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Oteng-Frimpong R, Karikari B, Sie EK, Kassim YB, Puozaa DK, Rasheed MA, Fonceka D, Okello DK, Balota M, Burow M, Ozias-Akins P. Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut ( Arachis hypogaea L.) germplasm. FRONTIERS IN PLANT SCIENCE 2023; 13:1076744. [PMID: 36684745 PMCID: PMC9849250 DOI: 10.3389/fpls.2022.1076744] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.
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Affiliation(s)
- Richard Oteng-Frimpong
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Benjamin Karikari
- Department of Agricultural Biotechnology, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, Tamale, Ghana
| | - Emmanuel Kofi Sie
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Yussif Baba Kassim
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Doris Kanvenaa Puozaa
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Masawudu Abdul Rasheed
- Groundnut Improvement Program, Council for Scientific and Industrial Research (CSIR)-Savanna Agricultural Research Institute, Tamale, Ghana
| | - Daniel Fonceka
- Centre d’Etude Régional pour l’Amélioration de l’Adaptation àla Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Thiès, Senegal
| | - David Kallule Okello
- Oil Crops Research Program, National Semi-Arid Resources Research Institute (NaSARRI), Soroti, Uganda
| | - Maria Balota
- School of Plant and Environmental Sciences, Tidewater Agricultural Research and Extension Center (AREC), Virginia Tech, Suffolk, VA, United States
| | - Mark Burow
- Texas A&M AgriLife Research and Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, United States
| | - Peggy Ozias-Akins
- Institute of Plant Breeding Genetics and Genomics, University of Georgia, Tifton, GA, United States
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Ma B, Nian L, Ain NU, Liu X, Yang Y, Zhu X, Haider FU, Lv Y, Bai P, Zhang X, Li Q, Mao Z, Xue Z. Genome-Wide Identification and Expression Profiling of the SRS Gene Family in Melilotus albus Reveals Functions in Various Stress Conditions. PLANTS (BASEL, SWITZERLAND) 2022; 11:3101. [PMID: 36432830 PMCID: PMC9693462 DOI: 10.3390/plants11223101] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/06/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
The plant-specific SHI-related sequence (SRS) family of transcription factors plays a vital role in growth regulation, plant development, phytohormone biosynthesis, and stress response. However, the genome-wide identification and role in the abiotic stress-related functions of the SRS gene family were not reported in white sweet clover (Melilotus albus). In this study, nine M. albus SRS genes (named MaSRS01-MaSRS09) were identified via a genome-wide search method. All nine genes were located on six out of eight chromosomes in the genome of M. albus and duplication analysis indicated eight segmentally duplicated genes in the MaSRS family. These MaSRS genes were classified into six groups based on their phylogenetic relationships. The gene structure and motif composition results indicated that MaSRS members in the same group contained analogous intron/exon and motif organizations. Further, promoter region analysis of MaSRS genes uncovered various growth, development, and stress-responsive cis-acting elements. Protein interaction networks showed that each gene has both functions of interacting with other genes and members within the family. Moreover, real-time quantitative PCR was also performed to verify the expression patterns of nine MaSRS genes in the leaves of M. albus. The results showed that nine MaSRSs were up- and down-regulated at different time points after various stress treatments, such as salinity, low-temperature, salicylic acid (SA), and methyl jasmonate (MeJA). This is the first systematic study of the M. albus SRS gene family, and it can serve as a strong foundation for further elucidation of the stress response and physiological improvement of the growth functions in M. albus.
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Affiliation(s)
- Biao Ma
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Lili Nian
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Noor ul Ain
- Centre of Genomics and Biotechnology, Fujian Agriculture and Forestry University, Jinshan, Fuzhou 350002, China
| | - Xuelu Liu
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Yingbo Yang
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Fasih Ullah Haider
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100039, China
| | - Ying Lv
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Pengpeng Bai
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Xiaoning Zhang
- College of Forestry, Gansu Agricultural University, Lanzhou 730070, China
| | - Quanxi Li
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Zixuan Mao
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
| | - Zongyang Xue
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou 730070, China
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Li Y, Liu X, Xiao Y, Wen Y, Li K, Ma Z, Yang L, Zhu Y, Yin J. Genome-wide characterization and function analysis uncovered roles of wheat LIMs in responding to adverse stresses and TaLIM8-4D function as a susceptible gene. THE PLANT GENOME 2022; 15:e20246. [PMID: 35894660 DOI: 10.1002/tpg2.20246] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 06/14/2022] [Indexed: 05/27/2023]
Abstract
The Lin-11, Isl-1, and Mec-3 domains (LIM) transcription factors play essential roles in regulating plant biological processes. Despite that, there is a lack of a full understanding of LIMs in wheat (Triticum aestivum L.). In this study, 28 wheat LIM s (TaLIMs) were identified and designated as TaLIM1-1A to TaLIM12-7D. The cis-regulatory element analysis showed that TaLIMs were rich in elements related to biological and abiotic stresses. Expression profiling analysis showed that certain members of TaLIMs were responsive to biotic and abiotic stresses, such as TaLIM1-1A, TaLIM3-2B, TaLIM8-4D, and TaLIM10-5D, were significantly induced by heat, drought, sodium chloride (NaCl), abscisic acid (ABA) and Fusarium graminearum stresses. Furthermore, the biological function of TaLIM8-4D was analyzed and results showed that it was subcellular localization in the nucleus and could induce weak cell death in Nicotiana benthamiana leaves. Additionally, overexpression of TaLIM8-4D could upregulate plant pathogenesis-related (PR) genes, promoting the infection of hemibiotrophic pathogen, implying that TaLIM8-4D could function as susceptible gene in the nucleus by upregulating PR genes and inducing cell death to promote the colonization of hemibiotrophic agent F. graminearum. Overall, the systematic identification, characterization, expression profiling, evolutionary, and function analyses provided the ability to understand TaLIMs and laid a foundation for the further function study of LIM family members in wheat.
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Affiliation(s)
- Yiting Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Xi Liu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Yongxin Xiao
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Yong Wen
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Keke Li
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Zhaolan Ma
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Lijun Yang
- Key Laboratory of Integrated Pest Management of Crops in Central China, Ministry of Agriculture/Hubei Key Laboratory of Crop Diseases, Insect Pests and Weeds Control, Institute of Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences, Wuhan, Hubei, 430064, China
| | - Yongxing Zhu
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
| | - Junliang Yin
- Hubei Key Laboratory of Waterlogging Disaster and Agricultural Use of Wetland/College of Agriculture/College of Horticulture and Gardening, Yangtze Univ., Jingzhou, Hubei, 434025, China
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Wei Y, Lu X, Bao J, Zhang C, Yan H, Li K, Gong M, Li S, Ma S. Identification and expression analysis of chlorophyll a/b binding protein gene family in grape ( Vitis vinifera). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1147-1158. [PMID: 35910436 PMCID: PMC9334500 DOI: 10.1007/s12298-022-01204-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 06/27/2022] [Accepted: 06/27/2022] [Indexed: 06/01/2023]
Abstract
UNLABELLED In higher plants, light capture of chlorophyll a/b binding protein (Lhc) plays a crucial role in the plant's response to adverse environment. So far, the family has not been systematically identified in grapes. In this study, 20 VvLhcs were identified in the grape genome, which were distributed in 13 of 19 grape chromosomes and divided into 7 developing branches. The results of gene duplication analysis showed that 6 VvLhcs formed fragment duplication events, while there was no tandem duplication in VvLhcs. Exon-intron structure analysis showed that they had a wide number of exons. Protein conserved motif analysis showed that VvLhcs contained more similar motif structures in the same phylogenetic branch. The cis-acting elements in the VvLhcs promoter region mainly respond to light, plant hormones and abiotic stresses. In addition, qRT-PCR results showed that different proportions of salt stress and red-blue light affected the expression of VvLhcs and the expression patterns of genes in different grape varieties were different. The results for further study on different grape varieties in different combinations of red and blue light of the Lhc provide a theoretical basis. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-022-01204-5.
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Affiliation(s)
- Yunchun Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xu Lu
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Jinyu Bao
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Congcong Zhang
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Haokai Yan
- College of Horticulture, Gansu Agricultural University, Lanzhou, 730070 China
| | - Kang Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Meishuang Gong
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
| | - Sheng Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Lab of Arid Land Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Shaoying Ma
- Basical Experimental Teaching Center, Gansu Agricultural University, Lanzhou, 730070 China
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Basu D, South PF. Design and Analysis of Native Photorespiration Gene Motifs of Promoter Untranslated Region Combinations Under Short Term Abiotic Stress Conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:828729. [PMID: 35251099 PMCID: PMC8888687 DOI: 10.3389/fpls.2022.828729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/18/2022] [Indexed: 05/09/2023]
Abstract
Quantitative traits are rarely controlled by a single gene, thereby making multi-gene transformation an indispensable component of modern synthetic biology approaches. However, the shortage of unique gene regulatory elements (GREs) for the robust simultaneous expression of multiple nuclear transgenes is a major bottleneck that impedes the engineering of complex pathways in plants. In this study, we compared the transcriptional efficacies of a comprehensive list of well-documented promoter and untranslated region (UTR) sequences side by side. The strength of GREs was examined by a dual-luciferase assay in conjunction with transient expression in tobacco. In addition, we created suites of new GREs with higher transcriptional efficacies by combining the best performing promoter-UTR sequences. We also tested the impact of elevated temperature and high irradiance on the effectiveness of these GREs. While constitutive promoters ensure robust expression of transgenes, they lack spatiotemporal regulations exhibited by native promoters. Here, we present a proof-of-principle study on the characterization of synthetic promoters based on cis-regulatory elements of three key photorespiratory genes. This conserved biochemical process normally increases under elevated temperature, low CO2, and high irradiance stress conditions and results in ∼25% loss in fixed CO2. To select stress-responsive cis-regulatory elements involved in photorespiration, we analyzed promoters of two chloroplast transporters (AtPLGG1 and AtBASS6) and a key plastidial enzyme, AtPGLP using PlantPAN3.0 and AthaMap. Our results suggest that these motifs play a critical role for PLGG1, BASS6, and PGLP in mediating response to elevated temperature and high-intensity light stress. These findings will not only enable the advancement of metabolic and genetic engineering of photorespiration but will also be instrumental in related synthetic biology approaches.
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Affiliation(s)
| | - Paul F. South
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
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Zhu X, Wang B, Wang X, Zhang C, Wei X. Genome-wide identification, characterization and expression analysis of the LIM transcription factor family in quinoa. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:787-800. [PMID: 33967462 PMCID: PMC8055757 DOI: 10.1007/s12298-021-00988-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/28/2021] [Accepted: 04/03/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED Lim family members play an important role in the regulation of plant cell development and stress response. However, there are few studies on LIM family in quinoa. In this study, we identified nine LIMS (named cqlim01-cqlim09) from quinoa, which were divided into three subfamilies (α Lim1, γ lim2 and δ lim2) according to phylogeny. The differences in gene structure and motif composition among different subfamilies have been observed. In addition, we studied the repetitive events of the members of the family. The Ka/Ks (non synchronous substitution rate / synchronous substitution rate) ratio analysis showed that the repetitive CqLIMs probably experienced purifying selection pressure. Promoter analysis showed that the family genes contained a variety of hormones, stress and tissue-specific expression elements, and protein interactions showed that these genes had actin stabilizing effect. In addition, QRT PCR results showed that all CqLIM genes were positively regulated under three stresses (low temperature, salt and ABA). These results provide a theoretical basis of further study of LIM gene in quinoa. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-00988-2.
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Affiliation(s)
- Xiaolin Zhu
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Baoqiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xian Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Chaoyang Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
| | - Xiaohong Wei
- College of Agronomy, Gansu Agricultural University, Lanzhou, 730070 China
- Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, 730070 China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070 China
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