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Gong W, Proud C, Vinarao R, Fukai S, Mitchell J. Genome-Wide Association Study of Early Vigour-Related Traits for a Rice ( Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions. Biology (Basel) 2024; 13:261. [PMID: 38666873 PMCID: PMC11048181 DOI: 10.3390/biology13040261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.
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Affiliation(s)
- Wenliu Gong
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD 4072, Australia (J.M.)
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Wang Y, Jiang C, Zhang X, Yan H, Yin Z, Sun X, Gao F, Zhao Y, Liu W, Han S, Zhang J, Zhang Y, Zhang Z, Zhang H, Li J, Xie X, Zhao Q, Wang X, Ye G, Li J, Ming R, Li Z. Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding. Plant Biotechnol J 2024; 22:662-677. [PMID: 37909415 PMCID: PMC10893945 DOI: 10.1111/pbi.14215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/31/2023] [Accepted: 10/16/2023] [Indexed: 11/03/2023]
Abstract
Upland rice is a distinctive drought-aerobic ecotype of cultivated rice highly resistant to drought stress. However, the genetic and genomic basis for the drought-aerobic adaptation of upland rice remains largely unclear due to the lack of genomic resources. In this study, we identified 25 typical upland rice accessions and assembled a high-quality genome of one of the typical upland rice varieties, IRAT109, comprising 384 Mb with a contig N50 of 19.6 Mb. Phylogenetic analysis revealed upland and lowland rice have distinct ecotype differentiation within the japonica subgroup. Comparative genomic analyses revealed that adaptive differentiation of lowland and upland rice is likely attributable to the natural variation of many genes in promoter regions, formation of specific genes in upland rice, and expansion of gene families. We revealed differentiated gene expression patterns in the leaves and roots of the two ecotypes and found that lignin synthesis mediated by the phenylpropane pathway plays an important role in the adaptive differentiation of upland and lowland rice. We identified 28 selective sweeps that occurred during domestication and validated that the qRT9 gene in selective regions can positively regulate drought resistance in rice. Eighty key genes closely associated with drought resistance were appraised for their appreciable potential in drought resistance breeding. Our study enhances the understanding of the adaptation of upland rice and provides a genome navigation map of drought resistance breeding, which will facilitate the breeding of drought-resistant rice and the "blue revolution" in agriculture.
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Affiliation(s)
- Yulong Wang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Conghui Jiang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Institute of Wetland Agriculture and EcologyShandong Academy of Agricultural SciencesJinanShandongChina
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
| | - Huimin Yan
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhigang Yin
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xingming Sun
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Fenghua Gao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yan Zhao
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Wei Liu
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Shichen Han
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jingjing Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Yage Zhang
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
| | - Zhanying Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Hongliang Zhang
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Jinjie Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
| | - Xianzhi Xie
- Institute of Wetland Agriculture and EcologyShandong Academy of Agricultural SciencesJinanShandongChina
| | - Quanzhi Zhao
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Xiaoning Wang
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
| | - Guoyou Ye
- Agricultural Genomics Institute in ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdongChina
- Institution International Rice Research InstituteLos BañosLagunaPhilippines
| | - Junzhou Li
- Collaborative Innovation Center of Henan Grain Crops, Henan Key Laboratory of Rice BiologyHenan Agricultural UniversityZhengzhouHenanChina
| | - Ray Ming
- Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Zichao Li
- Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and BiotechnologyChina Agricultural UniversityBeijingChina
- Sanya Institute of Hainan Academy of Agricultural SciencesSanyaHainanChina
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Padmashree R, Barbadikar KM, Honnappa, Magar ND, Balakrishnan D, Lokesha R, Gireesh C, Siddaiah AM, Madhav MS, Ramesha YM, Bharamappanavara M, Phule AS, Senguttuvel P, Diwan JR, Subrahmanyam D, Sundaram RM. Genome-wide association studies in rice germplasm reveal significant genomic regions for root and yield-related traits under aerobic and irrigated conditions. Front Plant Sci 2023; 14:1143853. [PMID: 37538056 PMCID: PMC10395336 DOI: 10.3389/fpls.2023.1143853] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 04/19/2023] [Indexed: 08/05/2023]
Abstract
The development of nutrient-use efficient rice lines is a priority amidst the changing climate and depleting resources viz., water, land, and labor for achieving sustainability in rice cultivation. Along with the traditional transplanted irrigated system of cultivation, the dry direct-seeded aerobic system is gaining ground nationwide. The root-related traits play a crucial role in nutrient acquisition, adaptation and need to be concentrated along with the yield-attributing traits. We phenotyped an association panel of 118 rice lines for seedling vigour index (SVI) traits at 14 and 21 days after sowing (DAS), root-related traits at panicle initiation (PI) stage in polythene bags under controlled aerobic condition, yield and yield-related traits under the irrigated condition at ICAR-IIRR, Hyderabad, Telangana; irrigated and aerobic conditions at ARS, Dhadesugur, Raichur, Karnataka. The panel was genotyped using simple sequence repeats (SSR) markers and genome-wide association studies were conducted for identifying marker-trait associations (MTAs). Significant correlations were recorded for root length, root dry weight with SVI, root volume at the PI stage, number of productive tillers per plant, spikelet fertility, the total number of grains per panicle with grain yield per plant under irrigated conditions, and the total number of grains per panicle with grain yield per plant under aerobic condition. The panel was divided into three sub-groups (K = 3) and correlated with the principal component analysis. The maximum number of MTAs were found on chromosomes 2, 3, and 12 with considerable phenotypic variability. Consistent MTAs were recorded for SVI traits at 14 and 21 DAS (RM25310, RM80, RM22961, RM1385), yield traits under irrigated conditions (RM2584, RM5179, RM410, RM20698, RM14753) across years at ICAR-IIRR, grain yield per plant (RM22961, RM1146) under the aerobic condition, grain yield per plant at irrigated ICAR-IIRR and SVI (RM5501), root traits at PI stage (RM2584, RM80, RM410, RM1146, RM18472). Functionally relevant genes near the MTAs through in-silico expression analysis in root and panicle tissues viz., HBF2 bZIP transcription factor, WD40 repeat-like domain, OsPILS6a auxin efflux carrier, WRKY108, OsSCP42, OsMADS80, nodulin-like domain-containing protein, amino acid transporter using various rice expression databases were identified. The identified MTAs and rice lines having high SVI traits (Langphou, TI-128, Mouli, TI-124, JBB-631-1), high yield under aerobic (Phouren, NPK-43, JBB-684, Ratnamudi, TI-112), irrigated conditions (KR-209, KR-262, Phouren, Keibi-Phou, TI-17), robust root traits like root length (MoirangPhou-Angouba, Wangoo-Phou, JBB-661, Dissi, NPK-45), root volume (Ratnachudi, KJ-221, Mow, Heimang-Phou, PUP-229) can be further employed in breeding programs for the targeted environments aimed at improving seedling vigour, yield-related traits under irrigated condition, aerobic condition as adaptability to water-saving technology.
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Affiliation(s)
- Revadi Padmashree
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Kalyani M. Barbadikar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Honnappa
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- University of Agricultural Sciences (UAS), Raichur, India
| | - Nakul D. Magar
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
- Chaudhary Charan Singh University, Meerut, India
| | - Divya Balakrishnan
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - R. Lokesha
- University of Agricultural Sciences (UAS), Raichur, India
| | - C. Gireesh
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Anantha M. Siddaiah
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Maganti Sheshu Madhav
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Y. M Ramesha
- Agricultural Research Station (ARS) Dhadesugur, University of Agricultural Sciences (UAS), Raichur, India
| | | | - Amol S. Phule
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - P. Senguttuvel
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - J. R. Diwan
- University of Agricultural Sciences (UAS), Raichur, India
| | - D. Subrahmanyam
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
| | - Raman Menakshi Sundaram
- Indian Council of Agricultural Research (ICAR)-Indian Institute of Rice Research (IIRR), Hyderabad, India
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Yue L, Xie B, Cao X, Chen F, Wang C, Xiao Z, Jiao L, Wang Z. The Mechanism of Manganese Ferrite Nanomaterials Promoting Drought Resistance in Rice. Nanomaterials (Basel) 2023; 13:nano13091484. [PMID: 37177029 PMCID: PMC10180523 DOI: 10.3390/nano13091484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
Strategies to reduce the risk of drought damage are urgently needed as intensified climate change threatens agricultural production. One potential strategy was using nanomaterials (NMs) to enhance plant resistance by regulating various physiological and biochemical processes. In the present study, 10 mg kg-1 manganese ferrite (MnFe2O4) NMs had the optimal enhancement to elevate the levels of biomass, photosynthesis, nutrient elements, and polysaccharide in rice by 10.9-525.0%, respectively, under drought stress. The MnFe2O4 NMs were internalized by rice plants, which provided the possibility for rice to better cope with drought. Furthermore, as compared with drought control and equivalent ion control, the introduction of MnFe2O4 NMs into the roots significantly upregulated the drought-sensing gene CLE25 (29.4%) and the receptor gene NCED3 (59.9%). This activation stimulated downstream abscisic acid, proline, malondialdehyde, and wax biosynthesis by 23.3%, 38.9%, 7.2%, and 26.2%, respectively. In addition, 10 mg·kg-1 MnFe2O4 NMs significantly upregulated the relative expressions of OR1, AUX2, AUX3, PIN1a, and PIN2, and increased IAA content significantly, resulting in an enlarged root angle and a deeper and denser root to help the plant withstand drought stresses. The nutritional quality of rice grains was also improved. Our study provides crucial insight for developing nano-enabled strategies to improve crop productivity and resilience to climate change.
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Affiliation(s)
- Le Yue
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Budiao Xie
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Xuesong Cao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Feiran Chen
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Chuanxi Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Zhenggao Xiao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Liya Jiao
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Jiangsu Engineering Laboratory for Biomass Energy and Carbon Reduction Technology, Wuxi 214122, China
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Proud C, Campbell B, Susanti Z, Fukai S, Godwin I, Ovenden B, Snell P, Mitchell J. Quantitative trait loci (QTL) for low temperature tolerance at the young microspore stage in rice ( Oryza sativa L.) in Australian breeding material. Breed Sci 2022; 72:238-247. [PMID: 36408321 PMCID: PMC9653190 DOI: 10.1270/jsbbs.21096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 04/07/2022] [Indexed: 06/15/2023]
Abstract
Low temperatures at the young microspore stage (YMS) decreases spikelet fertility and is a major limiting factor to rice production in temperate Australia. Low temperature tolerance is a difficult trait to phenotype, hence there is a strong desire for the identification of quantitative trait loci (QTL) for their use in marker-assisted selection (MAS). Association mapping was used in several breeding populations with a known source of low temperature tolerance, Norin PL8, to identify QTL for low temperature tolerance. A novel QTL for spikelet fertility was identified on chromosome 6, qYMCT6.1, in which the Australian variety, Kyeema, was the donor for increased fertility. Additional five genomics regions were identified that co-located with previously reported QTL, two of which have been previously cloned. Additionally, for the first time a QTL for spikelet fertility qYMCT10.1, has been shown to co-locate with the number of dehisced anthers qYMCTF10.1 which increases the shedding of pollen from the anthers. This study revealed one new QTL for low temperature tolerance at YMS in temperate japonica germplasm and identified an additional five previously reported. These QTL will be utilised for MAS in the Australian rice breeding program and may have merit for temperate breeding programs globally.
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Affiliation(s)
- Christopher Proud
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Bradley Campbell
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Zuziana Susanti
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
- Indonesian Centre for Rice Research, Agency for Agricultural Research and Development, Subang, West-Java, Indonesia
| | - Shu Fukai
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
| | - Ian Godwin
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Ben Ovenden
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW 2703, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW 2703, Australia
| | - Jaquie Mitchell
- The University of Queensland, School of Agriculture and Food Sciences, St Lucia, Queensland 4072, Australia
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Vinarao R, Proud C, Snell P, Fukai S, Mitchell J. Genomic Regions and Floral Traits Contributing to Low Temperature Tolerance at Young Microspore Stage in a Rice ( Oryza sativa L.) Recombinant Inbred Line Population of Sherpa/IRAT109. Front Plant Sci 2022; 13:873677. [PMID: 35574104 PMCID: PMC9100824 DOI: 10.3389/fpls.2022.873677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/31/2022] [Indexed: 06/15/2023]
Abstract
Aerobic rice production (AP) consumes less water compared to flooded systems. Developing genotypes and identifying genomic regions associated with low temperature (LT) tolerance at the young microspore stage (YMS) is imperative for AP, particularly for temperate regions. Using a recombinant inbred line population derived from the Australian LT tolerant variety Sherpa, experiments were conducted to map and dissect quantitative trait loci (QTL) associated with spikelet sterility (SS) after exposure to LT and to investigate floral traits contributing to the development of lower SS. Significant genotypic variation for SS was observed in the population after exposure to LT at YMS. Three genomic regions associated with SS, qYMCT3, qYMCT4, and qYMCT8.1 were identified in chromosomes 3, 4, and 8 respectively, using multiple QTL models explaining 22.4% of the genotypic variation. Introgression of the favorable allele from qYMCT3 was estimated to reduce SS by up to 15.4%. A co-locating genomic region with qYMCT3, qDTHW3.1 was identified as the major QTL affecting days to heading and explained as much as 44.7% of the genotypic variation. Whole-genome sequence and bioinformatic analyses demonstrated OsMADS50 as the candidate gene for qYMCT3/qDTHW3.1 and to our knowledge, this was the first attempt in connecting the role of OsMADS50 in both LT and flowering in rice. Differential sets selected for extreme SS showed LT tolerant genotype group produced higher total pollen per spikelet resulting in a higher number of dehisced anthers and pollen on stigma and eventually, lower SS than THE sensitive group. The relationship between these key floral traits with SS was induced only after exposure to LT and was not observed in warm ideal temperature conditions. Identification of elite germplasm with favorable QTL allele and combinations, gene cloning, and pyramiding with additional high-value QTL for key traits should empower breeders to develop AP adapted genotypes for temperate growing regions, and ultimately produce climate-resilient rice.
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Affiliation(s)
- Ricky Vinarao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Christopher Proud
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW, Australia
| | - Shu Fukai
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Jaquie Mitchell
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD, Australia
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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 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Vinarao R, Proud C, Snell P, Fukai S, Mitchell J. QTL Validation and Development of SNP-Based High Throughput Molecular Markers Targeting a Genomic Region Conferring Narrow Root Cone Angle in Aerobic Rice Production Systems. Plants (Basel) 2021; 10:2099. [PMID: 34685908 PMCID: PMC8537842 DOI: 10.3390/plants10102099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/29/2021] [Accepted: 09/30/2021] [Indexed: 06/13/2023]
Abstract
Aerobic rice production (AP) provides potential solutions to the global water crisis by consuming less water than traditional permanent water culture. Narrow root cone angle (RCA), development of deeper rooting and associated genomic regions are key for AP adaptation. However, their usefulness depends on validation across genetic backgrounds and development of linked markers. Using three F2 populations derived from IRAT109, qRCA4 was shown to be effective in multiple backgrounds, explaining 9.3-17.3% of the genotypic variation and introgression of the favourable allele resulted in 11.7-15.1° narrower RCA. Novel kompetitive allele specific PCR (KASP) markers were developed targeting narrow RCA and revealed robust quality metrics. Candidate genes related with plant response to abiotic stress and root development were identified along with 178 potential donors across rice subpopulations. This study validated qRCA4's effect in multiple genetic backgrounds further strengthening its value in rice improvement for AP adaptation. Furthermore, the development of novel KASP markers ensured the opportunity for its seamless introgression across pertinent breeding programs. This work provides the tools and opportunity to accelerate development of genotypes with narrow RCA through marker assisted selection in breeding programs targeting AP, which may ultimately contribute to more sustainable rice production where water availability is limited.
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Affiliation(s)
- Ricky Vinarao
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
| | - Christopher Proud
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
| | - Peter Snell
- Department of Primary Industries, Yanco Agricultural Institute, Yanco, NSW 2703, Australia;
| | - Shu Fukai
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
| | - Jaquie Mitchell
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia; (R.V.); (C.P.); (S.F.)
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