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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.
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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.
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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.
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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.
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Xu N, Chen B, Cheng Y, Su Y, Song M, Guo R, Wang M, Deng K, Lan T, Bao S, Wang G, Guo Z, Yu L. Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean. Genes (Basel) 2023; 14:1294. [PMID: 37372474 DOI: 10.3390/genes14061294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/13/2023] [Accepted: 06/16/2023] [Indexed: 06/29/2023] Open
Abstract
Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132-346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean.
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Affiliation(s)
- Ning Xu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Bingru Chen
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yuxin Cheng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Yufei Su
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Mengyuan Song
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Rongqiu Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Minghai Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Kunpeng Deng
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Tianjiao Lan
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Shuying Bao
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Guifang Wang
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Zhongxiao Guo
- Institute of Crop Germplasm Resources, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, China
| | - Lihe Yu
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, China
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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.
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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
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