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Noh E, Fallen B, Payero J, Narayanan S. Parsimonious root systems and better root distribution can improve biomass production and yield of soybean. PLoS One 2022; 17:e0270109. [PMID: 35737677 PMCID: PMC9223306 DOI: 10.1371/journal.pone.0270109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 06/05/2022] [Indexed: 11/19/2022] Open
Abstract
Enhancing the acquisition of belowground resources has been identified as an opportunity for improving soybean productivity worldwide. Root system architecture is gaining interest as a selection criterion in breeding programs for enhancing soil resource acquisition and developing climate-resilient varieties. Here we are presenting two novel characteristics of soybean root system architecture that improve aboveground growth and yield. Eleven selected soybean genotypes were tested under rain-fed conditions in 2019 and 2020 at two locations in South Carolina, in which one of the locations was characterized by compacted soils. The elite SC breeding line SC07-1518RR, exotic pedigree line N09-12854, and slow wilting line N09-13890 were superior genotypes in terms of biomass production, seed yield, and/or water use efficiency. Genotypes N09-12854 and N09-13890 demonstrated reduced root development (based on total root count and length), likely to restrict belowground growth and allocate more resources for shoot growth. This characteristic, which can be referred as a parsimonious root phenotype, might be advantageous for soybean improvement in high-input production systems (characterized by adequate fertilizer application and soil fertility) that exist in many parts of the world. Genotype SC07-1518RR exhibited a similar strategy: while it maintained its root system at an intermediate size through reduced levels of total root count and length, it selectively distributed more roots at deeper depths (53-70 cm). The increased root distribution of SC07-1518RR at deeper depths in compacted soil indicates its root penetrability and suitability for clayey soils with high penetration resistance. The beneficial root phenotypes identified in this study (parsimonious root development and selective root distribution in deeper depths) and the genotypes that possessed those phenotypes (SC07-1518RR, N09-12854, and N09-13890) will be useful for breeding programs in developing varieties for optimal, drought, and compacted-soil conditions.
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Affiliation(s)
- Enoch Noh
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Benjamin Fallen
- Soybean and Nitrogen Fixation Unit, USDA-ARS, Raleigh, North Carolina, United States of America
| | - Jose Payero
- Edisto Research and Education Center, Department of Agricultural Sciences, Clemson University, Blackville, South Carolina, United States of America
| | - Sruthi Narayanan
- Department of Plant and Environmental Sciences, Clemson University, Clemson, South Carolina, United States of America
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Liao Q, Chebotarov D, Islam MS, Quintana MR, Natividad MA, De Ocampo M, Beredo JC, Torres RO, Zhang Z, Song H, Price AH, McNally KL, Henry A. Aus rice root architecture variation contributing to grain yield under drought suggests a key role of nodal root diameter class. PLANT, CELL & ENVIRONMENT 2022; 45:854-870. [PMID: 35099814 DOI: 10.1111/pce.14272] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 01/25/2022] [Indexed: 06/14/2023]
Abstract
The aus rice variety group originated in stress-prone regions and is a promising source for the development of new stress-tolerant rice cultivars. In this study, an aus panel (~220 genotypes) was evaluated in field trials under well-watered and drought conditions and in the greenhouse (basket, herbicide and lysimeter studies) to investigate relationships between grain yield and root architecture, and to identify component root traits behind the composite trait of deep root growth. In the field trials, high and stable grain yield was positively related to high and stable deep root growth (r = 0.16), which may indicate response to within-season soil moisture fluctuations (i.e., plasticity). When dissecting component traits related to deep root growth (including angle, elongation and branching), the number of nodal roots classified as 'large-diameter' was positively related to deep root growth (r = 0.24), and showed the highest number of colocated genome-wide association study (GWAS) peaks with grain yield under drought. The role of large-diameter nodal roots in deep root growth may be related to their branching potential. Two candidate loci that colocated for yield and root traits were identified that showed distinct haplotype distributions between contrasting yield/stability groups and could be good candidates to contribute to rice improvement.
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Affiliation(s)
- Qiong Liao
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Dmytro Chebotarov
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Mohammad S Islam
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Marinell R Quintana
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Mignon A Natividad
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Marjorie De Ocampo
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Joseph C Beredo
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Rolando O Torres
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Zhenhua Zhang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Haixing Song
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Resources and Environmental Sciences, Hunan Agricultural University, Changsha, China
| | - Adam H Price
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, AB24 3UU, UK
| | - Kenneth L McNally
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
| | - Amelia Henry
- Rice Breeding Innovations, International Rice Research Institute, Pili Drive, UPLB Compound, Los Baños, Laguna, Philippines, 4031, Philippines
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Heredia MC, Kant J, Prodhan MA, Dixit S, Wissuwa M. Breeding rice for a changing climate by improving adaptations to water saving technologies. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:17-33. [PMID: 34218290 DOI: 10.1007/s00122-021-03899-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 06/25/2021] [Indexed: 06/13/2023]
Abstract
Climate change is expected to increasingly affect rice production through rising temperatures and decreasing water availability. Unlike other crops, rice is a main contributor to greenhouse gas emissions due to methane emissions from flooded paddy fields. Climate change can therefore be addressed in two ways in rice: through making the crop more climate resilient and through changes in management practices that reduce methane emissions and thereby slow global warming. In this review, we focus on two water saving technologies that reduce the periods lowland rice will be grown under fully flooded conditions, thereby improving water use efficiency and reducing methane emissions. Rice breeding over the past decades has mostly focused on developing high-yielding varieties adapted to continuously flooded conditions where seedlings were raised in a nursery and transplanted into a puddled flooded soil. Shifting cultivation to direct-seeded rice or to introducing non-flooded periods as in alternate wetting and drying gives rise to new challenges which need to be addressed in rice breeding. New adaptive traits such as rapid uniform germination even under anaerobic conditions, seedling vigor, weed competitiveness, root plasticity, and moderate drought tolerance need to be bred into the current elite germplasm and to what extent this is being addressed through trait discovery, marker-assisted selection and population improvement are reviewed.
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Affiliation(s)
| | | | - M Asaduzzaman Prodhan
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Shalabh Dixit
- International Rice Research Institute (IRRI), Los Baños, The Philippines
| | - Matthias Wissuwa
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan.
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Santos-Medellín C, Liechty Z, Edwards J, Nguyen B, Huang B, Weimer BC, Sundaresan V. Prolonged drought imparts lasting compositional changes to the rice root microbiome. NATURE PLANTS 2021; 7:1065-1077. [PMID: 34294907 DOI: 10.1038/s41477-021-00967-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 06/14/2021] [Indexed: 05/20/2023]
Abstract
Microbial symbioses can mitigate drought stress in crops but harnessing these beneficial interactions will require an in-depth understanding of root microbiome responses to drought cycles. Here, by detailed temporal characterization of root-associated microbiomes of rice plants during drought stress and recovery, we find that endosphere communities remained compositionally altered after rewatering, with prolonged droughts leading to decreased resilience. Several endospheric Actinobacteria were significantly enriched during drought and for weeks after rewatering. Notably, the most abundant endosphere taxon during this period was a Streptomyces, and a corresponding isolate promoted root growth. Additionally, drought stress disrupted the temporal dynamics of late-colonizing microorganisms, permanently altering the normal successional trends of root microbiota. These findings reveal that severe drought results in enduring impacts on rice root microbiomes, including enrichment of taxonomic groups that could shape the recovery response of the host, and have implications relevant to drought protection strategies using root microbiota.
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Affiliation(s)
- Christian Santos-Medellín
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Department of Plant Pathology, University of California, Davis, Davis, CA, USA
| | - Zachary Liechty
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Joseph Edwards
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Bao Nguyen
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Microbiology and Environmental Toxicology Department, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Bihua Huang
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, USA
| | - Bart C Weimer
- Department of Population Health and Reproduction, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, USA
| | - Venkatesan Sundaresan
- Department of Plant Biology, University of California, Davis, Davis, CA, USA.
- Department of Plant Sciences, University of California, Davis, Davis, CA, USA.
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Lucob-Agustin N, Kawai T, Kano-Nakata M, Suralta RR, Niones JM, Hasegawa T, Inari-Ikeda M, Yamauchi A, Inukai Y. Morpho-physiological and molecular mechanisms of phenotypic root plasticity for rice adaptation to water stress conditions. BREEDING SCIENCE 2021; 71:20-29. [PMID: 33762873 PMCID: PMC7973496 DOI: 10.1270/jsbbs.20106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 11/04/2020] [Indexed: 05/23/2023]
Abstract
Different types of water stress severely affect crop production, and the plant root system plays a critical role in stress avoidance. In the case of rice, a cereal crop cultivated under the widest range of soil hydrologic conditions, from irrigated anaerobic conditions to rainfed conditions, phenotypic root plasticity is of particular relevance. Recently, important plastic root traits under different water stress conditions, and their physiological and molecular mechanisms have been gradually understood. In this review, we summarize these plastic root traits and their contributions to dry matter production through enhancement of water uptake under different water stress conditions. We also discuss the physiological and molecular mechanisms regulating the phenotypic plasticity of root systems.
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Affiliation(s)
- Nonawin Lucob-Agustin
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
- Philippine Rice Research Institute, Central Experiment Station, Science City of Muñoz, Nueva Ecija, 3119, Philippines
| | - Tsubasa Kawai
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mana Kano-Nakata
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Roel R. Suralta
- Philippine Rice Research Institute, Central Experiment Station, Science City of Muñoz, Nueva Ecija, 3119, Philippines
| | - Jonathan M. Niones
- Philippine Rice Research Institute, Central Experiment Station, Science City of Muñoz, Nueva Ecija, 3119, Philippines
| | - Tomomi Hasegawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Mayuko Inari-Ikeda
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Yoshiaki Inukai
- International Center for Research and Education in Agriculture, Nagoya University, Nagoya, Aichi 464-8601, Japan
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Uga Y. Challenges to design-oriented breeding of root system architecture adapted to climate change. BREEDING SCIENCE 2021; 71:3-12. [PMID: 33762871 PMCID: PMC7973499 DOI: 10.1270/jsbbs.20118] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 10/18/2020] [Indexed: 05/12/2023]
Abstract
Roots are essential organs for capturing water and nutrients from the soil. In particular, root system architecture (RSA) determines the extent of the region of the soil where water and nutrients can be gathered. As global climate change accelerates, it will be important to improve belowground plant parts, as well as aboveground ones, because roots are front-line organs in the response to abiotic stresses such as drought, flooding, and salinity stress. However, using conventional breeding based on phenotypic selection, it is difficult to select breeding lines possessing promising RSAs to adapted to abiotic stress because roots remain hidden underground. Therefore, new breeding strategies that do not require phenotypic selection are necessary. Recent advances in molecular biology and biotechnology can be applied to the design-oriented breeding of RSA without phenotypic selection. Here I summarize recent progress in RSA ideotypes as "design" and RSA-related gene resources as "materials" that will be needed in leveraging these technologies for the RSA breeding. I also highlight the future challenges to design-oriented breeding of RSA and explore solutions to these challenges.
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Affiliation(s)
- Yusaku Uga
- Institute of Crop Science, National Agriculture and Food Research Organization, Kannondai, Tsukuba, Ibaraki 305-8518, Japan
- Corresponding author (e-mail: )
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Dwivedi SL, Stoddard FL, Ortiz R. Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 295:110365. [PMID: 32534611 DOI: 10.1016/j.plantsci.2019.110365] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 11/15/2019] [Accepted: 12/01/2019] [Indexed: 06/11/2023]
Abstract
Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.
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Affiliation(s)
| | | | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Department of Plant Breeding, Sundsvagen, 14 Box 101, SE 23053, Alnarp, Sweden.
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Mitsuya S, Murakami N, Sato T, Kazama T, Toriyama K, Skoulding NS, Kano-Nakata M, Yamauchi A. Evaluation of rice grain yield and yield components of Nona Bokra chromosome segment substitution lines with the genetic background of Koshihikari, in a saline paddy field. AOB PLANTS 2019; 11:plz040. [PMID: 31632626 PMCID: PMC6790112 DOI: 10.1093/aobpla/plz040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2018] [Accepted: 07/11/2019] [Indexed: 05/27/2023]
Abstract
The ability to tolerate salt differs with the growth stages of rice and thus the yield components that are determined during various growth stages, are differentially affected by salt stress. In this study, we utilized chromosome segment substitution lines (CSSLs) from Nona Bokra, a salt-tolerant indica landrace, with the genetic background of Koshihikari, a salt-susceptible japonica variety. These were screened to find superior CSSLs under long-term saline conditions that showed higher grain yield and yield components in comparison to Koshihikari. One-month-old seedlings were transplanted into a paddy field without salinity. These were allowed to establish for 1 month further, then the field was flooded, with saline water maintained at 7.41 dS m-1 salinity until harvest. The experiments were performed twice, once in 2015 and a targeted study in 2016. Salt tolerance of growth and reproductive stage parameters was evaluated as the Salt Effect Index (SEI) which was computed as the difference in each parameter within each line between control and saline conditions. All CSSLs and Koshihikari showed a decrease in grain yield and yield components except panicle number under salinity. SL538 showed a higher SEI for grain yield compared with Koshihikari under salinity throughout the two experiments. This was attributed to the retained grain filling and harvest index, yet the mechanism was not due to maintaining Na+, Cl- and K+ homeostasis. Few other CSSLs showed greater SEI for grain weight under salinity compared with Koshihikari, which might be related to low concentration of Na+ in leaves and panicles. These data indicate that substitution of different Nona Bokra chromosome segments independently contributed to the maintenance of grain filling and grain weight of Koshihikari under saline conditions.
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Affiliation(s)
- Shiro Mitsuya
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Norifumi Murakami
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Tadashi Sato
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Tomohiko Kazama
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | - Kinya Toriyama
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Japan
| | | | - Mana Kano-Nakata
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
- Institute for Advanced Research, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
| | - Akira Yamauchi
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Japan
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