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Zhao N, Yuan R, Usman B, Qin J, Yang J, Peng L, Mackon E, Liu F, Qin B, Li R. Detection of QTLs Regulating Six Agronomic Traits of Rice Based on Chromosome Segment Substitution Lines of Common Wild Rice ( Oryza rufipogon Griff.) and Mapping of qPH1.1 and qLMC6.1. Biomolecules 2022; 12:biom12121850. [PMID: 36551278 PMCID: PMC9775987 DOI: 10.3390/biom12121850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/06/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022] Open
Abstract
Wild rice is a primary source of genes that can be utilized to generate rice cultivars with advantageous traits. Chromosome segment substitution lines (CSSLs) are consisting of a set of consecutive and overlapping donor chromosome segments in a recipient's genetic background. CSSLs are an ideal genetic population for mapping quantitative traits loci (QTLs). In this study, 59 CSSLs from the common wild rice (Oryza rufipogon Griff.) accession DP15 under the indica rice cultivar (O. sativa L. ssp. indica) variety 93-11 background were constructed through multiple backcrosses and marker-assisted selection (MAS). Through high-throughput whole genome re-sequencing (WGRS) of parental lines, 12,565 mapped InDels were identified and designed for polymorphic molecular markers. The 59 CSSLs library covered 91.72% of the genome of common wild rice accession DP15. The DP15-CSSLs displayed variation in six economic traits including grain length (GL), grain width (GW), thousand-grain weight (TGW), grain length-width ratio (GLWR), plant height (PH), and leaf margin color (LMC), which were finally attributed to 22 QTLs. A homozygous CSSL line and a purple leave margin CSSL line were selected to construct two secondary genetic populations for the QTLs mapping. Thus, the PH-controlling QTL qPH1.1 was mapped to a region of 4.31-Mb on chromosome 1, and the LMC-controlling QTL qLMC6.1 was mapped to a region of 370-kb on chromosome 6. Taken together, these identified novel QTLs/genes from common wild rice can potentially promote theoretical knowledge and genetic applications to rice breeders worldwide.
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Affiliation(s)
- Neng Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Ruizhi Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Babar Usman
- Graduate School of Green-Bio Science and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
| | - Jiaming Qin
- Maize Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
| | - Jinlian Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Liyun Peng
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Enerand Mackon
- State Key Laboratory of Conservation and Utilization of Subtropical Agro-Bioresources, College of Life Science and Technology, Guangxi University, Nanning 530005, China
| | - Fang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Baoxiang Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
| | - Rongbai Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Agriculture, Guangxi University, Nanning 530004, China
- Correspondence:
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Khanna A, Anumalla M, Catolos M, Bartholomé J, Fritsche-Neto R, Platten JD, Pisano DJ, Gulles A, Sta Cruz MT, Ramos J, Faustino G, Bhosale S, Hussain W. Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines. RICE (NEW YORK, N.Y.) 2022; 15:14. [PMID: 35247120 PMCID: PMC8898209 DOI: 10.1186/s12284-022-00559-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Estimating genetic trends using historical data is an important parameter to check the success of the breeding programs. The estimated genetic trends can act as a guideline to target the appropriate breeding strategies and optimize the breeding program for improved genetic gains. In this study, 17 years of historical data from IRRI's rice drought breeding program was used to estimate the genetic trends and assess the breeding program's success. We also identified top-performing lines based on grain yield breeding values as an elite panel for implementing future population improvement-based breeding schemes. A two-stage approach of pedigree-based mixed model analysis was used to analyze the data and extract the breeding values and estimate the genetic trends for grain yield under non-stress, drought, and in combined data of non-stress and drought. Lower grain yield values were observed in all the drought trials. Heritability for grain yield estimates ranged between 0.20 and 0.94 under the drought trials and 0.43-0.83 under non-stress trials. Under non-stress conditions, the genetic gain of 0.21% (10.22 kg/ha/year) for genotypes and 0.17% (7.90 kg/ha/year) for checks was observed. The genetic trend under drought conditions exhibited a positive trend with the genetic gain of 0.13% (2.29 kg/ha/year) for genotypes and 0.55% (9.52 kg/ha/year) for checks. For combined analysis showed a genetic gain of 0.27% (8.32 kg/ha/year) for genotypes and 0.60% (13.69 kg/ha/year) for checks was observed. For elite panel selection, 200 promising lines were selected based on higher breeding values for grain yield and prediction accuracy of > 0.40. The breeding values of the 200 genotypes formulating the core panel ranged between 2366.17 and 4622.59 (kg/ha). A positive genetic rate was observed under all the three conditions; however, the rate of increase was lower than the required rate of 1.5% genetic gain. We propose a recurrent selection breeding strategy within the elite population with the integration of modern tools and technologies to boost the genetic gains in IRRI's drought breeding program. The elite breeding panel identified in this study forms an easily available and highly enriched genetic resource for future recurrent selection programs to boost the genetic gains.
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Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Jérôme Bartholomé
- AGAP Institute, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Roberto Fritsche-Neto
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - John Damien Platten
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Daniel Joseph Pisano
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Alaine Gulles
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Joie Ramos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Gem Faustino
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
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Fernandes T, Melo F, Vieira MB, Lourenço TF, Pucciariello C, Saibo NJM, Abreu IA, Oliveira MM. Screening for Abiotic Stress Response in Rice. Methods Mol Biol 2022; 2494:161-194. [PMID: 35467207 DOI: 10.1007/978-1-0716-2297-1_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rice (Oryza sativa L.) is the staple food for over half of the world population. However, most rice varieties are severely injured by abiotic stresses, with strong social and economic impacts. Understanding rice responses to stress may guide breeding for more tolerant varieties. However, the lack of consistency in the design of the stress experiments described in the literature limits comparative studies and output assessments. The use of identical setups is the only way to generate comparable data. This chapter comprises three sections, describing the experimental conditions established at the Genomics of Plant Stress (GPlantS) unit of ITQB NOVA to assess the response of rice plants to different abiotic stresses-high salinity, cold, drought, simulated drought, and submergence-and their recovery capacity when intended. All sections include a detailed description of the materials and methodology and useful notes gathered from our team experience. We use seedlings since rice plants at this stage show high sensitivity to abiotic stresses. For the salt, cold, and simulated drought (PEG, polyethylene glycol) stress assays, we grow rice seedlings in a hydroponic system, while for the drought assay, plants are grown in soil and subjected to water withholding. For submergence, we use water-filled Magenta boxes. All setups enable visual score determination and are suitable for sample collection during stress imposition and also recovery. The proposed methodologies are affordable and straightforward to implement in most labs, allowing the discrimination of several rice genotypes at the molecular and phenotypic levels.
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Affiliation(s)
- Telma Fernandes
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Fredilson Melo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Maria Beatriz Vieira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Tiago F Lourenço
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Chiara Pucciariello
- PlantLab, Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy
| | - Nelson J M Saibo
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - Isabel A Abreu
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit, Oeiras, Portugal.
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Hussain T, Hussain N, Ahmed M, Nualsri C, Duangpan S. Responses of Lowland Rice Genotypes under Terminal Water Stress and Identification of Drought Tolerance to Stabilize Rice Productivity in Southern Thailand. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122565. [PMID: 34961039 PMCID: PMC8706981 DOI: 10.3390/plants10122565] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 05/11/2023]
Abstract
Lowland rice is an important cereal crop that plays a key role in the food security and the economy of Thailand. Terminal water stress (TWS) in rainfed lowland areas poses threats to rice productivity due to stress occurrence at terminal crop stages and extreme sensitivity of rice to TWS. A two-year study was conducted to characterize the performance of yield and yield attributes of twelve Thai lowland rice genotypes under TWS, to identify stress-tolerant genotypes using stress response indices and to identify promising stress indices which are correlated with grain yield (GY) under well-watered (WW) and TWS conditions for their use as rapid identifiers in a rice crop breeding program for enhancing drought stress tolerance. Measurements were recorded under WW and TWS conditions. Highly significant variations were observed amongst assessed genotypes for their yield productivity responses. According to stress response indices, genotypes were categorized into stress-tolerant and stress susceptible genotypes. Genotypes Hom Pathum, Sang Yod, Dum Ja and Pathum Thani-1 were found highly stress tolerant and relatively high yielding; genotypes Look Pla and Lep Nok were stress tolerant, whereas genotypes Chor Lung, Hom Nang Kaew and Hom Chan were moderately tolerant genotypes. Hence, stress-tolerant genotypes could be potentially used for cultivation under rainfed and water-limited conditions, where TWS is predicted particularly in southern Thailand to stabilize rice productivity. Stress tolerance indices, including stress tolerance index (STI), geometric mean productivity (GMP), mean productivity index (MPRO) and harmonic mean index (MHAR), indicated strong and positive associations with GY under WW and TWS; thus, these indices could be used to indicate stress tolerance in rice crop breeding program aimed at a rapid screening of lowland rice genotypes for stress tolerance.
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Affiliation(s)
- Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Songkhla 90110, Thailand; (T.H.); (N.H.)
| | - Nurda Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Songkhla 90110, Thailand; (T.H.); (N.H.)
- Energy Technology Program, Faculty of Engineering, Prince of Songkla University, Songkhla 90110, Thailand
| | - Mukhtar Ahmed
- Department of Agronomy, Faculty of Crop and Food Sciences, PMAS Arid Agriculture University, Rawalpindi 46300, Punjab, Pakistan;
| | - Charassri Nualsri
- Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Songkhla 90110, Thailand;
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Songkhla 90110, Thailand; (T.H.); (N.H.)
- Correspondence: ; Tel.: +66-74-286-138
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Dar JS, Cheema MA, Rehmani MIA, Khuhro S, Rajput S, Virk AL, Hussain S, Bashir MA, Alghanem SM, Al-Zuaibr FM, Ansari MJ, Hessini K. Potassium fertilization improves growth, yield and seed quality of sunflower (Helianthus annuus L.) under drought stress at different growth stages. PLoS One 2021; 16:e0256075. [PMID: 34543316 PMCID: PMC8452053 DOI: 10.1371/journal.pone.0256075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/31/2021] [Indexed: 11/18/2022] Open
Abstract
Water scarcity is a major concern for sunflower production in the semi-arid and arid regions of the world. Potassium (K) application has been found effective to alleviate the influence of drought stress; however, the impact of drought stress on seed quality of sunflower has not been reported frequently. Therefore, a field experiment was performed to determine the optimum K requirement for mitigating the adverse effects of water stress and improving growth and seed quality of spring-planted sunflower. Sunflower plants were exposed to water stress at different growth stages, i.e., Io = no stress (normal irrigation), I1 = pre-anthesisi stress (irrigation skipped at pre-anthesis stage), I2 = anthesis stress (irrigation skipped at anthesis stage) and I3 = post-anthesis stress (irrigation skipped at post-anthesis stage). Potassium was applied at four different rates, i.e., Ko = 0, K1 = 50, K2 = 100 and K3 = 150 kg ha-1. The results revealed that water stress at pre- and post-anthesis stages significantly reduced plant height, head diameter, number of achenes, oleic acid contents, and phosphorus (P) uptake. However, pre-anthesis stress improved linoleic acid contents. Treatment IoK3 (stress-free with 150 kg ha-1 K) was optimum combination for 1000-achene weight, biological and achene yields, oil contents, protein contents, and N and P uptake. Results indicated that a higher amount of K and irrigation resulted in higher yield, whereas yield and yield components decreased with early-stage water stress. Nevertheless, potassium application lowered the impacts of waters stress compared to no application. Keeping in view these results, it is recommended that sunflower must be supplied 150 kg ha-1 K in arid and semi-arid regions to achieve higher yield and better seed quality.
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Affiliation(s)
| | - Mumtaz Akhtar Cheema
- School of Science and the Environment, Memorial University of Newfoundland, Corner Brook, Newfoundland and Labrador, Canada
| | | | | | | | - Ahmad Latif Virk
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Sajid Hussain
- Institute of Hydrobiology, Chinese Academy of Science, Wuhan, China
| | - Muhammad Amjad Bashir
- Department of Plant Protection Faculty of Agricultural Sciences, Ghazi University, Dera Ghazi Khan Punjab, Pakistan
| | - Suliman M. Alghanem
- Department of Biology Faculty of Science, Tabuk University, Tabuk, Saudia Arabia
| | | | - Mohammad Javed Ansari
- Department of Botany, Hindu College Moradabad (Mahatma Jyotiba Phule Rohilkhand University Bareilly), Moradabad, India
| | - Kamel Hessini
- Department of Biology, College of Sciences, Taif University, Taif, Saudi Arabia
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Pei X, Wang X, Fu G, Chen B, Nazir MF, Pan Z, He S, Du X. Identification and functional analysis of 9-cis-epoxy carotenoid dioxygenase (NCED) homologs in G. hirsutum. Int J Biol Macromol 2021; 182:298-310. [PMID: 33811933 DOI: 10.1016/j.ijbiomac.2021.03.154] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 03/19/2021] [Accepted: 03/23/2021] [Indexed: 11/20/2022]
Abstract
9-cis-epoxy carotenoid dioxygenase (NCED) is a fundamental enzyme, which plays an essential role in the process of organ development and stress resistance by regulating abscisic acid (ABA) synthesis in plant. In this study, a total of 7, 7, 14 and 14 NCED genes were identified from the genomes of G. arboreum, G. raimondii, G. barbadense and G. hirsutum, respectively. Phylogenetic tree showed that all forty-two NCED genes could be classified into three groups in cotton genus. Collinear analysis revealed that the NCED genes in G. hirsutum were not amplified by tandem repeats after polyploidy events. The function of NCED genes was evaluated between two accessions with contrasting plant height. The results showed that expression of the NCED genes in dwarf accession was higher than that in taller ones. GhNCED1-silenced cotton plants confirmed that suppression of NCED genes could increase the plant height, but reduce the resistance abilities to drought and salt stress. Our study systematically identified the homologs of NCED genes and their functions in cotton, which could provide new genetic resources for improving plant height and stress in future cotton breeding.
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Affiliation(s)
- Xinxin Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Xiaoyang Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Guoyong Fu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Baojun Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Mian Faisal Nazir
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
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Melo FV, Oliveira MM, Saibo NJM, Lourenço TF. Modulation of Abiotic Stress Responses in Rice by E3-Ubiquitin Ligases: A Promising Way to Develop Stress-Tolerant Crops. FRONTIERS IN PLANT SCIENCE 2021; 12:640193. [PMID: 33833769 PMCID: PMC8021960 DOI: 10.3389/fpls.2021.640193] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/17/2021] [Indexed: 05/25/2023]
Abstract
Plants are unable to physically escape environmental constraints and have, therefore, evolved a range of molecular and physiological mechanisms to maximize survival in an ever-changing environment. Among these, the post-translational modification of ubiquitination has emerged as an important mechanism to understand and improve the stress response. The ubiquitination of a given protein can change its abundance (through degradation), alter its localization, or even modulate its activity. Hence, ubiquitination increases the plasticity of the plant proteome in response to different environmental cues and can contribute to improve stress tolerance. Although ubiquitination is mediated by different enzymes, in this review, we focus on the importance of E3-ubiquitin ligases, which interact with the target proteins and are, therefore, highly associated with the mechanism specificity. We discuss their involvement in abiotic stress response and place them as putative candidates for ubiquitination-based development of stress-tolerant crops. This review covers recent developments in this field using rice as a reference for crops, highlighting the questions still unanswered.
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Çulha Erdal Ş, Eyidoğan F, Ekmekçi Y. Comparative physiological and proteomic analysis of cultivated and wild safflower response to drought stress and re-watering. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:281-295. [PMID: 33707869 PMCID: PMC7907392 DOI: 10.1007/s12298-021-00934-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 12/01/2020] [Accepted: 01/13/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Drought is one of the major environmental stress that adversely affect the growth and development of oil seed plant, safflower. There is a limited knowledge on proteomic responses to support physiological, biochemical changes in how safflowers can regulate growth and metabolism under drought conditions and followed by re-watering. The changes in morphological, physiological, biochemical and proteomics of safflower genotypes (Carthamus tinctorius L.; Remzibey-05 and Linas, tolerant and sensitive cultivars, respectively, and C. oxyacantha M. Bieb., wild type) after exposure to drought and followed by re-watering have been examined. Drought negatively affected the shoot weight, water content, chlorophyll fluorescence, and biochemical parameters, including photosynthetic pigment, proline, MDA, and H2O2 contents and antioxidant enzyme activities in all genotypes, while the re-watering period allowed Remzibey-05 to recover, and it even provided the wild type completely recovered (approximately 100%). A total of 72 protein spots were observed as differently accumulated under treatments. The identified proteins were mainly involved in photosynthesis and carbohydrate, protein, defense, and energy metabolisms. Protein accumulation related to these metabolisms in Remzibey-05 were decreased under drought, while increased following re-watering. However, sensitive cultivar, Linas, could not exhibit an effective performance under drought and recovery when compared with other safflower genotypes. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at (10.1007/s12298-021-00934-2).
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Affiliation(s)
- Şeküre Çulha Erdal
- Faculty of Science, Department of Biology, Hacettepe University, 06800 Ankara, Turkey
| | - Füsun Eyidoğan
- Faculty of Education, Department of Elementary Education, Başkent University, 06810 Ankara, Turkey
| | - Yasemin Ekmekçi
- Faculty of Science, Department of Biology, Hacettepe University, 06800 Ankara, Turkey
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Chen L, Czechowski T, Graham IA, Hartley SE. Impact of osmotic stress on the growth and root architecture of introgression lines derived from a wild ancestor of rice and a modern cultivar. PLANT-ENVIRONMENT INTERACTIONS (HOBOKEN, N.J.) 2020; 1:122-133. [PMID: 37283730 PMCID: PMC10168093 DOI: 10.1002/pei3.10026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/03/2020] [Accepted: 07/14/2020] [Indexed: 06/08/2023]
Abstract
Many modern rice varieties have been intensively selected for high-yielding performance under irrigated conditions, reducing their genetic diversity and potentially increasing their susceptibility to abiotic stresses such as drought. In this study, we tested benefits for stress tolerance of introducing DNA segments from wild ancestor Oryza rufipogon to the modern cultivar O. sativa cv Curinga (CUR) by applying a gradient of osmotic stress to both parents and seven introgressed lines. Shoot growth of O. rufipogon had a high tolerance to osmotic stress, and the number of total root tips increased under mild osmotic stress. One introgression line showed greater shoot growth, root growth, and higher number of total root tips than the parent line CUR under osmotic stress. Abscisic acid (ABA) is a key hormone mediating plant responses to abiotic stresses. Both root and shoot growth of O. rufipogon were much more sensitive to ABA than CUR. Introgression lines varied in the extent to which the sensitivity of their growth responses to ABA and some lines correlated with their sensitivity to osmotic stress. Our results suggest that rice responses to ABA and osmotic stress are genotype dependent, and growth responses of rice to ABA are not a consistent indicator of resilience to abiotic stress in introgression lines.
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Affiliation(s)
- Lin Chen
- Department of BiologyUniversity of YorkYorkUK
| | | | | | - Sue E. Hartley
- Department of BiologyUniversity of YorkYorkUK
- Present address:
Department of Animal and Plant SciencesUniversity of SheffieldSheffieldS10 2TNUK
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Sabar M, Shabir G, Shah SM, Aslam K, Naveed SA, Arif M. Identification and mapping of QTLs associated with drought tolerance traits in rice by a cross between Super Basmati and IR55419-04. BREEDING SCIENCE 2019; 69:169-178. [PMID: 31086495 PMCID: PMC6507710 DOI: 10.1270/jsbbs.18068] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Accepted: 11/30/2018] [Indexed: 05/19/2023]
Abstract
Water stress, in a climate change scenario is one of the major threats for sustainable rice productivity. Combining drought resistance with yield and desirable economic traits is the most promising solution for the researchers. Although several studies resulted in the identification of QTLs for drought resistance in rice, but none of them serve as a milestone. Therefore, there is always a quest to find the new QTLs. The present investigation was carried out to map QTLs involved in drought resistance and yield related parameter in a cross of IR55419-04 and Super Basmati. An F2 population of 418 individuals was used as the mapping population. The raised nursery was transplanted in lyzimeters. Two extreme sets of tolerant (23 Nos.) and sensitive (23 Nos.) individuals were selected based on total water uptake under water stress conditions. Two hundred thirty microsatellite markers staggered on the whole genome were used for identifying polymorphic markers between the two parents. The selected 73 polymorphic microsatellites were used to genotype individuals and were scattered on a distance of 1735 cM on all 12 linkage groups. QTL analysis was performed by using the WinQTL Cartographer 2.5 V. A total of 21 QTLs were detected using composite interval mapping. The QTLs relating to drought tolerance at the vegetative stage were found on chromosome 1. Novel genomic regions were detected in the marker interval RM520-RM143 and RM168-RM520. The region has a significant QTL qTWU3.1 for total water uptake. Root morphological trait QTLs were found on chromosome 3. QTLs responsible for additive effects were due to the alleles of the IR55419-04. These novel QTLs can be used for marker assisted breeding to develop new drought-tolerant rice varieties and fine mapping can be used to explore the functional relationship between the QTLs and phenotypic traits.
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Affiliation(s)
- Muhammad Sabar
- Rice Research Institute, Kala Shah Kaku,
Lahore,
Pakistan
| | - Ghulam Shabir
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University,
Multan,
Pakistan
| | - Shahid Masood Shah
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad Campus,
Abbottabad, 22010,
Pakistan
- Corresponding author (e-mail: )
| | - Kashif Aslam
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University,
Multan,
Pakistan
| | - Shahzad Amir Naveed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences,
Beijing,
China
| | - Muhammad Arif
- National Institute for Biotechnology and Genetic Engineering (NIBGE),
Faisalabad, 38000,
Pakistan
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A High-Density EST-SSR-Based Genetic Map and QTL Analysis of Dwarf Trait in Cucurbita pepo L. Int J Mol Sci 2018; 19:ijms19103140. [PMID: 30322052 PMCID: PMC6213718 DOI: 10.3390/ijms19103140] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 10/06/2018] [Accepted: 10/10/2018] [Indexed: 11/17/2022] Open
Abstract
As one of the earliest domesticated species, Cucurbita pepo (including squash and pumpkin) is rich in phenotypic polymorphism and has huge economic value. In this research, using 1660 expressed sequence tags-simple sequence repeats (EST-SSRs) and 632 genomic simple sequence repeats (gSSRs), we constructed the highest-density EST-SSR-based genetic map in Cucurbita genus, which spanned 2199.1 cM in total and harbored 623 loci distributed in 20 linkage groups. Using this map as a bridge, the two previous gSSR maps were integrated by common gSSRs and the corresponding relationships around chromosomes in three sets of genomes were also collated. Meanwhile, one large segmental inversion that existed between our map and the C. pepo genome was detected. Furthermore, three Quantitative Trait Loci (QTLs) of the dwarf trait (gibberellin-sensitive dwarf type) in C. pepo were located, and the candidate region that covered the major QTL spanned 1.39 Mb, which harbored a predicted gibberellin 2-β-oxidase gene. Considering the rich phenotypic polymorphism, the important economic value in the Cucurbita genus species and several advantages of the SSR marker were identified; thus, this high-density EST-SSR-based genetic map will be useful in Pumpkin and Squash breeding work in the future.
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12
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Brew-Appiah RAT, Sanguinet KA. Considerations of AOX Functionality Revealed by Critical Motifs and Unique Domains. Int J Mol Sci 2018; 19:ijms19102972. [PMID: 30274246 PMCID: PMC6213860 DOI: 10.3390/ijms19102972] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 09/14/2018] [Accepted: 09/28/2018] [Indexed: 12/28/2022] Open
Abstract
An understanding of the genes and mechanisms regulating environmental stress in crops is critical for boosting agricultural yield and safeguarding food security. Under adverse conditions, response pathways are activated for tolerance or resistance. In multiple species, the alternative oxidase (AOX) genes encode proteins which help in this process. Recently, this gene family has been extensively investigated in the vital crop plants, wheat, barley and rice. Cumulatively, these three species and/or their wild ancestors contain the genes for AOX1a, AOX1c, AOX1e, and AOX1d, and common patterns in the protein isoforms have been documented. Here, we add more information on these trends by emphasizing motifs that could affect expression, and by utilizing the most recent discoveries from the AOX isoform in Trypanosoma brucei to highlight clade-dependent biases. The new perspectives may have implications on how the AOX gene family has evolved and functions in monocots. The common or divergent amino acid substitutions between these grasses and the parasite are noted, and the potential effects of these changes are discussed. There is the hope that the insights gained will inform the way future AOX research is performed in monocots, in order to optimize crop production for food, feed, and fuel.
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Affiliation(s)
- Rhoda A T Brew-Appiah
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
| | - Karen A Sanguinet
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164-6420, USA.
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