1
|
Bhatia N, Tiwari JK, Kumari C, Zinta R, Sharma S, Buckseth T, Thakur AK, Singh RK, Kumar V. Transcriptome analysis reveals genes associated with late blight resistance in potato. Sci Rep 2024; 14:15501. [PMID: 38969681 PMCID: PMC11226683 DOI: 10.1038/s41598-024-60608-3] [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: 01/21/2024] [Accepted: 04/25/2024] [Indexed: 07/07/2024] Open
Abstract
Late blight is a serious disease of potato worldwide. Our study aimed to unveil genes involved in late blight resistance in potato by RNA-seq analysis after artificial inoculation under controlled conditions. In this study, two potato somatic hybrids (P7 and Crd6) and three varieties such as Kufri Girdhari, Kufri Jyoti and Kufri Bahar (control) were used. Transcriptiome analysis revealed statistically significant (p < 0.05) differentially expressed genes (DEGs), which were analysed into up-regulated and down-regulated genes. Further, DEGs were functionally characterized by the Gene Ontology annotations and the Kyoto Encyclopedia of Genes and Genomes pathways. Overall, some of the up-regulated genes in resistant genotypes were disease resistance proteins such as CC-NBS-LRR resistance protein, ankyrin repeat family protein, cytochrome P450, leucine-rich repeat family protein/protein kinase family, and MYB transcription factor. Sequence diversity analysis based on 38 peptide sequences representing 18 genes showed distinct variation and the presence of three motifs in 15 amino acid sequences. Selected genes were also validated by real-time quantitative polymerase chain reaction analysis. Interestingly, gene expression markers were developed for late blight resistant genotypes. Our study elucidates genes involved in imparting late blight resistance in potato, which will be beneficial for its management strategies in the future.
Collapse
Affiliation(s)
- Nisha Bhatia
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Jagesh Kumar Tiwari
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India.
- ICAR-Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India.
| | - Chandresh Kumari
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Rasna Zinta
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sanjeev Sharma
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay K Thakur
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh K Singh
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Vinod Kumar
- ICAR-Central Potato Research Institute, Shimla, Himachal Pradesh, India
| |
Collapse
|
2
|
Basso MF, Contaldi F, Lo Celso F, Baratto CM, Grossi-de-Sa MF, Barone G, Ferrante A, Martinelli F. Identification and expression profile of the SMAX/SMXL family genes in chickpea and lentil provide important players of biotechnological interest involved in plant branching. PLANTA 2023; 259:1. [PMID: 37966555 PMCID: PMC10651550 DOI: 10.1007/s00425-023-04277-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 10/28/2023] [Indexed: 11/16/2023]
Abstract
MAIN CONCLUSION SMAX/SMXL family genes were successfully identified and characterized in the chickpea and lentil and gene expression data revealed several genes associated with the modulation of plant branching and powerful targets for use in transgenesis and genome editing. Strigolactones (SL) play essential roles in plant growth, rooting, development, and branching, and are associated with plant resilience to abiotic and biotic stress conditions. Likewise, karrikins (KAR) are "plant smoke-derived molecules" that act in a hormonal signaling pathway similar to SL playing an important role in seed germination and hairy root elongation. The SMAX/SMXL family genes are part of these two signaling pathways, in addition to some of these members acting in a still little known SL- and KAR-independent signaling pathway. To date, the identification and functional characterization of the SMAX/SMXL family genes has not been performed in the chickpea and lentil. In this study, nine SMAX/SMXL genes were systematically identified and characterized in the chickpea and lentil, and their expression profiles were explored under different unstressless or different stress conditions. After a comprehensive in silico characterization of the genes, promoters, proteins, and protein-protein interaction network, the expression profile for each gene was determined using a meta-analysis from the RNAseq datasets and complemented with real-time PCR analysis. The expression profiles of the SMAX/SMXL family genes were very dynamic in different chickpea and lentil organs, with some genes assuming a tissue-specific expression pattern. In addition, these genes were significantly modulated by different stress conditions, indicating that SMAX/SMXL genes, although working in three distinct signaling pathways, can act to modulate plant resilience. Most CaSMAX/SMXL and partner genes such as CaTiE1 and CaLAP1, have a positive correlation with the plant branching level, while most LcSMAX/SMXL genes were less correlated with the plant branching level. The SMXL6, SMXL7, SMXL8, TiE1, LAP1, BES1, and BRC1 genes were highlighted as powerful targets for use in transgenesis and genome editing aiming to develop chickpea and lentil cultivars with improved architecture. Therefore, this study presented a detailed characterization of the SMAX/SMXL genes in the chickpea and lentil, and provided new insights for further studies focused on each SMAX/SMXL gene.
Collapse
Affiliation(s)
| | - Felice Contaldi
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy
| | - Fabrizio Lo Celso
- Department of Physics and Chemical, University of Palermo, Viale Delle Scienze, Edificio 17, 90128, Palermo, Italy
| | - César Milton Baratto
- University of Western Santa Catarina, Biotechnological Center, UNOESC, Videira, SC, 89566-252, Brazil
| | | | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale Delle Scienze, Edificio 17, 90128, Palermo, Italy
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, University of Milan, Via Festa del Perdono, 20122, Milan, Italy
| | - Federico Martinelli
- Department of Biology, University of Florence, 50019, Sesto Fiorentino, Italy.
| |
Collapse
|
3
|
Basso MF, Contaldi F, Celso FL, Karalija E, Paz-Carrasco LC, Barone G, Ferrante A, Martinelli F. Expression profile of the NCED/CCD genes in chickpea and lentil during abiotic stress reveals a positive correlation with increased plant tolerance. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111817. [PMID: 37562731 DOI: 10.1016/j.plantsci.2023.111817] [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: 03/23/2023] [Revised: 07/28/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023]
Abstract
Carotenoid cleavage dioxygenase (CCD) gene family is organized in two subfamilies: (i) 9-cis epoxycarotenoid dioxygenase (NCED) genes and (ii) CCD genes. NCED genes are essential for catalyzing the first step of the abscisic-acid (ABA) biosynthesis, while CCD genes produce precursors of the strigolactones hormone. The functional characterization of these gene subfamilies has not been yet performed in chickpea and lentil. Herein, were identified and systematically characterized two NCED and five CCD genes in the chickpea and two NCED and six CCD genes in lentil. After in silico sequence analysis and phylogeny, the expression profile of the NCED/CCD genes was determined by meta-analysis and real-time PCR in plants under different stress conditions. Sequence data revealed that NCED/CCD genes are highly conserved between chickpea and lentil. This conservation was observed both at gene and protein sequence levels and phylogenetic relationships. Analysis of the promoter sequences revealed that all NCED/CCD genes have a considerable number of cis-regulatory elements responsive to biotic and abiotic stress. Protein sequence analysis evidenced that NCED/CCD genes share several conserved motifs and that they have a highly interconnected interaction network. Furthermore, the three-dimensional structure of these proteins was determined and indicated that some proteins have structures with considerable similarity. The meta-analysis revealed that NCED/CCD genes are dynamically modulated in different organs and under different stress conditions, but they have a positive correlation with plant tolerance. In accordance, real-time PCR data showed that both NCED and CCD genes are differentially modulated in plants under drought stress. In particular, CaNCED2, CaCCD5, LcNCED2, LcCCD1, and LcCCD2 genes have a positive correlation with improved plant tolerance to drought stress. Therefore, this study presented a detailed characterization of the chickpea and lentil NCED/CCD genes and provided new insights to improve abiotic stress tolerance in these two important crops.
Collapse
Affiliation(s)
- Marcos Fernando Basso
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy; University of Western Santa Catarina, Biotechnological Center, UNOESC, Videira, SC 89566-252, Brazil
| | - Felice Contaldi
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy
| | - Fabrizio Lo Celso
- Department of Physics and Chemical, University of Palermo, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | - Erna Karalija
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy; Department of Biology, Faculty of science, University of Sarajevo, Zmaja od Bosne 33-35, 71000 Sarajevo, Bosnia and Herzegovina
| | - Lenin Celiano Paz-Carrasco
- National Institute of Agricultural Research (INIAP), Plant Pathology Department and Rice Breeding Program, Km 26 vía Duran-Tambo, Yaguachi, Guayas, Ecuador
| | - Giampaolo Barone
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Viale delle Scienze, Edificio 17, 90128 Palermo, Italy
| | - Antonio Ferrante
- Department of Agricultural and Environmental Sciences, Università degli Studi di Milano, Via Celoria 2, 20133 Milan, Italy
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino 50019, Florence, Italy.
| |
Collapse
|
4
|
Bhatia N, Tiwari JK, Kumari C, Zinta R, Sharma S, Thakur AK, Buckseth T, Dalamu D, Singh RK, Kumar V. Screening of wild species and transcriptome profiling to identify differentially regulated genes in response to late blight resistance in potato. FRONTIERS IN PLANT SCIENCE 2023; 14:1212135. [PMID: 37502703 PMCID: PMC10368984 DOI: 10.3389/fpls.2023.1212135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 06/27/2023] [Indexed: 07/29/2023]
Abstract
Late blight (Phytophthora infestans) is a serious disease of potatoes. The aim of this study was to screen wild potato species and identify differentially expressed genes (DEGs) associated with late blight resistance. Wild potato species such as PIN45 (Solanum pinnatisectum), CPH62 (Solanum cardiophyllum), JAM07 (Solanum jamesii), MCD24 (Solanum microdontum), PLD47 (Solanum polyadenium), and cv. Kufri Bahar (control) were tested by artificial inoculation of P. infestans under controlled conditions. Transcriptomes of the leaf tissues (96 h post-inoculation) were sequenced using the Illumina platform. Statistically significant (p < 0.05) DEGs were analyzed in wild species by comparison with the control, and upregulated (>2 log2 fold change, FC) and downregulated (<-2 log2 FC) genes were identified. DEGs were functionally characterized with Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Selected genes were validated by real-time PCR analysis to confirm RNA-seq results. We identified some upregulated genes associated with late blight resistance in wild species such as cytochrome P450, proline-rich protein, MYB transcription factor MYB139, ankyrin repeat-containing protein, and LRR receptor-like serine/threonine-protein kinase in PIN45; glucosyltransferase, fructose-bisphosphate aldolase, and phytophthora-inhibited protease 1 in CPH62; steroid binding protein and cysteine proteinase 3 in JAM07; glycine-rich cell wall structural protein 1 and RING finger protein in MCD24; and cysteine proteinase 3 and major latex protein in PLD47. On the other hand, downregulated genes in these species were snakin-2 and WRKY transcription factor 3 in PIN45; lichenase and phenylalanine ammonia-lyase 1 in CPH62; metallothionein and LRR receptor-like serine/threonine-protein kinase in JAM07; UDP-glucoronosyl/UDP-glucosyl transferase family protein and steroid binding protein in MCD24; and cytoplasmic small heat shock protein class I and phosphatase PLD47. Our study identified highly resistant wild potato species and underlying genes such as disease resistance, stress response, phytohormones, and transcription factors (e.g., MYB, WRKY, AP2/ERF, and AN1) associated with late blight resistance in wild potato species.
Collapse
Affiliation(s)
- Nisha Bhatia
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Jagesh Kumar Tiwari
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Chandresh Kumari
- School of Biotechnology, Shoolini University, Solan, Himachal Pradesh, India
| | - Rasna Zinta
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, India
| | - Sanjeev Sharma
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Ajay Kumar Thakur
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Tanuja Buckseth
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Dalamu Dalamu
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| | - Rajesh Kumar Singh
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
- Division of Vegetable Improvement, Indian Council of Agricultural Research—Indian Institute of Vegetable Research, Varanasi, Uttar Pradesh, India
| | - Vinod Kumar
- Division of Crop Improvement, Indian Council of Agricultural Research—Central Potato Research Institute, Shimla, Himachal Pradesh, India
| |
Collapse
|
5
|
Lopes NDS, Santos AS, de Novais DPS, Pirovani CP, Micheli F. Pathogenesis-related protein 10 in resistance to biotic stress: progress in elucidating functions, regulation and modes of action. FRONTIERS IN PLANT SCIENCE 2023; 14:1193873. [PMID: 37469770 PMCID: PMC10352611 DOI: 10.3389/fpls.2023.1193873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 05/08/2023] [Indexed: 07/21/2023]
Abstract
Introduction The Family of pathogenesis-related proteins 10 (PR-10) is widely distributed in the plant kingdom. PR-10 are multifunctional proteins, constitutively expressed in all plant tissues, playing a role in growth and development or being induced in stress situations. Several studies have investigated the preponderant role of PR-10 in plant defense against biotic stresses; however, little is known about the mechanisms of action of these proteins. This is the first systematic review conducted to gather information on the subject and to reveal the possible mechanisms of action that PR-10 perform. Methods Therefore, three databases were used for the article search: PubMed, Web of Science, and Scopus. To avoid bias, a protocol with inclusion and exclusion criteria was prepared. In total, 216 articles related to the proposed objective of this study were selected. Results The participation of PR-10 was revealed in the plant's defense against several stressor agents such as viruses, bacteria, fungi, oomycetes, nematodes and insects, and studies involving fungi and bacteria were predominant in the selected articles. Studies with combined techniques showed a compilation of relevant information about PR-10 in biotic stress that collaborate with the understanding of the mechanisms of action of these molecules. The up-regulation of PR-10 was predominant under different conditions of biotic stress, in addition to being more expressive in resistant varieties both at the transcriptional and translational level. Discussion Biological models that have been proposed reveal an intrinsic network of molecular interactions involving the modes of action of PR-10. These include hormonal pathways, transcription factors, physical interactions with effector proteins or pattern recognition receptors and other molecules involved with the plant's defense system. Conclusion The molecular networks involving PR-10 reveal how the plant's defense response is mediated, either to trigger susceptibility or, based on data systematized in this review, more frequently, to have plant resistance to the disease.
Collapse
Affiliation(s)
- Natasha dos Santos Lopes
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Ariana Silva Santos
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Diogo Pereira Silva de Novais
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Carlos Priminho Pirovani
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
| | - Fabienne Micheli
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Ilhéus-Bahia, Brazil
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Unité Mixte de Recherche Amélioration Génétique et Adaptation des Plantes Meditérranéennes et Tropicales (UMR AGAP Institut), Montpellier, France
| |
Collapse
|
6
|
Li M, He P, Zhao Z, Liu J, Liu H, Ma S, Shen Y, Li B. Effect of temperature on betacyanins synthesis and the transcriptome of Suaeda salsa. FRONTIERS IN PLANT SCIENCE 2023; 14:1203089. [PMID: 37434603 PMCID: PMC10330703 DOI: 10.3389/fpls.2023.1203089] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 06/02/2023] [Indexed: 07/13/2023]
Abstract
Introduction Suaeda salsa (Linn.) Pall. is an important tourist resource and ecological restoration species in coastal wetlands. Environmental factors such as low temperature, darkness, phytohormone, salt stress and seawater flflooding, and light can induce betalain synthesis in S. salsa, which plays an important role in plant adaptation to abiotic stress processes and in shaping the beautiful "red beach" landscape. Methods In this study, Illumina sequencing was used to profifile the transcriptome sequence (RNA-Seq) of S. salsa leaves at different temperatures (5° C, 10°C, 15°C, 20°C, 25°C, and 30°C) and to validate differentially expressed genes (DEGs) indicated by real-time PCR (RT-qPCR). Results The betacyanin content was highest in S. salsa leaves at 15°C. Transcription group data showed that compared to the control group (15°C), the "betacyanin biosynthesis pathway" was signifificantly enriched in the fifive different temperature groups. KEGG analysis showed that the DEGs were mainly involved in pathways of phenylpropanoid biosynthesis, carbon fifixation in photosynthetic organisms, flflavonoid biosynthesis, and betacyanin biosynthesis. Among the key enzymes involved in biosynthesis of betacyanin, genes for tyrosinase, CYP76AD1 and 4,5-DOPA dioxygenase were signifificantly upregulated and most abundantly expressed at 15°C. It is possible that the gene for betacyanin synthesis from S. salsa is primarily regulated by the MYB1R1 and MYB1 transcription factor. Four DEGs were randomly selected for quantitative PCR analysis, and DEG expression was generally consistent with the RNA-Seq data, verifying the validity of the transcriptome sequencing data. Discussion Relative to other temperatures, 15°C was optimum for S. salsa betacyanin synthesis, and this provides a theoretical reference for coastal wetland ecological remediation, reveals mechanisms of S. salsa discoloration, and further mines its potential application for landscape vegetation.
Collapse
Affiliation(s)
- Min Li
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Peimin He
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Engineering Research Center for Water Environment Ecology in Shanghai, Shanghai, China
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Zitao Zhao
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Jinlin Liu
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Hongtao Liu
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Shaozu Ma
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Yifei Shen
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| | - Bin Li
- School of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
| |
Collapse
|
7
|
Zhang Q, Luo T, Yuan D, Liu J, Fu Y, Yuan J. Qilongtian ameliorate bleomycin-induced pulmonary fibrosis in mice via inhibiting IL-17 signal pathway. Sci Rep 2023; 13:6002. [PMID: 37045911 PMCID: PMC10092933 DOI: 10.1038/s41598-023-31439-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 03/11/2023] [Indexed: 04/14/2023] Open
Abstract
Pulmonary fibrosis (PF) is a special type of pulmonary parenchymal disease, with chronic, progressive, fibrosis, and high mortality. There is a lack of safe, effective, and affordable treatment methods. Qilongtian (QLT) is a traditional Chinese prescription that is composed of Panax notoginseng, Earthworm, and Rhodiola, and shows the remarkable clinical curative effect of PF. However, the mechanism of QLT remains to be clarified. Therefore, we studied the effectivity of QLT in treating Bleomycin (BLM) induced PF mice. 36 C57BL/6 J mice were randomized into the control group, the model group, the low-, medium- and high-dose QLT group, and Pirfenidone group. After establishing a model of pulmonary fibrosis in mice, the control and model groups were infused with a normal saline solution, and the delivery group was infused with QLT. Pulmonary function in the mice from each group was detected. Pulmonary tissue morphologies and collagen deposition were stained by HE and Masson. The content of hydroxyproline (HYP) was detected by alkaline hydrolysis and the mRNA and protein expression of related genes in pulmonary tissues were detected by using q-PCR, ELISA, and Western blot. Our studies have shown that QLT significantly reduced the inflammatory injury, hydroxy-proline content, and collagen deposition of pulmonary tissue in BLM-induced PF mice and down-regulated the cytokine related to inflammation and fibrosis and PF expression on the mRNA and protein level in PF mice. To identify the mechanism of QLT, the Transcriptome was measured and the IL-17 signal pathway was screened out for further research. Further studies indicated that QLT reduced the mRNAs and protein levels of interleukin 17 (IL-17), c-c motif chemokine ligand 12 (CCL12), c-x-c motif chemokine ligand 5 (CXCL5), fos-like antigen 1 (FOSL1), matrix metalloproteinase-9 (MMP9), and amphiregulin (AREG), which are inflammation and fibrosis-related genes in the IL-17 signal pathway. The results indicated that the potential mechanism for QLT in the prevention of PF progression was by inhibiting inflammation resulting in the IL-17 signal pathway. Our study provides the novel scientific basis of QLT and represents new therapeutics for PF in clinical.
Collapse
Affiliation(s)
- Qiang Zhang
- School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong District, Shanghai, 201203, China.
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, 650500, China.
| | - Ting Luo
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
- Yunnan University of Chinese Medicine, Kunming, 650500, China
| | - Dezheng Yuan
- Yunnan University of Chinese Medicine, Kunming, 650500, China
- The third Affiliated Hospital of Yunnan University of Chinese Medicine: Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, 650500, China
| | - Jing Liu
- Yunnan University of Chinese Medicine, Kunming, 650500, China
- The third Affiliated Hospital of Yunnan University of Chinese Medicine: Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, 650500, China
| | - Yi Fu
- Yunnan University of Chinese Medicine, Kunming, 650500, China
- The third Affiliated Hospital of Yunnan University of Chinese Medicine: Kunming Municipal Hospital of Traditional Chinese Medicine, Kunming, 650500, China
| | - Jiali Yuan
- School of Basic Medicine, Shanghai University of Traditional Chinese Medicine, 1200 Cailun Road, Pudong District, Shanghai, 201203, China
- Yunnan Provincial Key Laboratory of Molecular Biology for Sinomedicine, Yunnan University of Chinese Medicine, Kunming, 650500, China
- Yunnan University of Chinese Medicine, Kunming, 650500, China
| |
Collapse
|
8
|
Rajpal VR, Singh A, Kathpalia R, Thakur RK, Khan MK, Pandey A, Hamurcu M, Raina SN. The Prospects of gene introgression from crop wild relatives into cultivated lentil for climate change mitigation. FRONTIERS IN PLANT SCIENCE 2023; 14:1127239. [PMID: 36998696 PMCID: PMC10044020 DOI: 10.3389/fpls.2023.1127239] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/22/2023] [Indexed: 05/31/2023]
Abstract
Crop wild relatives (CWRs), landraces and exotic germplasm are important sources of genetic variability, alien alleles, and useful crop traits that can help mitigate a plethora of abiotic and biotic stresses and crop yield reduction arising due to global climatic changes. In the pulse crop genus Lens, the cultivated varieties have a narrow genetic base due to recurrent selections, genetic bottleneck and linkage drag. The collection and characterization of wild Lens germplasm resources have offered new avenues for the genetic improvement and development of stress-tolerant, climate-resilient lentil varieties with sustainable yield gains to meet future food and nutritional requirements. Most of the lentil breeding traits such as high-yield, adaptation to abiotic stresses and resistance to diseases are quantitative and require the identification of quantitative trait loci (QTLs) for marker assisted selection and breeding. Advances in genetic diversity studies, genome mapping and advanced high-throughput sequencing technologies have helped identify many stress-responsive adaptive genes, quantitative trait loci (QTLs) and other useful crop traits in the CWRs. The recent integration of genomics technologies with plant breeding has resulted in the generation of dense genomic linkage maps, massive global genotyping, large transcriptomic datasets, single nucleotide polymorphisms (SNPs), expressed sequence tags (ESTs) that have advanced lentil genomic research substantially and allowed for the identification of QTLs for marker-assisted selection (MAS) and breeding. Assembly of lentil and its wild species genomes (~4Gbp) opens up newer possibilities for understanding genomic architecture and evolution of this important legume crop. This review highlights the recent strides in the characterization of wild genetic resources for useful alleles, development of high-density genetic maps, high-resolution QTL mapping, genome-wide studies, MAS, genomic selections, new databases and genome assemblies in traditionally bred genus Lens for future crop improvement amidst the impending global climate change.
Collapse
Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Apekshita Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Renu Kathpalia
- Department of Botany, Kirori Mal College, University of Delhi, Delhi, India
| | - Rakesh Kr. Thakur
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| | - Mohd. Kamran Khan
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Anamika Pandey
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Mehmet Hamurcu
- Department of Soil Science and Plant Nutrition, Faculty of Agriculture, Selcuk University, Konya, Türkiye
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Sector 125, Noida, U.P., India
| |
Collapse
|
9
|
He L, Han Z, Zang Y, Dai F, Chen J, Jin S, Huang C, Cheng Y, Zhang J, Xu B, Qi G, Cao Y, Yan S, Xuan L, Zhang T, Si Z, Hu Y. Advanced genes expression pattern greatly contributes to divergence in Verticillium wilt resistance between Gossypium barbadense and Gossupium hirsutum. FRONTIERS IN PLANT SCIENCE 2022; 13:979585. [PMID: 35979082 PMCID: PMC9376480 DOI: 10.3389/fpls.2022.979585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
Verticillium, representing one of the world's major pathogens, causes Verticillium wilt in important woody species, ornamentals, agricultural, etc., consequently resulting in a serious decline in production and quality, especially in cotton. Gossupium hirutum and Gossypium barbadense are two kinds of widely cultivated cotton species that suffer from Verticillium wilt, while G. barbadense has much higher resistance toward it than G. hirsutum. However, the molecular mechanism regarding their divergence in Verticillium wilt resistance remains largely unknown. In the current study, G. barbadense cv. Hai7124 and G. hirsutum acc. TM-1 were compared at 0, 12, 24, 48, 72, 96, 120, and 144 h post-inoculation (hpi) utilizing high throughput RNA-Sequencing. As a result, a total of 3,549 and 4,725 differentially expressed genes (DEGs) were identified, respectively. In particular, the resistant type Hai7124 displayed an earlier and faster detection and signaling response to the Verticillium dahliae infection and demonstrated higher expression levels of defense-related genes over TM-1 with respect to transcription factors, plant hormone signal transduction, plant-pathogen interaction, and nucleotide-binding leucine-rich repeat (NLR) genes. This study provides new insights into the molecular mechanisms of divergence in Verticillium wilt resistance between G. barbadense and G. hirsutum and important candidate genes for breeding V. dahliae resistant cotton cultivars.
Collapse
Affiliation(s)
- Lu He
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zegang Han
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yihao Zang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Fan Dai
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Chen
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Shangkun Jin
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chujun Huang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yu Cheng
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Juncheng Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Biyu Xu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Guoan Qi
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiwen Cao
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunyi Yan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Lisha Xuan
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Tianzhen Zhang
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhanfeng Si
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- The Rural Development Academy, Zhejiang University, Hangzhou, China
| | - Yan Hu
- Department of Agronomy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| |
Collapse
|
10
|
Jha UC, Sharma KD, Nayyar H, Parida SK, Siddique KHM. Breeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes. Int J Mol Sci 2022; 23:ijms23042217. [PMID: 35216334 PMCID: PMC8880496 DOI: 10.3390/ijms23042217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/04/2022] Open
Abstract
Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.
Collapse
Affiliation(s)
- Uday C. Jha
- Indian Institute of Pulses Research, Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Kamal Dev Sharma
- Department of Agricultural Biotechnology, CSK Himachal Pradesh Agricultural University, Palampur 176062, India;
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 0172, India;
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi 110001, India;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
| |
Collapse
|
11
|
Sohrabi SS, Ismaili A, Nazarian-Firouzabadi F, Fallahi H, Hosseini SZ. Identification of key genes and molecular mechanisms associated with temperature stress in lentil. Gene 2022; 807:145952. [PMID: 34500049 DOI: 10.1016/j.gene.2021.145952] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 08/24/2021] [Accepted: 09/03/2021] [Indexed: 02/03/2023]
Abstract
Extreme temperature is one of the serious threats to crop production in present and future scenarios of global climate changes. Lentil (Lens culinaris) is an important crop, and there is a serious lack of genetic information regarding environmental and temperature stresses responses. This study is the first report of evaluation of key genes and molecular mechanisms related to temperature stresses in lentil using the RNA sequencing technique. De novo transcriptome assembly created 44,673 contigs and differential gene expression analysis revealed 7494 differentially expressed genes between the temperature stresses and control group. Basic annotation of generated transcriptome assembly in our study led to the identification of 2765 novel transcripts that have not been identified yet in lentil genome draft v1.2. In addition, several unigenes involved in mechanisms of temperature sensing, calcium and hormone signaling and DNA-binding transcription factor activity were identified. Also, common mechanisms in response to temperature stresses, including the proline biosynthesis, the photosynthetic light reactions balancing, chaperone activity and circadian rhythms, are determined by the hub genes through the protein-protein interaction networks analysis. Deciphering the mechanisms of extreme temperature tolerance would be a new way for developing crops with enhanced plasticity against climate change. In general, this study has identified set of mechanisms and various genes related to cold and heat stresses which will be useful in better understanding of the lentil's reaction to temperature stresses.
Collapse
Affiliation(s)
- Seyed Sajad Sohrabi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Ahmad Ismaili
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Farhad Nazarian-Firouzabadi
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| | - Hossein Fallahi
- Department of Biology, School of Sciences, Razi University, Kermanshah, Iran.
| | - Seyedeh Zahra Hosseini
- Department of Plant Production and Genetic Engineering, Faculty of Agriculture, Lorestan University, Khorramabad, Iran.
| |
Collapse
|
12
|
Tiwari M, Singh B, Min D, Jagadish SVK. Omics Path to Increasing Productivity in Less-Studied Crops Under Changing Climate-Lentil a Case Study. FRONTIERS IN PLANT SCIENCE 2022; 13:813985. [PMID: 35615121 PMCID: PMC9125188 DOI: 10.3389/fpls.2022.813985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Accepted: 04/04/2022] [Indexed: 05/08/2023]
Abstract
Conventional breeding techniques for crop improvement have reached their full potential, and hence, alternative routes are required to ensure a sustained genetic gain in lentils. Although high-throughput omics technologies have been effectively employed in major crops, less-studied crops such as lentils have primarily relied on conventional breeding. Application of genomics and transcriptomics in lentils has resulted in linkage maps and identification of QTLs and candidate genes related to agronomically relevant traits and biotic and abiotic stress tolerance. Next-generation sequencing (NGS) complemented with high-throughput phenotyping (HTP) technologies is shown to provide new opportunities to identify genomic regions and marker-trait associations to increase lentil breeding efficiency. Recent introduction of image-based phenotyping has facilitated to discern lentil responses undergoing biotic and abiotic stresses. In lentil, proteomics has been performed using conventional methods such as 2-D gel electrophoresis, leading to the identification of seed-specific proteome. Metabolomic studies have led to identifying key metabolites that help differentiate genotypic responses to drought and salinity stresses. Independent analysis of differentially expressed genes from publicly available transcriptomic studies in lentils identified 329 common transcripts between heat and biotic stresses. Similarly, 19 metabolites were common across legumes, while 31 were common in genotypes exposed to drought and salinity stress. These common but differentially expressed genes/proteins/metabolites provide the starting point for developing high-yielding multi-stress-tolerant lentils. Finally, the review summarizes the current findings from omic studies in lentils and provides directions for integrating these findings into a systems approach to increase lentil productivity and enhance resilience to biotic and abiotic stresses under changing climate.
Collapse
Affiliation(s)
- Manish Tiwari
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- *Correspondence: Manish Tiwari,
| | - Baljinder Singh
- National Institute of Plant Genome Research, New Delhi, India
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
| | - S. V. Krishna Jagadish
- Department of Agronomy, Kansas State University, Manhattan, KS, United States
- S. V. Krishna Jagadish,
| |
Collapse
|
13
|
Mishra GP, Aski MS, Bosamia T, Chaurasia S, Mishra DC, Bhati J, Kumar A, Javeria S, Tripathi K, Kohli M, Kumar RR, Singh AK, Devi J, Kumar S, Dikshit HK. Insights into the Host-Pathogen Interaction Pathways through RNA-Seq Analysis of Lens culinaris Medik. in Response to Rhizoctonia bataticola Infection. Genes (Basel) 2021; 13:genes13010090. [PMID: 35052429 PMCID: PMC8774501 DOI: 10.3390/genes13010090] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
Dry root rot (Rhizoctonia bataticola) is an important disease of lentils (Lens culinaris Medik.).To gain an insight into the molecular aspects of host-pathogen interactions, the RNA-seq approach was used in lentils following inoculation with R.bataticola. The RNA-Seq has generated >450 million high-quality reads (HQRs) and nearly 96.97% were properly aligned to the reference genome. Very high similarity in FPKM (fragments per kilobase of exon per million mapped fragments) values (R > 0.9) among biological replicates showed the consistency of the RNA-Seq results. The study revealed various DEGs (differentially expressed genes) that were associated with changes in phenolic compounds, transcription factors (TFs), antioxidants, receptor kinases, hormone signals which corresponded to the cell wall modification enzymes, defense-related metabolites, and jasmonic acid (JA)/ethylene (ET) pathways. Gene ontology (GO) categorization also showed similar kinds of significantly enriched similar GO terms. Interestingly, of the total unigenes (42,606), 12,648 got assembled and showed significant hit with Rhizoctonia species. String analysis also revealed the role of various disease responsive proteins viz., LRR family proteins, LRR-RLKs, protein kinases, etc. in the host-pathogen interaction. Insilico validation analysis was performed using Genevestigator® and DEGs belonging to six major defense-response groups viz., defense-related enzymes, disease responsive genes, hormones, kinases, PR (pathogenesis related) proteins, and TFs were validated. For the first time some key miRNA targets viz. miR156, miR159, miR167, miR169, and miR482 were identified from the studied transcriptome, which may have some vital role in Rhizoctonia-based responses in lentils. The study has revealed the molecular mechanisms of the lentil/R.bataticola interactions and also provided a theoretical approach for the development of lentil genotypes resistant to R.bataticola.
Collapse
Affiliation(s)
- Gyan P. Mishra
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Muraleedhar S. Aski
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Tejas Bosamia
- Plant Omics Division, Central Salt and Marine Chemicals Research Institute, Bhavnagar 364002, India;
| | - Shiksha Chaurasia
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Dwijesh Chandra Mishra
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (D.C.M.); (J.B.)
| | - Jyotika Bhati
- Agricultural Bioinformatics, Indian Agricultural Statistics Research Institute, New Delhi 110012, India; (D.C.M.); (J.B.)
| | - Atul Kumar
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.); (S.J.)
| | - Shaily Javeria
- Division of Seed Science and Technology, Indian Agricultural Research Institute, New Delhi 110012, India; (A.K.); (S.J.)
| | - Kuldeep Tripathi
- Germplasm Evaluation Division, National Bureau of Plant Genetic Resources, New Delhi 110012, India;
| | - Manju Kohli
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Amit Kumar Singh
- Division of Genomic Resources, National Bureau of Plant Genetic Resources, New Delhi 110012, India;
| | - Jyoti Devi
- Division of Crop Improvement, Indian Institute of Vegetable Research, Varanasi 221305, India;
| | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, Avenue HafianeCherkaoui, Rabat 10112, Morocco
- Correspondence: (S.K.); (H.K.D.)
| | - Harsh Kumar Dikshit
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110012, India; (G.P.M.); (M.S.A.); (S.C.); (M.K.)
- Correspondence: (S.K.); (H.K.D.)
| |
Collapse
|
14
|
Zhang Z, Chen Q, Tan Y, Shuang S, Dai R, Jiang X, Temuer B. Combined Transcriptome and Metabolome Analysis of Alfalfa Response to Thrips Infection. Genes (Basel) 2021; 12:genes12121967. [PMID: 34946916 PMCID: PMC8701657 DOI: 10.3390/genes12121967] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/07/2021] [Accepted: 12/07/2021] [Indexed: 11/22/2022] Open
Abstract
Thrips (Thysanoptera: Thripidae) is a major insect pest for alfalfa which can result in decreased plant nutrients, low yields, and even plant death. To identify the differentially expressed genes and metabolites in response to thrips in alfalfa, a combination of metabolomics and transcriptomics was employed using alfalfa (Caoyuan No. 2) with and without thrips infestation. The results showed that the flavonoid biosynthesis and isoflavonoid biosynthesis pathways were the most significantly enriched pathways in response to thrips infection, as shown by the combined transcriptome and metabolome analysis. The transcriptome results showed that SA and JA signal transduction and PAPM-triggered immunity and the MAPK signaling pathway–plant pathways played a crucial role in thrips-induced plant resistance in alfalfa. In addition, we found that thrips infestation could also induce numerous changes in plant primary metabolism, such as carbohydrate and amino acid metabolism as compared to the control. Overall, our results described here should improve fundamental knowledge of molecular responses to herbivore-inducible plant defenses and contribute to the design of strategies against thrips in alfalfa.
Collapse
Affiliation(s)
- Zhiqiang Zhang
- Key Laboratory of Grassland Resources of the Ministry of Education, Technology Engineering Center of Drought and Cold-Resistant Grass Breeding in North of the National Forestry and Grassland Administration, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.Z.); (Q.C.); (S.S.); (X.J.)
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China;
| | - Qi Chen
- Key Laboratory of Grassland Resources of the Ministry of Education, Technology Engineering Center of Drought and Cold-Resistant Grass Breeding in North of the National Forestry and Grassland Administration, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.Z.); (Q.C.); (S.S.); (X.J.)
| | - Yao Tan
- College of Horticulture and Plant Protection, Inner Mongolia Agricultural University, Hohhot 010011, China;
| | - Shuang Shuang
- Key Laboratory of Grassland Resources of the Ministry of Education, Technology Engineering Center of Drought and Cold-Resistant Grass Breeding in North of the National Forestry and Grassland Administration, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.Z.); (Q.C.); (S.S.); (X.J.)
| | - Rui Dai
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China;
| | - Xiaohong Jiang
- Key Laboratory of Grassland Resources of the Ministry of Education, Technology Engineering Center of Drought and Cold-Resistant Grass Breeding in North of the National Forestry and Grassland Administration, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.Z.); (Q.C.); (S.S.); (X.J.)
| | - Buhe Temuer
- Key Laboratory of Grassland Resources of the Ministry of Education, Technology Engineering Center of Drought and Cold-Resistant Grass Breeding in North of the National Forestry and Grassland Administration, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China; (Z.Z.); (Q.C.); (S.S.); (X.J.)
- Key Laboratory of Grassland Resources of the Ministry of Education, College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot 010011, China;
- Correspondence: ; Tel.: +86-0471-4316259
| |
Collapse
|
15
|
Kumar J, Gupta DS, Kesari R, Verma R, Murugesan S, Basu PS, Soren KR, Gupta S, Singh NP. Comprehensive RNAseq analysis for identification of genes expressed under heat stress in lentil. PHYSIOLOGIA PLANTARUM 2021; 173:1785-1807. [PMID: 33829491 DOI: 10.1111/ppl.13419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Lentils are highly sensitive to abrupt increases in temperature during the mid to late reproductive stages, leading to severe biomass and seed yield reduction. Therefore, we carried out an RNAseq analysis between IG4258 (heat tolerant) and IG3973 (heat sensitive) lentil genotypes at the reproductive stage under both normal and heat stress conditions in the field. It resulted in 209,549 assembled transcripts and among these 161,809 transcripts had coding regions, of which 94,437 transcripts were annotated. The differential gene expression analysis showed upregulation of 678 transcripts and downregulation of 680 transcripts between the tolerant and sensitive genotypes at the early reproductive stage. While 76 transcripts were upregulated and 47 transcripts were downregulated at the late reproductive stage under heat stress conditions. The validation of 12 up-or downregulated transcripts through RT-PCR corresponded well with the expression analysis data of RNAseq, with a correlation of R2 = 0.89. Among these transcripts, the DN364_c1_g1_i9 and DN2218_c0_g1_i5 transcripts encoded enzymes involved in the tryptophan pathway, indicating that tryptophan biosynthesis plays a role under heat stress in lentil. Moreover, KEGG pathways enrichment analysis identified transcripts associated with genes encoding proteins/regulating factors related to different metabolic pathways including signal transduction, fatty acid biosynthesis, rRNA processing, ribosome biogenesis, gibberellin (GA) biosynthesis, and riboflavin biosynthesis. This analysis also identified 6852 genic-SSRs leading to the development of 4968 SSR primers that are potential genomic resources for molecular mapping of heat-tolerant genes in lentil.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Ravi Kesari
- Department of Plant Breeding and Genetics, Bhola Paswan Shastri Agricultural College, Purnea, India
| | - Renu Verma
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | | - Partha Sarathi Basu
- Division of Basic Sciences, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Khela Ram Soren
- Division of Biotechnology, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Sanjeev Gupta
- All India Co-ordinated Research Project on MULLaRP, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | | |
Collapse
|
16
|
Singh CK, Singh D, Taunk J, Chaudhary P, Tomar RSS, Chandra S, Singh D, Pal M, Konjengbam NS, Singh MP, Singh Sengar R, Sarker A. Comparative Inter- and IntraSpecies Transcriptomics Revealed Key Differential Pathways Associated With Aluminium Stress Tolerance in Lentil. FRONTIERS IN PLANT SCIENCE 2021; 12:693630. [PMID: 34531881 PMCID: PMC8438445 DOI: 10.3389/fpls.2021.693630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Accepted: 07/30/2021] [Indexed: 05/28/2023]
Abstract
Aluminium stress causes plant growth retardation and engenders productivity loss under acidic soil conditions. This study accentuates morpho-physiological and molecular bases of aluminium (Al) tolerance within and between wild (ILWL-15) and cultivated (L-4602 and BM-4) lentil species. Morpho-physiological studies revealed better cyto-morphology of tolerant genotypes over sensitive under Al3+ stress conditions. Mitotic lesions were observed in root cells under these conditions. Transcriptome analysis under Al3+ stress revealed 30,158 specifically up-regulated genes in different comparison groups showing contigs between 15,305 and 18,861 bp. In tolerant genotypes, top up-regulated differentially expressed genes (DEGs) were found to be involved in organic acid synthesis and exudation, production of antioxidants, callose synthesis, protein degradation, and phytohormone- and calcium-mediated signalling under stress conditions. DEGs associated with epigenetic regulation and Al3+ sequestration inside vacuole were specifically upregulated in wild and cultivars, respectively. Based on assembled unigenes, an average of 6,645.7 simple sequence repeats (SSRs) and 14,953.7 high-quality single nucleotide polymorphisms (SNPs) were spotted. By quantitative real-time polymerase chain reaction (qRT-PCR), 12 selected genes were validated. Gene ontology (GO) annotation revealed a total of 8,757 GO terms in three categories, viz., molecular, biological, and cellular processes. Kyoto Encyclopaedia of Genes and Genomes pathway scanning also revealed another probable pathway pertaining to metacaspase-1,-4, and -9 for programmed cell death under Al-stress conditions. This investigation reveals key inter- and intraspecies metabolic pathways associated with Al-stress tolerance in lentil species that can be utilised in designing future breeding programmes to improve lentil and related species towards Al3+ stress.
Collapse
Affiliation(s)
- Chandan Kumar Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Dharmendra Singh
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Jyoti Taunk
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Priya Chaudhary
- Division of Genetics, Indian Agricultural Research Institute, New Delhi, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi, India
| | - Shivani Chandra
- Amity Institute of Biotechnology, Amity University, Noida, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut, India
| | - Madan Pal
- Division of Plant Physiology, Indian Agricultural Research Institute, New Delhi, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University—Imphal, Umiam, India
| | - M. Premjit Singh
- College of Agriculture, Central Agricultural University—Imphal, Iroisemba, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut, India
| | - Ashutosh Sarker
- International Center for Agriculture Research in the Dry Areas, New Delhi, India
| |
Collapse
|
17
|
Dadu RHR, Bar I, Ford R, Sambasivam P, Croser J, Ribalta F, Kaur S, Sudheesh S, Gupta D. Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil. FRONTIERS IN PLANT SCIENCE 2021; 12:703283. [PMID: 34539696 PMCID: PMC8442733 DOI: 10.3389/fpls.2021.703283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/28/2021] [Indexed: 05/24/2023]
Abstract
Australian lentil production is affected by several major biotic constraints including Ascochyta blight (AB), caused by Ascochyta lentis, a devastating fungal disease. Cultivation of AB resistant cultivars, alongside agronomic management including fungicide application, is the current most economically viable control strategy. However, the breakdown of AB resistance in cultivars, such as Northfield and Nipper, suggests the need for introgression of new and diverse resistance genes. Successful introgression entails an understanding of the genetic basis of resistance. In this context, a biparental mapping population derived from a cross between a recently identified AB resistant accession ILWL 180 (Lens orientalis) and a susceptible cultivar ILL 6002 was produced. A genetic linkage map was constructed from single-nucleotide polymorphism markers generated using a genotyping-by-sequencing transcript approach. Genetic dissection of the mapping population revealed a major quantitative trait loci (QTL) region nested with three QTLs on linkage group 5 and explained 9.5-11.5 percent (%) of phenotypic variance for AB resistance. Another QTL was identified on LG2 with phenotypic variance of 9.6%. The identified QTL regions harbored putative candidate genes potentially associated with defense responses to A. lentis infection. The QTL analysis and the candidate gene information are expected to contribute to the development of diagnostic markers and enable marker-assisted resistance selection in lentil breeding programmes.
Collapse
Affiliation(s)
- Rama Harinath Reddy Dadu
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, Dookie College, The University of Melbourne, Dookie, VIC, Australia
- Grains Innovation Park, Agriculture Victoria, DJPR, Horsham, VIC, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Prabhakaran Sambasivam
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Janine Croser
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Federico Ribalta
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Shimna Sudheesh
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Dorin Gupta
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, Dookie College, The University of Melbourne, Dookie, VIC, Australia
| |
Collapse
|
18
|
Grapevine-Downy Mildew Rendezvous: Proteome Analysis of the First Hours of an Incompatible Interaction. PLANTS 2020; 9:plants9111498. [PMID: 33167573 PMCID: PMC7694532 DOI: 10.3390/plants9111498] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/23/2020] [Accepted: 11/02/2020] [Indexed: 12/26/2022]
Abstract
Grapevine is one of the most relevant crops in the world being used for economically important products such as wine. However, relevant grapevine cultivars are heavily affected by diseases such as the downy mildew disease caused by Plasmopara viticola. Improvements on grapevine resistance are made mainly by breeding techniques where resistance traits are introgressed into cultivars with desired grape characteristics. However, there is still a lack of knowledge on how resistant or tolerant cultivars tackle the P. viticola pathogen. In this study, using a shotgun proteomics LC-MS/MS approach, we unravel the protein modulation of a highly tolerant grapevine cultivar, Vitis vinifera “Regent”, in the first hours post inoculation (hpi) with P. viticola. At 6 hpi, proteins related to defense and to response to stimuli are negatively modulated while at 12 hpi there is an accumulation of proteins belonging to both categories. The co-occurrence of indicators of effector-triggered susceptibility (ETS) and effector-triggered immunity (ETI) is detected at both time-points, showing that these defense processes present high plasticity. The results obtained in this study unravel the tolerant grapevine defense strategy towards P. viticola and may provide valuable insights on resistance associated candidates and mechanisms, which may play an important role in the definition of new strategies for breeding approaches.
Collapse
|
19
|
Kumar J, Sen Gupta D. Prospects of next generation sequencing in lentil breeding. Mol Biol Rep 2020; 47:9043-9053. [PMID: 33037962 DOI: 10.1007/s11033-020-05891-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 10/03/2020] [Indexed: 11/28/2022]
Abstract
Lentil is an important food legume crop that has large and complex genome. During past years, considerable attention has been given on the use of next generation sequencing for enriching the genomic resources including identification of SSR and SNP markers, development of unigenes, transcripts, and identification of candidate genes for biotic and abiotic stresses, analysis of genetic diversity and identification of genes/ QTLs for agronomically important traits. However, in other crops including pulses, next generation sequencing has revolutionized the genomic research and helped in genomic assisted breeding rapidly and cost effectively. The present review discuss current status and future prospects of the use NGS based breeding in lentil.
Collapse
Affiliation(s)
- Jitendra Kumar
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India.
| | - Debjyoti Sen Gupta
- Division of Crop Improvement, ICAR-Indian Institute of Pulses Research, Kalyanpur, Kanpur, 208024, India
| |
Collapse
|
20
|
Cao Z, Kapoor K, Li L, Banniza S. Interactive Gene Expression Patterns of Susceptible and Resistant Lens ervoides Recombinant Inbred Lines and the Necrotroph Ascochyta lentis. Front Microbiol 2020; 11:1259. [PMID: 32670221 PMCID: PMC7326948 DOI: 10.3389/fmicb.2020.01259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 05/18/2020] [Indexed: 11/13/2022] Open
Abstract
Ascochyta lentis is a foliar pathogen of Lens species and is of worldwide importance in cultivated lentil production. High levels of resistance were identified in the wild species Lens ervoides. This resistance was explored through histopathology, qPCR estimation of fungal biomass and transcriptome sequencing in a susceptible and a resistant recombinant inbred line (RIL) of L. ervoides infected with an aggressive isolate of A. lentis. Necrotrophic growth was delayed in the resistant RIL compared to accelerated necrotrophy of A. lentis in the susceptible RIL. Analysis of the fungal secretome indicated that the early activation of cell wall-degrading enzymes contributed to increased virulence of A. lentis. On the host side, gene co-expression analysis revealed that the invasion by A. lentis caused mRNA, DNA and protein decay in infected plants regardless of the level of resistance in the host. The resistant RIL exhibited a stronger gene co-expression in lipid localization and sulfur processes, and cellular responses to nutrients and stimuli than the susceptible RIL. In addition, differential gene analysis revealed that the repression of both, gibberellin signaling and cell death associated with the hypersensitive response (HR), were associated with enhanced A. lentis resistance.
Collapse
Affiliation(s)
- Zhe Cao
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Karan Kapoor
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Li Li
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Sabine Banniza
- Crop Development Centre, Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| |
Collapse
|
21
|
Comparative Transcriptome Profiling Reveals Compatible and Incompatible Patterns of Potato Toward Phytophthora infestans. G3-GENES GENOMES GENETICS 2020; 10:623-634. [PMID: 31818876 PMCID: PMC7003068 DOI: 10.1534/g3.119.400818] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Late blight, caused by Phytophthora infestans (P. infestans), is a devastating disease in potato worldwide. Our previous study revealed that the Solanum andigena genotype 03112-233 is resistant to P. infestans isolate 90128, but susceptible to the super race isolate, CN152. In this study, we confirmed by diagnostic resistance gene enrichment sequencing (dRenSeq) that the resistance of 03112-233 toward 90128 is most likely based on a distinct new R gene(s). To gain an insight into the mechanism that governs resistance or susceptibility in 03112-223, comparative transcriptomic profiling analysis based on RNAseq was initiated. Changes in transcription at two time points (24 h and 72 h) after inoculation with isolates 90128 or CN152 were analyzed. A total of 8,881 and 7,209 genes were differentially expressed in response to 90128 and CN152, respectively, and 1,083 differentially expressed genes (DEGs) were common to both time points and isolates. A substantial number of genes were differentially expressed in an isolate-specific manner with 3,837 genes showing induction or suppression following infection with 90128 and 2,165 genes induced or suppressed after colonization by CN152. Hierarchical clustering analysis suggested that isolates with different virulence profiles can induce different defense responses at different time points. Further analysis revealed that the compatible interaction caused higher induction of susceptibility genes such as SWEET compared with the incompatible interaction. The salicylic acid, jasmonic acid, and abscisic acid mediated signaling pathways were involved in the response against both isolates, while ethylene and brassinosteroids mediated defense pathways were suppressed. Our results provide a valuable resource for understanding the interactions between P. infestans and potato.
Collapse
|
22
|
Agrobacterium tumefaciens-mediated transformation and expression of GFP in Ascochyta lentis to characterize ascochyta blight disease progression in lentil. PLoS One 2019; 14:e0223419. [PMID: 31647840 PMCID: PMC6812748 DOI: 10.1371/journal.pone.0223419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/20/2019] [Indexed: 11/25/2022] Open
Abstract
The plant immune system is made up of a complex response network that involves several lines of defense to fight invading pathogens. Fungal plant pathogens on the other hand, have evolved a range of ways to infect their host. The interaction between Ascochyta lentis and two lentil genotypes was explored to investigate the progression of ascochyta blight (AB) in lentils. In this study, we developed an Agrobacterium tumefaciens-mediated transformation system for A. lentis by constructing a new binary vector, pATMT-GpdGFP, for the constitutive expression of green fluorescent protein (EGFP). Green fluorescence was used as a highly efficient vital marker to study the developmental changes in A. lentis during AB disease progression on the susceptible and resistant lentil accessions, ILL6002 and ILL7537, respectively. The initial infection stages were similar in both the resistant and susceptible accessions where A. lentis uses infection structures such as germ tubes and appressoria to gain entry into the host while the host uses defense mechanisms to prevent pathogen entry. Penetration was observed at the junctions between neighbouring epidermal cells and occasionally, through the stomata. The pathogen attempted to penetrate and colonize ILL7537, but further fungal advancement appeared to be halted, and A. lentis did not enter the mesophyll. Successful entry and colonization of ILL6002 coincided with structural changes in A. lentis and the onset of necrotic lesions 5–7 days post inoculation. Once inside the leaf, A. lentis continued to grow, colonizing all parts of the leaf followed by plant cell collapse. Pycnidia-bearing spores appeared 14 days post inoculation, which marks the completion of the infection cycle. The use of fluorescent proteins in plant pathogenic fungi together with confocal laser scanning microscopy, provide a valuable tool to study the intracellular dynamics, colonization strategy and infection mechanisms during plant-pathogen interaction.
Collapse
|
23
|
Cheng A, Raai MN, Zain NAM, Massawe F, Singh A, Wan-Mohtar WAAQI. In search of alternative proteins: unlocking the potential of underutilized tropical legumes. Food Secur 2019. [DOI: 10.1007/s12571-019-00977-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
24
|
Cao Z, Li L, Kapoor K, Banniza S. Using a transcriptome sequencing approach to explore candidate resistance genes against stemphylium blight in the wild lentil species Lens ervoides. BMC PLANT BIOLOGY 2019; 19:399. [PMID: 31510924 PMCID: PMC6740027 DOI: 10.1186/s12870-019-2013-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 08/30/2019] [Indexed: 05/24/2023]
Abstract
BACKGROUND Stemphylium blight (SB), caused by Stemphylium botryosum, is a devastating disease in lentil production. Although it is known that accessions of Lens ervoides possess superior SB resistance at much higher frequency than the cultivated lentil species, very little is known about the molecular basis regulating SB resistance in L. ervoides. Therefore, a comprehensive molecular study of SB resistance in L. ervoides was needed to exploit this wild resource available at genebanks for use by plant breeders in resistance breeding. RESULTS Microscopic and qPCR quantification of fungal growth revealed that 48, 96, and 144 h post-inoculation (hpi) were interesting time points for disease development in L. ervoides recombinant inbred lines (RILs) LR-66-637 (resistant to SB) and LR-66-577 (susceptible to SB). Results of transcriptome sequencing at 0, 48, 96 and 144 hpi showed that 8810 genes were disease-responsive genes after challenge by S. botryosum. Among them, 7526 genes displayed a similar expression trend in both RILs, and some of them were likely involved in non-host resistance. The remaining 1284 genes were differentially expressed genes (DEGs) between RILs. Of those, 712 DEGs upregulated in LR-66-637 were mostly enriched in 'carbohydrate metabolic process', 'cell wall organization or biogenesis', and 'polysaccharide metabolic process'. In contrast, there were another 572 DEGs that were upregulated in LR-66-577, and some of them were enriched in 'oxidation-reduction process', 'asparagine metabolic process' and 'asparagine biosynthetic process'. After comparing DEGs to genes identified in previously described quantitative trait loci (QTLs) for resistance to SB, nine genes were common and three of them showed differential gene expression between a resistant and a susceptible bulk consisting of five RILs each. Results showed that two genes encoding calcium-transporting ATPase and glutamate receptor3.2 were candidate resistance genes, whereas one gene with unknown function was a candidate susceptibility gene. CONCLUSION This study provides new insights into the mechanisms of resistance and susceptibility in L. ervoides RILs responding to S. botryosum infection. Furthermore, we identified candidate resistance or susceptibility genes which warrant further gene function analyses, and which could be valuable for resistance breeding, if their role in resistance or susceptibility can be confirmed.
Collapse
Affiliation(s)
- Zhe Cao
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Li Li
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Karan Kapoor
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| | - Sabine Banniza
- Crop Development Centre / Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan S7N 5A8 Canada
| |
Collapse
|
25
|
Zhou Z, Bar I, Sambasivam PT, Ford R. Determination of the Key Resistance Gene Analogs Involved in Ascochyta rabiei Recognition in Chickpea. FRONTIERS IN PLANT SCIENCE 2019; 10:644. [PMID: 31191572 PMCID: PMC6546118 DOI: 10.3389/fpls.2019.00644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/29/2019] [Indexed: 05/21/2023]
Abstract
Chickpea (Cicer arietinum L.) is an important cool season food legume, however, its production is severely constrained by the foliar disease Ascochyta blight caused by the fungus Ascochyta rabiei (syn. Phoma rabiei). Several disease management options have been developed to control the pathogen, including breeding for host plant resistance. However, the pathogen population is evolving to produce more aggressive isolates. For host resistance to be effective, the plant must quickly recognize the pathogen and instigate initial defense mechanisms, optimally at the point of contact. Given that the most resistant host genotypes display rapid pathogen recognition and response, the approach taken was to assess the type, speed and pattern of recognition via Resistance Gene Analog (RGA) transcription among resistant and susceptible cultivated chickpea varieties. RGAs are key factors in the recognition of plant pathogens and the signaling of inducible defenses. In this study, a suite of RGA loci were chosen for further investigation from both published literature and from newly mined homologous sequences within the National Center for Biotechnology Information (NCBI) database. Following their validation in the chickpea genome, 10 target RGAs were selected for differential expression analysis in response to A. rabiei infection. This was performed in a set of four chickpea varieties including two resistant cultivars (ICC3996 and PBA Seamer), one moderately resistant cultivar (PBA HatTrick) and one susceptible cultivar (Kyabra). Gene expression at each RGA locus was assessed via qPCR at 2, 6, and 24 h after A. rabiei inoculation with a previously characterized highly aggressive isolate. As a result, all loci were differentially transcribed in response to pathogen infection in at least one genotype and at least one time point after inoculation. Among these, the differential expression of four RGAs was significant and consistently increased in the most resistant genotype ICC3996 immediately following inoculation, when spore germination began and ahead of penetration into the plant's epidermal tissues. Further in silico analyses indicated that the differentially transcribed RGAs function through ADP-binding within the pathogen recognition pathway. These represent clear targets for future functional validation and potential for selective resistance breeding for introgression into elite cultivars.
Collapse
Affiliation(s)
| | | | | | - Rebecca Ford
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Nathan, QLD, Australia
| |
Collapse
|
26
|
Polanco C, Sáenz de Miera LE, González AI, García P, Fratini R, Vaquero F, Vences FJ, Pérez de la Vega M. Construction of a high-density interspecific (Lens culinaris x L. odemensis) genetic map based on functional markers for mapping morphological and agronomical traits, and QTLs affecting resistance to Ascochyta in lentil. PLoS One 2019; 14:e0214409. [PMID: 30917174 PMCID: PMC6436743 DOI: 10.1371/journal.pone.0214409] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/12/2019] [Indexed: 01/13/2023] Open
Abstract
Usage of high-throughput sequencing approaches allow for the generation and characterization of reference transcriptome datasets that support gene-based marker discovery, which in turn can be used to build genetic maps among other purposes. We have obtained a transcriptome assembly including 49,453 genes for the lentil (Lens culinaris Medik.) cultivar Alpo using RNAseq methodology. This transcriptome was used as reference to obtain 6,306 quality polymorphic markers (SNPs and short indels) analyzing genotype data from a RIL population at F7 generation derived from the interspecific cross between L. culinaris cv. Alpo and L. odemensis accession ILWL235. L. odemensis is a wild species included in the secondary gene pool and can be used as a source for gene introgression in lentil breeding programs. Marker data were used to construct the first genetic interspecific map between these two species. This linkage map has been used to precisely identify regions of the CDC-Redberry lentil draft genome in which the candidate genes for some qualitative traits (seed coat spotting pattern, flower color, and stem pigmentation) could be located. The genome regions corresponding to a significant single quantitative trait locus (QTL) controlling "time to flowering" located in chromosome 6 and three QTLs regulating seed size and positioned in chromosomes 1 and 5 (two QTLs) were also identified. Significant QTLs for Ascochyta blight resistance in lentil were mapped to chromosome 6 in the genome region or close to it where QTLs for Ascochyta blight resistance have previously been reported.
Collapse
Affiliation(s)
- Carlos Polanco
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
- * E-mail:
| | | | - Ana Isabel González
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Pedro García
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Richard Fratini
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Francisca Vaquero
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | | | | |
Collapse
|
27
|
Sari E, Bhadauria V, Ramsay L, Borhan MH, Lichtenzveig J, Bett KE, Vandenberg A, Banniza S. Defense responses of lentil (Lens culinaris) genotypes carrying non-allelic ascochyta blight resistance genes to Ascochyta lentis infection. PLoS One 2018; 13:e0204124. [PMID: 30235263 PMCID: PMC6147436 DOI: 10.1371/journal.pone.0204124] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 09/03/2018] [Indexed: 12/24/2022] Open
Abstract
Ascochyta blight of lentil is an important fungal disease in many lentil-producing regions of the world causing major yield and grain quality losses. Quick shifts in aggressiveness of the population of the causal agent Ascochyta lentis mandates developing germplasm with novel and durable resistance. In the absence of complete resistance, lentil genotypes CDC Robin and 964a-46 have frequently been used as sources of partial resistance to ascochyta blight and carry non-allelic ascochyta blight resistance genes. RNA-seq analysis was conducted to identify differences in the transcriptome of CDC Robin, 964a-46 and the susceptible check Eston after inoculation with A. lentis. Candidate defense genes differentially expressed among the genotypes had hypothetical functions in various layers of plant defense, including pathogen recognition, phytohormone signaling pathways and downstream defense responses. CDC Robin and 964a-46 activated cell surface receptors (e.g. receptor like kinases) tentatively associated with pathogen-associated molecular patterns (PAMP) recognition and nucleotide-binding site leucine-rich repeat (NBS-LRR) receptors associated with intracellular effector recognition upon A. lentis infection, and differed in their activation of salicylic acid, abscisic acid and jasmonic acid / ethylene signal transduction pathways. These differences were reflected in the differential expression of downstream defense responses such as pathogenesis-related proteins, and genes associated with the induction of cell death and cell-wall reinforcement. A significant correlation between expression levels of a selection of genes based on quantitative real-time PCR and their expression levels estimated through RNA-seq demonstrated the technical and analytical accuracy of RNA-seq for identification of genes differentially expressed among genotypes. The presence of different resistance mechanisms in 964a-46 and CDC Robin indicates their value for pyramiding gene leading to more durable resistance to ascochyta blight.
Collapse
Affiliation(s)
- Ehsan Sari
- Department of Plant Sciences/Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Vijai Bhadauria
- Department of Plant Sciences/Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Larissa Ramsay
- Department of Plant Sciences/Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - M. Hossein Borhan
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, Saskatoon, Saskatchewan, Canada
| | - Judith Lichtenzveig
- School of Agriculture and Environment, University of Western Australia, Perth, Western Australia, Australia
| | - Kirstin E. Bett
- Department of Plant Sciences/Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Albert Vandenberg
- Department of Plant Sciences/Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Sabine Banniza
- Department of Plant Sciences/Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- * E-mail:
| |
Collapse
|