of Seed Science and Technology, Guangdong Key Laboratory of Plant Molecular Breeding, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, 510642, Guangzhou, China.
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Skovbjerg CK, Angra D, Robertson-Shersby-Harvie T, Kreplak J, Keeble-Gagnère G, Kaur S, Ecke W, Windhorst A, Nielsen LK, Schiemann A, Knudsen J, Gutierrez N, Tagkouli V, Fechete LI, Janss L, Stougaard J, Warsame A, Alves S, Khazaei H, Link W, Torres AM, O'Sullivan DM, Andersen SU. Genetic analysis of global faba bean diversity, agronomic traits and selection signatures. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:114. [PMID: 37074596 PMCID: PMC10115707 DOI: 10.1007/s00122-023-04360-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 03/31/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE We identified marker-trait associations for key faba bean agronomic traits and genomic signatures of selection within a global germplasm collection. Faba bean (Vicia faba L.) is a high-protein grain legume crop with great potential for sustainable protein production. However, little is known about the genetics underlying trait diversity. In this study, we used 21,345 high-quality SNP markers to genetically characterize 2678 faba bean genotypes. We performed genome-wide association studies of key agronomic traits using a seven-parent-MAGIC population and detected 238 significant marker-trait associations linked to 12 traits of agronomic importance. Sixty-five of these were stable across multiple environments. Using a non-redundant diversity panel of 685 accessions from 52 countries, we identified three subpopulations differentiated by geographical origin and 33 genomic regions subjected to strong diversifying selection between subpopulations. We found that SNP markers associated with the differentiation of northern and southern accessions explained a significant proportion of agronomic trait variance in the seven-parent-MAGIC population, suggesting that some of these traits were targets of selection during breeding. Our findings point to genomic regions associated with important agronomic traits and selection, facilitating faba bean genomics-based breeding.
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Affiliation(s)
- Cathrine Kiel Skovbjerg
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark.
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark.
| | - Deepti Angra
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | | | - Jonathan Kreplak
- Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, Dijon, France
| | | | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Wolfgang Ecke
- Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Alex Windhorst
- Georg-August-Universität Göttingen, DNPW, Carl-Sprengel 1, Germany
| | | | | | | | - Natalia Gutierrez
- Área de Mejora Vegetal y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo 3092, 14080, Córdoba, Spain
| | - Vasiliki Tagkouli
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Lavinia Ioana Fechete
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, 8000, Aarhus, Denmark
| | - Jens Stougaard
- Department of Molecular Biology and Genetics, Aarhus University, 8000, Aarhus, Denmark
| | - Ahmed Warsame
- School of Agriculture, Policy and Development, University of Reading, Reading, UK
| | - Sheila Alves
- Crops Research, Teagasc, Oak Park, Carlow, Ireland
| | - Hamid Khazaei
- Production Systems, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Wolfgang Link
- Georg-August-Universität Göttingen, DNPW, Carl-Sprengel 1, Germany
| | - Ana Maria Torres
- Área de Mejora Vegetal y Biotecnología, IFAPA Centro "Alameda del Obispo", Apdo 3092, 14080, Córdoba, Spain
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Osnato M. Evolution of flowering time genes in rice: From the paleolithic to the anthropocene. PLANT, CELL & ENVIRONMENT 2023; 46:1046-1059. [PMID: 36411270 DOI: 10.1111/pce.14495] [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: 07/19/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 06/16/2023]
Abstract
The evolutionary paths of humans and plants have crossed more than once throughout millennia. While agriculture contributed to the evolution of societies in prehistory, human selection of desirable traits contributed to the evolution of crops during centuries of cultivation. Among cereal crops, rice is currently grown around the globe and represents staple food for almost half of the world population. Over time, rice cultivation has expanded from subtropical to temperate regions thanks to artificial selection of mutants with impaired response to photoperiod. Additional regulatory mechanisms control flowering in response to diverse environmental cues, anticipating or delaying the floral transition to produce seeds in more favourable conditions. Nevertheless, the changing climate is threatening grain production because modern cultivars are sensitive to external fluctuations that go beyond their physiological range. One possibility to guarantee food production could be the exploitation of novel varieties obtained by crossing highly productive Asian rice with stress tolerant African rice. This review explores the genetic basis of the key traits that marked the long journey of rice cultivation from the end of the paleolithic to the anthropocene, with a focus on heading date. By 2050, will rice plants of the future flower in the outer space?
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Affiliation(s)
- Michela Osnato
- Institut de Ciència i Tecnologia Ambientals, Universitat Autónoma de Barcelona (ICTA-UAB), Bellaterra, Spain
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46
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Hong J, Su S, Wang L, Bai S, Xu J, Li Z, Betts N, Liang W, Wang W, Shi J, Zhang D. Combined genome-wide association study and epistasis analysis reveal multifaceted genetic architectures of plant height in Asian cultivated rice. PLANT, CELL & ENVIRONMENT 2023; 46:1295-1311. [PMID: 36734269 DOI: 10.1111/pce.14557] [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: 10/25/2022] [Revised: 01/08/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
Plant height (PH) in rice (Oryza sativa) is an important trait for its adaptation and agricultural performance. Discovery of the semi-dwarf1 (SD1) mutation initiated the Green Revolution, boosting rice yield and fitness, but the underlying genetic regulation of PH in rice remains largely unknown. Here, we performed genome-wide association study (GWAS) and identified 12 non-repetitive QTL/genes regulating PH variation in 619 Asian cultivated rice accessions. One of these was an SD1 structural variant, not normally detected in standard GWAS analyses. Given the strong effect of SD1 on PH, we also divided 619 accessions into subgroups harbouring distinct SD1 haplotypes, and found a further 85 QTL/genes for PH, revealing genetic heterogeneity that may be missed by analysing a broad, diverse population. Moreover, we uncovered two epistatic interaction networks of PH-associated QTL/genes in the japonica (Geng)-dominant SD1NIP subgroup. In one of them, the hub QTL/gene qphSN1.4/GAMYB interacted with qphSN3.1/OsINO80, qphSN3.4/HD16/EL1, qphSN6.2/LOC_Os06g11130, and qphSN10.2/MADS56. Sequence variations in GAMYB and MADS56 were associated with their expression levels and PH variations, and MADS56 was shown to physically interact with MADS57 to coregulate expression of gibberellin (GA) metabolic genes OsGA2ox3 and Elongated Uppermost Internode1 (EUI1). Our study uncovered the multifaceted genetic architectures of rice PH, and provided novel and abundant genetic resources for breeding semi-dwarf rice and new candidates for further mechanistic studies on regulation of PH in rice.
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Affiliation(s)
- Jun Hong
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Su Su
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Li Wang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Shaoxing Bai
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Jianlong Xu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhikang Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Natalie Betts
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
| | - Wanqi Liang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Wensheng Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianxin Shi
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
| | - Dabing Zhang
- Joint International Research Laboratory of Metabolic and Developmental Sciences, State Key Laboratory of Hybrid Rice, School of Life Sciences and Biotechnology, Yazhou Bay Institute of Deepsea Sci-Tech, Shanghai Jiao Tong University, Shanghai, China
- School of Agriculture, Food and Wine, University of Adelaide, Urrbrae, South Australia, Australia
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Wang J, Zhou F, Li C, Yin N, Liu H, Zhuang B, Huang Q, Wen Y. Gene Association Analysis of Quantitative Trait Based on Functional Linear Regression Model with Local Sparse Estimator. Genes (Basel) 2023; 14:genes14040834. [PMID: 37107592 PMCID: PMC10137544 DOI: 10.3390/genes14040834] [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: 02/16/2023] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/03/2023] Open
Abstract
Functional linear regression models have been widely used in the gene association analysis of complex traits. These models retain all the genetic information in the data and take full advantage of spatial information in genetic variation data, which leads to brilliant detection power. However, the significant association signals identified by the high-power methods are not all the real causal SNPs, because it is easy to regard noise information as significant association signals, leading to a false association. In this paper, a method based on the sparse functional data association test (SFDAT) of gene region association analysis is developed based on a functional linear regression model with local sparse estimation. The evaluation indicators CSR and DL are defined to evaluate the feasibility and performance of the proposed method with other indicators. Simulation studies show that: (1) SFDAT performs well under both linkage equilibrium and linkage disequilibrium simulation; (2) SFDAT performs successfully for gene regions (including common variants, low-frequency variants, rare variants and mix variants); (3) With power and type I error rates comparable to OLS and Smooth, SFDAT has a better ability to handle the zero regions. The Oryza sativa data set is analyzed by SFDAT. It is shown that SFDAT can better perform gene association analysis and eliminate the false positive of gene localization. This study showed that SFDAT can lower the interference caused by noise while maintaining high power. SFDAT provides a new method for the association analysis between gene regions and phenotypic quantitative traits.
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Affiliation(s)
- Jingyu Wang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Fujie Zhou
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cheng Li
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Ning Yin
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Huiming Liu
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Binxian Zhuang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qingyu Huang
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongxian Wen
- College of Computer and Information Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Institute of Statistics and Application, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence:
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48
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Chen D, Zou W, Zhang M, Liu J, Chen L, Peng T, Ye G. Genome-Wide Association Study for Seed Dormancy Using Re-Sequenced Germplasm under Multiple Conditions in Rice. Int J Mol Sci 2023; 24:ijms24076117. [PMID: 37047087 PMCID: PMC10094323 DOI: 10.3390/ijms24076117] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Revised: 03/08/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Seed dormancy is a key factor used to determine seed germination in rice production. So far, only a few genes controlling seed dormancy have been reported, and the genetic mechanism of rice seed dormancy is still elusive. In this study, a population of 195 diverse re-sequenced accessions from 40 countries was evaluated for the seed germination rate (GR) without dormancy breaking (WDB) as a control and under dry heating (DH) and gibberellic acid (GA) treatments, as dormancy breaking agents to identify QTLs for seed dormancy. Phenotypic assessment revealed that these accessions had abundant variations in seed dormancy. GWAS using 1,120,223 high-quality single nucleotide polymorphisms (SNPs) and a mixed linear model (MLM) incorporating both principal components (PCs) and kinship (K) identified 30 QTLs on 10 chromosomes, accounting for 7.3-20.4% of the phenotypic variance in GR. Ten of the QTLs were located in the regions of previously reported QTLs, while the rest were novel ones. Thirteen high-confidence candidate genes were predicted for the four QTLs detected in two or three conditions (qGR4-4, qGR4-5, qGR8 and qGR11-4) and one QTL with a large effect (qGR3). These genes were highly expressed during seed development and were significantly regulated by various hormone treatments. This study provides new insights into the genetic and molecular basis of rice seed dormancy/germination. The accessions with moderate and strong dormancy and markers for the QTLs and candidate genes are useful for attaining a proper level of seed dormancy.
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Affiliation(s)
- Dandan Chen
- Key Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Wenli Zou
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Mingpei Zhang
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China
- Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Jindong Liu
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Liang Chen
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Ting Peng
- Key Laboratory of Rice Biology in Henan Province, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, China
| | - Guoyou Ye
- CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Rice Breeding Innovations Platform, International Rice Research Institute (IRRI), Metro Manila 1301, Philippines
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Chen J, Xuan Y, Yi J, Xiao G, Yuan DP, Li D. Progress in rice sheath blight resistance research. FRONTIERS IN PLANT SCIENCE 2023; 14:1141697. [PMID: 37035075 PMCID: PMC10080073 DOI: 10.3389/fpls.2023.1141697] [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: 01/10/2023] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
Rice sheath blight (ShB) disease poses a major threat to rice yield throughout the world. However, the defense mechanisms against ShB in rice remain largely unknown. ShB resistance is a typical quantitative trait controlled by multiple genes. With the rapid development of molecular methods, many quantitative trait loci (QTLs) related to agronomic traits, biotic and abiotic stresses, and yield have been identified by genome-wide association studies. The interactions between plants and pathogens are controlled by various plant hormone signaling pathways, and the pathways synergistically or antagonistically interact with each other, regulating plant growth and development as well as the defense response. This review summarizes the regulatory effects of hormones including auxin, ethylene, salicylic acid, jasmonic acid, brassinosteroids, gibberellin, abscisic acid, strigolactone, and cytokinin on ShB and the crosstalk between the various hormones. Furthermore, the effects of sugar and nitrogen on rice ShB resistance, as well as information on genes related to ShB resistance in rice and their effects on ShB are also discussed. In summary, this review is a comprehensive description of the QTLs, hormones, nutrition, and other defense-related genes related to ShB in rice. The prospects of targeting the resistance mechanism as a strategy for controlling ShB in rice are also discussed.
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Affiliation(s)
- Jingsheng Chen
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Yuanhu Xuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Jianghui Yi
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - Guosheng Xiao
- College of Biology and Food Engineering, Chongqing Three Gorges University, Wanzhou, China
| | - De Peng Yuan
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Dandan Li
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
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50
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Kim TH, Kim SM. Identification of Candidate Genes for Salt Tolerance at the Seedling Stage Using Integrated Genome-Wide Association Study and Transcriptome Analysis in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:1401. [PMID: 36987089 PMCID: PMC10056360 DOI: 10.3390/plants12061401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Salt stress is a major constraint in rice production worldwide. Salt stress is estimated to cause annual losses of 30-50% in rice production. Discovering and deploying salt-resistance genes are the most effective ways to control salt stress. We performed a genome-wide association study (GWAS) to detect QTLs related to salt tolerance at the seedling stage using the japonica-multiparent advanced generation intercross (MAGIC) population. Four QTLs (qDTS1-1, qDTS1-2, qDTS2, and qDTS9) associated with salt tolerance were identified on chromosomes 1, 2, and 9. Among these QTLs, a novel QTL, qDTS1-2, was located between flanking SNPs (1354576 and id1028360) on chromosome 1, with the largest -log10(P) value of 5.81 and a total phenotypic variance of 15.2%. RNA-seq analysis revealed that among the seven differentially expressed genes (DEGs) commonly identified in both P6 and JM298 showing salt tolerance, two upregulated genes, Os01g0963600 (ASR transcription factor) and Os01g0975300 (OsMYB48), related to salt and drought tolerance, were also involved in the target region of qDTS1-2. The results of this study can provide insights into further understanding of salt tolerance mechanisms and developing DNA markers for marker-assisted selection (MAS) breeding to improve the salt tolerance of cultivars in rice breeding programs.
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Affiliation(s)
- Tae-Heon Kim
- Institute of Agricultural Science and Technology, Kyungpook National University, Daegu 41566, Republic of Korea;
- Department of Ecological & Environmental System, Kyungpook National University, Sangju 37224, Republic of Korea
| | - Suk-Man Kim
- Department of Ecological & Environmental System, Kyungpook National University, Sangju 37224, Republic of Korea
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