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Liu J, Wang X, Wu H, Zhu Y, Ahmad I, Dong G, Zhou G, Wu Y. Association between Reactive Oxygen Species, Transcription Factors, and Candidate Genes in Drought-Resistant Sorghum. Int J Mol Sci 2024; 25:6464. [PMID: 38928168 PMCID: PMC11203540 DOI: 10.3390/ijms25126464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/04/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024] Open
Abstract
Drought stress is one of the most severe natural disasters in terms of its frequency, length, impact intensity, and associated losses, making it a significant threat to agricultural productivity. Sorghum (Sorghum bicolor), a C4 plant, shows a wide range of morphological, physiological, and biochemical adaptations in response to drought stress, paving the way for it to endure harsh environments. In arid environments, sorghum exhibits enhanced water uptake and reduced dissipation through its morphological activity, allowing it to withstand drought stress. Sorghum exhibits physiological and biochemical resistance to drought, primarily by adjusting its osmotic potential, scavenging reactive oxygen species, and changing the activities of its antioxidant enzymes. In addition, certain sorghum genes exhibit downregulation capabilities in response to drought stress. Therefore, in the current review, we explore drought tolerance in sorghum, encompassing its morphological characteristics and physiological mechanisms and the identification and selection of its functional genes. The use of modern biotechnological and molecular biological approaches to improving sorghum resistance is critical for selecting and breeding drought-tolerant sorghum varieties.
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Affiliation(s)
- Jiao Liu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Xin Wang
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Hao Wu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Yiming Zhu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Irshad Ahmad
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Guichun Dong
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Guisheng Zhou
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
| | - Yanqing Wu
- Joint International Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou 225000, China; (J.L.); (X.W.); (H.W.); (Y.Z.); (I.A.)
- Jiangsu Key Laboratory of Crop Cultivation and Physiology, Yangzhou University, Yangzhou 225000, China;
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McGrath JM, Siebers MH, Fu P, Long SP, Bernacchi CJ. To have value, comparisons of high-throughput phenotyping methods need statistical tests of bias and variance. FRONTIERS IN PLANT SCIENCE 2024; 14:1325221. [PMID: 38312358 PMCID: PMC10835710 DOI: 10.3389/fpls.2023.1325221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/20/2023] [Indexed: 02/06/2024]
Abstract
The gap between genomics and phenomics is narrowing. The rate at which it is narrowing, however, is being slowed by improper statistical comparison of methods. Quantification using Pearson's correlation coefficient (r) is commonly used to assess method quality, but it is an often misleading statistic for this purpose as it is unable to provide information about the relative quality of two methods. Using r can both erroneously discount methods that are inherently more precise and validate methods that are less accurate. These errors occur because of logical flaws inherent in the use of r when comparing methods, not as a problem of limited sample size or the unavoidable possibility of a type I error. A popular alternative to using r is to measure the limits of agreement (LOA). However both r and LOA fail to identify which instrument is more or less variable than the other and can lead to incorrect conclusions about method quality. An alternative approach, comparing variances of methods, requires repeated measurements of the same subject, but avoids incorrect conclusions. Variance comparison is arguably the most important component of method validation and, thus, when repeated measurements are possible, variance comparison provides considerable value to these studies. Statistical tests to compare variances presented here are well established, easy to interpret and ubiquitously available. The widespread use of r has potentially led to numerous incorrect conclusions about method quality, hampering development, and the approach described here would be useful to advance high throughput phenotyping methods but can also extend into any branch of science. The adoption of the statistical techniques outlined in this paper will help speed the adoption of new high throughput phenotyping techniques by indicating when one should reject a new method, outright replace an old method or conditionally use a new method.
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Affiliation(s)
- Justin M. McGrath
- Global Change and Photosynthesis Research Unit, USDA-Agricultural Research Service (ARS), Urbana, IL, United States
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Matthew H. Siebers
- Global Change and Photosynthesis Research Unit, USDA-Agricultural Research Service (ARS), Urbana, IL, United States
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Peng Fu
- Center for Advanced Agriculture and Sustainability, Harrisburg University of Science and Technology, Harrisburg, PA, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Stephen P. Long
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, Urbana, IL, United States
| | - Carl J. Bernacchi
- Global Change and Photosynthesis Research Unit, USDA-Agricultural Research Service (ARS), Urbana, IL, United States
- Department of Plant Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States
- Carl R. Woese Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Urbana, IL, United States
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Rahmati Ishka M, Julkowska M. Tapping into the plasticity of plant architecture for increased stress resilience. F1000Res 2023; 12:1257. [PMID: 38434638 PMCID: PMC10905174 DOI: 10.12688/f1000research.140649.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/24/2023] [Indexed: 03/05/2024] Open
Abstract
Plant architecture develops post-embryonically and emerges from a dialogue between the developmental signals and environmental cues. Length and branching of the vegetative and reproductive tissues were the focus of improvement of plant performance from the early days of plant breeding. Current breeding priorities are changing, as we need to prioritize plant productivity under increasingly challenging environmental conditions. While it has been widely recognized that plant architecture changes in response to the environment, its contribution to plant productivity in the changing climate remains to be fully explored. This review will summarize prior discoveries of genetic control of plant architecture traits and their effect on plant performance under environmental stress. We review new tools in phenotyping that will guide future discoveries of genes contributing to plant architecture, its plasticity, and its contributions to stress resilience. Subsequently, we provide a perspective into how integrating the study of new species, modern phenotyping techniques, and modeling can lead to discovering new genetic targets underlying the plasticity of plant architecture and stress resilience. Altogether, this review provides a new perspective on the plasticity of plant architecture and how it can be harnessed for increased performance under environmental stress.
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Kumar N, Boatwright JL, Sapkota S, Brenton ZW, Ballén-Taborda C, Myers MT, Cox WA, Jordan KE, Kresovich S, Boyles RE. Discovering useful genetic variation in the seed parent gene pool for sorghum improvement. Front Genet 2023; 14:1221148. [PMID: 37790706 PMCID: PMC10544336 DOI: 10.3389/fgene.2023.1221148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/04/2023] [Indexed: 10/05/2023] Open
Abstract
Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.
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Affiliation(s)
- Neeraj Kumar
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - J. Lucas Boatwright
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Sirjan Sapkota
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
| | - Zachary W. Brenton
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Carolina Seed Systems, Darlington, SC, United States
| | - Carolina Ballén-Taborda
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Pee Dee Research and Education Center, Clemson University, Florence, SC, United States
| | - Matthew T. Myers
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - William A. Cox
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Kathleen E. Jordan
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
| | - Stephen Kresovich
- Advanced Plant Technology, Clemson University, Clemson, SC, United States
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Feed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United States
| | - Richard E. Boyles
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, United States
- Pee Dee Research and Education Center, Clemson University, Florence, SC, United States
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Menamo T, Borrell AK, Mace E, Jordan DR, Tao Y, Hunt C, Kassahun B. Genetic dissection of root architecture in Ethiopian sorghum landraces. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:209. [PMID: 37715848 DOI: 10.1007/s00122-023-04457-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 08/28/2023] [Indexed: 09/18/2023]
Abstract
KEY MESSAGE This study quantified genetic variation in root system architecture (root number, angle, length and dry mass) within a diversity panel of 1771 Ethiopian sorghum landraces and identified 22 genomic regions associated with the root variations. The root system architecture (RSA) of crop plants influences adaptation to water-limited conditions and determines the capacity of a plant to access soil water and nutrients. Four key root traits (number, angle, length and dry mass) were evaluated in a diversity panel of 1771 Ethiopian sorghum landraces using purpose-built root chambers. Significant genetic variation was observed in all studied root traits, with nodal root angle ranging from 16.4° to 26.6°, with a high repeatability of 78.9%. Genome wide association studies identified a total of 22 genomic regions associated with root traits which were distributed on all chromosomes except chromosome SBI-10. Among the 22 root genomic regions, 15 co-located with RSA trait QTL previously identified in sorghum, with the remaining seven representing novel RSA QTL. The majority (85.7%) of identified root angle QTL also co-localized with QTL previously identified for stay-green in sorghum. This suggests that the stay-green phenotype might be associated with root architecture that enhances water extraction during water stress conditions. The results open avenues for manipulating root phenotypes to improve productivity in abiotic stress environments via marker-assisted selection.
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Affiliation(s)
- Temesgen Menamo
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia
| | - Andrew K Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Emma Mace
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
- Agri-Science Queensland, Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - David R Jordan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Yongfu Tao
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), University of Queensland, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Colleen Hunt
- Agri-Science Queensland, Department of Agriculture and Fisheries, Hermitage Research Facility, Warwick, QLD, 4370, Australia
| | - Bantte Kassahun
- College of Agriculture and Veterinary Medicine, Jimma University, P.O. Box 307, Jimma, Ethiopia.
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Wong ACS, van Oosterom EJ, Godwin ID, Borrell AK. Integrating stay-green and PIN-FORMED genes: PIN-FORMED genes as potential targets for designing climate-resilient cereal ideotypes. AOB PLANTS 2023; 15:plad040. [PMID: 37448862 PMCID: PMC10337860 DOI: 10.1093/aobpla/plad040] [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: 11/27/2022] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Plant architecture modification (e.g. short-stature crops) is one of the key outcomes of modern crop breeding for high-yielding crop varieties. In cereals, delayed senescence, or stay-green, is an important trait that enables post-anthesis drought stress adaptation. Stay-green crops can prolong photosynthetic capacity during grain-filling period under post-anthesis drought stress, which is essential to ensure grain yield is not impacted under drought stress conditions. Although various stay-green quantitative trait loci have been identified in cereals, the underlying molecular mechanisms regulating stay-green remain elusive. Recent advances in various gene-editing technologies have provided avenues to fast-track crop improvement, such as the breeding of climate-resilient crops in the face of climate change. We present in this viewpoint the focus on using sorghum as the model cereal crop, to study PIN-FORMED (PIN) auxin efflux carriers as means to modulate plant architecture, and the potential to employ it as an adaptive strategy to address the environmental challenges posed by climate uncertainties.
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Affiliation(s)
- Albert Chern Sun Wong
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
| | - Erik J van Oosterom
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
| | - Ian D Godwin
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, 306 Carmody Road, Brisbane, Queensland 4072, Australia
| | - Andrew K Borrell
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Hermitage Research Facility, 604 Yangan Road, Warwick, Queensland 4370, Australia
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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Wang L, Shang L, Wu X, Hao H, Jing HC. Genomic architecture of leaf senescence in sorghum (Sorghum bicolor). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:45. [PMID: 36905488 DOI: 10.1007/s00122-023-04315-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 01/28/2023] [Indexed: 06/18/2023]
Abstract
Leaf senescence in sorghum is primarily controlled by the progression, but not by the onset of senescence. The senescence-delaying haplotypes of 45 key genes accentuated from landraces to improved lines. Leaf senescence is a genetically programmed developmental process and plays a central role for plant survival and crop production by remobilising nutrients accumulated in senescent leaves. In theory, the ultimate outcome of leaf senescence is determined by the onset and progression of senescence, but how these two processes contribute to senescence is not fully illustrated in crops and the genetic basis for them is not well understood. Sorghum (Sorghum bicolor), which is known for the remarkable stay-green trait, is ideal for dissecting the genomic architecture underlying the regulation of senescence. In this study, a diverse panel of 333 sorghum lines was explored for the onset and progression of leaf senescence. Trait correlation analysis showed that the progression of leaf senescence, rather than the onset of leaf senescence, significantly correlated with variations of the final leaf greenness. This notion was further supported by GWAS, which identified 31 senescence-associated genomic regions containing 148 genes, of which 124 were related to the progression of leaf senescence. The senescence-delaying haplotypes of 45 key candidate genes were enriched in lines with extremely prolonged senescence duration, while senescence-promoting haplotypes in those with extremely accelerated senescence. Haplotype combinations of these genes could well explain the segregation of the senescence trait in a recombinant inbred population. We also demonstrated that senescence-delaying haplotypes of candidate genes were under strong selection during sorghum domestication and genetic improvement. Together, this research advanced our understanding of crop leaf senescence and provided a suite of candidate genes for functional genomics and molecular breeding.
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Affiliation(s)
- Lidong Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Shang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiaoyuan Wu
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Huaiqing Hao
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Hai-Chun Jing
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Engineering Laboratory for Grass-Based Livestock Husbandry, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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9
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Mulugeta B, Tesfaye K, Ortiz R, Johansson E, Hailesilassie T, Hammenhag C, Hailu F, Geleta M. Marker-trait association analyses revealed major novel QTLs for grain yield and related traits in durum wheat. FRONTIERS IN PLANT SCIENCE 2023; 13:1009244. [PMID: 36777537 PMCID: PMC9909559 DOI: 10.3389/fpls.2022.1009244] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
The growing global demand for wheat for food is rising due to the influence of population growth and climate change. The dissection of complex traits by employing a genome-wide association study (GWAS) allows the identification of DNA markers associated with complex traits to improve the productivity of crops. We used GWAS with 10,045 single nucleotide polymorphism (SNP) markers to search for genomic regions associated with grain yield and related traits based on diverse panels of Ethiopian durum wheat. In Ethiopia, multi-environment trials of the genotypes were carried out at five locations. The genotyping was conducted using the 25k Illumina Wheat SNP array to explore population structure, linkage disequilibrium (LD), and marker-trait associations (MTAs). For GWAS, the multi-locus Fixed and Random Model Circulating Probability Unification (FarmCPU) model was applied. Broad-sense heritability estimates were high, ranging from 0.63 (for grain yield) to 0.97 (for thousand-kernel weight). The population structure based on principal component analysis, and model-based cluster analysis revealed two genetically distinct clusters with limited admixtures. The LD among SNPs declined within the range of 2.02-10.04 Mbp with an average of 4.28 Mbp. The GWAS scan based on the mean performance of the genotypes across the environments identified 44 significant MTAs across the chromosomes. Twenty-six of these MTAs are novel, whereas the remaining 18 were previously reported and confirmed in this study. We also identified candidate genes for the novel loci potentially regulating the traits. Hence, this study highlights the significance of the Ethiopian durum wheat gene pool for improving durum wheat globally. Furthermore, a breeding strategy focusing on accumulating favorable alleles at these loci could improve durum wheat production in the East African highlands and elsewhere.
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Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Director General, Bio and Emerging Technology Institute (BETin), Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Eva Johansson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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10
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Borrell AK, Wong ACS, George-Jaeggli B, van Oosterom EJ, Mace ES, Godwin ID, Liu G, Mullet JE, Klein PE, Hammer GL, McLean G, Hunt C, Jordan DR. Genetic modification of PIN genes induces causal mechanisms of stay-green drought adaptation phenotype. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6711-6726. [PMID: 35961690 PMCID: PMC9629789 DOI: 10.1093/jxb/erac336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 08/10/2022] [Indexed: 05/27/2023]
Abstract
The stay-green trait is recognized as a key drought adaptation mechanism in cereals worldwide. Stay-green sorghum plants exhibit delayed senescence of leaves and stems, leading to prolonged growth, a reduced risk of lodging, and higher grain yield under end-of-season drought stress. More than 45 quantitative trait loci (QTL) associated with stay-green have been identified, including two major QTL (Stg1 and Stg2). However, the contributing genes that regulate functional stay-green are not known. Here we show that the PIN FORMED family of auxin efflux carrier genes induce some of the causal mechanisms driving the stay-green phenotype in sorghum, with SbPIN4 and SbPIN2 located in Stg1 and Stg2, respectively. We found that nine of 11 sorghum PIN genes aligned with known stay-green QTL. In transgenic studies, we demonstrated that PIN genes located within the Stg1 (SbPIN4), Stg2 (SbPIN2), and Stg3b (SbPIN1) QTL regions acted pleiotropically to modulate canopy development, root architecture, and panicle growth in sorghum, with SbPIN1, SbPIN2, and SbPIN4 differentially expressed in various organs relative to the non-stay-green control. The emergent consequence of such modifications in canopy and root architecture is a stay-green phenotype. Crop simulation modelling shows that the SbPIN2 phenotype can increase grain yield under drought.
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Affiliation(s)
- Andrew K Borrell
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
| | - Albert C S Wong
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Barbara George-Jaeggli
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | | | - Emma S Mace
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | - Ian D Godwin
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Guoquan Liu
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - John E Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Patricia E Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX 77843, USA
| | - Graeme L Hammer
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Greg McLean
- University of Queensland, QAAFI, Brisbane, QLD 4072, Australia
| | - Colleen Hunt
- Agri-Science Queensland, Department of Agriculture & Fisheries, Warwick, QLD 4370, Australia
| | - David R Jordan
- University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), Warwick, QLD 4370, Australia
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11
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Ortiz D, Salas-Fernandez MG. Dissecting the genetic control of natural variation in sorghum photosynthetic response to drought stress. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3251-3267. [PMID: 34791180 PMCID: PMC9126735 DOI: 10.1093/jxb/erab502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/12/2021] [Indexed: 06/13/2023]
Abstract
Drought stress causes crop yield losses worldwide. Sorghum is a C4 species tolerant to moderate drought stress, and its extensive natural variation for photosynthetic traits under water-limiting conditions can be exploited for developing cultivars with enhanced stress tolerance. The objective of this study was to discover genes/genomic regions that control the sorghum photosynthetic capacity under pre-anthesis water-limiting conditions. We performed a genome-wide association study for seven photosynthetic gas exchange and chlorophyll fluorescence traits during three periods of contrasting soil volumetric water content (VWC): control (30% VWC), drought (15% VWC), and recovery (30% VWC). Water stress was imposed with an automated irrigation system that generated a controlled dry-down period for all plants, to perform an unbiased genotypic comparison. A total of 60 genomic regions were associated with natural variation in one or more photosynthetic traits in a particular treatment or with derived variables. We identified 33 promising candidate genes with predicted functions related to stress signaling, oxidative stress protection, hormonal response to stress, and dehydration protection. Our results provide new knowledge about the natural variation and genetic control of sorghum photosynthetic response to drought with the ultimate goal of improving its adaptation and productivity under water stress scenarios.
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Affiliation(s)
- Diego Ortiz
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
- Instituto Nacional de Tecnologia Agropecuaria, Manfredi, Cordoba 5988, Argentina
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12
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Chiluwal A, Perumal R, Poudel HP, Muleta K, Ostmeyer T, Fedenia L, Pokharel M, Bean SR, Sebela D, Bheemanahalli R, Oumarou H, Klein P, Rooney WL, Jagadish SVK. Genetic control of source-sink relationships in grain sorghum. PLANTA 2022; 255:40. [PMID: 35038036 DOI: 10.1007/s00425-022-03822-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
QTL hotspots identified for selected source-sink-related traits provide the opportunity for pyramiding favorable alleles for improving sorghum productivity under diverse environments. A sorghum bi-parental mapping population was evaluated under six different environments at Hays and Manhattan, Kansas, USA, in 2016 and 2017, to identify genomic regions controlling source-sink relationships. The population consisted of 210 recombinant inbred lines developed from US elite post-flowering drought susceptible (RTx430) and a known post-flowering drought tolerant cultivar (SC35). Selected physiological traits related to source (effective quantum yield of photosystem II and chlorophyll index), sink (grain yield per panicle) and panicle neck diameter were recorded during grain filling. The results showed strong phenotypic and genotypic association between panicle neck diameter and grain yield per panicle during mid-grain filling and at maturity. Multiple QTL model revealed 5-12 including 2-5 major QTL for each trait. Among them 3, 7 and 8 QTL for quantum yield, panicle neck diameter and chlorophyll index, respectively, have not been identified previously in sorghum. Phenotypic variation explained by QTL identified across target traits ranged between 5.5 and 25.4%. Panicle neck diameter and grain yield per panicle were positively associated, indicating the possibility of targeting common co-localized QTL to improve both traits simultaneously through marker-assisted selection. Three major QTL hotspots, controlling multiple traits were identified on chromosome 1 (52.23-61.18 Mb), 2 (2.52-11.43 Mb) and 3 (1.32-3.95 Mb). The identified genomic regions and underlying candidate genes can be utilized in pyramiding favorable alleles for improving source-sink relationships in sorghum under diverse environments.
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Affiliation(s)
- Anuj Chiluwal
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Ramasamy Perumal
- Agricultural Research Center, Kansas State University, Hays, KS, 67601, USA
| | - Hari P Poudel
- Agriculture and Agri-Food Canada, 5403 First Ave. South, Lethbridge, AB, T1J 4B1, Canada
| | - Kebede Muleta
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Troy Ostmeyer
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Lauren Fedenia
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Meghnath Pokharel
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Scott R Bean
- Grain Quality and Structure Research Unit, CGAHR, USDA-ARS, 1515 College Avenue, Manhattan, KS, 66502, USA
| | - David Sebela
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Raju Bheemanahalli
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
- Department of Plant and Soil Sciences, Mississippi State University, Mississippi State, MS, 39762, USA
| | - Halilou Oumarou
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA
| | - Patricia Klein
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - William L Rooney
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - S V Krishna Jagadish
- Department of Agronomy, Kansas State University, 2004 Throckmorton Plant Sciences Center, 1712 Claflin Road, Manhattan, KS, 66506-5501, USA.
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13
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Abreha KB, Enyew M, Carlsson AS, Vetukuri RR, Feyissa T, Motlhaodi T, Ng'uni D, Geleta M. Sorghum in dryland: morphological, physiological, and molecular responses of sorghum under drought stress. PLANTA 2021; 255:20. [PMID: 34894286 PMCID: PMC8665920 DOI: 10.1007/s00425-021-03799-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/19/2021] [Indexed: 05/10/2023]
Abstract
Droughts negatively affect sorghum's productivity and nutritional quality. Across its diversity centers, however, there exist resilient genotypes that function differently under drought stress at various levels, including molecular and physiological. Sorghum is an economically important and a staple food crop for over half a billion people in developing countries, mostly in arid and semi-arid regions where drought stress is a major limiting factor. Although sorghum is generally considered tolerant, drought stress still significantly hampers its productivity and nutritional quality across its major cultivation areas. Hence, understanding both the effects of the stress and plant response is indispensable for improving drought tolerance of the crop. This review aimed at enhancing our understanding and provide more insights on drought tolerance in sorghum as a contribution to the development of climate resilient sorghum cultivars. We summarized findings on the effects of drought on the growth and development of sorghum including osmotic potential that impedes germination process and embryonic structures, photosynthetic rates, and imbalance in source-sink relations that in turn affect seed filling often manifested in the form of substantial reduction in grain yield and quality. Mechanisms of sorghum response to drought-stress involving morphological, physiological, and molecular alterations are presented. We highlighted the current understanding about the genetic basis of drought tolerance in sorghum, which is important for maximizing utilization of its germplasm for development of improved cultivars. Furthermore, we discussed interactions of drought with other abiotic stresses and biotic factors, which may increase the vulnerability of the crop or enhance its tolerance to drought stress. Based on the research reviewed in this article, it appears possible to develop locally adapted cultivars of sorghum that are drought tolerant and nutrient rich using modern plant breeding techniques.
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Affiliation(s)
- Kibrom B Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden.
| | - Muluken Enyew
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
- Institute of Biotechnology, Addis Ababa University, Box 1176, Addis Ababa, Ethiopia
| | - Anders S Carlsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
| | - Ramesh R Vetukuri
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Box 1176, Addis Ababa, Ethiopia
| | - Tiny Motlhaodi
- Department of Agricultural Research, Private Bag, 0033, Gaborone, Botswana
| | - Dickson Ng'uni
- Zambia Agriculture Research Institute, Mount Makulu Research Station, P/B 7, Chilanga, Zambia
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 190, 234 22, Lomma, Sweden
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14
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Pardo J, VanBuren R. Evolutionary innovations driving abiotic stress tolerance in C4 grasses and cereals. THE PLANT CELL 2021; 33:3391-3401. [PMID: 34387354 PMCID: PMC8566246 DOI: 10.1093/plcell/koab205] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/07/2021] [Indexed: 06/13/2023]
Abstract
Grasslands dominate the terrestrial landscape, and grasses have evolved complex and elegant strategies to overcome abiotic stresses. The C4 grasses are particularly stress tolerant and thrive in tropical and dry temperate ecosystems. Growing evidence suggests that the presence of C4 photosynthesis alone is insufficient to account for drought resilience in grasses, pointing to other adaptations as contributing to tolerance traits. The majority of grasses from the Chloridoideae subfamily are tolerant to drought, salt, and desiccation, making this subfamily a hub of resilience. Here, we discuss the evolutionary innovations that make C4 grasses so resilient, with a particular emphasis on grasses from the Chloridoideae (chloridoid) and Panicoideae (panicoid) subfamilies. We propose that a baseline level of resilience in chloridoid ancestors allowed them to colonize harsh habitats, and these environments drove selective pressure that enabled the repeated evolution of abiotic stress tolerance traits. Furthermore, we suggest that a lack of evolutionary access to stressful environments is partially responsible for the relatively poor stress resilience of major C4 crops compared to their wild relatives. We propose that chloridoid crops and the subfamily more broadly represent an untapped reservoir for improving resilience to drought and other abiotic stresses in cereals.
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Affiliation(s)
- Jeremy Pardo
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
| | - Robert VanBuren
- Department of Horticulture, Michigan State University, East Lansing, Michigan 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, Michigan 48824, USA
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15
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Souza VFD, Pereira GDS, Pastina MM, Parrella RADC, Simeone MLF, Barros BDA, Noda RW, da Costa e Silva L, Magalhães JVD, Schaffert RE, Garcia AAF, Damasceno CMB. QTL mapping for bioenergy traits in sweet sorghum recombinant inbred lines. G3 GENES|GENOMES|GENETICS 2021; 11:6370150. [PMID: 34519766 PMCID: PMC8527507 DOI: 10.1093/g3journal/jkab314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/26/2021] [Indexed: 11/13/2022]
Abstract
Abstract
During the past decade, sweet sorghum (Sorghum bicolor Moench L.) has shown great potential for bioenergy production, especially biofuels. In this study, 223 recombinant inbred lines (RILs) derived from a cross between two sweet sorghum lines (Brandes × Wray) were evaluated in three trials. Single-nucleotide polymorphisms (SNPs) derived from genotyping by sequencing of 272 RILs were used to build a high-density genetic map comprising 3,767 SNPs spanning 1,368.83 cM. Multitrait multiple interval mapping (MT-MIM) was carried out to map quantitative trait loci (QTL) for eight bioenergy traits. A total of 33 QTLs were identified for flowering time, plant height, total soluble solids and sucrose (five QTLs each), fibers (four QTLs), and fresh biomass yield, juice extraction yield, and reducing sugars (three QTLs each). QTL hotspots were found on chromosomes 1, 3, 6, 9, and 10, in addition to other QTLs detected on chromosomes 4 and 8. We observed that 14 out of the 33 mapped QTLs were found in all three trials. Upon further development and validation in other crosses, the results provided by the present study have a great potential to be used in marker-assisted selection in sorghum breeding programs for biofuel production.
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Affiliation(s)
| | - Guilherme da Silva Pereira
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | | | | | | | | | | | | | | | - Antonio Augusto Franco Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
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16
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Fatiukha A, Deblieck M, Klymiuk V, Merchuk-Ovnat L, Peleg Z, Ordon F, Fahima T, Korol A, Saranga Y, Krugman T. Genomic Architecture of Phenotypic Plasticity in Response to Water Stress in Tetraploid Wheat. Int J Mol Sci 2021; 22:ijms22041723. [PMID: 33572141 PMCID: PMC7915520 DOI: 10.3390/ijms22041723] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 02/04/2021] [Accepted: 02/05/2021] [Indexed: 01/12/2023] Open
Abstract
Phenotypic plasticity is one of the main mechanisms of adaptation to abiotic stresses via changes in critical developmental stages. Altering flowering phenology is a key evolutionary strategy of plant adaptation to abiotic stresses, to achieve the maximum possible reproduction. The current study is the first to apply the linear regression residuals as drought plasticity scores while considering the variation in flowering phenology and traits under non-stress conditions. We characterized the genomic architecture of 17 complex traits and their drought plasticity scores for quantitative trait loci (QTL) mapping, using a mapping population derived from a cross between durum wheat (Triticum turgidum ssp. durum) and wild emmer wheat (T. turgidum ssp. dicoccoides). We identified 79 QTLs affected observed traits and their plasticity scores, of which 33 reflected plasticity in response to water stress and exhibited epistatic interactions and/or pleiotropy between the observed and plasticity traits. Vrn-B3 (TaTF1) residing within an interval of a major drought-escape QTL was proposed as a candidate gene. The favorable alleles for most of the plasticity QTLs were contributed by wild emmer wheat, demonstrating its high potential for wheat improvement. Our study presents a new approach for the quantification of plant adaptation to various stresses and provides new insights into the genetic basis of wheat complex traits under water-deficit stress.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Mathieu Deblieck
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Lianne Merchuk-Ovnat
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Zvi Peleg
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Frank Ordon
- Julius Kühn-Institut (JKI) Federal Research Centre for Cultivated Plants, Institute for Resistance Research and Stress Tolerance, 06484 Quedlinburg, Germany; (M.D.); (F.O.)
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Department of Evolutionary and Environmental Biology, University of Haifa, Haifa 3498838, Israel
| | - Yehoshua Saranga
- R. H. Smith Institute of Plant Science & Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel; (L.M.-O.); (Z.P.); (Y.S.)
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Haifa 3498838, Israel; (A.F.); (V.K.); (T.F.); (A.K.)
- Correspondence: ; Tel.: +972-04-8240783
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17
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Bernardino KC, de Menezes CB, de Sousa SM, Guimarães CT, Carneiro PCS, Schaffert RE, Kochian LV, Hufnagel B, Pastina MM, Magalhaes JV. Association mapping and genomic selection for sorghum adaptation to tropical soils of Brazil in a sorghum multiparental random mating population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:295-312. [PMID: 33052425 DOI: 10.1007/s00122-020-03697-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 09/28/2020] [Indexed: 06/11/2023]
Abstract
A multiparental random mating population used in sorghum breeding is amenable for the detection of QTLs related to tropical soil adaptation, fine mapping of underlying genes and genomic selection approaches. Tropical soils where low phosphorus (P) and aluminum (Al) toxicity limit sorghum [Sorghum bicolor (L.) Moench] production are widespread in the developing world. We report on BRP13R, a multiparental random mating population (MP-RMP), which is commonly used in sorghum recurrent selection targeting tropical soil adaptation. Recombination dissipated much of BRP13R's likely original population structure and average linkage disequilibrium (LD) persisted up to 2.5 Mb, establishing BRP13R as a middle ground between biparental populations and sorghum association panels. Genome-wide association mapping (GWAS) identified conserved QTL from previous studies, such as for root morphology and grain yield under low-P, and indicated the importance of dominance in the genetic architecture of grain yield. By overlapping consensus QTL regions, we mapped two candidate P efficiency genes to a ~ 5 Mb region on chromosomes 6 (ALMT) and 9 (PHO2). Remarkably, we find that only 200 progeny genotyped with ~ 45,000 markers in BRP13R can lead to GWAS-based positional cloning of naturally rare, subpopulation-specific alleles, such as for SbMATE-conditioned Al tolerance. Genomic selection was found to be useful in such MP-RMP, particularly if markers in LD with major genes are fitted as fixed effects into GBLUP models accommodating dominance. Shifts in allele frequencies in progeny contrasting for grain yield indicated that intermediate to minor-effect genes on P efficiency, such as SbPSTOL1 genes, can be employed in pre-breeding via allele mining in the base population. Therefore, MP-RMPs such as BRP13R emerge as multipurpose resources for efficient gene discovery and deployment for breeding sorghum cultivars adapted to tropical soils.
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Affiliation(s)
- Karine C Bernardino
- Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil
| | - Cícero B de Menezes
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil
| | - Sylvia M de Sousa
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil
| | - Claudia T Guimarães
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil
| | - Pedro C S Carneiro
- Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Viçosa, MG, 36570-900, Brazil
| | - Robert E Schaffert
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil
| | - Leon V Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Barbara Hufnagel
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil
- BPMP, CNRS, INRAE, SupAgro, University of Montpellier, 34060, Montpellier, France
| | - Maria Marta Pastina
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil.
| | - Jurandir V Magalhaes
- Embrapa Milho e Sorgo, Rodovia MG 424 km 65, Sete Lagoas, MG, 35701-970, Brazil.
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18
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Ogden AJ, Abdali S, Engbrecht KM, Zhou M, Handakumbura PP. Distinct Preflowering Drought Tolerance Strategies of Sorghum bicolor Genotype RTx430 Revealed by Subcellular Protein Profiling. Int J Mol Sci 2020; 21:ijms21249706. [PMID: 33352693 PMCID: PMC7767018 DOI: 10.3390/ijms21249706] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Revised: 12/12/2020] [Accepted: 12/13/2020] [Indexed: 11/16/2022] Open
Abstract
Drought is the largest stress affecting agricultural crops, resulting in substantial reductions in yield. Plant adaptation to water stress is a complex trait involving changes in hormone signaling, physiology, and morphology. Sorghum (Sorghum bicolor (L.) Moench) is a C4 cereal grass; it is an agricultural staple, and it is particularly drought-tolerant. To better understand drought adaptation strategies, we compared the cytosolic- and organelle-enriched protein profiles of leaves from two Sorghum bicolor genotypes, RTx430 and BTx642, with differing preflowering drought tolerances after 8 weeks of growth under water limitation in the field. In agreement with previous findings, we observed significant drought-induced changes in the abundance of multiple heat shock proteins and dehydrins in both genotypes. Interestingly, our data suggest a larger genotype-specific drought response in protein profiles of organelles, while cytosolic responses are largely similar between genotypes. Organelle-enriched proteins whose abundance significantly changed exclusively in the preflowering drought-tolerant genotype RTx430 upon drought stress suggest multiple mechanisms of drought tolerance. These include an RTx430-specific change in proteins associated with ABA metabolism and signal transduction, Rubisco activation, reactive oxygen species scavenging, flowering time regulation, and epicuticular wax production. We discuss the current understanding of these processes in relation to drought tolerance and their potential implications.
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Affiliation(s)
- Aaron J. Ogden
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, Richland, WA 99354, USA; (A.J.O.); (S.A.); (K.M.E.)
| | - Shadan Abdali
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, Richland, WA 99354, USA; (A.J.O.); (S.A.); (K.M.E.)
| | - Kristin M. Engbrecht
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratories, Richland, WA 99354, USA; (A.J.O.); (S.A.); (K.M.E.)
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
| | - Pubudu P. Handakumbura
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354, USA;
- Correspondence:
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Naoura G, Sawadogo N, Atchozou EA, Emendack Y, Hassan MA, Reoungal D, Amos DN, Djirabaye N, Tabo R, Laza H. Assessment of agro-morphological variability of dry-season sorghum cultivars in Chad as novel sources of drought tolerance. Sci Rep 2019; 9:19581. [PMID: 31863053 PMCID: PMC6925278 DOI: 10.1038/s41598-019-56192-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/08/2019] [Indexed: 11/17/2022] Open
Abstract
Dry-season sorghum is a type of sorghum whose establishment ends at the end of the rainy season and its development takes place during the dry and cold harmattan period. Its root system is particularly well developed with deep penetration for water withdrawal. This study was conducted to assess the level of genetic diversity present among dry-season sorghum in Chad’s Sudanese zone using phenotypic traits, and to identify new sources of drought tolerance that could be used in sorghum breeding programs. A high variability in qualitative traits was observed except for the botanical race which showed that all cultivars were of durra race. It was also observed that most cultivars had compact panicles (66.67%), mostly black glumes (66.67%), glume hairiness (58.33%) and did not have aristation (91.67%). Most qualitative traits showed a coefficient of variation of less than 30%, and the analysis of the variance showed that at 0.1% probability, there were significant differences between cultivars for all traits except botanical race. It was observed that the potential productivity of dry-season sorghum of this collection was strongly related to their staygreen characteristic; a trait of enormous importance in breeding for postflowering drought tolerance in sorghum. Plant height was highly heritable (91.9%), followed by the peduncle length (90.2%), panicle length (87.5%) and the internodes number (86.5%). Structuring of diversity separated the cultivars into four statistically distinct groups; with group 2 clustering cultivars with panicle productivity, early maturity and high staygreen, and other traits that contribute to the performance of cultivars. The findings will help to enhance the selection and production of dry-season sorghum in Chad and also provide alternative sources for staygreen introgression into the larger sorghum breeding community.
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Affiliation(s)
- Gapili Naoura
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Nerbewende Sawadogo
- Equipe Génétique et Amélioration des plantes, Laboratoire Biosciences, Université Ouaga I Pr Joseph KI-ZERBO 03 BP 7021, Ouagadougou, 03, Burkina Faso
| | | | - Yves Emendack
- USDA-ARS, Cropping Systems Research Laboratory, Lubbock, TX, USA.
| | - Mahamat A Hassan
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Djinodji Reoungal
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Doyam N Amos
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Nadjiam Djirabaye
- Institut Tchadien de Recherche Agronomique pour le Développement (ITRAD), B.P. 5400, N'Djaména, Tchad
| | - Ramadjita Tabo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, BP 320, Bamako, Mali
| | - Haydee Laza
- USDA-ARS, Cropping Systems Research Laboratory, Lubbock, TX, USA
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Rosati VC, Blomstedt CK, Møller BL, Garnett T, Gleadow R. The Interplay Between Water Limitation, Dhurrin, and Nitrate in the Low-Cyanogenic Sorghum Mutant adult cyanide deficient class 1. FRONTIERS IN PLANT SCIENCE 2019; 10:1458. [PMID: 31798611 PMCID: PMC6874135 DOI: 10.3389/fpls.2019.01458] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 10/21/2019] [Indexed: 05/27/2023]
Abstract
Sorghum bicolor (L.) Moench produces the nitrogen-containing natural product dhurrin that provides chemical defense against herbivores and pathogens via the release of toxic hydrogen cyanide gas. Drought can increase dhurrin in shoot tissues to concentrations toxic to livestock. As dhurrin is also a remobilizable store of reduced nitrogen and plays a role in stress mitigation, reductions in dhurrin may come at a cost to plant growth and stress tolerance. Here, we investigated the response to an extended period of water limitation in a unique EMS-mutant adult cyanide deficient class 1 (acdc1) that has a low dhurrin content in the leaves of mature plants. A mutant sibling line was included to assess the impact of unknown background mutations. Plants were grown under three watering regimes using a gravimetric platform, with growth parameters and dhurrin and nitrate concentrations assessed over four successive harvests. Tissue type was an important determinant of dhurrin and nitrate concentrations, with the response to water limitation differing between above and below ground tissues. Water limitation increased dhurrin concentration in the acdc1 shoots to the same extent as in wild-type plants and no growth advantage or disadvantage between the lines was observed. Lower dhurrin concentrations in the acdc1 leaf tissue when fully watered correlated with an increase in nitrate content in the shoot and roots of the mutant. In targeted breeding efforts to down-regulate dhurrin concentration, parallel effects on the level of stored nitrates should be considered in all vegetative tissues of this important forage crop to avoid potential toxic effects.
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Affiliation(s)
- Viviana C. Rosati
- School of Biological Sciences Faculty of Science Monash University, Clayton, Victoria, Australia
| | - Cecilia K. Blomstedt
- School of Biological Sciences Faculty of Science Monash University, Clayton, Victoria, Australia
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory and VILLUM Research Centre for Plant Plasticity, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Trevor Garnett
- The Australian Plant Phenomics Facility, The University of Adelaide, Adelaide, Australia
| | - Ros Gleadow
- School of Biological Sciences Faculty of Science Monash University, Clayton, Victoria, Australia
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Ohnishi N, Wacera W F, Sakamoto W. Photosynthetic Responses to High Temperature and Strong Light Suggest Potential Post-flowering Drought Tolerance of Sorghum Japanese Landrace Takakibi. PLANT & CELL PHYSIOLOGY 2019; 60:2086-2099. [PMID: 31147706 DOI: 10.1093/pcp/pcz107] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 05/20/2019] [Indexed: 05/09/2023]
Abstract
Sorghum [Sorghum bicolor (L.) Moench] is a C4 crop known to be adaptable to harsh environments such as those under high temperature and water deficit. In this study, we focused on a Japanese sorghum landrace Takakibi (NOG) and employed chlorophyll fluorescence measurements to assess its response to environmental stress. Comparison of photosynthetic rate evaluated using two parameters (effective quantum yield and electron transfer rate) indicated that NOG showed less activity than BTx623 in the pre-flowering stage, which was consistent with the higher susceptibility of NOG seedlings to drought than BTx623. The observed differences in photosynthetic activity between the two cultivars were detectable without drought conditions on days with high temperature and strong light. Interestingly, the photosynthetic activity of NOG leaves in stress conditions increased soon after heading, and the trend was similar to that in BTx642, a well-characterized post-flowering drought-tolerant cultivar. In contrast, BTx623 showed a gradual decline in photosynthetic rate. Thus, we inferred that Japanese Takakibi has the potential to show pre-flowering drought susceptibility and post-flowering drought tolerance, through which it adapts to local climates with high temperature and strong light at harvest.
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Affiliation(s)
- Norikazu Ohnishi
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, Japan
| | - Fiona Wacera W
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, Japan
| | - Wataru Sakamoto
- Institute of Plant Science and Resources, Okayama University, 2-20-1 Chuo, Kurashiki, Okayama, Japan
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22
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Schröder P, Sauvêtre A, Gnädinger F, Pesaresi P, Chmeliková L, Doğan N, Gerl G, Gökçe A, Hamel C, Millan R, Persson T, Ravnskov S, Rutkowska B, Schmid T, Szulc W, Teodosiu C, Terzi V. Discussion paper: Sustainable increase of crop production through improved technical strategies, breeding and adapted management - A European perspective. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 678:146-161. [PMID: 31075581 DOI: 10.1016/j.scitotenv.2019.04.212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 03/29/2019] [Accepted: 04/13/2019] [Indexed: 06/09/2023]
Abstract
During the next decade it will be necessary to develop novel combinations of management strategies to sustainably increase crop production and soil resilience. Improving agricultural productivity, while conserving and enhancing biotic and abiotic resources, is an essential requirement to increase global food production on a sustainable basis. The role of farmers in increasing agricultural productivity growth sustainably will be crucial. Farmers are at the center of any process of change involving natural resources and for this reason they need to be encouraged and guided, through appropriate incentives and governance practices, to conserve natural ecosystems and their biodiversity, and minimize the negative impact agriculture can have on the environment. Farmers and stakeholders need to revise traditional approaches not as productive as the modern approaches but more friendly with natural and environmental ecosystems values as well as emerging novel tools and approaches addressing precise farming, organic amendments, lowered water consumption, integrated pest control and beneficial plant-microbe interactions. While practical solutions are developing, science based recommendations for crop rotations, breeding and harvest/postharvest strategies leading to environmentally sound and pollinator friendly production and better life in rural areas have to be provided.
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Affiliation(s)
- Peter Schröder
- Helmholtz Zentrum München, Comparative Microbiome Analysis, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany.
| | - Andrés Sauvêtre
- Helmholtz Zentrum München, Comparative Microbiome Analysis, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Friederike Gnädinger
- Helmholtz Zentrum München, Comparative Microbiome Analysis, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Paolo Pesaresi
- University of Milan, Department of Biosciences, Via Celoria, 26, I-20133 Milano, Italy
| | - Lucie Chmeliková
- Technical University of Munich, Chair Organic Agriculture and Agronomy, Liesel Beckmann Str. 2, D-85354 Freising, Germany
| | - Nedim Doğan
- Adnan Menderes University, Department of Plant Protection, Bitki Koruma Bolumu, Aydin, Turkey
| | - Georg Gerl
- Helmholtz Zentrum München, Research Unit Environmental Simulation, Ingolstädter Landstrasse 1, D-85764 Neuherberg, Germany
| | - Ayhan Gökçe
- Niğde Ömer Halisdemir University, Faculty of Agricultural Sciences and Technologies, Niğde, Turkey
| | - Chantal Hamel
- Quebec Research and Development Centre, Agriculture and Agri-Food, 2560 Blvd. Hochelaga, Québec, QC G1V 2J3, Canada
| | - Rocio Millan
- CIEMAT, Environment Department/Soil Conservation and Recuperation Unit, Avenida Complutense 40, E-28040 Madrid, Spain
| | - Tomas Persson
- NIBIO-Norwegian Institute of Bioeconomy Research, Særheim, Postvegen 213, N-4353 Klepp Stasjon, Norway
| | - Sabine Ravnskov
- Dept. of Agroecology, Aarhus University, Forsøgsvej 1, DK-4200 Slagelse, Denmark
| | - Beata Rutkowska
- Warsaw University of Life Sciences - SGGW, Noworsynowska 166 St., P-02-787 Warsaw, Poland
| | - Thomas Schmid
- CIEMAT, Environment Department/Soil Conservation and Recuperation Unit, Avenida Complutense 40, E-28040 Madrid, Spain
| | - Wiesław Szulc
- Warsaw University of Life Sciences - SGGW, Noworsynowska 166 St., P-02-787 Warsaw, Poland
| | - Carmen Teodosiu
- Dept. Environmental Engineering & Management, "Gheorghe Asachi" Technical University of Iasi, 73 Prof.Dr. D. Mangeron Street, 700050 Iasi, Romania
| | - Valeria Terzi
- Genomics Research Centre, Via S. Protaso, 302, I-29017 Fiorenzuola d'Arda, PC, Italy
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Unraveling the genetic complexity underlying sorghum response to water availability. PLoS One 2019; 14:e0215515. [PMID: 30998785 PMCID: PMC6472798 DOI: 10.1371/journal.pone.0215515] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 02/28/2019] [Indexed: 11/19/2022] Open
Abstract
Understanding the adaptation mechanisms of sorghum to drought and the underlying genetic architecture may help to improve its production in a wide range of environments. By crossing a high yielding parent (HYP) and a drought tolerant parent (DTP), we obtained 140 recombinant inbred lines (RILs), which were genotyped with 120 DArT and SSR markers covering 14 linkage groups (LGs). A subset of 100 RILs was evaluated three times in control and drought treatments to genetically dissect their response to water availability. Plants with early heading date (HD) in the drought treatment maintained yield (YLD) level by reducing seed number SN and increasing hundred seed weight (HSW). In contrast, early HD in the control treatment increased SN, HSW and YLD. In total, 133 significant QTL associated with the measured traits were detected in ten hotspot regions. Antagonistic, pleiotropic effects of a QTL cluster mapped on LG-6 may explain the observed trade-offs between SN and HSW: Alleles from DTP reduced SN and the alleles from HYP increased HSW under drought stress, but not in the control treatment. Our results illustrate the importance of considering genetic and environmental factors in QTL mapping to better understand plant responses to drought and to improve breeding programs.
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24
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Bernardino KC, Pastina MM, Menezes CB, de Sousa SM, Maciel LS, Jr GC, Guimarães CT, Barros BA, da Costa e Silva L, Carneiro PCS, Schaffert RE, Kochian LV, Magalhaes JV. The genetic architecture of phosphorus efficiency in sorghum involves pleiotropic QTL for root morphology and grain yield under low phosphorus availability in the soil. BMC PLANT BIOLOGY 2019; 19:87. [PMID: 30819116 PMCID: PMC6394046 DOI: 10.1186/s12870-019-1689-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 02/19/2019] [Indexed: 05/18/2023]
Abstract
BACKGROUND Phosphorus (P) fixation on aluminum (Al) and iron (Fe) oxides in soil clays restricts P availability for crops cultivated on highly weathered tropical soils, which are common in developing countries. Hence, P deficiency becomes a major obstacle for global food security. We used multi-trait quantitative trait loci (QTL) mapping to study the genetic architecture of P efficiency and to explore the importance of root traits on sorghum grain yield on a tropical low-P soil. RESULTS P acquisition efficiency was the most important component of P efficiency, and both traits were highly correlated with grain yield under low P availability. Root surface area was positively associated with grain yield. The guinea parent, SC283, contributed 58% of all favorable alleles detected by single-trait mapping. Multi-trait mapping detected 14 grain yield and/or root morphology QTLs. Tightly linked or pleiotropic QTL underlying the surface area of fine roots (1-2 mm in diameter) and grain yield were detected at positions 1-7 megabase pairs (Mb) and 71 Mb on chromosome 3, respectively, and a root diameter/grain yield QTL was detected at 7 Mb on chromosome 7. All these QTLs were near sorghum homologs of the rice serine/threonine kinase, OsPSTOL1. The SbPSTOL1 genes on chromosome 3, Sb03g006765 at 7 Mb and Sb03g031690 at 60 Mb were more highly expressed in SC283, which donated the favorable alleles at all QTLs found nearby SbPSTOL1 genes. The Al tolerance gene, SbMATE, may also influence a grain yield QTL on chromosome 3. Another PSTOL1-like gene, Sb07g02840, appears to enhance grain yield via small increases in root diameter. Co-localization analyses suggested a role for other genes, such as a sorghum homolog of the Arabidopsis ubiquitin-conjugating E2 enzyme, phosphate 2 (PHO2), on grain yield advantage conferred by the elite parent, BR007 allele. CONCLUSIONS Genetic determinants conferring higher root surface area and slight increases in fine root diameter may favor P uptake, thereby enhancing grain yield under low-P availability in the soil. Molecular markers for SbPSTOL1 genes and for QTL increasing grain yield by non-root morphology-based mechanisms hold promise in breeding strategies aimed at developing sorghum cultivars adapted to low-P soils.
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Affiliation(s)
- Karine C. Bernardino
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
- Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Viçosa, MG 36570-900 Brazil
| | - Maria Marta Pastina
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
| | - Cícero B. Menezes
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
| | - Sylvia M. de Sousa
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
| | - Laiane S. Maciel
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Belo Horizonte, MG 31270-901 Brazil
| | - Geraldo Carvalho Jr
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
- Present Address: Helix Sementes, Rua Arnaldo Luiz de Oliveira, 75, Setor D, Bela Vista, Patos de Minas, MG 38703-240 Brazil
| | - Claudia T. Guimarães
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
| | - Beatriz A. Barros
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
| | - Luciano da Costa e Silva
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
| | - Pedro C. S. Carneiro
- Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n, Viçosa, MG 36570-900 Brazil
| | - Robert E. Schaffert
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
| | - Leon V. Kochian
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK S7N 4J8 Canada
| | - Jurandir V. Magalhaes
- Embrapa Milho e Sorgo, Rodovia MG 424, km 65, Caixa Postal 151, Sete Lagoas, MG 35701-970 Brazil
- Departamento de Biologia Geral, Universidade Federal de Minas Gerais, Avenida Presidente Antônio Carlos, 6627, Belo Horizonte, MG 31270-901 Brazil
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25
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Kamal NM, Gorafi YSA, Tsujimoto H, Ghanim AMA. Stay-Green QTLs Response in Adaptation to Post-Flowering Drought Depends on the Drought Severity. BIOMED RESEARCH INTERNATIONAL 2018; 2018:7082095. [PMID: 30584537 PMCID: PMC6280221 DOI: 10.1155/2018/7082095] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Accepted: 10/03/2018] [Indexed: 11/26/2022]
Abstract
Stay-green trait enhances sorghum adaptation to post-flowering drought. Six stay-green backcross introgression lines (BILs) carrying one or more stay-green QTLs (Stg1-4) and their parents were characterized under non-stress (W100: 100% of soil field capacity (FC)) and two levels of post-flowering drought (W75: 75% FC; W50: 50% FC) in a controlled condition. We aimed to study the response and identify the drought threshold of these QTLs under different levels of post-flowering drought and find traits closely contributing to grain yield (GY) under different drought severity. W50 caused the highest reduction in BILs performance. From W100 to W50, the GY of the recurrent parent reduced by 70%, whereas that of the BILs reduced by only 36%. W75 and W50 induce different behavior/response compared to W100. Harvest index contributed to the GY under the three water regimes. For high GY under drought transpiration rate at the beginning of drought and mid-grain filling was important at W75, whereas it was important at mid-grain filling and late-grain filling at W50. Stay-green trait can be scored simply with the relative number of green leaves/plants under both irrigated and stress environments. QTL pyramiding might not always be necessary to stabilize or increase the GY under post-flowering drought. The stay-green QTLs increase GY under drought by manipulating water utilization depending on drought severity.
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Affiliation(s)
- Nasrein Mohamed Kamal
- Biotechnology and Biosafety Research Center, Agricultural Research Corporation, P.O. Box 30, Shambat, Khartoum North, Sudan
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Yasir Serag Alnor Gorafi
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
- Agricultural Research Corporation, P.O. Box 126, Wad Medani, Sudan
| | - Hisashi Tsujimoto
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Abdelbagi Mukhtar Ali Ghanim
- Biotechnology and Biosafety Research Center, Agricultural Research Corporation, P.O. Box 30, Shambat, Khartoum North, Sudan
- Plant Breeding and Genetics Laboratory, FAO/IAEA Joint Division of Nuclear Techniques in Food and Agriculture, International Atomic Energy Agency (IAEA), Seibersdorf, Austria
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26
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Woldesemayat AA, Modise DM, Gemeildien J, Ndimba BK, Christoffels A. Cross-species multiple environmental stress responses: An integrated approach to identify candidate genes for multiple stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and related model species. PLoS One 2018; 13:e0192678. [PMID: 29590108 PMCID: PMC5873934 DOI: 10.1371/journal.pone.0192678] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 01/29/2018] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Crop response to the changing climate and unpredictable effects of global warming with adverse conditions such as drought stress has brought concerns about food security to the fore; crop yield loss is a major cause of concern in this regard. Identification of genes with multiple responses across environmental stresses is the genetic foundation that leads to crop adaptation to environmental perturbations. METHODS In this paper, we introduce an integrated approach to assess candidate genes for multiple stress responses across-species. The approach combines ontology based semantic data integration with expression profiling, comparative genomics, phylogenomics, functional gene enrichment and gene enrichment network analysis to identify genes associated with plant stress phenotypes. Five different ontologies, viz., Gene Ontology (GO), Trait Ontology (TO), Plant Ontology (PO), Growth Ontology (GRO) and Environment Ontology (EO) were used to semantically integrate drought related information. RESULTS Target genes linked to Quantitative Trait Loci (QTLs) controlling yield and stress tolerance in sorghum (Sorghum bicolor (L.) Moench) and closely related species were identified. Based on the enriched GO terms of the biological processes, 1116 sorghum genes with potential responses to 5 different stresses, such as drought (18%), salt (32%), cold (20%), heat (8%) and oxidative stress (25%) were identified to be over-expressed. Out of 169 sorghum drought responsive QTLs associated genes that were identified based on expression datasets, 56% were shown to have multiple stress responses. On the other hand, out of 168 additional genes that have been evaluated for orthologous pairs, 90% were conserved across species for drought tolerance. Over 50% of identified maize and rice genes were responsive to drought and salt stresses and were co-located within multifunctional QTLs. Among the total identified multi-stress responsive genes, 272 targets were shown to be co-localized within QTLs associated with different traits that are responsive to multiple stresses. Ontology mapping was used to validate the identified genes, while reconstruction of the phylogenetic tree was instrumental to infer the evolutionary relationship of the sorghum orthologs. The results also show specific genes responsible for various interrelated components of drought response mechanism such as drought tolerance, drought avoidance and drought escape. CONCLUSIONS We submit that this approach is novel and to our knowledge, has not been used previously in any other research; it enables us to perform cross-species queries for genes that are likely to be associated with multiple stress tolerance, as a means to identify novel targets for engineering stress resistance in sorghum and possibly, in other crop species.
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Affiliation(s)
- Adugna Abdi Woldesemayat
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Belleville, South Africa
- Department of Life and Consumer Sciences, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Florida, Johannesburg, South Africa
- * E-mail: ,
| | - David M. Modise
- Department of Agriculture and Animal Health, College of Agriculture and Environmental Sciences, University of South Africa, Science Campus, Florida, Johannesburg, South Africa
| | - Junaid Gemeildien
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Belleville, South Africa
| | - Bongani K. Ndimba
- Department of Biotechnology, University of the Western Cape, Cape Town, Western Cape, South Africa
- Agricultural Research Council, Infruitech-Nietvoorbij, Stellenbosch, South Africa
| | - Alan Christoffels
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Belleville, South Africa
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Naylor D, DeGraaf S, Purdom E, Coleman-Derr D. Drought and host selection influence bacterial community dynamics in the grass root microbiome. THE ISME JOURNAL 2017; 11:2691-2704. [PMID: 28753209 PMCID: PMC5702725 DOI: 10.1038/ismej.2017.118] [Citation(s) in RCA: 267] [Impact Index Per Article: 38.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/20/2017] [Accepted: 06/07/2017] [Indexed: 12/30/2022]
Abstract
Root endophytes have been shown to have important roles in determining host fitness under periods of drought stress, and yet the effect of drought on the broader root endosphere bacterial community remains largely uncharacterized. In this study, we present phylogenetic profiles of bacterial communities associated with drought-treated root and rhizosphere tissues of 18 species of plants with varying degrees of drought tolerance belonging to the Poaceae family, including important crop plants. Through 16S rRNA gene profiling across two distinct watering regimes and two developmental time points, we demonstrate that there is a strong correlation between host phylogenetic distance and the microbiome dissimilarity within root tissues, and that drought weakens this correlation by inducing conserved shifts in bacterial community composition. We identify a significant enrichment in a wide variety of Actinobacteria during drought within the roots of all hosts, and demonstrate that this enrichment is higher within the root than it is in the surrounding environments. Furthermore, we show that this observed enrichment is the result of an absolute increase in Actinobacterial abundance and that previously hypothesized mechanisms for observed enrichments in Actinobacteria in drought-treated soils are unlikely to fully account for the phenomena observed here within the plant root.
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Affiliation(s)
- Dan Naylor
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA, USA
- Plant Gene Expression Center, UC Berkeley, USDA-ARS, Albany, CA, USA
| | - Stephanie DeGraaf
- Department of Statistics, University of California, Berkeley, CA, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, 111 Koshland Hall, University of California, Berkeley, CA, USA
- Plant Gene Expression Center, UC Berkeley, USDA-ARS, Albany, CA, USA
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Briñez B, Perseguini JMKC, Rosa JS, Bassi D, Gonçalves JGR, Almeida C, Paulino JFDC, Blair MW, Chioratto AF, Carbonell SAM, Valdisser PAMR, Vianello RP, Benchimol-Reis LL. Mapping QTLs for drought tolerance in a SEA 5 x AND 277 common bean cross with SSRs and SNP markers. Genet Mol Biol 2017; 40:813-823. [PMID: 29064511 PMCID: PMC5738610 DOI: 10.1590/1678-4685-gmb-2016-0222] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 04/03/2017] [Indexed: 11/21/2022] Open
Abstract
The common bean is characterized by high sensitivity to drought and low productivity. Breeding for drought resistance in this species involves genes of different genetic groups. In this work, we used a SEA 5 x AND 277 cross to map quantitative trait loci associated with drought tolerance in order to assess the factors that determine the magnitude of drought response in common beans. A total of 438 polymorphic markers were used to genotype the F8 mapping population. Phenotyping was done in two greenhouses, one used to simulate drought and the other to simulate irrigated conditions. Fourteen traits associated with drought tolerance were measured to identify the quantitative trait loci (QTLs). The map was constructed with 331 markers that covered all 11 chromosomes and had a total length of 1515 cM. Twenty-two QTLs were discovered for chlorophyll, leaf and stem fresh biomass, leaf biomass dry weight, leaf temperature, number of pods per plant, number of seeds per plant, seed weight, days to flowering, dry pod weight and total yield under well-watered and drought (stress) conditions. All the QTLs detected under drought conditions showed positive effects of the SEA 5 allele. This study provides a better understanding of the genetic inheritance of drought tolerance in common bean.
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Affiliation(s)
- Boris Briñez
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico
(IAC), Campinas, SP, Brazil
| | - Juliana Morini Küpper Cardoso Perseguini
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico
(IAC), Campinas, SP, Brazil
- Ciências Biológicas, Universidade Tecnológica Federal do Paraná
(UTFPR), Dois Vizinhos, PR, Brazil
| | - Juliana Santa Rosa
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico
(IAC), Campinas, SP, Brazil
| | - Denis Bassi
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico
(IAC), Campinas, SP, Brazil
| | | | - Caléo Almeida
- Centro de Recursos Genéticos Vegetais, Instituto Agronômico
(IAC), Campinas, SP, Brazil
| | | | - Matthew Ward Blair
- Department of Agriculture and Natural Sciences, Tennessee State
University, Nashville, TN, USA
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Gorim L, Asch F. Seed Coating with Hydro-Absorbers as Potential Mitigation of Early Season Drought in Sorghum (Sorghum bicolor L. Moench). BIOLOGY 2017; 6:E33. [PMID: 28758977 PMCID: PMC5617921 DOI: 10.3390/biology6030033] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/20/2017] [Accepted: 07/21/2017] [Indexed: 11/25/2022]
Abstract
Climate change poses a threat to sorghum production systems by shifting the onset of the rainy season to a later date, increasing the risk of crop failure during crop establishment. The effects of drought on sorghum during seedling establishment have not been determined. Coating seeds with a water absorbing substance offers a way to buffer the seed against insufficient moisture in the surrounding soil. Seeds of two different sorghum varieties were coated with one of two commercially available hydro-absorbers: Stokosorb® and Geohumus®. These hydro-absorbers have the capacity to store water several times their own weight. The aim of this study was to compare the effects of the cited hydro-absorbers on early seedling growth of two sorghum landraces under different levels of soil water deficit. Seedlings were grown for 12 days under three water availability levels (Field capacity (FC), 50% of FC, and 25% of FC). The seedlings under water limited treatments were subsequently re-watered. Biomass, root length, plant height, leaf area, and leaf extension rate were monitored in two-day intervals for 24 days. Coating strongly affected seedling growth both under fully watered and water deficit conditions. Sorghum varieties differed in their responses to both soil water deficit and coating materials. In general, Stockosorb improved seedling performance under water limited conditions particularly by promoting root growth, whereas Geohumus did not.
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Affiliation(s)
- Linda Gorim
- 51 Campus Drive Saskatoon, Department of Plant Sciences College of Agriculture and Bioresources, University of Saskatchewan, SK S7N5A8, Canada.
| | - Folkard Asch
- Institute for Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute) Garbenstr. 13, University of Hohenheim, 70599 Stuttgart, Germany.
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Zhang L, Gezan SA, Eduardo Vallejos C, Jones JW, Boote KJ, Clavijo-Michelangeli JA, Bhakta M, Osorno JM, Rao I, Beebe S, Roman-Paoli E, Gonzalez A, Beaver J, Ricaurte J, Colbert R, Correll MJ. Development of a QTL-environment-based predictive model for node addition rate in common bean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1065-1079. [PMID: 28343247 DOI: 10.1007/s00122-017-2871-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 02/02/2017] [Indexed: 06/06/2023]
Abstract
This work reports the effects of the genetic makeup, the environment and the genotype by environment interactions for node addition rate in an RIL population of common bean. This information was used to build a predictive model for node addition rate. To select a plant genotype that will thrive in targeted environments it is critical to understand the genotype by environment interaction (GEI). In this study, multi-environment QTL analysis was used to characterize node addition rate (NAR, node day- 1) on the main stem of the common bean (Phaseolus vulgaris L). This analysis was carried out with field data of 171 recombinant inbred lines that were grown at five sites (Florida, Puerto Rico, 2 sites in Colombia, and North Dakota). Four QTLs (Nar1, Nar2, Nar3 and Nar4) were identified, one of which had significant QTL by environment interactions (QEI), that is, Nar2 with temperature. Temperature was identified as the main environmental factor affecting NAR while day length and solar radiation played a minor role. Integration of sites as covariates into a QTL mixed site-effect model, and further replacing the site component with explanatory environmental covariates (i.e., temperature, day length and solar radiation) yielded a model that explained 73% of the phenotypic variation for NAR with root mean square error of 16.25% of the mean. The QTL consistency and stability was examined through a tenfold cross validation with different sets of genotypes and these four QTLs were always detected with 50-90% probability. The final model was evaluated using leave-one-site-out method to assess the influence of site on node addition rate. These analyses provided a quantitative measure of the effects on NAR of common beans exerted by the genetic makeup, the environment and their interactions.
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Affiliation(s)
- Li Zhang
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, 32611, USA
| | - Salvador A Gezan
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, 32611, USA
| | - C Eduardo Vallejos
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - James W Jones
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, 32611, USA
| | - Kenneth J Boote
- Agronomy Department, University of Florida, Gainesville, FL, 32611, USA
| | | | - Mehul Bhakta
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Juan M Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | | | | | | | | | - James Beaver
- University of Puerto Rico, Mayagüez, 00682, Puerto Rico
| | | | - Raphael Colbert
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Melanie J Correll
- Agricultural and Biological Engineering Department, University of Florida, Gainesville, FL, 32611, USA.
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Simnadis TG, Tapsell LC, Beck EJ. Effect of sorghum consumption on health outcomes: a systematic review. Nutr Rev 2016; 74:690-707. [PMID: 27694643 DOI: 10.1093/nutrit/nuw036] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
CONTEXT Sorghum, an ancient grain originating in Africa, may have health-protective properties that could encourage its consumption among those who do not traditionally consume it. OBJECTIVE The aim of this systematic review was to evaluate the health effects associated with the consumption of sorghum among humans. DATA SOURCES Academic databases were searched for relevant studies published between 1985 and November 2015. STUDY SELECTION Nineteen studies -13 interventional and 6 observational - were identified for inclusion. DATA EXTRACTION Participant characteristics, study country, health outcomes, main findings, and study quality were reported. Interventional and observational studies were summarized separately. RESULTS Studies were divided into those that investigated the effect of sorghum on chronic disease and those that investigated other effects of sorghum on health. There was evidence that the consumption of sorghum attenuated blood glucose responses and decreased the expression of markers of oxidative stress. Sorghum was also observed to be a suitable ingredient for the formulation of oral rehydration solutions and showed potential for use as a medical adjunct to boost immune responses in HIV-positive patients CONCLUSIONS: The implication is that sorghum may have attributes superior to those of other staple grains, indicating its potential for innovative uses in commercial foods. More work is required to elucidate the health effects of sorghum when consumed by population groups that have not been traditional consumers of the grain.
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Affiliation(s)
- Thomas G Simnadis
- T.G. Simnadis, L.C. Tapsell, and E.J. Beck are with the School of Medicine, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Linda C Tapsell
- T.G. Simnadis, L.C. Tapsell, and E.J. Beck are with the School of Medicine, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia
| | - Eleanor J Beck
- T.G. Simnadis, L.C. Tapsell, and E.J. Beck are with the School of Medicine, Illawarra Health and Medical Research Institute, University of Wollongong, Wollongong, New South Wales, Australia
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Onogi A, Ideta O, Yoshioka T, Ebana K, Yamasaki M, Iwata H. Uncovering a Nuisance Influence of a Phenological Trait of Plants Using a Nonlinear Structural Equation: Application to Days to Heading and Culm Length in Asian Cultivated Rice (Oryza Sativa L.). PLoS One 2016; 11:e0148609. [PMID: 26859143 PMCID: PMC4747597 DOI: 10.1371/journal.pone.0148609] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2015] [Accepted: 01/20/2016] [Indexed: 12/17/2022] Open
Abstract
Phenological traits of plants, such as flowering time, are linked to growth phase transition. Thus, phenological traits often influence other traits through the modification of the duration of growth period. This influence is a nuisance in plant breeding because it hampers genetic evaluation of the influenced traits. Genetic effects on the influenced traits have two components, one that directly affects the traits and one that indirectly affects the traits via the phenological trait. These cannot be distinguished by phenotypic evaluation and ordinary linear regression models. Consequently, if a phenological trait is modified by introgression or editing of the responsible genes, the phenotypes of the influenced traits can change unexpectedly. To uncover the influence of the phenological trait and evaluate the direct genetic effects on the influenced traits, we developed a nonlinear structural equation (NSE) incorporating a nonlinear influence of the phenological trait. We applied the NSE to real data for cultivated rice (Oryza sativa L.): days to heading (DH) as a phenological trait and culm length (CL) as the influenced trait. This showed that CL of the cultivars that showed extremely early heading was shortened by the strong influence of DH. In a simulation study, it was shown that the NSE was able to infer the nonlinear influence and direct genetic effects with reasonable accuracy. However, the NSE failed to infer the linear influence in this study. When no influence was simulated, an ordinary bi-trait linear model (OLM) tended to infer the genetic effects more accurately. In such cases, however, by comparing the NSE and OLM using an information criterion, we could assess whether the nonlinear assumption of the NSE was appropriate for the data analyzed. This study demonstrates the usefulness of the NSE in revealing the phenotypic influence of phenological traits.
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Affiliation(s)
- Akio Onogi
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Osamu Ideta
- Western Region Agricultural Research Center, National Agriculture and Food Research Organization, Fukuyama, Hiroshima, Japan
| | - Takuma Yoshioka
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo, Japan
| | - Kaworu Ebana
- Genetic Resources Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Masanori Yamasaki
- Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Kasai, Hyogo, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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Albert E, Gricourt J, Bertin N, Bonnefoi J, Pateyron S, Tamby JP, Bitton F, Causse M. Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:395-418. [PMID: 26582510 DOI: 10.1007/s00122-015-2635-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 11/04/2015] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE In tomato, genotype by watering interaction resulted from genotype re-ranking more than scale changes. Interactive QTLs according to watering regime were detected. Differentially expressed genes were identified in some intervals. ABSTRACT As a result of climate change, drought will increasingly limit crop production in the future. Studying genotype by watering regime interactions is necessary to improve plant adaptation to low water availability. In cultivated tomato (Solanum lycopersicum L.), extensively grown in dry areas, well-mastered water deficits can stimulate metabolite production, increasing plant defenses and concentration of compounds involved in fruit quality, at the same time. However, few tomato Quantitative Trait Loci (QTLs) and genes involved in response to drought are identified or only in wild species. In this study, we phenotyped a population of 119 recombinant inbred lines derived from a cross between a cherry tomato and a large fruit tomato, grown in greenhouse under two watering regimes, in two locations. A large genetic variability was measured for 19 plant and fruit traits, under the two watering treatments. Highly significant genotype by watering regime interactions were detected and resulted from re-ranking more than scale changes. The population was genotyped for 679 SNP markers to develop a genetic map. In total, 56 QTLs were identified among which 11 were interactive between watering regimes. These later mainly exhibited antagonist effects according to watering treatment. Variation in gene expression in leaves of parental accessions revealed 2259 differentially expressed genes, among which candidate genes presenting sequence polymorphisms were identified under two main interactive QTLs. Our results provide knowledge about the genetic control of genotype by watering regime interactions in cultivated tomato and the possible use of deficit irrigation to improve tomato quality.
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Affiliation(s)
- Elise Albert
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Justine Gricourt
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Nadia Bertin
- INRA, UR 1115, Plante et Système de cultures Horticoles, 228 Route de l'aérodrome, Centre de Recherche PACA, Domaine Saint Paul, CS40509, 84914, Avignon Cedex 9, France
| | | | - Stéphanie Pateyron
- INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France
| | - Jean-Philippe Tamby
- INRA, Institut of Plant Sciences Paris-Saclay (IPS2), UMR 9213/UMR1403, CNRS, INRA, Université Paris-Sud, Université d'Evry, Université Paris-Diderot, Sorbonne Paris-Cité, Rue de Noetzlin, Plateau du Moulon, 91405, Orsay, France
| | - Frédérique Bitton
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, 67 Allée des chênes, Centre de Recherche PACA, Domaine Saint Maurice, CS60094, 84143, Montfavet, France.
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Back to Acid Soil Fields: The Citrate Transporter SbMATE Is a Major Asset for Sustainable Grain Yield for Sorghum Cultivated on Acid Soils. G3-GENES GENOMES GENETICS 2015; 6:475-84. [PMID: 26681519 PMCID: PMC4751565 DOI: 10.1534/g3.115.025791] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Aluminum (Al) toxicity damages plant roots and limits crop production on acid soils, which comprise up to 50% of the world’s arable lands. A major Al tolerance locus on chromosome 3, AltSB, controls aluminum tolerance in sorghum [Sorghum bicolor (L.) Moench] via SbMATE, an Al-activated plasma membrane transporter that mediates Al exclusion from sensitive regions in the root apex. As is the case with other known Al tolerance genes, SbMATE was cloned based on studies conducted under controlled environmental conditions, in nutrient solution. Therefore, its impact on grain yield on acid soils remains undetermined. To determine the real world impact of SbMATE, multi-trait quantitative trait loci (QTL) mapping in hydroponics, and, in the field, revealed a large-effect QTL colocalized with the Al tolerance locus AltSB, where SbMATE lies, conferring a 0.6 ton ha–1 grain yield increase on acid soils. A second QTL for Al tolerance in hydroponics, where the positive allele was also donated by the Al tolerant parent, SC283, was found on chromosome 9, indicating the presence of distinct Al tolerance genes in the sorghum genome, or genes acting in the SbMATE pathway leading to Al-activated citrate release. There was no yield penalty for AltSB, consistent with the highly localized Al regulated SbMATE expression in the root tip, and Al-dependent transport activity. A female effect of 0.5 ton ha–1 independently demonstrated the effectiveness of AltSB in hybrids. Al tolerance conferred by AltSB is thus an indispensable asset for sorghum production and food security on acid soils, many of which are located in developing countries.
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Vikram P, Swamy BPM, Dixit S, Singh R, Singh BP, Miro B, Kohli A, Henry A, Singh NK, Kumar A. Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits. Sci Rep 2015; 5:14799. [PMID: 26458744 PMCID: PMC4602206 DOI: 10.1038/srep14799] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/02/2015] [Indexed: 12/15/2022] Open
Abstract
Green Revolution (GR) rice varieties are high yielding but typically drought sensitive. This is partly due to the tight linkage between the loci governing plant height and drought tolerance. This linkage is illustrated here through characterization of qDTY1.1, a QTL for grain yield under drought that co-segregates with the GR gene sd1 for semi-dwarf plant height. We report that the loss of the qDTY1.1 allele during the GR was due to its tight linkage in repulsion with the sd1 allele. Other drought-yield QTLs (qDTY) also showed tight linkage with traits rejected in GR varieties. Genetic diversity analysis for 11 different qDTY regions grouped GR varieties separately from traditional drought-tolerant varieties, and showed lower frequency of drought tolerance alleles. The increased understanding and breaking of the linkage between drought tolerance and undesirable traits has led to the development of high-yielding drought-tolerant dwarf lines with positive qDTY alleles and provides new hope for extending the benefits of the GR to drought-prone rice-growing regions.
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Affiliation(s)
- Prashant Vikram
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - B. P. Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Shalabh Dixit
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Renu Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Bikram P. Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Berta Miro
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Ajay Kohli
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
| | - Amelia Henry
- Crop and Environmental Sciences Division, International Rice Research Institute, Los Baños, Philippines
| | - N. K. Singh
- National Research Center for Plant Biology, Indian Agricultural Research Institute, New Delhi, India 110012
| | - Arvind Kumar
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, Los Baños, Philippines
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Anami SE, Zhang L, Xia Y, Zhang Y, Liu Z, Jing H. Sweet sorghum ideotypes: genetic improvement of the biofuel syndrome. Food Energy Secur 2015. [DOI: 10.1002/fes3.63] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Affiliation(s)
- Sylvester Elikana Anami
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- Institute of Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya
| | - Li‐Min Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yan Xia
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yu‐Miao Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Zhi‐Quan Liu
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Hai‐Chun Jing
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
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Lasky JR, Upadhyaya HD, Ramu P, Deshpande S, Hash CT, Bonnette J, Juenger TE, Hyma K, Acharya C, Mitchell SE, Buckler ES, Brenton Z, Kresovich S, Morris GP. Genome-environment associations in sorghum landraces predict adaptive traits. SCIENCE ADVANCES 2015; 1:e1400218. [PMID: 26601206 PMCID: PMC4646766 DOI: 10.1126/sciadv.1400218] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 04/26/2015] [Indexed: 05/15/2023]
Abstract
Improving environmental adaptation in crops is essential for food security under global change, but phenotyping adaptive traits remains a major bottleneck. If associations between single-nucleotide polymorphism (SNP) alleles and environment of origin in crop landraces reflect adaptation, then these could be used to predict phenotypic variation for adaptive traits. We tested this proposition in the global food crop Sorghum bicolor, characterizing 1943 georeferenced landraces at 404,627 SNPs and quantifying allelic associations with bioclimatic and soil gradients. Environment explained a substantial portion of SNP variation, independent of geographical distance, and genic SNPs were enriched for environmental associations. Further, environment-associated SNPs predicted genotype-by-environment interactions under experimental drought stress and aluminum toxicity. Our results suggest that genomic signatures of environmental adaptation may be useful for crop improvement, enhancing germplasm identification and marker-assisted selection. Together, genome-environment associations and phenotypic analyses may reveal the basis of environmental adaptation.
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Affiliation(s)
- Jesse R. Lasky
- Earth Institute, and Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY 10025, USA
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- UWA Institute of Agriculture, University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Punna Ramu
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
| | - C. Tom Hash
- ICRISAT Sahelian Center, BP 12404, Niamey, Niger
| | - Jason Bonnette
- Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA
| | - Thomas E. Juenger
- Department of Integrative Biology, Institute for Cellular and Molecular Biology, and Brackenridge Field Laboratory, University of Texas at Austin, Austin, TX 78712, USA
| | - Katie Hyma
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Charlotte Acharya
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Sharon E. Mitchell
- Genomic Diversity Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA
| | - Edward S. Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA
- U.S. Department of Agriculture–Agricultural Research Service, Ithaca, NY 14853, USA
| | - Zachary Brenton
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Stephen Kresovich
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, USA
| | - Geoffrey P. Morris
- Department of Agronomy, Kansas State University, Manhattan, KS 66506, USA
- Corresponding author. E-mail:
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Anami SE, Zhang L, Xia Y, Zhang Y, Liu Z, Jing H. Sweet sorghum ideotypes: genetic improvement of stress tolerance. Food Energy Secur 2015. [DOI: 10.1002/fes3.54] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Sylvester Elikana Anami
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
- Institute of Biotechnology Research Jomo Kenyatta University of Agriculture and Technology Nairobi Kenya
| | - Li‐Min Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yan Xia
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Yu‐Miao Zhang
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Zhi‐Quan Liu
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
| | - Hai‐Chun Jing
- Key Laboratory of Plant Resources Institute of Botany Chinese Academy of Sciences Beijing 100093 China
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Farfan IDB, De La Fuente GN, Murray SC, Isakeit T, Huang PC, Warburton M, Williams P, Windham GL, Kolomiets M. Genome wide association study for drought, aflatoxin resistance, and important agronomic traits of maize hybrids in the sub-tropics. PLoS One 2015; 10:e0117737. [PMID: 25714370 PMCID: PMC4340625 DOI: 10.1371/journal.pone.0117737] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2013] [Accepted: 12/31/2014] [Indexed: 11/24/2022] Open
Abstract
The primary maize (Zea mays L.) production areas are in temperate regions throughout the world and this is where most maize breeding is focused. Important but lower yielding maize growing regions such as the sub-tropics experience unique challenges, the greatest of which are drought stress and aflatoxin contamination. Here we used a diversity panel consisting of 346 maize inbred lines originating in temperate, sub-tropical and tropical areas testcrossed to stiff-stalk line Tx714 to investigate these traits. Testcross hybrids were evaluated under irrigated and non-irrigated trials for yield, plant height, ear height, days to anthesis, days to silking and other agronomic traits. Irrigated trials were also inoculated with Aspergillus flavus and evaluated for aflatoxin content. Diverse maize testcrosses out-yielded commercial checks in most trials, which indicated the potential for genetic diversity to improve sub-tropical breeding programs. To identify genomic regions associated with yield, aflatoxin resistance and other important agronomic traits, a genome wide association analysis was performed. Using 60,000 SNPs, this study found 10 quantitative trait variants for grain yield, plant and ear height, and flowering time after stringent multiple test corrections, and after fitting different models. Three of these variants explained 5-10% of the variation in grain yield under both water conditions. Multiple identified SNPs co-localized with previously reported QTL, which narrows the possible location of causal polymorphisms. Novel significant SNPs were also identified. This study demonstrated the potential to use genome wide association studies to identify major variants of quantitative and complex traits such as yield under drought that are still segregating between elite inbred lines.
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Affiliation(s)
- Ivan D. Barrero Farfan
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Gerald N. De La Fuente
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Seth C. Murray
- Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas, United States of America
| | - Thomas Isakeit
- Department of Plant Pathology, Texas A&M University, College Station, Texas, United States of America
| | - Pei-Cheng Huang
- Department of Plant Pathology, Texas A&M University, College Station, Texas, United States of America
| | - Marilyn Warburton
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, Mississippi, United States of America
| | - Paul Williams
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, Mississippi, United States of America
| | - Gary L. Windham
- USDA ARS Corn Host Plant Resistance Research Unit, Mississippi State, Mississippi, United States of America
| | - Mike Kolomiets
- Department of Plant Pathology, Texas A&M University, College Station, Texas, United States of America
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Rama Reddy NR, Ragimasalawada M, Sabbavarapu MM, Nadoor S, Patil JV. Detection and validation of stay-green QTL in post-rainy sorghum involving widely adapted cultivar, M35-1 and a popular stay-green genotype B35. BMC Genomics 2014; 15:909. [PMID: 25326366 PMCID: PMC4219115 DOI: 10.1186/1471-2164-15-909] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Accepted: 09/24/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Sorghum [Sorghum bicolor (L.) Moench] is an important dry-land cereal of the world providing food, fodder, feed and fuel. Stay-green (delayed-leaf senescence) is a key attribute in sorghum determining its adaptation to terminal drought stress. The objective of this study was to validate sorghum stay-green quantitative trait loci (QTL) identified in the past, and to identify new QTL in the genetic background of a post-rainy adapted genotype M35-1. RESULTS A genetic linkage map based on 245 F9 Recombinant Inbred Lines (RILs) derived from a cross between M35-1 (more senescent) and B35 (less senescent) with 237 markers consisting of 174 genomic, 60 genic and 3 morphological markers was used. The phenotypic data collected for three consecutive post-rainy crop seasons on the RIL population (M35-1 × B35) was used for QTL analysis. Sixty-one QTL were identified for various measures of stay-green trait and each trait was controlled by one to ten QTL. The phenotypic variation explained by each QTL ranged from 3.8 to 18.7%. Co-localization of QTL for more than five traits was observed on two linkage groups i.e. on SBI-09-3 flanked by S18 and Xgap206 markers and, on SBI-03 flanked by XnhsbSFCILP67 and Xtxp31. QTL identified in this study were stable across environments and corresponded to sorghum stay-green and grain yield QTL reported previously. Of the 60 genic SSRs mapped, 14 were closely linked with QTL for ten traits. A genic marker, XnhsbSFCILP67 (Sb03g028240) encoding Indole-3-acetic acid-amido synthetase GH3.5, was co-located with QTL for GLB, GLM, PGLM and GLAM on SBI-03. Genes underlying key enzymes of chlorophyll metabolism were also found in the stay-green QTL regions. CONCLUSIONS We validated important stay-green QTL reported in the past in sorghum and detected new QTL influencing the stay-green related traits consistently. Stg2, Stg3 and StgB were prominent in their expression. Collectively, the QTL/markers identified are likely candidates for subsequent verification for their involvement in stay-green phenotype using NILs and to develop drought tolerant sorghum varieties through marker-assisted breeding for terminal drought tolerance in sorghum.
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Affiliation(s)
- Nagaraja Reddy Rama Reddy
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
- />ICAR-Directorate of Medicinal and Aromatic Plants Research (DMAPR), Anand, Gujarat 387 310 India
| | - Madhusudhana Ragimasalawada
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
| | - Murali Mohan Sabbavarapu
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
| | - Seetharama Nadoor
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
| | - Jagannatha Vishnu Patil
- />Marker-assisted selection Lab, ICAR-Directorate of Sorghum Research (DSR), Rajendranagar, Hyderabad, 500 030 India
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42
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El-Soda M, Malosetti M, Zwaan BJ, Koornneef M, Aarts MGM. Genotype×environment interaction QTL mapping in plants: lessons from Arabidopsis. TRENDS IN PLANT SCIENCE 2014; 19:390-8. [PMID: 24491827 DOI: 10.1016/j.tplants.2014.01.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Revised: 12/23/2013] [Accepted: 01/06/2014] [Indexed: 05/23/2023]
Abstract
Plant growth and development are influenced by the genetic composition of the plant (G), the environment (E), and the interaction between them (G×E). To produce suitable genotypes for multiple environments, G×E should be accounted for and assessed in plant-breeding programs. Here, we review the genetic basis of G×E and its consequence for quantitative trait loci (QTL) mapping in biparental and genome-wide association (GWA) mapping populations. We also consider the implications of G×E for understanding plant fitness trade-offs and evolutionary ecology.
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Affiliation(s)
- Mohamed El-Soda
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Department of Genetics, Faculty of Agriculture, Cairo University, Giza, 12613, Egypt
| | - Marcos Malosetti
- Biometris - Applied Statistics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Bas J Zwaan
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maarten Koornneef
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands; Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, D-50829 Cologne, Germany
| | - Mark G M Aarts
- Laboratory of Genetics, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands.
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O'Donnell NH, Møller BL, Neale AD, Hamill JD, Blomstedt CK, Gleadow RM. Effects of PEG-induced osmotic stress on growth and dhurrin levels of forage sorghum. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2013; 73:83-92. [PMID: 24080394 DOI: 10.1016/j.plaphy.2013.09.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 09/05/2013] [Indexed: 05/27/2023]
Abstract
Sorghum (Sorghum bicolor L. Moench) is a valuable forage crop in regions with low soil moisture. Sorghum may accumulate high concentrations of the cyanogenic glucoside dhurrin when drought stressed resulting in possible cyanide (HCN) intoxication of grazing animals. In addition, high concentrations of nitrate, also potentially toxic to ruminants, may accumulate during or shortly after periods of drought. Little is known about the degree and duration of drought-stress required to induce dhurrin accumulation, or how changes in dhurrin concentration are influenced by plant size or nitrate metabolism. Given that finely regulating soil moisture under controlled conditions is notoriously difficult, we exposed sorghum plants to varying degrees of osmotic stress by growing them for different lengths of time in hydroponic solutions containing polyethylene glycol (PEG). Plants grown in medium containing 20% PEG (-0.5 MPa) for an extended period had significantly higher concentrations of dhurrin in their shoots but lower dhurrin concentrations in their roots. The total amount of dhurrin in the shoots of plants from the various treatments was not significantly different on a per mass basis, although a greater proportion of shoot N was allocated to dhurrin. Following transfer from medium containing 20% PEG to medium lacking PEG, shoot dhurrin concentrations decreased but nitrate concentrations increased to levels potentially toxic to grazing ruminants. This response is likely due to the resumption of plant growth and root activity, increasing the rate of nitrate uptake. Data presented in this article support a role for cyanogenic glucosides in mitigating oxidative stress.
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Affiliation(s)
- Natalie H O'Donnell
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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Des Marais DL, Hernandez KM, Juenger TE. Genotype-by-Environment Interaction and Plasticity: Exploring Genomic Responses of Plants to the Abiotic Environment. ANNUAL REVIEW OF ECOLOGY EVOLUTION AND SYSTEMATICS 2013. [DOI: 10.1146/annurev-ecolsys-110512-135806] [Citation(s) in RCA: 256] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- David L. Des Marais
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
| | - Kyle M. Hernandez
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
| | - Thomas E. Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712;
- Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas 78712
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45
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Malosetti M, Ribaut JM, van Eeuwijk FA. The statistical analysis of multi-environment data: modeling genotype-by-environment interaction and its genetic basis. Front Physiol 2013; 4:44. [PMID: 23487515 PMCID: PMC3594989 DOI: 10.3389/fphys.2013.00044] [Citation(s) in RCA: 147] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 02/25/2013] [Indexed: 12/04/2022] Open
Abstract
Genotype-by-environment interaction (GEI) is an important phenomenon in plant breeding. This paper presents a series of models for describing, exploring, understanding, and predicting GEI. All models depart from a two-way table of genotype by environment means. First, a series of descriptive and explorative models/approaches are presented: Finlay–Wilkinson model, AMMI model, GGE biplot. All of these approaches have in common that they merely try to group genotypes and environments and do not use other information than the two-way table of means. Next, factorial regression is introduced as an approach to explicitly introduce genotypic and environmental covariates for describing and explaining GEI. Finally, QTL modeling is presented as a natural extension of factorial regression, where marker information is translated into genetic predictors. Tests for regression coefficients corresponding to these genetic predictors are tests for main effect QTL expression and QTL by environment interaction (QEI). QTL models for which QEI depends on environmental covariables form an interesting model class for predicting GEI for new genotypes and new environments. For realistic modeling of genotypic differences across multiple environments, sophisticated mixed models are necessary to allow for heterogeneity of genetic variances and correlations across environments. The use and interpretation of all models is illustrated by an example data set from the CIMMYT maize breeding program, containing environments differing in drought and nitrogen stress. To help readers to carry out the statistical analyses, GenStat® programs, 15th Edition and Discovery® version, are presented as “Appendix.”
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Affiliation(s)
- Marcos Malosetti
- Biometris - Applied Statistics, Department of Plant Science, Wageningen University Wageningen, Netherlands
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46
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Tuberosa R. Phenotyping for drought tolerance of crops in the genomics era. Front Physiol 2012; 3:347. [PMID: 23049510 PMCID: PMC3446691 DOI: 10.3389/fphys.2012.00347] [Citation(s) in RCA: 181] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2012] [Accepted: 08/09/2012] [Indexed: 12/11/2022] Open
Abstract
Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.
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Affiliation(s)
- Roberto Tuberosa
- Department of Agroenvironmental Science and Technology, University of BolognaBologna, Italy
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