151
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Seidenthal K, Panjvani K, Chandnani R, Kochian L, Eramian M. Iterative image segmentation of plant roots for high-throughput phenotyping. Sci Rep 2022; 12:16563. [PMID: 36195610 PMCID: PMC9532414 DOI: 10.1038/s41598-022-19754-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/02/2022] [Indexed: 11/24/2022] Open
Abstract
Accurate segmentation of root system architecture (RSA) from 2D images is an important step in studying phenotypic traits of root systems. Various approaches to image segmentation exist but many of them are not well suited to the thin and reticulated structures characteristic of root systems. The findings presented here describe an approach to RSA segmentation that takes advantage of the inherent structural properties of the root system, a segmentation network architecture we call ITErRoot. We have also generated a novel 2D root image dataset which utilizes an annotation tool developed for producing high quality ground truth segmentation of root systems. Our approach makes use of an iterative neural network architecture to leverage the thin and highly branched properties of root systems for accurate segmentation. Rigorous analysis of model properties was carried out to obtain a high-quality model for 2D root segmentation. Results show a significant improvement over other recent approaches to root segmentation. Validation results show that the model generalizes to plant species with fine and highly branched RSA’s, and performs particularly well in the presence of non-root objects.
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Affiliation(s)
- Kyle Seidenthal
- Department of Computer Science, University of Saskatchewan, 110 Science Place, Saskatoon, SK, S7N 5C9, Canada
| | - Karim Panjvani
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, Saskatoon, SK, S7N 4L8, Canada
| | - Rahul Chandnani
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, Saskatoon, SK, S7N 4L8, Canada
| | - Leon Kochian
- Global Institute for Food Security, University of Saskatchewan, 421 Downey Road, Saskatoon, SK, S7N 4L8, Canada
| | - Mark Eramian
- Department of Computer Science, University of Saskatchewan, 110 Science Place, Saskatoon, SK, S7N 5C9, Canada.
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152
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Barnhart MH, Masalia RR, Mosley LJ, Burke JM. Phenotypic and transcriptomic responses of cultivated sunflower seedlings (Helianthus annuus L.) to four abiotic stresses. PLoS One 2022; 17:e0275462. [PMID: 36178944 PMCID: PMC9524668 DOI: 10.1371/journal.pone.0275462] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 09/18/2022] [Indexed: 11/19/2022] Open
Abstract
Plants encounter and respond to numerous abiotic stresses during their lifetimes. These stresses are often related and could therefore elicit related responses. There are, however, relatively few detailed comparisons between multiple different stresses at the molecular level. Here, we investigated the phenotypic and transcriptomic response of cultivated sunflower (Helianthus annuus L.) seedlings to three water-related stresses (i.e., dry-down, an osmotic challenge, and salt stress), as well as a generalized low-nutrient stress. All four stresses negatively impacted seedling growth, with the nutrient stress having a more divergent response from control as compared to the water-related stresses. Phenotypic responses were consistent with expectations for growth in low-resource environments, including increased (i.e., less negative) carbon fractionation values and leaf C:N ratios, as well as increased belowground biomass allocation. The number of differentially expressed genes (DEGs) under stress was greater in leaf tissue, but roots exhibited a higher proportion of DEGs unique to individual stresses. Overall, the three water-related stresses had a more similar transcriptomic response to each other vs. nutrient stress, though this pattern was more pronounced in root vs. leaf tissue. In contrast to our DEG analyses, co-expression network analysis revealed that there was little indication of a shared response between the four stresses in despite the majority of DEGs being shared between multiple stresses. Importantly, osmotic stress, which is often used to simulate drought stress in experimental settings, had little transcriptomic resemblance to true water limitation (i.e., dry-down) in our study, calling into question its utility as a means for simulating drought.
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Affiliation(s)
- Max H. Barnhart
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
- * E-mail:
| | - Rishi R. Masalia
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
| | - Liana J. Mosley
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, GA, United States of America
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153
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Qin T, Kazim A, Wang Y, Richard D, Yao P, Bi Z, Liu Y, Sun C, Bai J. Root-Related Genes in Crops and Their Application under Drought Stress Resistance—A Review. Int J Mol Sci 2022; 23:ijms231911477. [PMID: 36232779 PMCID: PMC9569943 DOI: 10.3390/ijms231911477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/25/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Crop growth and development are frequently affected by biotic and abiotic stresses. The adaptation of crops to stress is mostly achieved by regulating specific genes. The root system is the primary organ for nutrient and water uptake, and has an important role in drought stress response. The improvement of stress tolerance to increase crop yield potential and yield stability is a traditional goal of breeders in cultivar development using integrated breeding methods. An improved understanding of genes that control root development will enable the formulation of strategies to incorporate stress-tolerant genes into breeding for complex agronomic traits and provide opportunities for developing stress-tolerant germplasm. We screened the genes associated with root growth and development from diverse plants including Arabidopsis, rice, maize, pepper and tomato. This paper provides a theoretical basis for the application of root-related genes in molecular breeding to achieve crop drought tolerance by the improvement of root architecture.
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Affiliation(s)
- Tianyuan Qin
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Ali Kazim
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Yihao Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Dormatey Richard
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Panfeng Yao
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Zhenzhen Bi
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuhui Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Chao Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (C.S.); (J.B.); Tel.: +86-189-9319-8496 (C.S.); +86-181-0942-4020 (J.B.)
| | - Jiangping Bai
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
- Correspondence: (C.S.); (J.B.); Tel.: +86-189-9319-8496 (C.S.); +86-181-0942-4020 (J.B.)
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154
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Xiang J, Zhang C, Wang N, Liang Z, Zhenzhen Z, Liang L, Yuan H, Shi Y. Genome-Wide Association Study Reveals Candidate Genes for Root-Related Traits in Rice. Curr Issues Mol Biol 2022; 44:4386-4405. [PMID: 36286016 PMCID: PMC9601093 DOI: 10.3390/cimb44100301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 12/04/2022] Open
Abstract
Root architecture is a determinant factor of drought resistance in rice and plays essential roles in the absorption of water and nutrients for the survival of rice plants. Dissection of the genetic basis for root structure can help to improve stress-resistance and grain yield in rice breeding. In this study, a total of 391 rice (Oryz asativa L.) accessions were used to perform a genome-wide association study (GWAS) on three root-related traits in rice, including main root length (MRL), average root length (ARL), and total root number (TRN). As a result, 13 quantitative trait loci (QTLs) (qMRL1.1, qMRL1.2, qMRL3.1, qMRL3.2, qMRL3.3, qMRL4.1, qMRL7.1, qMRL8.1, qARL1.1, qARL9.1, qTRN9.1, qTRN9.2, and qTRN11.1) significantly associated with the three traits were identified, among which three (qMRL3.2, qMRL4.1 and qMRL8.1) were overlapped with OsGNOM1, OsARF12 and qRL8.1, respectively, and ten were novel QTLs. Moreover, we also detected epistatic interactions affecting root-related traits and identified 19 related genetic interactions. These results lay a foundation for cloning the corresponding genes for rice root structure, as well as provide important genomic resources for breeding high yield rice varieties.
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Affiliation(s)
| | | | | | | | | | | | | | - Yingyao Shi
- College of Agronomy, Anhui Agricultural University, Hefei 230000, China
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155
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Chen H, Zhao C, Yang Y, Zeng Z, Li W, Liu Y, Tang H, Xu Q, Deng M, Jiang Q, Chen G, Peng Y, Jiang Y, Jiang Y, Wei Y, Zheng Y, Lan X, Ma J. Identification and validation of a locus for wheat maximum root length independent of parental reproductive environment. FRONTIERS IN PLANT SCIENCE 2022; 13:999414. [PMID: 36172559 PMCID: PMC9511226 DOI: 10.3389/fpls.2022.999414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023]
Abstract
Maximum root length (MRL) plays an important role in the uptake of nutrients and resisting abiotic stresses. Understanding the genetic mechanism of root development is of great significance for genetic improvement of wheat. Previous studies have confirmed that parental reproductive environment (PRE) has a significant impact on growth and development of the next generation in the whole life cycle of a given plant. In this study, a recombinant inbred line population genotyped using the Wheat55K SNP array, was used to map quantitative trait loci (QTL) for wheat seedling MRL based on the harvested seeds from five different PREs. A total of 5 QTL located on chromosomes 3D and 7A were identified. Among them, QMrl.sicau-2SY-3D.2 located in a 4.0 cM interval on chromosome 3D was likely independent of PREs. QMrl.sicau-2SY-7A.2 was detected in two tests and probably influenced by PREs. The effect of QMrl.sicau-2SY-3D.2 was further validated using the tightly linked kompetitive allele specific PCR (KASP) marker, KASP-AX-111589572, in populations with different genetic backgrounds. Lines with a combination of positive alleles from QMrl.sicau-2SY-3D.2 and QMrl.sicau-2SY-7A.2 have significantly longer MRL. Furthermore, four genes (TraesCS3D03G0612000, TraesCS3D03G0608400, TraesCS3D03G0613600, and TraesCS3D03G0602400) mainly expressed in wheat root were predicted to be associated with root growth. Taken together, this study reports on a major QTL independent of PREs and lays a foundation for understanding the regulation mechanism of wheat MRL at the seedling stage.
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Affiliation(s)
- Huangxin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Conghao Zhao
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaoyao Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhaoyong Zeng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yuanying Peng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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156
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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157
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Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez‐Alfonso Y, Varshney RK. Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:1701-1715. [PMID: 35534989 PMCID: PMC9398337 DOI: 10.1111/pbi.13840] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/28/2022] [Indexed: 05/26/2023]
Abstract
Chickpea production is vulnerable to drought stress. Identifying the genetic components underlying drought adaptation is crucial for enhancing chickpea productivity. Here, we present the fine mapping and characterization of 'QTL-hotspot', a genomic region controlling chickpea growth with positive consequences on crop production under drought. We report that a non-synonymous substitution in the transcription factor CaTIFY4b regulates seed weight and organ size in chickpea. Ectopic expression of CaTIFY4b in Medicago truncatula enhances root growth under water deficit. Our results suggest that allelic variation in 'QTL-hotspot' improves pre-anthesis water use, transpiration efficiency, root architecture and canopy development, enabling high-yield performance under terminal drought conditions. Gene expression analysis indicated that CaTIFY4b may regulate organ size under water deficit by modulating the expression of GRF-INTERACTING FACTOR1 (GIF1), a transcriptional co-activator of Growth-Regulating Factors. Taken together, our study offers new insights into the role of CaTIFY4b and on diverse physiological and molecular mechanisms underpinning chickpea growth and production under specific drought scenarios.
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Affiliation(s)
- Rutwik Barmukh
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Department of GeneticsOsmania UniversityHyderabadIndia
| | - Manish Roorkiwal
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- Khalifa Center for Genetic Engineering and BiotechnologyUnited Arab Emirates UniversityAl‐AinUnited Arab Emirates
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
| | - Vanika Garg
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Liam German
- Centre for Plant ScienceSchool of BiologyUniversity of LeedsLeedsUK
| | - Deepa Jaganathan
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Annapurna Chitikineni
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Jana Kholova
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Himabindu Kudapa
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Kaliamoorthy Sivasakthi
- Crop Physiology and ModellingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Srinivasan Samineni
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sandip M. Kale
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pooran M. Gaur
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Crop BreedingInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | | | - Rajeev K. Varshney
- Centre of Excellence in Genomics and Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- The UWA Institute of AgricultureThe University of Western AustraliaPerthWestern AustraliaAustralia
- Murdoch’s Centre for Crop & Food InnovationState Agricultural Biotechnology CentreFood Futures InstituteMurdoch UniversityMurdochWestern AustraliaAustralia
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158
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Verma PK, Verma S, Pandey N. Root system architecture in rice: impacts of genes, phytohormones and root microbiota. 3 Biotech 2022; 12:239. [PMID: 36016841 PMCID: PMC9395555 DOI: 10.1007/s13205-022-03299-9] [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: 03/14/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
To feed the continuously expanding world's population, new crop varieties have been generated, which significantly contribute to the world's food security. However, the growth of these improved plant varieties relies primarily on synthetic fertilizers, which negatively affect the environment and human health; therefore, continuous improvement is needed for sustainable agriculture. Several plants, including cereal crops, have the adaptive capability to combat adverse environmental changes by altering physiological and molecular mechanisms and modifying their root system to improve nutrient uptake efficiency. These plants operate distinct pathways at various developmental stages to optimally establish their root system. These processes include changes in the expression profile of genes, changes in phytohormone level, and microbiome-induced root system architecture (RSA) modification. Several studies have been performed to understand microbial colonization and their involvement in RSA improvement through changes in phytohormone and transcriptomic levels. This review highlights the impact of genes, phytohormones, and particularly root microbiota in influencing RSA and provides new insights resulting from recent studies on rice root as a model system and summarizes the current knowledge about biochemical and central molecular mechanisms.
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Affiliation(s)
- Pankaj Kumar Verma
- Department of Botany, University of Lucknow, Lucknow, India
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Shikha Verma
- Present Address: French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus, Israel
| | - Nalini Pandey
- Department of Botany, University of Lucknow, Lucknow, India
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159
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All Are in a Drought, but Some Stand Out: Multivariate Analysis in the Selection of Agronomic Efficient Popcorn Genotypes. PLANTS 2022; 11:plants11172275. [PMID: 36079656 PMCID: PMC9460328 DOI: 10.3390/plants11172275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/17/2022]
Abstract
The search for productive germplasm adapted to adverse conditions is an important action to mitigate the harmful effects of climate change. The aim was to identify the yield potential of 50 popcorn inbred lines grown in field conditions, in two crop seasons (CS), and under contrasting water conditions (WC). Morphoagronomic, physiological, and root system traits were evaluated. Joint and individual analyses of variance were performed, in addition to the multivariate GT bip-lot analysis. Expressive reductions between WC were observed in 100-grain weight (100 GW), popping expansion (PE), grain yield (GY), expanded popcorn volume per ha (EPV), row number per ear (RNE), plant height (PH), relative chlorophyll content (SPAD), and nitrogen balance index (NBI). It was found that the SPAD, 100 GW, GY, PE, and grain number per ear (GNE) traits had the most significant impact on the selection of genotypes. Regardless of WC and CS, the ideal lines were L294 and L688 for PE; L691 and L480 for GY; and L291 and L292 for both traits. SPAD, 100 GW, and GNE can contribute to the indirect selection. Our work contributes to understanding the damage caused by drought and the integration of traits for the indirect selection of drought-tolerant popcorn genotypes.
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160
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Shoaib M, Banerjee BP, Hayden M, Kant S. Roots’ Drought Adaptive Traits in Crop Improvement. PLANTS 2022; 11:plants11172256. [PMID: 36079644 PMCID: PMC9460784 DOI: 10.3390/plants11172256] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022]
Abstract
Drought is one of the biggest concerns in agriculture due to the projected reduction of global freshwater supply with a concurrent increase in global food demand. Roots can significantly contribute to improving drought adaptation and productivity. Plants increase water uptake by adjusting root architecture and cooperating with symbiotic soil microbes. Thus, emphasis has been given to root architectural responses and root–microbe relationships in drought-resilient crop development. However, root responses to drought adaptation are continuous and complex processes and involve additional root traits and interactions among themselves. This review comprehensively compiles and discusses several of these root traits such as structural, physiological, molecular, hydraulic, anatomical, and plasticity, which are important to consider together, with architectural changes, when developing drought resilient crop varieties. In addition, it describes the significance of root contribution in improving soil structure and water holding capacity and its implication on long-term resilience to drought. In addition, various drought adaptive root ideotypes of monocot and dicot crops are compared and proposed for given agroclimatic conditions. Overall, this review provides a broader perspective of understanding root structural, physiological, and molecular regulators, and describes the considerations for simultaneously integrating multiple traits for drought tolerance and crop improvement, under specific growing environments.
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Affiliation(s)
- Mirza Shoaib
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, VIC 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC 3083, Australia
| | - Bikram P. Banerjee
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, VIC 3400, Australia
| | - Matthew Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Melbourne, VIC 3083, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, 110 Natimuk Road, Horsham, VIC 3400, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Melbourne, VIC 3083, Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, Melbourne, VIC 3083, Australia
- Correspondence:
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161
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Zhao J, Jiang L, Bai H, Dai Y, Li K, Li S, Wang X, Wu L, Fu Q, Yang Y, Dong Q, Yu S, Wang M, Liu H, Peng Z, Zhu H, Zhang X, He X, Lei Y, Liang Y, Guo L, Zhang H, Yu D, Liu Y, Huang H, Liu C, Peng S, Du Y. Characteristics of members of IGT family genes in controlling rice root system architecture and tiller development. FRONTIERS IN PLANT SCIENCE 2022; 13:961658. [PMID: 36147240 PMCID: PMC9487910 DOI: 10.3389/fpls.2022.961658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 07/27/2022] [Indexed: 06/16/2023]
Abstract
Root system architecture (RSA) and tiller are important agronomic traits. However, the mechanisms of the IGT family genes regulate RSA and tiller development in different rice varieties remain unclear. In this study, we demonstrated that 38 rice varieties obtained from Yuanyang Hani's terraced fields with different RSA and could be classified into six groups based on the ratio of root length and width. We found a positive correlation between RSA (including root width, length, and area) and tiller number in most of rice varieties. Furthermore, the IGT family genes Deeper Rooting 1 (DRO1), LAZY1, TAC1, and qSOR1 showed different expression patterns when rice grown under irrigation and drought conditions. Moreover, the qSOR1 gene had higher levels in the roots and tillers, and accompanied with higher levels of PIN1b gene in roots when rice grown under drought environmental condition. DRO1 gene had two single nucleotide polymorphisms (SNPs) in the exon 3 sequences and showed different expression patterns in the roots and tillers of the 38 rice varieties. Overexpression of DRO1 with a deletion of exon 5 caused shorter root length, less lateral roots and lower levels of LAZY1, TAC1, and qSOR1. Further protein interaction network, microRNA targeting and co-expression analysis showed that DRO1 plays a critical role in the root and tiller development associated with auxin transport. These data suggest that the RSA and tiller development are regulated by the IGT family genes in an intricate network way, which is tightly related to rice genetic background in rice adapting to different environmental conditions.
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Affiliation(s)
- Jianping Zhao
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Lihui Jiang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Hanrui Bai
- Division of Life Sciences and Medicine, College of Life Sciences, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Yuliang Dai
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Kuixiu Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Saijie Li
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Xiaoran Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Lixia Wu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qijing Fu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yanfen Yang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Qian Dong
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Si Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Meixian Wang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Haiyan Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
| | - Ziai Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Haiyan Zhu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xiaoyan Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Xie He
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yan Lei
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yan Liang
- Yuguopu District Agricultural Comprehensive Service Center, Mengzi, China
| | - Liwei Guo
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Hongji Zhang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Decai Yu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yixiang Liu
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Huichuan Huang
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Changning Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Sheng Peng
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
| | - Yunlong Du
- College of Plant Protection, Yunnan Agricultural University, Kunming, China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
- Key Laboratory of Agro-Biodiversity and Pest Management of Education Ministry of China, Yunnan Agricultural University, Kunming, China
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Chen H, Wei J, Tian R, Zeng Z, Tang H, Liu Y, Xu Q, Deng M, Jiang Q, Chen G, Liu Y, Li W, Qi P, Jiang Y, Jiang Y, Tang L, Wei Y, Zheng Y, Lan X, Ma J. A major quantitative trait locus for wheat total root length associated with precipitation distribution. FRONTIERS IN PLANT SCIENCE 2022; 13:995183. [PMID: 36092437 PMCID: PMC9451531 DOI: 10.3389/fpls.2022.995183] [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: 07/18/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Optimizing root system architecture (RSA) allows crops to better capture water and nutrients and adapt to harsh environment. Parental reproductive environment (PRE) has been reported to significantly affect growth and development throughout the life cycle of the next generation. In this study, 10 RSA-related traits were evaluated in seedling stage from five independent hydroponic tests using seeds harvested from five different PREs. Based on the Wheat55K SNP array-based genetic map, quantitative trait loci (QTL) for these traits were detected in a recombinant inbred line population. Twenty-eight putative QTL for RSA-related traits were detected, covering thirteen chromosomal regions. A major QTL, QTrl.sicau-2SY-4D for total root length (TRL), which was likely independent of PREs, explained 15.81-38.48% of phenotypic variations and was located at 14.96-19.59 Mb on chromosome arm 4DS. Interestingly, it showed pleiotropic effects on TRL, root area, root volume, root forks, root dry weight, and shoot dry weight. The functional marker KASP-Rht-D1 for Rht-D1 was used to genotype 2SY population and remapping QTL for TRL showed that QTrl.sicau-2SY-4D was not linked to Rht-D1. The kompetitive allele-specific PCR (KASP) marker, KASP-AX-110527441 linked to this major QTL, was developed and used to successfully validate its effect in three different genetic populations. Further analysis suggested that the positive allele at QTrl.sicau-2SY-4D was mainly utilized in wheat breeding of northwest China where precipitation was significantly lower, indicating that wheat requires longer TRL to capture water and nutrients in arid or semi-arid regions due to deficient precipitation. Additionally, four genes (TraesCS4D03G0059800, TraesCS4D03G0057800, TraesCS4D03G0064000, and TraesCS4D03G0064400) possibly related to root development were predicted in physical interval of QTrl.sicau-2SY-4D. Taken together, these results enrich our understanding on the genetic basis of RSA and provide a potentially valuable TRL QTL for wheat breeding.
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Affiliation(s)
- Huangxin Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jiatai Wei
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Rong Tian
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zhaoyong Zeng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Huaping Tang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yanlin Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiang Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Mei Deng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Li
- College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yun Jiang
- Institute of Biotechnology and Nuclear Technology Research, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Liwei Tang
- Panzhihua Academy of Agricultural and Forestry Sciences, Panzhihua, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Youliang Zheng
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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163
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Blocking Rice Shoot Gravitropism by Altering One Amino Acid in LAZY1. Int J Mol Sci 2022; 23:ijms23169452. [PMID: 36012716 PMCID: PMC9409014 DOI: 10.3390/ijms23169452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022] Open
Abstract
Tiller angle is an important trait that determines plant architecture and yield in cereal crops. Tiller angle is partially controlled during gravistimulation by the dynamic re-allocation of LAZY1 (LA1) protein between the nucleus and plasma membrane, but the underlying mechanism remains unclear. In this study, we identified and characterized a new allele of LA1 based on analysis of a rice (Oryza sativa L.) spreading-tiller mutant la1G74V, which harbors a non-synonymous mutation in the predicted transmembrane (TM) domain-encoding region of this gene. The mutation causes complete loss of shoot gravitropism, leading to prostrate growth of plants. Our results showed that LA1 localizes not only to the nucleus and plasma membrane but also to the endoplasmic reticulum. Removal of the TM domain in LA1 showed spreading-tiller phenotype of plants similar to la1G74V but did not affect the plasma membrane localization; thus, making it distinct from its ortholog ZmLA1 in Zea mays. Therefore, we propose that the TM domain is indispensable for the biological function of LA1, but this domain does not determine the localization of the protein to the plasma membrane. Our study provides new insights into the LA1-mediated regulation of shoot gravitropism.
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164
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Crop Root Responses to Drought Stress: Molecular Mechanisms, Nutrient Regulations, and Interactions with Microorganisms in the Rhizosphere. Int J Mol Sci 2022; 23:ijms23169310. [PMID: 36012575 PMCID: PMC9409098 DOI: 10.3390/ijms23169310] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/03/2022] [Accepted: 08/17/2022] [Indexed: 12/03/2022] Open
Abstract
Roots play important roles in determining crop development under drought. Under such conditions, the molecular mechanisms underlying key responses and interactions with the rhizosphere in crop roots remain limited compared with model species such as Arabidopsis. This article reviews the molecular mechanisms of the morphological, physiological, and metabolic responses to drought stress in typical crop roots, along with the regulation of soil nutrients and microorganisms to these responses. Firstly, we summarize how root growth and architecture are regulated by essential genes and metabolic processes under water-deficit conditions. Secondly, the functions of the fundamental plant hormone, abscisic acid, on regulating crop root growth under drought are highlighted. Moreover, we discuss how the responses of crop roots to altered water status are impacted by nutrients, and vice versa. Finally, this article explores current knowledge of the feedback between plant and soil microbial responses to drought and the manipulation of rhizosphere microbes for improving the resilience of crop production to water stress. Through these insights, we conclude that to gain a more comprehensive understanding of drought adaption mechanisms in crop roots, future studies should have a network view, linking key responses of roots with environmental factors.
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165
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Root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism. Proc Natl Acad Sci U S A 2022; 119:e2201350119. [PMID: 35881796 PMCID: PMC9351459 DOI: 10.1073/pnas.2201350119] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The growth angle roots adopt are critical for capturing soil resources, such as nutrients and water. Despite its agronomic importance, few regulatory genes have been identified in crops. Here we identify the root angle regulatory gene ENHANCED GRAVITROPISM 1 (EGT1) in barley. Strikingly, mutants lacking EGT1 exhibit a steeper angle in every root class. EGT1 appears to function as a component of an antigravitropic offset mechanism that regulates tissue stiffness, which impacts final root growth angle. EGT1 is a hot spot for selection as natural allelic variation within a conserved Tubby domain that is linked with steeper root angle. Analogous EGT1-dependent regulation of root angle in wheat demonstrates broad significance of EGT1 for trait improvement in cereal crops. Root angle in crops represents a key trait for efficient capture of soil resources. Root angle is determined by competing gravitropic versus antigravitropic offset (AGO) mechanisms. Here we report a root angle regulatory gene termed ENHANCED GRAVITROPISM1 (EGT1) that encodes a putative AGO component, whose loss-of-function enhances root gravitropism. Mutations in barley and wheat EGT1 genes confer a striking root phenotype, where every root class adopts a steeper growth angle. EGT1 encodes an F-box and Tubby domain-containing protein that is highly conserved across plant species. Haplotype analysis found that natural allelic variation at the barley EGT1 locus impacts root angle. Gravitropic assays indicated that Hvegt1 roots bend more rapidly than wild-type. Transcript profiling revealed Hvegt1 roots deregulate reactive oxygen species (ROS) homeostasis and cell wall-loosening enzymes and cofactors. ROS imaging shows that Hvegt1 root basal meristem and elongation zone tissues have reduced levels. Atomic force microscopy measurements detected elongating Hvegt1 root cortical cell walls are significantly less stiff than wild-type. In situ analysis identified HvEGT1 is expressed in elongating cortical and stele tissues, which are distinct from known root gravitropic perception and response tissues in the columella and epidermis, respectively. We propose that EGT1 controls root angle by regulating cell wall stiffness in elongating root cortical tissue, counteracting the gravitropic machinery’s known ability to bend the root via its outermost tissues. We conclude that root angle is controlled by EGT1 in cereal crops employing an antigravitropic mechanism.
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166
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Favero BT, Tan Y, Chen X, Müller R, Lütken H. Kalanchoë blossfeldiana naturally transformed with Rhizobium rhizogenes exhibits superior root phenotype. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 321:111323. [PMID: 35696923 DOI: 10.1016/j.plantsci.2022.111323] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 03/04/2022] [Accepted: 05/11/2022] [Indexed: 06/15/2023]
Abstract
Plant transformation with root oncogenic loci (rol) genes and open reading frames (ORFs) from Rhizobium rhizogenes have not yet targeted the underground root phenotype of these transformants. Hence, there is a need to develop plants with more efficient root system architecture (RSA). Here, RSA was assessed in naturally transformed (NT) and single rol/ORF Kalanchoë blossfeldiana 'Molly' lines in an aeroponic growth system combined with gene expression analysis. Three NT lines; 306, 324 and 331; exhibited better-developed RSA with longer roots and increased root biomass. In line 306, longest root was 6.3 ± 0.3 cm while WT had 4.8 ± 0.1 cm. However, root length of all overexpressing lines was ca. 30% shorter than WT. Root fresh weight of NT lines was 4.5-fold higher than WT. The expression of rolB, ∆ORF13a and ORF14 in the leaves of overexpressing lines was many folds higher than in NT lines. Increased expression of ∆ORF13a and ORF14 in leaves and roots may contribute more to a stronger compact phenotype than previously assumed. The moderate compact phenotype of NT lines combined with improved RSA compared to the overexpressing lines and WT strongly indicate that the use of R. rhizogenes has great potential to produce Kalanchoë phenotypes with enhanced RSA.
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Affiliation(s)
- Bruno Trevenzoli Favero
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, 2630 Tåstrup, Denmark.
| | - Yi Tan
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, 2630 Tåstrup, Denmark
| | - Xuefei Chen
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, 2630 Tåstrup, Denmark
| | - Renate Müller
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, 2630 Tåstrup, Denmark
| | - Henrik Lütken
- Section for Crop Sciences, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Højbakkegård Allé 13, 2630 Tåstrup, Denmark
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Jian C, Hao P, Hao C, Liu S, Mao H, Song Q, Zhou Y, Yin S, Hou J, Zhang W, Zhao H, Zhang X, Li T. The miR319/TaGAMYB3 module regulates plant architecture and improves grain yield in common wheat (Triticum aestivum). THE NEW PHYTOLOGIST 2022; 235:1515-1530. [PMID: 35538666 DOI: 10.1111/nph.18216] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
Plant architecture is a key determinant of crop productivity and adaptation. The highly conserved microRNA319 (miR319) family functions in various biological processes, but little is known about how miR319 regulates plant architecture in wheat (Triticum aestivum). Here, we determined that the miR319/TaGAMYB3 module controls plant architecture and grain yield in common wheat. Repressing tae-miR319 using short tandem target mimics resulted in favorable plant architecture traits, including increased plant height, reduced tiller number, enlarged spikes and flag leaves, and thicker culms, as well as enhanced grain yield in field plot tests. Overexpressing tae-miR319 had the opposite effects on plant architecture and grain yield. Although both TaPCF8 and TaGAMYB3 were identified as miR319 target genes, genetic complementation assays demonstrated that only miR319-resistant TaGAMYB3 (rTaGAMYB3) abolished tae-miR319-mediated growth inhibition of flag leaves and spikes. TaGAMYB3 functions as a transcriptional activator of downstream genes, including TaPSKR1, TaXTH23, TaMADS5 and TaMADS51, by binding to their promoters. Furthermore, TaGAMYB3 physically interacts with TaBA1, an important regulator of spike development, to additively activate the transcription of downstream genes such as TaMADS5. Our findings provide insight into how the miR319/TaGAMYB3 module regulates plant architecture and improves grain yield in common wheat.
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Affiliation(s)
- Chao Jian
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pingan Hao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Chenyang Hao
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shujuan Liu
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hude Mao
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Qilu Song
- College of Plant Protection, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yongbin Zhou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Shuining Yin
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology & Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jian Hou
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weijun Zhang
- Crop Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, 750002, Ningxia, China
| | - Huixian Zhao
- College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xueyong Zhang
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tian Li
- Key Laboratory of Crop Gene Resources and Germplasm Enhancement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Luo Z, Xiong J, Xia H, Wang L, Hou G, Li Z, Li J, Zhou H, Li T, Luo L. Pentatricopeptide Repeat Gene-Mediated Mitochondrial RNA Editing Impacts on Rice Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:926285. [PMID: 35928709 PMCID: PMC9343880 DOI: 10.3389/fpls.2022.926285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/21/2022] [Indexed: 05/27/2023]
Abstract
Mitochondrial RNA editing plays crucial roles in the plant development and environmental adaptation. Pentatricopeptide repeat (PPR) genes, which are involved in the regulating mitochondrial RNA editing, are potential gene resources in the improvement of rice drought tolerance. In this study, we investigated genome-wide mitochondrial RNA editing in response to drought between upland and lowland rice. Responses of mitochondrial RNA editing to drought exhibit site-specific and genotype-specific patterns. We detected 22 and 57 ecotype-differentiated editing sites under well-watered and drought-treated conditions, respectively. Interestingly, the RNA editing efficiency was positively correlated with many agronomic traits, while it was negatively correlated with drought tolerance. We further selected two mitochondrial-localized PPR proteins, PPR035 and PPR406, to validate their functions in drought tolerance. PPR035 regulated RNA editing at rps4-926 and orfX-406, while PPR406 regulated RNA editing at orfX-355. The defectiveness in RNA editing at these sites had no apparent penalties in rice respiration and vegetative growth. Meanwhile, the knockout mutants of ppr035 and ppr406 show enhanced drought- and salt tolerance. PPR035 and PPR406 were under the balancing selection in upland rice and highly differentiated between upland and lowland rice ecotypes. The upland-dominant haplotypes of PPR035 and PPR406 shall contribute to the better drought tolerance in upland rice. They have great prospective in the improvement of rice drought tolerance.
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Affiliation(s)
- Zhi Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jie Xiong
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hui Xia
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lei Wang
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Guihua Hou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Zhaoyang Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Jing Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Hengling Zhou
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
| | - Tianfei Li
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
| | - Lijun Luo
- College of Plant Sciences & Technology, Huazhong Agricultural University, Wuhan, China
- Shanghai Collaborative Innovation Center of Agri-Seeds (SCCAS), Shanghai Agrobiological Gene Center, Shanghai, China
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs, Shanghai, China
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Abstract
Climate change adversely affects plant nutrition, which serves as a major hurdle in the production of enough nutritious food to meet the needs of the growing global population. Here, we discuss how various climatic stressors impact nutrient homeostasis and how natural variation studies can yield resilient crop production systems to ensure future food security.
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170
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Li J, Lin S, Ma H, Wang Y, He H, Fang C. Spatial-Temporal Distribution of Allelopathic Rice Roots in Paddy Soil and Its Impact on Weed-Suppressive Activity at the Seedling Stages. FRONTIERS IN PLANT SCIENCE 2022; 13:940218. [PMID: 35865295 PMCID: PMC9294529 DOI: 10.3389/fpls.2022.940218] [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: 05/10/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Allelochemicals secreted by allelopathic rice roots are transmitted to the receptor rhizosphere through the soil medium to inhibit the growth of the surrounding weeds. This research aimed to explore the relationships between the spatial-temporal distribution of rice roots in soil and weed-suppression ability at its seedling stage. RESULTS This study first examined the root distribution of three rice cultivars in paddy soil in both vertical and horizontal directions at 3-6 leaf stage. Then, an experiment using rice-barnyardgrass mixed culture was conducted to analyze the allelopathic potential and allelochemical content secreted by rice roots in different lateral soil layers. The results showed that allelopathic rice had a smaller root diameter and larger root length density, root surface area density, and root dry weight density than those of non-allelopathic rice, in the top 5 cm at 5- and 6-leaf stages. In particular, there were significant differences in root distribution at the horizontal distance of 6-12 cm. Besides, allelopathic rice significantly inhibited the above-ground growth of barnyardgrass co-cultured at 12 cm lateral distance in situ, and the content of benzoic acid derivatives in allelopathic rice in a 6-12 cm soil circle was higher than that observed at 0-6 cm distance. Moreover, correlation analysis confirmed that the distribution of roots in the horizontal distance was significantly correlated with weed inhibition effect and allelochemical content. CONCLUSION These results implied that spatial distribution of allelopathic rice roots in paddy soil, particularly at the lateral distance, appears to have important impact on its weed-suppressive activity at the seedling stage, suggesting that modifying root distribution in soil may be a novel method to strengthen the ability of rice seedlings to resist paddy weeds.
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Affiliation(s)
- Jiayu Li
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shunxian Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huayan Ma
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanping Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haibin He
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Changxun Fang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Crop Ecology and Molecular Physiology, Fujian Agriculture and Forestry University, Fuzhou, China
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171
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Kim G, Ryu H, Sung J. Hormonal Crosstalk and Root Suberization for Drought Stress Tolerance in Plants. Biomolecules 2022; 12:811. [PMID: 35740936 PMCID: PMC9220869 DOI: 10.3390/biom12060811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/05/2022] [Accepted: 06/06/2022] [Indexed: 12/10/2022] Open
Abstract
Higher plants in terrestrial environments face to numerous unpredictable environmental challenges, which lead to a significant impact on plant growth and development. In particular, the climate change caused by global warming is causing drought stress and rapid desertification in agricultural fields. Many scientific advances have been achieved to solve these problems for agricultural and plant ecosystems. In this review, we handled recent advances in our understanding of the physiological changes and strategies for plants undergoing drought stress. The activation of ABA synthesis and signaling pathways by drought stress regulates root development via the formation of complicated signaling networks with auxin, cytokinin, and ethylene signaling. An abundance of intrinsic soluble sugar, especially trehalose-6-phosphate, promotes the SnRK-mediated stress-resistance mechanism. Suberin deposition in the root endodermis is a physical barrier that regulates the influx/efflux of water and nutrients through complex hormonal and metabolic networks, and suberization is essential for drought-stressed plants to survive. It is highly anticipated that this work will contribute to the reproduction and productivity improvements of drought-resistant crops in the future.
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Affiliation(s)
- Gaeun Kim
- Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Korea;
| | - Hojin Ryu
- Department of Biology, Chungbuk National University, Cheong-ju 28644, Korea
- Department of Biological Sciences and Biotechnology, Chungbuk National University, Cheong-ju 28644, Korea
| | - Jwakyung Sung
- Department of Crop Science, Chungbuk National University, Cheong-ju 28644, Korea;
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172
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An Isolated Arthrobacter sp. Enhances Rice ( Oryza sativa L.) Plant Growth. Microorganisms 2022; 10:microorganisms10061187. [PMID: 35744704 PMCID: PMC9228311 DOI: 10.3390/microorganisms10061187] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/07/2022] [Accepted: 06/07/2022] [Indexed: 12/28/2022] Open
Abstract
Rice is a symbol of life and a representation of prosperity in South Korea. However, studies on the diversity of the bacterial communities in the rhizosphere of rice plants are limited. In this study, four bundles of root samples were collected from the same rice field located in Goyang, South Korea. These were systematically analyzed to discover the diversity of culturable bacterial communities through culture-dependent methods. A total of 504 culturable bacteria were isolated and evaluated for their plant growth-promoting abilities in vitro. Among them, Arthrobacter sp. GN70 was selected for inoculation into the rice plants under laboratory and greenhouse conditions. The results showed a significantly positive effect on shoot length, root length, fresh plant weight, and dry plant weight. Moreover, scanning electron microscopic (SEM) images demonstrated the accumulation of bacterial biofilm networks at the junction of the primary roots, confirming the root-colonizing ability of the bacterium. The strain also exhibited a broad spectrum of in vitro antimicrobial activities against bacteria and fungi. Here, we first report the rice plant growth-promoting ability of the Arthrobacter species with the biofilm-producing and antimicrobial activities against plant and human pathogens. Genome analyses revealed features attributable to enhance rice plant growth, including the genes involved in the synthesis of plant hormones, biofilm production, and secondary metabolites. This study revealed that the rhizobacteria isolated from the roots of rice plants have dual potential to be utilized as a plant growth promoter and antimicrobial agent.
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173
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Pachamuthu K, Hari Sundar V, Narjala A, Singh RR, Das S, Avik Pal HCY, Shivaprasad PV. Nitrate-dependent regulation of miR444-OsMADS27 signalling cascade controls root development in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3511-3530. [PMID: 35243491 DOI: 10.1093/jxb/erac083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Nitrate is an important nutrient and a key signalling molecule for plant development. A number of transcription factors involved in the response to nitrate and their regulatory mechanisms have been identified. However, little is known about the transcription factors involved in nitrate sensing and their regulatory mechanisms among crop plants. In this study, we identified functions of a nitrate-responsive miR444:MADS-box transcription factor OsMADS27 module and its downstream targets mediating rice root growth and stress responses. Transgenic rice plants expressing miR444 target mimic improved rice root growth. Although miR444 has the potential to target multiple genes, we identified OsMADS27 as the major miR444 target that regulates the expression of nitrate transporters, as well as several key genes including expansins, and those associated with auxin signalling, to promote root growth. In agreement with this, overexpression of miRNA-resistant OsMADS27 improved root development and tolerance to abiotic stresses, while its silencing suppressed root growth. OsMADS27 mediated robust stress tolerance in plants through its ability to bind to the promoters of specific stress regulators, as observed in ChIP-seq analysis. Our results provide evidence of a nitrate-dependent miR444-OsMADS27 signalling cascade involved in the regulation of rice root growth, as well as its surprising role in stress responses.
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Affiliation(s)
- Kannan Pachamuthu
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris- Saclay, Versailles, France
| | - Vivek Hari Sundar
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Anushree Narjala
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- SASTRA University, Thirumalaisamudram, Thanjavur, India
| | - Rahul R Singh
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
- Department of Biological Sciences, North Dakota State University, Fargo, ND, USA
| | - Soumita Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Harshith C Y Avik Pal
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
| | - Padubidri V Shivaprasad
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bangalore, India
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174
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Luo L, Zhu M, Jia L, Xie Y, Wang Z, Xuan W. Ammonium transporters cooperatively regulate rice crown root formation responding to ammonium nitrogen. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3671-3685. [PMID: 35176162 DOI: 10.1093/jxb/erac059] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 02/16/2022] [Indexed: 06/14/2023]
Abstract
Crown roots (CRs) are major components of the rice root system. They form at the basal node of the shoot, and their development is greatly influenced by environmental factors. Ammonium nitrogen is known to impact plant root development through ammonium transporters (AMTs), but it remains unclear whether ammonium and AMTs play roles in rice CR formation. In this study, we revealed a significant role of ammonium, rather than nitrate, in regulating rice CR development. High ammonium supply increases CR formation but inhibits CR elongation. Genetic evidence showed that ammonium regulation of CR development relies on ammonium uptake mediated jointly by ammonium transporters OsAMT1;1, OsAMT1;2; OsAMT1;3, and OsAMT2;1, but not on root acidification which was the result of ammonium uptake. OsAMTs are also needed for glutamine-induced CR formation. Furthermore, we showed that polar auxin transport dependent on the PIN auxin efflux carriers acts downstream of ammonium uptake and assimilation to activate local auxin signaling at CR primordia, in turn promoting CR formation. Taken together, our results highlight a critical role for OsAMTs in cooperatively regulating CR formation through regulating auxin transport under nitrogen-rich conditions.
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Affiliation(s)
- Long Luo
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ming Zhu
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Letian Jia
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuanming Xie
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Ziniu Wang
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
| | - Wei Xuan
- MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River and State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China
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175
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Urfan M, Sharma S, Hakla HR, Rajput P, Andotra S, Lehana PK, Bhardwaj R, Khan MS, Das R, Kumar S, Pal S. Recent trends in root phenomics of plant systems with available methods- discrepancies and consonances. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1311-1321. [PMID: 35910442 PMCID: PMC9334470 DOI: 10.1007/s12298-022-01209-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 07/02/2022] [Accepted: 07/12/2022] [Indexed: 06/03/2023]
Abstract
The phenotyping of plant roots is a challenging task and poses a major lacuna in plant root research. Roots rhizospheric zone is affected by several environmental cues among which salinity, drought, heavy metal and soil pH are key players. Among biological factors, fungal, nematode and bacterial interactions with roots are vital for improving nutrient uptake efficiency in plants. The subterranean nature of a plant root and the limited number of approaches for root phenotyping offers a great challenge to the plant breeders to select a desirable root trait under different stress conditions. Identification of key root traits can provide a basic understanding for generating crop plants with enhanced ability to withstand various biotic or abiotic stresses. For instance, crops with improved soil exploration potential, phosphate uptake efficiency, water use efficiency and others. Laboratory methods such as hydroponics, rhizotron, rhizoslide and luminescence observatory for roots do not provide precise and desired root quantification attributes. Though 3D imaging by X-ray computed tomography (X-ray-CT) and magnetic resonance imaging techniques are complex, however, it provides the most applicable and practically relevant data for quantifying root system architecture traits. This review outlines the current developments in root studies including recent approaches viz. X-ray-CT, MRI, thermal infrared imaging and minirhizotron. Although root phenotyping is a laborious procedure, it offers multiple advantages by removing discrepancies and providing the actual practical significance of plant roots for breeding programs.
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Affiliation(s)
- Mohammad Urfan
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006 India
| | - Shubham Sharma
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006 India
| | - Haroon Rashid Hakla
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006 India
| | - Prakriti Rajput
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006 India
| | - Sonali Andotra
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006 India
| | | | - Renu Bhardwaj
- Department of Botanical and Environmental Sciences, Guru Nanak Dev University, Amritsar, 143001 India
| | - M Suhail Khan
- USBT, Guru Gobind Singh Indraprastha University, Dwarka, 110 078 New Delhi India
| | - Ranjan Das
- Department of Crop Physiology, Assam Agricultural University, Jorhat, 785013 India
| | - Sunil Kumar
- Department of Statistics, University of Jammu, Jammu, 180006 India
| | - Sikander Pal
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, 180006 India
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176
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Teramoto S, Yamasaki M, Uga Y. Identification of a unique allele in the quantitative trait locus for crown root number in japonica rice from Japan using genome-wide association studies. BREEDING SCIENCE 2022; 72:222-231. [PMID: 36408322 PMCID: PMC9653191 DOI: 10.1270/jsbbs.22010] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/10/2022] [Indexed: 06/16/2023]
Abstract
To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo 675-2103, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
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177
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Hickey K, Wood M, Sexton T, Sahin Y, Nazarov T, Fisher J, Sanguinet KA, Cousins A, Kirchhoff H, Smertenko A. Drought Tolerance Strategies and Autophagy in Resilient Wheat Genotypes. Cells 2022; 11:1765. [PMID: 35681460 PMCID: PMC9179661 DOI: 10.3390/cells11111765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/14/2022] [Accepted: 05/15/2022] [Indexed: 01/18/2023] Open
Abstract
Drought resiliency strategies combine developmental, physiological, cellular, and molecular mechanisms. Here, we compare drought responses in two resilient spring wheat (Triticum aestivum) genotypes: a well-studied drought-resilient Drysdale and a resilient genotype from the US Pacific North-West Hollis. While both genotypes utilize higher water use efficiency through the reduction of stomatal conductance, other mechanisms differ. First, Hollis deploys the drought escape mechanism to a greater extent than Drysdale by accelerating the flowering time and reducing root growth. Second, Drysdale uses physiological mechanisms such as non-photochemical quenching (NPQ) to dissipate the excess of harvested light energy and sustain higher Fv/Fm and ϕPSII, whereas Hollis maintains constant NPQ but lower Fv/Fm and ϕPSII values. Furthermore, more electron donors of the electron transport chain are in the oxidized state in Hollis than in Drysdale. Third, many ROS homeostasis parameters, including peroxisome abundance, transcription of peroxisome biogenesis genes PEX11 and CAT, catalase protein level, and enzymatic activity, are higher in Hollis than in Drysdale. Fourth, transcription of autophagy flux marker ATG8.4 is upregulated to a greater degree in Hollis than in Drysdale under drought, whereas relative ATG8 protein abundance under drought stress is lower in Hollis than in Drysdale. These data demonstrate the activation of autophagy in both genotypes and a greater autophagic flux in Hollis. In conclusion, wheat varieties utilize different drought tolerance mechanisms. Combining these mechanisms within one genotype offers a promising strategy to advance crop resiliency.
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Affiliation(s)
- Kahleen Hickey
- Institute of Biological Chemistry, Washington State University, 1772 NE Stadium Way, P.O. Box 99163, Pullman, WA 99164, USA; (K.H.); (M.W.); (Y.S.); (T.N.); (J.F.)
| | - Magnus Wood
- Institute of Biological Chemistry, Washington State University, 1772 NE Stadium Way, P.O. Box 99163, Pullman, WA 99164, USA; (K.H.); (M.W.); (Y.S.); (T.N.); (J.F.)
| | - Tom Sexton
- School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, WA 99164, USA; (T.S.); (A.C.)
| | - Yunus Sahin
- Institute of Biological Chemistry, Washington State University, 1772 NE Stadium Way, P.O. Box 99163, Pullman, WA 99164, USA; (K.H.); (M.W.); (Y.S.); (T.N.); (J.F.)
| | - Taras Nazarov
- Institute of Biological Chemistry, Washington State University, 1772 NE Stadium Way, P.O. Box 99163, Pullman, WA 99164, USA; (K.H.); (M.W.); (Y.S.); (T.N.); (J.F.)
| | - Jessica Fisher
- Institute of Biological Chemistry, Washington State University, 1772 NE Stadium Way, P.O. Box 99163, Pullman, WA 99164, USA; (K.H.); (M.W.); (Y.S.); (T.N.); (J.F.)
| | - Karen A. Sanguinet
- Department of Crop and Soil Sciences, Washington State University, P.O. Box 646420, Pullman, WA 99164, USA;
| | - Asaph Cousins
- School of Biological Sciences, Washington State University, P.O. Box 644236, Pullman, WA 99164, USA; (T.S.); (A.C.)
| | - Helmut Kirchhoff
- Institute of Biological Chemistry, Washington State University, 1772 NE Stadium Way, P.O. Box 99163, Pullman, WA 99164, USA; (K.H.); (M.W.); (Y.S.); (T.N.); (J.F.)
| | - Andrei Smertenko
- Institute of Biological Chemistry, Washington State University, 1772 NE Stadium Way, P.O. Box 99163, Pullman, WA 99164, USA; (K.H.); (M.W.); (Y.S.); (T.N.); (J.F.)
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178
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Sun C, Liang W, Yan K, Xu D, Qin T, Fiaz S, Kear P, Bi Z, Liu Y, Liu Z, Zhang J, Bai J. Expression of Potato StDRO1 in Arabidopsis Alters Root Architecture and Drought Tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:836063. [PMID: 35665176 PMCID: PMC9161210 DOI: 10.3389/fpls.2022.836063] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Potato (Solanum tuberosum L) is the third important crop for providing calories to a large human population, and is considered sensitive to moderately sensitive to drought stress conditions. The development of drought-tolerant, elite varieties of potato is a challenging task, which can be achieved through molecular breeding. Recently, the DEEPER ROOTING 1 (DRO1) gene has been identified in rice, which influences plant root system and regulates grain yield under drought stress conditions. The potato StDRO1 protein is mainly localized in the plasma membrane of tobacco leaf cells, and overexpression analysis of StDRO1 in Arabidopsis resulted in an increased lateral root number, but decreased lateral root angle, lateral branch angle, and silique angle. Additionally, the drought treatment analysis indicated that StDRO1 regulated drought tolerance and rescued the defective root architecture and drought-tolerant phenotypes of Atdro1, an Arabidopsis AtDRO1 null mutant. Furthermore, StDRO1 expression was significantly higher in the drought-tolerant potato cultivar "Unica" compared to the drought-sensitive cultivar "Atlantic." The transcriptional response of StDRO1 under drought stress occurred significantly earlier in Unica than in Atlantic. Collectively, the outcome of the present investigation elucidated the role of DRO1 function in the alternation of root architecture, which potentially acts as a key gene in the development of a drought stress-tolerant cultivar. Furthermore, these findings will provide the theoretical basis for molecular breeding of drought-tolerant potato cultivars for the farming community.
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Affiliation(s)
- Chao Sun
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Wenjun Liang
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Kan Yan
- School of Biological and Pharmaceutical Engineering, Lanzhou Jiaotong University, Lanzhou, China
| | - Derong Xu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Tianyuan Qin
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Sajid Fiaz
- Department of Plant Breeding and Genetics, The University of Haripur, Haripur, Pakistan
| | - Philip Kear
- International Potato Center (CIP), CIP China Center for Asia Pacific (CCCAP), Beijing, China
| | - Zhenzhen Bi
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Yuhui Liu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Zhen Liu
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Junlian Zhang
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
| | - Jiangping Bai
- Gansu Provincial Key Laboratory of Arid Land Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou, China
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179
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Hanzawa E, Kitomi Y, Uga Y, Sato T. Quantification of Soil-surface Roots in Seedlings and Mature Rice Plants. Bio Protoc 2022; 12:e4409. [PMID: 35800462 PMCID: PMC9090522 DOI: 10.21769/bioprotoc.4409] [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: 12/07/2021] [Accepted: 03/21/2022] [Indexed: 12/29/2022] Open
Abstract
Soil-surface roots (SORs) in rice are primary roots that elongate over or near the soil surface. SORs help avoid excessive reduction of stress that occurs in paddy, such as in saline conditions. SORs may also be beneficial for rice growth in phosphorus-deficient paddy fields. Thus, SOR is a useful trait for crop adaptation to certain environmental stresses. To identify a promising genetic material showing SOR, we established methods for evaluating SOR under different growth conditions. We introduced procedures to evaluate the genetic diversity of SOR in various growth stages and conditions: the Cup method allowed us to quantify SOR at the seedling stage, and the Basket method, using a basket buried in a pot or field, is useful in quantifying SOR at the adult stage. These protocols are expected to contribute not only to the evaluation of the genetic diversity of SOR, but also the isolation of related genes in rice.
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Affiliation(s)
- Eiko Hanzawa
- Graduate School of Life Sciences, Tohoku University, 980-8577 Sendai, Miyagi, Japan
| | - Yuka Kitomi
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 305-8518 Tsukuba, Ibaraki, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 305-8518 Tsukuba, Ibaraki, Japan
| | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University, 980-8572 Sendai, Miyagi, Japan
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*For correspondence: or
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180
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Zhou J, Qiao J, Wang J, Quan R, Huang R, Qin H. OsQHB Improves Salt Tolerance by Scavenging Reactive Oxygen Species in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:848891. [PMID: 35599895 PMCID: PMC9115556 DOI: 10.3389/fpls.2022.848891] [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: 01/05/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
Soil salinity is a major environmental stress that restricts the growth and yield of crops. Mining the key genes involved in the balance of rice salt tolerance and yield will be extremely important for us to cultivate salt-tolerance rice varieties. In this study, we report a WUSCHEL-related homeobox (WOX) gene, quiescent-center-specific homeobox (OsQHB), positively regulates yield-related traits and negatively regulates salt tolerance in rice. Mutation in OsQHB led to a decrease in plant height, tiller number, panicle length, grain length and grain width, and an increase in salt tolerance. Transcriptome and qPCR analysis showed that reactive oxygen species (ROS) scavenging-related genes were regulated by OsQHB. Moreover, the osqhb mutants have higher ROS-scavenging enzymes activities and lower accumulation of ROS and malondialdehyde (MDA) under salt stress. Thus, our findings provide new insights into the role of rice WOX gene family in rice development and salt tolerance, and suggest that OsQHB is a valuable target for improving rice production in environments characterized by salt stress.
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Affiliation(s)
- Jiahao Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinzhu Qiao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Juan Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
| | - Ruidang Quan
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
| | - Rongfeng Huang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
| | - Hua Qin
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, China
- National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing, China
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181
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Rasool F, Khan MR, Schneider M, Uzair M, Aqeel M, Ajmal W, Léon J, Naz AA. Transcriptome unveiled the gene expression patterns of root architecture in drought-tolerant and sensitive wheat genotypes. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:20-30. [PMID: 35247694 DOI: 10.1016/j.plaphy.2022.02.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/26/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
Drought is a big challenge for agricultural production. Root attributes are the important target traits for breeding high-yielding sustainable wheat varieties against ever changing climatic conditions. However, the transcriptomic of wheat concerning root architecture remained obscure. Here, we explored RNA-Seq based transcriptome to dissect putative genes involved in root system variations in naturally occurring six genotypes (drought-tolerant and sensitive) of wheat. Global RNA-Seq based root transcriptome analysis revealed single nucleotide polymorphisms (SNPs) variations and differentially expressed genes. Putative 56 SNPs were identified related to 15 genes involved in root architecture. Enrichment of these genes using GO terms demonstrated that differentially expressed genes (DEGs) are divided into sub-categories implicated in molecular functions, cellular components and biological processes. The KEGG analysis of DEGs in each comparison of genotype include metabolic, biosynthesis of secondary metabolites, microbial metabolism in diverse environments and biosynthesis of antibiotics. A deeper insight into DEGs unveiled various pathways involved in drought response and positive gravitropism. These genes belong to various transcription factor families such as DOF, C3H, MYB, and NAC involved in root developmental and stress-related pathways. Local White and UZ-11-CWA-8, which are drought-tolerant genotypes, harbor over-representation of most of DEGs or transcription factors. Notably, a microtubule-associated protein MAPRE1 belonging to RP/EB family recruited in positive gravitropism was enriched. Real-time PCR analysis revealed expression of MAPRE1 and PAL genes is consistent with RNA-seq data. The presented data and genetic resources seem valuable for providing genes involved in the root system architecture of drought-tolerant and susceptible genotypes.
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Affiliation(s)
- Fatima Rasool
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Ramzan Khan
- Genome Editing & Sequencing Lab, National Centre for Bioinformatics, Quaid-i-Azam University, Islamabad, 45320, Pakistan; National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan.
| | - Michael Schneider
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Muhammad Uzair
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Muhammad Aqeel
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Wajya Ajmal
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad, 45500, Pakistan
| | - Jens Léon
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany
| | - Ali Ahmed Naz
- Institute of Crop Science and Resource Conservation (INRES), Department of Crop Genetics and Biotechnology, Rheinische Friedrich-Wilhelms University of Bonn, Germany.
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182
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Suresh BV, Choudhary P, Aggarwal PR, Rana S, Singh RK, Ravikesavan R, Prasad M, Muthamilarasan M. De novo transcriptome analysis identifies key genes involved in dehydration stress response in kodo millet (Paspalum scrobiculatum L.). Genomics 2022; 114:110347. [PMID: 35337948 DOI: 10.1016/j.ygeno.2022.110347] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 02/08/2022] [Accepted: 03/18/2022] [Indexed: 01/14/2023]
Abstract
Kodo millet (Paspalum scrobiculatum L.) is a small millet species known for its excellent nutritional and climate-resilient traits. To understand the genes and pathways underlying dehydration stress tolerance of kodo millet, the transcriptome of cultivar 'CO3' subjected to dehydration stress (0 h, 3 h, and 6 h) was sequenced. The study generated 239.1 million clean reads that identified 9201, 9814, and 2346 differentially expressed genes (DEGs) in 0 h vs. 3 h, 0 h vs. 6 h, and 3 h vs. 6 h libraries, respectively. The DEGs were found to be associated with vital molecular pathways, including hormone metabolism and signaling, antioxidant scavenging, photosynthesis, and cellular metabolism, and were validated using qRT-PCR. Also, a higher abundance of uncharacterized genes expressed during stress warrants further studies to characterize this class of genes to understand their role in dehydration stress response. Altogether, the study provides insights into the transcriptomic response of kodo millet during dehydration stress.
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Affiliation(s)
- Bonthala Venkata Suresh
- Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf 40225, Germany.
| | - Pooja Choudhary
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Pooja Rani Aggarwal
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
| | - Sumi Rana
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
| | | | - Rajasekaran Ravikesavan
- Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India.
| | - Manoj Prasad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India; National Institute of Plant Genome Research, New Delhi 110067, India.
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India.
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183
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Characteristics of microRNAs and Target Genes in Maize Root under Drought Stress. Int J Mol Sci 2022; 23:ijms23094968. [PMID: 35563360 PMCID: PMC9104622 DOI: 10.3390/ijms23094968] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/23/2022] [Accepted: 04/26/2022] [Indexed: 02/06/2023] Open
Abstract
Maize (Zea mays) is an important multi-functional crop. The growth and yield of maize are severely affected by drought stress. Previous studies have shown that microRNAs (miRNAs) in maize play important roles in response to abiotic stress; however, their roles in response to drought stress in maize roots is unclear. In our study, we found 375 miRNAs in the roots of 16 inbred lines. Of the 16 lines, zma-MIR168, zma-MIR156, and zma-MIR166 were highly expressed, whereas zma-MIR399, zma-MIR2218, and zma-MIR2275 exhibited low expression levels. The expression patterns of miRNA in parental lines and their derived RILs are different. Over 50% of miRNAs exhibited a lower expression in recombinant inbred lines than in parents. The expression of 50 miRNAs was significantly altered under water stress (WS) in at least three inbred lines, and the expression of miRNAs in drought-tolerant lines changed markedly. To better understand the reasons for miRNA response to drought, the degree of histone modifications for miRNA genes was estimated. The methylation level of H3K4 and H3K9 in miRNA precursor regions changed more noticeably after WS, but no such phenomenon was seen for DNA methylation and m6A modification. After the prediction of miRNA targets using psRNATarget and psRobot, we used correlation analysis and qRT-PCR to further investigate the relationship between miRNAs and target genes. We found that 87 miRNA–target pairs were significantly negatively correlated. In addition, a weighted gene co-expression network analysis using miRNAs, as well as their predicted targets, was conducted to reveal that miR159, miR394, and miR319 may be related to maize root growth. The results demonstrated that miRNAs might play essential roles in the response to drought stress.
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184
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Reynoso MA, Borowsky AT, Pauluzzi GC, Yeung E, Zhang J, Formentin E, Velasco J, Cabanlit S, Duvenjian C, Prior MJ, Akmakjian GZ, Deal RB, Sinha NR, Brady SM, Girke T, Bailey-Serres J. Gene regulatory networks shape developmental plasticity of root cell types under water extremes in rice. Dev Cell 2022; 57:1177-1192.e6. [PMID: 35504287 DOI: 10.1016/j.devcel.2022.04.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 02/10/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022]
Abstract
Understanding how roots modulate development under varied irrigation or rainfall is crucial for development of climate-resilient crops. We established a toolbox of tagged rice lines to profile translating mRNAs and chromatin accessibility within specific cell populations. We used these to study roots in a range of environments: plates in the lab, controlled greenhouse stress and recovery conditions, and outdoors in a paddy. Integration of chromatin and mRNA data resolves regulatory networks of the following: cycle genes in proliferating cells that attenuate DNA synthesis under submergence; genes involved in auxin signaling, the circadian clock, and small RNA regulation in ground tissue; and suberin biosynthesis, iron transporters, and nitrogen assimilation in endodermal/exodermal cells modulated with water availability. By applying a systems approach, we identify known and candidate driver transcription factors of water-deficit responses and xylem development plasticity. Collectively, this resource will facilitate genetic improvements in root systems for optimal climate resilience.
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Affiliation(s)
- Mauricio A Reynoso
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; IBBM, FCE-UNLP CONICET, La Plata 1900, Argentina
| | - Alexander T Borowsky
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Germain C Pauluzzi
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elaine Yeung
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Jianhai Zhang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Elide Formentin
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Department of Biology, University of Padova, Padova, Italy
| | - Joel Velasco
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Sean Cabanlit
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Christine Duvenjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Matthew J Prior
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Garo Z Akmakjian
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Roger B Deal
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Neelima R Sinha
- Department of Plant Biology, University of California, Davis, Davis, CA 95616, USA
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, Davis, CA 95616, USA
| | - Thomas Girke
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, Riverside, CA 92521, USA; Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, 3584 Utrecht, the Netherlands.
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185
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Discovery of Genomic Regions and Candidate Genes Controlling Root Development Using a Recombinant Inbred Line Population in Rapeseed ( Brassica napus L.). Int J Mol Sci 2022; 23:ijms23094781. [PMID: 35563170 PMCID: PMC9102059 DOI: 10.3390/ijms23094781] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 11/16/2022] Open
Abstract
Marker-assisted selection enables breeders to quickly select excellent root architectural variations, which play an essential role in plant productivity. Here, ten root-related and shoot biomass traits of a new F6 recombinant inbred line (RIL) population were investigated under hydroponics and resulted in high heritabilities from 0.61 to 0.83. A high-density linkage map of the RIL population was constructed using a Brassica napus 50k Illumina single nucleotide polymorphism (SNP) array. A total of 86 quantitative trait loci (QTLs) explaining 4.16–14.1% of the phenotypic variances were detected and integrated into eight stable QTL clusters, which were repeatedly detected in different experiments. The codominant markers were developed to be tightly linked with three major QTL clusters, qcA09-2, qcC08-2, and qcC08-3, which controlled both root-related and shoot biomass traits and had phenotypic contributions greater than 10%. Among these, qcA09-2, renamed RT.A09, was further fine-mapped to a 129-kb interval with 19 annotated genes in the B. napus reference genome. By integrating the results of real-time PCR and comparative sequencing, five genes with expression differences and/or amino acid differences were identified as important candidate genes for RT.A09. Our findings laid the foundation for revealing the molecular mechanism of root development and developed valuable markers for root genetic improvement in rapeseed.
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186
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Xu Z, York LM, Seethepalli A, Bucciarelli B, Cheng H, Samac DA. Objective Phenotyping of Root System Architecture Using Image Augmentation and Machine Learning in Alfalfa (Medicago sativa L.). PLANT PHENOMICS (WASHINGTON, D.C.) 2022; 2022:9879610. [PMID: 35479182 PMCID: PMC9012978 DOI: 10.34133/2022/9879610] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/03/2022] [Indexed: 12/28/2022]
Abstract
Active breeding programs specifically for root system architecture (RSA) phenotypes remain rare; however, breeding for branch and taproot types in the perennial crop alfalfa is ongoing. Phenotyping in this and other crops for active RSA breeding has mostly used visual scoring of specific traits or subjective classification into different root types. While image-based methods have been developed, translation to applied breeding is limited. This research is aimed at developing and comparing image-based RSA phenotyping methods using machine and deep learning algorithms for objective classification of 617 root images from mature alfalfa plants collected from the field to support the ongoing breeding efforts. Our results show that unsupervised machine learning tends to incorrectly classify roots into a normal distribution with most lines predicted as the intermediate root type. Encouragingly, random forest and TensorFlow-based neural networks can classify the root types into branch-type, taproot-type, and an intermediate taproot-branch type with 86% accuracy. With image augmentation, the prediction accuracy was improved to 97%. Coupling the predicted root type with its prediction probability will give breeders a confidence level for better decisions to advance the best and exclude the worst lines from their breeding program. This machine and deep learning approach enables accurate classification of the RSA phenotypes for genomic breeding of climate-resilient alfalfa.
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Affiliation(s)
- Zhanyou Xu
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Larry M. York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | | | - Bruna Bucciarelli
- Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
| | - Hao Cheng
- Department of Animal Science, University of California, 2251 Meyer Hall, One Shields Ave., Davis, CA 95616, USA
| | - Deborah A. Samac
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN 55108, USA
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187
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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188
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Maqbool S, Hassan MA, Xia X, York LM, Rasheed A, He Z. Root system architecture in cereals: progress, challenges and perspective. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:23-42. [PMID: 35020968 DOI: 10.1111/tpj.15669] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/31/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
Roots are essential multifunctional plant organs involved in water and nutrient uptake, metabolite storage, anchorage, mechanical support, and interaction with the soil environment. Understanding of this 'hidden half' provides potential for manipulation of root system architecture (RSA) traits to optimize resource use efficiency and grain yield in cereal crops. Unfortunately, root traits are highly neglected in breeding due to the challenges of phenotyping, but could have large rewards if the variability in RSA traits can be fully exploited. Until now, a plethora of genes have been characterized in detail for their potential role in improving RSA. The use of forward genetics approaches to find sequence variations in genes underpinning desirable RSA would be highly beneficial. Advances in computer vision applications have allowed image-based approaches for high-throughput phenotyping of RSA traits that can be used by any laboratory worldwide to make progress in understanding root function and dissection of the genetics. At the same time, the frontiers of root measurement include non-invasive methods like X-ray computer tomography and magnetic resonance imaging that facilitate new types of temporal studies. Root physiology and ecology are further supported by spatiotemporal root simulation modeling. The discovery of component traits providing improved resilience and yield advantage in target environments is a key necessity for mainstreaming root-based cereal breeding. The integrated use of pan-genome resources, now available in most cereals, coupled with new in-field phenotyping platforms has the potential for precise selection of superior genotypes with improved RSA.
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Affiliation(s)
- Saman Maqbool
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Adeel Hassan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Xianchun Xia
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
| | - Larry M York
- Biosciences Division and Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Awais Rasheed
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Wheat and Maize Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Wheat and Maize Improvement Center (CIMMYT) China Office, c/o CAAS, 12 Zhongguancun South Street, Beijing, 100081, China
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189
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Isolation and Molecular Characterisation of TtDro1A and TtDro1B Genes from Triticum turgidum Subspecies durum and turgidum, Study of Their Influences on Seedling Root Angles. PLANTS 2022; 11:plants11060821. [PMID: 35336704 PMCID: PMC8954752 DOI: 10.3390/plants11060821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 12/03/2022]
Abstract
Durum wheat (Triticum turgidum, 2n = 4x = AABB) includes several subspecies with differential characteristics in their root system architecture (RSA). Subspecies durum has longer and more vertical roots, while subspecies turgidum has smaller and shallower roots. The homeologous genes TtDro1A and TtDro1B of both subspecies have been identified and found to differ in their sizes, sequences and the proteins they encode. To determine whether there is a relationship between the level of expression of these two genes and the angle adopted by the roots of durum wheat seedlings, their expressions has been studied by RT-qPCR, both in the primary seminal root and in the other seminal roots. The results of the analyses showed that the TtDro1A gene is expressed 1.4 times more in the primary seminal root than in the other seminal roots. Furthermore, this gene is expressed 2.49 to 8.76 times more than TtDro1B depending on root type (primary or seminal) and subspecies. There are positive correlations between the expression ratio of both genes (TtDro1A/TtDro1B) and the mean of all root angles, the most vertical root angle and the most horizontal root angle of the seedlings. The higher the expression of TtDro1B gene, the lower the root growth angles.
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190
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Jobson E, Roberts R. Genomic structural variation in tomato and its role in plant immunity. MOLECULAR HORTICULTURE 2022; 2:7. [PMID: 37789472 PMCID: PMC10515242 DOI: 10.1186/s43897-022-00029-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 02/22/2022] [Indexed: 10/05/2023]
Abstract
It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives.
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Affiliation(s)
- Emma Jobson
- Montana State University Extension, Montana State University, Bozeman, MT, 59717, United States
| | - Robyn Roberts
- Agricultural Biology Department, College of Agricultural Sciences, Colorado State University, Fort Collins, CO, USA.
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191
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Galindo-Castañeda T, Lynch JP, Six J, Hartmann M. Improving Soil Resource Uptake by Plants Through Capitalizing on Synergies Between Root Architecture and Anatomy and Root-Associated Microorganisms. FRONTIERS IN PLANT SCIENCE 2022; 13:827369. [PMID: 35356114 PMCID: PMC8959776 DOI: 10.3389/fpls.2022.827369] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/15/2022] [Indexed: 05/14/2023]
Abstract
Root architectural and anatomical phenotypes are highly diverse. Specific root phenotypes can be associated with better plant growth under low nutrient and water availability. Therefore, root ideotypes have been proposed as breeding targets for more stress-resilient and resource-efficient crops. For example, root phenotypes that correspond to the Topsoil Foraging ideotype are associated with better plant growth under suboptimal phosphorus availability, and root phenotypes that correspond to the Steep, Cheap and Deep ideotype are linked to better performance under suboptimal availability of nitrogen and water. We propose that natural variation in root phenotypes translates into a diversity of different niches for microbial associations in the rhizosphere, rhizoplane and root cortex, and that microbial traits could have synergistic effects with the beneficial effect of specific root phenotypes. Oxygen and water content, carbon rhizodeposition, nutrient availability, and root surface area are all factors that are modified by root anatomy and architecture and determine the structure and function of the associated microbial communities. Recent research results indicate that root characteristics that may modify microbial communities associated with maize include aerenchyma, rooting angle, root hairs, and lateral root branching density. Therefore, the selection of root phenotypes linked to better plant growth under specific edaphic conditions should be accompanied by investigating and selecting microbial partners better adapted to each set of conditions created by the corresponding root phenotype. Microbial traits such as nitrogen transformation, phosphorus solubilization, and water retention could have synergistic effects when correctly matched with promising plant root ideotypes for improved nutrient and water capture. We propose that elucidation of the interactive effects of root phenotypes and microbial functions on plant nutrient and water uptake offers new opportunities to increase crop yields and agroecosystem sustainability.
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Affiliation(s)
- Tania Galindo-Castañeda
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Jonathan P. Lynch
- Department of Plant Science, The Pennsylvania State University, University Park, PA, United States
| | - Johan Six
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
| | - Martin Hartmann
- Sustainable Agroecosystems, Institute of Agricultural Sciences, Department of Environmental System Science, ETH Zürich, Zurich, Switzerland
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192
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Bin Rahman ANMR, Zhang J. The Coexistence of Flood and Drought Tolerance: An Opinion on the Development of Climate-Smart Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:860802. [PMID: 35350297 PMCID: PMC8957971 DOI: 10.3389/fpls.2022.860802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Affiliation(s)
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
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193
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Shen X, He J, Ping Y, Guo J, Hou N, Cao F, Li X, Geng D, Wang S, Chen P, Qin G, Ma F, Guan Q. The positive feedback regulatory loop of miR160-Auxin Response Factor 17-HYPONASTIC LEAVES 1 mediates drought tolerance in apple trees. PLANT PHYSIOLOGY 2022; 188:1686-1708. [PMID: 34893896 PMCID: PMC8896624 DOI: 10.1093/plphys/kiab565] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 11/10/2021] [Indexed: 05/25/2023]
Abstract
Drought stress tolerance is a complex trait regulated by multiple factors. Here, we demonstrate that the miRNA160-Auxin Response Factor 17 (ARF17)-HYPONASTIC LEAVES 1 module is crucial for apple (Malus domestica) drought tolerance. Using stable transgenic plants, we found that drought tolerance was improved by higher levels of Mdm-miR160 or MdHYL1 and by decreased levels of MdARF17, whereas reductions in MdHYL1 or increases in MdARF17 led to greater drought sensitivity. Further study revealed that modulation of drought tolerance was achieved through regulation of drought-responsive miRNA levels by MdARF17 and MdHYL1; MdARF17 interacted with MdHYL1 and bound to the promoter of MdHYL1. Genetic analysis further suggested that MdHYL1 is a direct downstream target of MdARF17. Importantly, MdARF17 and MdHYL1 regulated the abundance of Mdm-miR160. In addition, the Mdm-miR160-MdARF17-MdHYL1 module regulated adventitious root development. We also found that Mdm-miR160 can move from the scion to the rootstock in apple and tomato (Solanum lycopersicum), thereby improving root development and drought tolerance of the rootstock. Our study revealed the mechanisms by which the positive feedback loop of Mdm-miR160-MdARF17-MdHYL1 influences apple drought tolerance.
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Affiliation(s)
- Xiaoxia Shen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yikun Ping
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Nan Hou
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fuguo Cao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dali Geng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Pengxiang Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gege Qin
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, Shaanxi 712100, China
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194
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Xie N, Li B, Yu J, Shi R, Zeng Q, Jiang Y, Zhao D. Transcriptomic and proteomic analyses uncover the drought adaption landscape of Phoebe zhennan. BMC PLANT BIOLOGY 2022; 22:95. [PMID: 35240986 PMCID: PMC8892755 DOI: 10.1186/s12870-022-03474-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Phoebe zhennan S.Lee (nanmu) is listed as a threatened tree species in China, whose growth and development, especially during the seedling stage, can be severely limited by drought. Previous studies on nanmu responses to drought stress involved physiological and biochemical analyses, while the molecular mechanisms remained unclear. Therefore, it is of great significance to carry out molecular biology research on the drought resistance of nanmu and reveal the genetic background and molecular regulation mechanism of nanmu drought resistance. RESULTS Drought stress enhanced the soluble sugar (SS), free proline(PRO), superoxide anion (O2·-), and hydrogen peroxide (H2O2) contents as well as the peroxidase (POD) and monodehydroascorbate reductase (MDHAR) activities of nanmu. However, glutathione S-transferase (GST) activity was sensitive to drought stress. Further transcriptomic and proteomic analyses revealed the abundant members of the differentially expressed genes(DEGs) and differentially expressed proteins(DEPs) that were related to phenylpropanoid and flavonoid biosynthesis, hormone biosynthesis and signal transduction, chlorophyll metabolism, photosynthesis, and oxidation-reduction reaction, which suggested their involvement in the drought response of nanmu. These enhanced the osmotic regulation, detoxification, and enzyme-induced and non-enzyme-induced antioxidant ability of nanmu. Moreover, 52% (447/867) of proteins that were up-regulated and 34% (307/892) down-regulated ones were attributed to the increase and decrease of transcription abundance. Transcript up (TU) and protein up (PU) groups had 447 overlaps, while transcript down (TD) and protein down (PD) groups had 307 overlaps, accounting for 54% of up and 35% of down-regulated proteins. The lack of overlap between DEGs and DEPs also suggested that post-transcriptional regulation has a critical role in nanmu response to drought. CONCLUSIONS Our research results provide significant insights into the regulatory mechanisms of drought stress in nanmu.
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Affiliation(s)
- Na Xie
- Institute of Agro-Bioengineering and College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
- Guizhou Academy of Agricultural Sciences, Guizhou Plant Conservation Technology Center, Guiyang, 550006, Guizhou, China
| | - Bo Li
- Institute of Agro-Bioengineering and College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
- Guizhou Academy of Agricultural Sciences, Guizhou Plant Conservation Technology Center, Guiyang, 550006, Guizhou, China
| | - Jing Yu
- Tobacco Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang, 550081, China
| | - Ruxia Shi
- Institute of Agro-Bioengineering and College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
- Guizhou Academy of Agricultural Sciences, Guizhou Plant Conservation Technology Center, Guiyang, 550006, Guizhou, China
| | - Qin Zeng
- Institute of Agro-Bioengineering and College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China
- Guizhou Academy of Agricultural Sciences, Guizhou Plant Conservation Technology Center, Guiyang, 550006, Guizhou, China
| | - Yunli Jiang
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
| | - Dan Zhao
- Institute of Agro-Bioengineering and College of Life Sciences, The Key Laboratory of Plant Resources Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, 550025, Guizhou, China.
- Guizhou Academy of Agricultural Sciences, Guizhou Plant Conservation Technology Center, Guiyang, 550006, Guizhou, China.
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195
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Chakraborty K, Jena P, Mondal S, Dash GK, Ray S, Baig MJ, Swain P. Relative contribution of different members of OsDREB gene family to osmotic stress tolerance in indica and japonica ecotypes of rice. PLANT BIOLOGY (STUTTGART, GERMANY) 2022; 24:356-366. [PMID: 34939275 DOI: 10.1111/plb.13379] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
Drought/osmotic stress is the single largest production constraint in rain-fed rice cultivation. Different members of the DREB gene family are known to contribute to osmotic stress tolerance. In this study, an attempt was made to understand their relative contribution towards osmotic stress tolerance in indica and japonica ecotypes of rice. Two genotypes (one tolerant and one susceptible) from each ecotype were grown hydroponically, and 21-day-old seedlings were subjected to polyethylene glycol-induced osmotic stress (15% PEG-6000, equivalent to -3.0 bars osmotic potential). The tolerant genotypes CR143 and Moroberekan were found to have superior root traits (total root length, surface area and volume), better plant water status and increased total dry biomass as compared to their susceptible counterparts after 10 days of osmotic stress. Different members of the DREB gene family were differentially induced in response to osmotic shock (1 h after stress) and osmotic stress (24 h after stress), which also differed between the two rice ecotypes. From the gene expression profiles of 10 DREB genes (both DREB1 and DREB2 families), in indica two DREB genes, DREB1B and DREB1G, were significantly correlated with stress tolerance indices, whereas in japonica significant correlations with five DREB genes (DREB1A, DREB1B, DREB1D, DREB1E and DREB2B) were observed. We found that only one member, i.e. DREB1B, showed a significant correlation with drought tolerance indices in both indica and japonica ecotypes. This study provides an overview of the relative contribution of different members of the DREB gene family and their association with drought/osmotic stress tolerance in rice.
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Affiliation(s)
- K Chakraborty
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - P Jena
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - S Mondal
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - G K Dash
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - S Ray
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - M J Baig
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
| | - P Swain
- Division of Crop Physiology & Biochemistry, ICAR-National Rice Research Institute, Cuttack, India
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196
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Xu F, Liao H, Zhang Y, Yao M, Liu J, Sun L, Zhang X, Yang J, Wang K, Wang X, Ding Y, Liu C, Rensing C, Zhang J, Yeh K, Xu W. Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying. THE ISME JOURNAL 2022; 16:801-811. [PMID: 34621017 PMCID: PMC8857228 DOI: 10.1038/s41396-021-01133-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 09/22/2021] [Accepted: 09/27/2021] [Indexed: 11/10/2022]
Abstract
Moderate soil drying (MSD) is a promising agricultural technique that can reduce water consumption and enhance rhizosheath formation promoting drought resistance in plants. The endophytic fungus Piriformospora indica (P. indica) with high auxin production may be beneficial for rhizosheath formation. However, the integrated role of P. indica with native soil microbiome in rhizosheath formation is unclear. Here, we investigated the roles of P. indica and native bacteria on rice rhizosheath formation under MSD using high-throughput sequencing and rice mutants. Under MSD, rice rhizosheath formation was significantly increased by around 30% with P. indica inoculation. Auxins in rice roots and P. indica were responsible for the rhizosheath formation under MSD. Next, the abundance of the genus Bacillus, known as plant growth-promoting rhizobacteria, was enriched in the rice rhizosheath and root endosphere with P. indica inoculation under MSD. Moreover, the abundance of Bacillus cereus (B. cereus) with high auxin production was further increased by P. indica inoculation. After inoculation with both P. indica and B. cereus, rhizosheath formation in wild-type or auxin efflux carrier OsPIN2 complemented line rice was higher than that of the ospin2 mutant. Together, our results suggest that the interaction of the endophytic fungus P. indica with the native soil bacterium B. cereus favors rice rhizosheath formation by auxins modulation in rice and microbes under MSD. This finding reveals a cooperative contribution of P. indica and native microbiota in rice rhizosheath formation under moderate soil drying, which is important for improving water use in agriculture.
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Affiliation(s)
- Feiyun Xu
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Hanpeng Liao
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yingjiao Zhang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Minjie Yao
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianping Liu
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Leyun Sun
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xue Zhang
- grid.256111.00000 0004 1760 2876Engineering Research Center of Soil Remediation of Fujian Province University, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jinyong Yang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Ke Wang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiaoyun Wang
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Yexin Ding
- grid.256111.00000 0004 1760 2876Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Chen Liu
- grid.256111.00000 0004 1760 2876Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Christopher Rensing
- grid.256111.00000 0004 1760 2876Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianhua Zhang
- grid.221309.b0000 0004 1764 5980Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Kaiwun Yeh
- grid.19188.390000 0004 0546 0241Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Weifeng Xu
- Center for Plant Water-use and Nutrition Regulation and College of Life Sciences, Joint International Research Laboratory of Water and Nutrient in Crop, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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197
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G. Viana W, Scharwies JD, Dinneny JR. Deconstructing the root system of grasses through an exploration of development, anatomy and function. PLANT, CELL & ENVIRONMENT 2022; 45:602-619. [PMID: 35092025 PMCID: PMC9303260 DOI: 10.1111/pce.14270] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 05/16/2023]
Abstract
Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.
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Affiliation(s)
| | | | - José R. Dinneny
- Department of BiologyStanford UniversityStanfordCaliforniaUSA
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198
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Ranjan A, Sinha R, Singla-Pareek SL, Pareek A, Singh AK. Shaping the root system architecture in plants for adaptation to drought stress. PHYSIOLOGIA PLANTARUM 2022; 174:e13651. [PMID: 35174506 DOI: 10.1111/ppl.13651] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 02/05/2022] [Accepted: 02/11/2022] [Indexed: 06/14/2023]
Abstract
Root system architecture plays an important role in plant adaptation to drought stress. The root system architecture (RSA) consists of several structural features, which includes number and length of main and lateral roots along with the density and length of root hairs. These features exhibit plasticity under water-limited environments and could be critical to developing crops with efficient root systems for adaptation under drought. Recent advances in the omics approaches have significantly improved our understanding of the regulatory mechanisms of RSA remodeling under drought and the identification of genes and other regulatory elements. Plant response to drought stress at physiological, morphological, biochemical, and molecular levels in root cells is regulated by various phytohormones and their crosstalk. Stress-induced reactive oxygen species play a significant role in regulating root growth and development under drought stress. Several transcription factors responsible for the regulation of RSA under drought have proven to be beneficial for developing drought tolerant crops. Molecular breeding programs for developing drought-tolerant crops have been greatly benefitted by the availability of quantitative trait loci (QTLs) associated with the RSA regulation. In the present review, we have discussed the role of various QTLs, signaling components, transcription factors, microRNAs and crosstalk among various phytohormones in shaping RSA and present future research directions to better understand various factors involved in RSA remodeling for adaptation to drought stress. We believe that the information provided herein may be helpful in devising strategies to develop crops with better RSA for efficient uptake and utilization of water and nutrients under drought conditions.
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Affiliation(s)
- Alok Ranjan
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Ragini Sinha
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
| | - Ashwani Pareek
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
- National Agri-Food Biotechnology Institute, Mohali, Punjab, India
| | - Anil Kumar Singh
- School of Genetic Engineering, ICAR-Indian Institute of Agricultural Biotechnology, Ranchi, India
- ICAR-National Institute for Plant Biotechnology, LBS Centre, New Delhi, India
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199
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Ajmera I, Henry A, Radanielson AM, Klein SP, Ianevski A, Bennett MJ, Band LR, Lynch JP. Integrated root phenotypes for improved rice performance under low nitrogen availability. PLANT, CELL & ENVIRONMENT 2022; 45:805-822. [PMID: 35141925 PMCID: PMC9303783 DOI: 10.1111/pce.14284] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/27/2021] [Accepted: 10/30/2021] [Indexed: 05/06/2023]
Abstract
Greater nitrogen efficiency would substantially reduce the economic, energy and environmental costs of rice production. We hypothesized that synergistic balancing of the costs and benefits for soil exploration among root architectural phenes is beneficial under suboptimal nitrogen availability. An enhanced implementation of the functional-structural model OpenSimRoot for rice integrated with the ORYZA_v3 crop model was used to evaluate the utility of combinations of root architectural phenes, namely nodal root angle, the proportion of smaller diameter nodal roots, nodal root number; and L-type and S-type lateral branching densities, for plant growth under low nitrogen. Multiple integrated root phenotypes were identified with greater shoot biomass under low nitrogen than the reference cultivar IR64. The superiority of these phenotypes was due to synergism among root phenes rather than the expected additive effects of phene states. Representative optimal phenotypes were predicted to have up to 80% greater grain yield with low N supply in the rainfed dry direct-seeded agroecosystem over future weather conditions, compared to IR64. These phenotypes merit consideration as root ideotypes for breeding rice cultivars with improved yield under rainfed dry direct-seeded conditions with limited nitrogen availability. The importance of phene synergism for the performance of integrated phenotypes has implications for crop breeding.
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Affiliation(s)
- Ishan Ajmera
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Amelia Henry
- Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLagunaPhilippines
| | - Ando M. Radanielson
- Strategic Innovation PlatformInternational Rice Research InstituteLos BañosLagunaPhilippines
- Centre for Sustainable Agricultural Systems, Institute for Life Sciences and the Environment, Toowoomba CampusUniversity of Southern QueenslandToowoombaQueenslandAustralia
| | - Stephanie P. Klein
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
| | - Aleksandr Ianevski
- Institute for Molecular Medicine Finland (FIMM)University of HelsinkiFinland
| | - Malcolm J. Bennett
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Leah R. Band
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Centre for Mathematical Medicine and Biology, School of Mathematical SciencesUniversity of NottinghamNottinghamUK
| | - Jonathan P. Lynch
- Division of Plant and Crop Sciences, School of BiosciencesUniversity of NottinghamSutton BoningtonUK
- Department of Plant ScienceThe Pennsylvania State UniversityUniversity ParkPennsylvaniaUSA
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200
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Teramoto S, Uga Y. Improving the efficiency of plant root system phenotyping through digitization and automation. BREEDING SCIENCE 2022; 72:48-55. [PMID: 36045896 PMCID: PMC8987843 DOI: 10.1270/jsbbs.21053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/11/2021] [Indexed: 05/19/2023]
Abstract
Root system architecture (RSA) determines unevenly distributed water and nutrient availability in soil. Genetic improvement of RSA, therefore, is related to crop production. However, RSA phenotyping has been carried out less frequently than above-ground phenotyping because measuring roots in the soil is difficult and labor intensive. Recent advancements have led to the digitalization of plant measurements; this digital phenotyping has been widely used for measurements of both above-ground and RSA traits. Digital phenotyping for RSA is slower and more difficult than for above-ground traits because the roots are hidden underground. In this review, we summarized recent trends in digital phenotyping for RSA traits. We classified the sample types into three categories: soil block containing roots, section of soil block, and root sample. Examples of the use of digital phenotyping are presented for each category. We also discussed room for improvement in digital phenotyping in each category.
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Affiliation(s)
- Shota Teramoto
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
| | - Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8518, Japan
- Corresponding author (e-mail: )
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