1
|
Perez-Rial A, Carmona A, Ali L, Rubio J, Millan T, Castro P, Die JV. Phenotypic and genetic characterization of a near-isogenic line pair: insights into flowering time in chickpea. BMC PLANT BIOLOGY 2024; 24:709. [PMID: 39054447 PMCID: PMC11270784 DOI: 10.1186/s12870-024-05411-y] [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: 03/01/2024] [Accepted: 07/11/2024] [Indexed: 07/27/2024]
Abstract
BACKGROUND Cicer arietinum is a significant legume crop cultivated mainly in short-season environments, where early-flowering is a desirable trait to overcome terminal constraints. Despite its agricultural significance, the genetic control of flowering time in chickpea is not fully understood. In this study, we developed, phenotyped, re-sequenced and genetically characterized a pair of near-isogenic lines (NILs) with contrasting days to flowering to identify candidate gene variants potentially associated with flowering time. RESULTS In addition to days to flowering, noticeable differences in multiple shoot architecture traits were observed between the NILs. The resequencing data confirms that the NILs developed in this study serve as appropriate plant materials, effectively constraining genetic variation to specific regions and thereby establishing a valuable resource for future genetic and functional investigations in chickpea research. Leveraging bioinformatics tools and public genomic datasets, we identified homologs of flowering-related genes from Arabidopsis thaliana, including ELF3 and, for the first time in chickpea, MED16 and STO/BBX24, with variants among the NILs. Analysis of the allelic distribution of these genes revealed their preservation within chickpea diversity and their potential association with flowering time. Variants were also identified in members of the ERF and ARF gene families. Furthermore, in silico expression analysis was conducted elucidating their putative roles in flowering. CONCLUSIONS While the gene CaELF3a is identified as a prominent candidate, this study also exposes new targets in chickpea, such as CaMED16b and LOC101499101 (BBX24-like), homologs of flowering-related genes in Arabidopsis, as well as ERF12 and ARF2. The in silico expression characterization and genetic variability analysis performed could contribute to their use as specific markers for chickpea breeding programs. This study lays the groundwork for future investigations utilizing this plant material, promising further insights into the complex mechanisms governing flowering time in chickpea.
Collapse
Affiliation(s)
- Adrian Perez-Rial
- Department of Genetics-ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, 14071, Spain
| | - Alejandro Carmona
- Department of Genetics-ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, 14071, Spain
| | - Latifah Ali
- Department of Plant Biology-Science Faculty, University of Tishreen, Lattakia City, Syria
| | - Josefa Rubio
- Área de Mejora y Biotecnología, IFAPA Centro 'Alameda del Obispo', Córdoba, 14080, Spain
| | - Teresa Millan
- Department of Genetics-ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, 14071, Spain
| | - Patricia Castro
- Department of Genetics-ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, 14071, Spain.
| | - Jose V Die
- Department of Genetics-ETSIAM, University of Córdoba, Campus de Rabanales, Córdoba, 14071, Spain
| |
Collapse
|
2
|
Clayton EJ, Islam NS, Pannunzio K, Kuflu K, Sirjani R, Kohalmi SE, Dhaubhadel S. Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity? FRONTIERS IN PLANT SCIENCE 2024; 15:1307489. [PMID: 38322824 PMCID: PMC10845154 DOI: 10.3389/fpls.2024.1307489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.
Collapse
Affiliation(s)
- Emily J. Clayton
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kelsey Pannunzio
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kuflom Kuflu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ramtin Sirjani
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| |
Collapse
|
3
|
Nandety RS, Wen J, Mysore KS. Medicago truncatula resources to study legume biology and symbiotic nitrogen fixation. FUNDAMENTAL RESEARCH 2023; 3:219-224. [PMID: 38932916 PMCID: PMC11197554 DOI: 10.1016/j.fmre.2022.06.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/01/2022] [Accepted: 06/19/2022] [Indexed: 10/17/2022] Open
Abstract
Medicago truncatula is a chosen model for legumes towards deciphering fundamental legume biology, especially symbiotic nitrogen fixation. Current genomic resources for M. truncatula include a completed whole genome sequence information for R108 and Jemalong A17 accessions along with the sparse draft genome sequences for other 226 M. truncatula accessions. These genomic resources are complemented by the availability of mutant resources such as retrotransposon (Tnt1) insertion mutants in R108 and fast neutron bombardment (FNB) mutants in A17. In addition, several M. truncatula databases such as small secreted peptides (SSPs) database, transporter protein database, gene expression atlas, proteomic atlas, and metabolite atlas are available to the research community. This review describes these resources and provide information regarding how to access these resources.
Collapse
Affiliation(s)
- Raja Sekhar Nandety
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND 58102, United States
| | - Jiangqi Wen
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
| | - Kirankumar S. Mysore
- Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401, United States
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, United States
| |
Collapse
|
4
|
González AM, Lebrón R, Yuste-Lisbona FJ, Gómez-Martín C, Ortiz-Atienza A, Hackenberg M, Oliver JL, Lozano R, Santalla M. Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean. Int J Mol Sci 2022; 23:ijms232314783. [PMID: 36499112 PMCID: PMC9739310 DOI: 10.3390/ijms232314783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.
Collapse
Affiliation(s)
- Ana M. González
- Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain
| | - Ricardo Lebrón
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Fernando J. Yuste-Lisbona
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Cristina Gómez-Martín
- Departamento de Genética, Facultad de Ciencias & Laboratorio de Bioinformática, Centro de Investigación Biomédica, Universidad de Granada, 18071 Granada, Spain
| | - Ana Ortiz-Atienza
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Michael Hackenberg
- Departamento de Genética, Facultad de Ciencias & Laboratorio de Bioinformática, Centro de Investigación Biomédica, Universidad de Granada, 18071 Granada, Spain
| | - José L. Oliver
- Departamento de Genética, Facultad de Ciencias & Laboratorio de Bioinformática, Centro de Investigación Biomédica, Universidad de Granada, 18071 Granada, Spain
| | - Rafael Lozano
- Centro de Investigación en Biotecnología Agroalimentaria (CIAIMBITAL), Universidad de Almería, 04120 Almería, Spain
| | - Marta Santalla
- Genética del Desarrollo de Plantas, Misión Biológica de Galicia-CSIC, P.O. Box 28, 36080 Pontevedra, Spain
- Correspondence: ; Tel.: +34-986-596134; Fax: +34-986-851362
| |
Collapse
|
5
|
Singh G, Gudi S, Amandeep, Upadhyay P, Shekhawat PK, Nayak G, Goyal L, Kumar D, Kumar P, Kamboj A, Thada A, Shekhar S, Koli GK, DP M, Halladakeri P, Kaur R, Kumar S, Saini P, Singh I, Ayoubi H. Unlocking the hidden variation from wild repository for accelerating genetic gain in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:1035878. [PMID: 36438090 PMCID: PMC9682257 DOI: 10.3389/fpls.2022.1035878] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 10/17/2022] [Indexed: 11/02/2023]
Abstract
The fluctuating climates, rising human population, and deteriorating arable lands necessitate sustainable crops to fulfil global food requirements. In the countryside, legumes with intriguing but enigmatic nitrogen-fixing abilities and thriving in harsh climatic conditions promise future food security. However, breaking the yield plateau and achieving higher genetic gain are the unsolved problems of legume improvement. Present study gives emphasis on 15 important legume crops, i.e., chickpea, pigeonpea, soybean, groundnut, lentil, common bean, faba bean, cowpea, lupin, pea, green gram, back gram, horse gram, moth bean, rice bean, and some forage legumes. We have given an overview of the world and India's area, production, and productivity trends for all legume crops from 1961 to 2020. Our review article investigates the importance of gene pools and wild relatives in broadening the genetic base of legumes through pre-breeding and alien gene introgression. We have also discussed the importance of integrating genomics, phenomics, speed breeding, genetic engineering and genome editing tools in legume improvement programmes. Overall, legume breeding may undergo a paradigm shift once genomics and conventional breeding are integrated in the near future.
Collapse
Affiliation(s)
- Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Amandeep
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Upadhyay
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pooja Kanwar Shekhawat
- Division of Crop Improvement, Plant Breeding and Genetics, Indian Council of Agricultural Research (ICAR)-Central Soil Salinity Research Institute, Karnal, Haryana, India
- Department of Plant Breeding and Genetics, Sri Karan Narendra Agriculture University, Jobner, Rajasthan, India
| | - Gyanisha Nayak
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Lakshay Goyal
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Deepak Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Akashdeep Kamboj
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Antra Thada
- Department of Genetics and Plant Breeding, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Shweta Shekhar
- Department of Plant Molecular Biology and Biotechnology, Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh, India
| | - Ganesh Kumar Koli
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh Haryana Agricultural University, Hisar, Haryana, India
| | - Meghana DP
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, Gujarat, India
| | - Rajvir Kaur
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Sumit Kumar
- Department of Agronomy, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Pawan Saini
- CSB-Central Sericultural Research & Training Institute (CSR&TI), Ministry of Textiles, Govt. of India, Jammu- Kashmir, Pampore, India
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Habiburahman Ayoubi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| |
Collapse
|
6
|
Yu K, Miao H, Liu H, Zhou J, Sui M, Zhan Y, Xia N, Zhao X, Han Y. Genome-wide association studies reveal novel QTLs, QTL-by-environment interactions and their candidate genes for tocopherol content in soybean seed. FRONTIERS IN PLANT SCIENCE 2022; 13:1026581. [PMID: 36388509 PMCID: PMC9647135 DOI: 10.3389/fpls.2022.1026581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
Genome-wide association studies (GWAS) is an efficient method to detect quantitative trait locus (QTL), and has dissected many complex traits in soybean [Glycine max (L.) Merr.]. Although these results have undoubtedly played a far-reaching role in the study of soybean biology, environmental interactions for complex traits in traditional GWAS models are frequently overlooked. Recently, a new GWAS model, 3VmrMLM, was established to identify QTLs and QTL-by-environment interactions (QEIs) for complex traits. In this study, the GLM, MLM, CMLM, FarmCPU, BLINK, and 3VmrMLM models were used to identify QTLs and QEIs for tocopherol (Toc) content in soybean seed, including δ-Tocotrienol (δ-Toc) content, γ-Tocotrienol (γ-Toc) content, α-Tocopherol (α-Toc) content, and total Tocopherol (T-Toc) content. As a result, 101 QTLs were detected by the above methods in single-environment analysis, and 57 QTLs and 13 QEIs were detected by 3VmrMLM in multi-environment analysis. Among these QTLs, some QTLs (Group I) were repeatedly detected three times or by at least two models, and some QTLs (Group II) were repeatedly detected only by 3VmrMLM. In the two Groups, 3VmrMLM was able to correctly detect all known QTLs in group I, while good results were achieved in Group II, for example, 8 novel QTLs were detected in Group II. In addition, comparative genomic analysis revealed that the proportion of Glyma_max specific genes near QEIs was higher, in other words, these QEIs nearby genes are more susceptible to environmental influences. Finally, around the 8 novel QTLs, 11 important candidate genes were identified using haplotype, and validated by RNA-Seq data and qRT-PCR analysis. In summary, we used phenotypic data of Toc content in soybean, and tested the accuracy and reliability of 3VmrMLM, and then revealed novel QTLs, QEIs and candidate genes for these traits. Hence, the 3VmrMLM model has broad prospects and potential for analyzing the genetic structure of complex quantitative traits in soybean.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Xue Zhao
- *Correspondence: Xue Zhao, ; Yingpeng Han,
| | | |
Collapse
|
7
|
Zhang Y, Zhang L, Xiao Q, Wu C, Zhang J, Xu Q, Yu Z, Bao S, Wang J, Li Y, Wang L, Wang J. Two independent allohexaploidizations and genomic fractionation in Solanales. FRONTIERS IN PLANT SCIENCE 2022; 13:1001402. [PMID: 36212355 PMCID: PMC9538396 DOI: 10.3389/fpls.2022.1001402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Solanales, an order of flowering plants, contains the most economically important vegetables among all plant orders. To date, many Solanales genomes have been sequenced. However, the evolutionary processes of polyploidization events in Solanales and the impact of polyploidy on species diversity remain poorly understood. We compared two representative Solanales genomes (Solanum lycopersicum L. and Ipomoea triloba L.) and the Vitis vinifera L. genome and confirmed two independent polyploidization events. Solanaceae common hexaploidization (SCH) and Convolvulaceae common hexaploidization (CCH) occurred ∼43-49 and ∼40-46 million years ago (Mya), respectively. Moreover, we identified homologous genes related to polyploidization and speciation and constructed multiple genomic alignments with V. vinifera genome, providing a genomic homology framework for future Solanales research. Notably, the three polyploidization-produced subgenomes in both S. lycopersicum and I. triloba showed significant genomic fractionation bias, suggesting the allohexaploid nature of the SCH and CCH events. However, we found that the higher genomic fractionation bias of polyploidization-produced subgenomes in Solanaceae was likely responsible for their more abundant species diversity than that in Convolvulaceae. Furthermore, through genomic fractionation and chromosomal structural variation comparisons, we revealed the allohexaploid natures of SCH and CCH, both of which were formed by two-step duplications. In addition, we found that the second step of two paleohexaploidization events promoted the expansion and diversity of β-amylase (BMY) genes in Solanales. These current efforts provide a solid foundation for future genomic and functional exploration of Solanales.
Collapse
Affiliation(s)
- Yan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Lan Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qimeng Xiao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Chunyang Wu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jiaqi Zhang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Qiang Xu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Zijian Yu
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Shoutong Bao
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jianyu Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yu Li
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Li Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
| | - Jinpeng Wang
- Center for Genomics and Computational Biology, School of Life Sciences, North China University of Science and Technology, Tangshan, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
8
|
Sudalaimuthuasari N, Ali R, Kottackal M, Rafi M, Al Nuaimi M, Kundu B, Al-Maskari RS, Wang X, Mishra AK, Balan J, Chaluvadi SR, Al Ansari F, Bennetzen JL, Purugganan MD, Hazzouri KM, Amiri KMA. The Genome of the Mimosoid Legume Prosopis cineraria, a Desert Tree. Int J Mol Sci 2022; 23:8503. [PMID: 35955640 PMCID: PMC9369113 DOI: 10.3390/ijms23158503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/26/2022] [Accepted: 07/28/2022] [Indexed: 11/16/2022] Open
Abstract
The mimosoid legumes are a clade of ~40 genera in the Caesalpinioideae subfamily of the Fabaceae that grow in tropical and subtropical regions. Unlike the better studied Papilionoideae, there are few genomic resources within this legume group. The tree Prosopis cineraria is native to the Near East and Indian subcontinent, where it thrives in very hot desert environments. To develop a tool to better understand desert plant adaptation mechanisms, we sequenced the P. cineraria genome to near-chromosomal assembly, with a total sequence length of ~691 Mb. We predicted 77,579 gene models (76,554 CDS, 361 rRNAs and 664 tRNAs) from the assembled genome, among them 55,325 (~72%) protein-coding genes that were functionally annotated. This genome was found to consist of over 58% repeat sequences, primarily long terminal repeats (LTR-)-retrotransposons. We find an expansion of terpenoid metabolism genes in P. cineraria and its relative Prosopis alba, but not in other legumes. We also observed an amplification of NBS-LRR disease-resistance genes correlated with LTR-associated retrotransposition, and identified 410 retrogenes with an active burst of chimeric retrogene creation that approximately occurred at the same time of divergence of P. cineraria from a common lineage with P. alba~23 Mya. These retrogenes include many biotic defense responses and abiotic stress stimulus responses, as well as the early Nodulin 93 gene. Nodulin 93 gene amplification is consistent with an adaptive response of the species to the low nitrogen in arid desert soil. Consistent with these results, our differentially expressed genes show a tissue specific expression of isoprenoid pathways in shoots, but not in roots, as well as important genes involved in abiotic salt stress in both tissues. Overall, the genome sequence of P. cineraria enriches our understanding of the genomic mechanisms of its disease resistance and abiotic stress tolerance. Thus, it is a very important step in crop and legume improvement.
Collapse
Affiliation(s)
- Naganeeswaran Sudalaimuthuasari
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Rashid Ali
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
- Mitrix Bio., 400 Farmington Ave., Farmington, CT 06032, USA
| | - Martin Kottackal
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Mohammed Rafi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Mariam Al Nuaimi
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Biduth Kundu
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
| | - Raja Saeed Al-Maskari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
| | - Xuewen Wang
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (X.W.); (S.R.C.); (J.L.B.)
| | - Ajay Kumar Mishra
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Jithin Balan
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Srinivasa R. Chaluvadi
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (X.W.); (S.R.C.); (J.L.B.)
| | - Fatima Al Ansari
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
| | - Jeffrey L. Bennetzen
- Department of Genetics, University of Georgia, Athens, GA 30602, USA; (X.W.); (S.R.C.); (J.L.B.)
| | - Michael D. Purugganan
- Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi P.O. Box. 129188, United Arab Emirates;
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Khaled M. Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
| | - Khaled M. A. Amiri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (N.S.); (R.A.); (M.K.); (M.R.); (M.A.N.); (A.K.M.); (J.B.)
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box. 15551, United Arab Emirates; (B.K.); (R.S.A.-M.); (F.A.A.)
| |
Collapse
|
9
|
Yu N, Sun H, Yang J, Li R. The Diesel Tree Sindora glabra Genome Provides Insights Into the Evolution of Oleoresin Biosynthesis. FRONTIERS IN PLANT SCIENCE 2022; 12:794830. [PMID: 35058955 PMCID: PMC8764381 DOI: 10.3389/fpls.2021.794830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
Sindora glabra is an economically important tree that produces abundant oleoresin in the trunk. Here, we present a high-quality chromosome-scale assembly of S. glabra genome by combining Illumina HiSeq, Pacific Biosciences sequencing, and Hi-C technologies. The size of S. glabra genome was 1.11 Gb, with a contig N50 of 1.27 Mb and 31,944 predicted genes. This is the first sequenced genome of the subfamily Caesalpinioideae. As a sister taxon to Papilionoideae, S. glabra underwent an ancient genome triplication shared by core eudicots and further whole-genome duplication shared by early-legume in the last 73.3 million years. S. glabra harbors specific genes and expanded genes largely involved in stress responses and biosynthesis of secondary metabolites. Moreover, 59 terpene backbone biosynthesis genes and 64 terpene synthase genes were identified, which together with co-expressed transcription factors could contribute to the diversity and specificity of terpene compounds and high terpene content in S. glabra stem. In addition, 63 disease resistance NBS-LRR genes were found to be unique in S. glabra genome and their expression levels were correlated with the accumulation of terpene profiles, suggesting potential defense function of terpenes in S. glabra. These together provide new resources for understanding genome evolution and oleoresin production.
Collapse
Affiliation(s)
- Niu Yu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Haixi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Jinchang Yang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Rongsheng Li
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| |
Collapse
|
10
|
Shimamura M, Kumaki T, Hashimoto S, Saeki K, Ayabe SI, Higashitani A, Akashi T, Sato S, Aoki T. Phenolic Acids Induce Nod Factor Production in <i>Lotus japonicus</i>–<i>Mesorhizobium</i> Symbiosis. Microbes Environ 2022; 37. [PMID: 35283370 PMCID: PMC8958295 DOI: 10.1264/jsme2.me21094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In legume–rhizobia symbiosis, partner recognition and the initiation of symbiosis processes require the mutual exchange of chemical signals. Chemicals, generally (iso)flavonoids, in the root exudates of the host plant induce the expression of nod genes in rhizobia, and, thus, are called nod gene inducers. The expression of nod genes leads to the production of lipochitooligosaccharides (LCOs) called Nod factors. Natural nod gene inducer(s) in Lotus japonicus–Mesorhizobium symbiosis remain unknown. Therefore, we developed an LCO detection method based on ultra-high-performance liquid chromatography–tandem-quadrupole mass spectrometry (UPLC-TQMS) to identify these inducers and used it herein to screen 40 phenolic compounds and aldonic acids for their ability to induce LCOs in Mesorhizobium japonicum MAFF303099. We identified five phenolic acids with LCO-inducing activities, including p-coumaric, caffeic, and ferulic acids. The induced LCOs caused root hair deformation, and nodule numbers in L. japonicus inoculated with M. japonicum were increased by these phenolic acids. The three phenolic acids listed above induced the expression of the nodA, nodB, and ttsI genes in a strain harboring a multicopy plasmid encoding NodD1, but not that encoding NodD2. The presence of p-coumaric and ferulic acids in the root exudates of L. japonicus was confirmed by UPLC-TQMS, and the induction of ttsI::lacZ in the strain harboring the nodD1 plasmid was detected in the rhizosphere of L. japonicus. Based on these results, we propose that phenolic acids are a novel type of nod gene inducer in L. japonicus–Mesorhizobium symbiosis.
Collapse
Affiliation(s)
| | | | | | - Kazuhiko Saeki
- Department of Biological Sciences and Kyousei Science Center for Life and Nature, Nara Women’s University
| | | | | | | | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University
| | - Toshio Aoki
- Department of Applied Biological Sciences, Nihon University
| |
Collapse
|
11
|
Zhou Z, Lakhssassi N, Knizia D, Cullen MA, El Baz A, Embaby MG, Liu S, Badad O, Vuong TD, AbuGhazaleh A, Nguyen HT, Meksem K. Genome-wide identification and analysis of soybean acyl-ACP thioesterase gene family reveals the role of GmFAT to improve fatty acid composition in soybean seed. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3611-3623. [PMID: 34319424 DOI: 10.1007/s00122-021-03917-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Soybean acyl-ACP thioesterase gene family have been characterized; GmFATA1A mutants were discovered to confer high oleic acid, while GmFATB mutants presented low palmitic and high oleic acid seed content. Soybean oil stability and quality are primarily determined by the relative proportions of saturated versus unsaturated fatty acids. Commodity soybean typically contains 11% palmitic acid, as the primary saturated fatty acids. Reducing palmitic acid content is the principal approach to minimize the levels of saturated fatty acids in soybean. Though high palmitic acid enhances oxidative stability of soybean oil, it is negatively correlated with oil and oleic acid content and can cause coronary heart diseases for humans. For plants, acyl-acyl carrier protein (ACP) thioesterases (TEs) are a group of enzymes to hydrolyze acyl group and release free fatty acid from plastid. Among them, GmFATB1A has become the main target to genetically reduce the palmitic acid content in soybean. However, the role of members in soybean acyl-ACP thioesterase gene family is largely unknown. In this study, we characterized two classes of TEs, GmFATA, and GmFATB in soybean. We also denominated two GmFATA members and discovered six additional members that belong to GmFATB gene family through phylogenetic, syntenic, and in silico analysis. Using TILLING-by-Sequencing+, we identified an allelic series of mutations in five soybean acyl-ACP thioesterase genes, including GmFATA1A, GmFATB1A, GmFATB1B, GmFATB2A, and GmFATB2B. Additionally, we discovered mutations at GmFATA1A to confer high oleic acid (up to 34.5%) content, while mutations at GmFATB presented low palmitic acid (as low as 5.6%) and high oleic acid (up to 36.5%) phenotypes. The obtained soybean mutants with altered fatty acid content can be used in soybean breeding program for improving soybean oil composition traits.
Collapse
Affiliation(s)
- Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
- Plant Science Department, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Mallory A Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Abdelhalim El Baz
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Mohamed G Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Oussama Badad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Tri D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA.
| |
Collapse
|
12
|
Singh D, Chaudhary P, Taunk J, Singh CK, Singh D, Tomar RSS, Aski M, Konjengbam NS, Raje RS, Singh S, Sengar RS, Yadav RK, Pal M. Fab Advances in Fabaceae for Abiotic Stress Resilience: From 'Omics' to Artificial Intelligence. Int J Mol Sci 2021; 22:10535. [PMID: 34638885 PMCID: PMC8509049 DOI: 10.3390/ijms221910535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/17/2021] [Accepted: 09/23/2021] [Indexed: 11/16/2022] Open
Abstract
Legumes are a better source of proteins and are richer in diverse micronutrients over the nutritional profile of widely consumed cereals. However, when exposed to a diverse range of abiotic stresses, their overall productivity and quality are hugely impacted. Our limited understanding of genetic determinants and novel variants associated with the abiotic stress response in food legume crops restricts its amelioration. Therefore, it is imperative to understand different molecular approaches in food legume crops that can be utilized in crop improvement programs to minimize the economic loss. 'Omics'-based molecular breeding provides better opportunities over conventional breeding for diversifying the natural germplasm together with improving yield and quality parameters. Due to molecular advancements, the technique is now equipped with novel 'omics' approaches such as ionomics, epigenomics, fluxomics, RNomics, glycomics, glycoproteomics, phosphoproteomics, lipidomics, regulomics, and secretomics. Pan-omics-which utilizes the molecular bases of the stress response to identify genes (genomics), mRNAs (transcriptomics), proteins (proteomics), and biomolecules (metabolomics) associated with stress regulation-has been widely used for abiotic stress amelioration in food legume crops. Integration of pan-omics with novel omics approaches will fast-track legume breeding programs. Moreover, artificial intelligence (AI)-based algorithms can be utilized for simulating crop yield under changing environments, which can help in predicting the genetic gain beforehand. Application of machine learning (ML) in quantitative trait loci (QTL) mining will further help in determining the genetic determinants of abiotic stress tolerance in pulses.
Collapse
Affiliation(s)
- Dharmendra Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Priya Chaudhary
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Jyoti Taunk
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Chandan Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Deepti Singh
- Department of Botany, Meerut College, Meerut 250001, India
| | - Ram Sewak Singh Tomar
- College of Horticulture and Forestry, Rani Lakshmi Bai Central Agricultural University, Jhansi 284003, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Noren Singh Konjengbam
- College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University, Imphal 793103, India
| | - Ranjeet Sharan Raje
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Sanjay Singh
- ICAR- National Institute of Plant Biotechnology, LBS Centre, Pusa Campus, New Delhi 110012, India
| | - Rakesh Singh Sengar
- College of Biotechnology, Sardar Vallabh Bhai Patel Agricultural University, Meerut 250001, India
| | - Rajendra Kumar Yadav
- Department of Genetics and Plant Breeding, Chandra Shekhar Azad University of Agriculture and Technology, Kanpur 208002, India
| | - Madan Pal
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| |
Collapse
|
13
|
Lakhssassi N, Zhou Z, Cullen MA, Badad O, El Baze A, Chetto O, Embaby MG, Knizia D, Liu S, Neves LG, Meksem K. TILLING-by-Sequencing + to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis. Int J Mol Sci 2021; 22:4219. [PMID: 33921707 PMCID: PMC8073088 DOI: 10.3390/ijms22084219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 12/25/2022] Open
Abstract
Reverse genetic approaches have been widely applied to study gene function in crop species; however, these techniques, including gel-based TILLING, present low efficiency to characterize genes in soybeans due to genome complexity, gene duplication, and the presence of multiple gene family members that share high homology in their DNA sequence. Chemical mutagenesis emerges as a genetically modified-free strategy to produce large-scale soybean mutants for economically important traits improvement. The current study uses an optimized high-throughput TILLING by target capture sequencing technology, or TILLING-by-Sequencing+ (TbyS+), coupled with universal bioinformatic tools to identify population-wide mutations in soybeans. Four ethyl methanesulfonate mutagenized populations (4032 mutant families) have been screened for the presence of induced mutations in targeted genes. The mutation types and effects have been characterized for a total of 138 soybean genes involved in soybean seed composition, disease resistance, and many other quality traits. To test the efficiency of TbyS+ in complex genomes, we used soybeans as a model with a focus on three desaturase gene families, GmSACPD, GmFAD2, and GmFAD3, that are involved in the soybean fatty acid biosynthesis pathway. We successfully isolated mutants from all the six gene family members. Unsurprisingly, most of the characterized mutants showed significant changes either in their stearic, oleic, or linolenic acids. By using TbyS+, we discovered novel sources of soybean oil traits, including high saturated and monosaturated fatty acids in addition to low polyunsaturated fatty acid contents. This technology provides an unprecedented platform for highly effective screening of polyploid mutant populations and functional gene analysis. The obtained soybean mutants from this study can be used in subsequent soybean breeding programs for improved oil composition traits.
Collapse
Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mallory A. Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oussama Badad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Abdelhalim El Baze
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oumaima Chetto
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mohamed G. Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | | | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| |
Collapse
|
14
|
Franco AL, Figueredo A, Pereira LDM, de Sousa SM, Souza G, Carvalho MA, Simon MF, Viccini LF. Low cytomolecular diversification in the genus Stylosanthes Sw. (Papilionoideae, Leguminosae). Genet Mol Biol 2020; 43:e20180250. [PMID: 31429856 PMCID: PMC7197990 DOI: 10.1590/1678-4685-gmb-2018-0250] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 03/07/2019] [Indexed: 12/02/2022] Open
Abstract
Stylosanthes (Papilionoideae, Leguminosae) is a predominantly Neotropical genus with ~48 species that include worldwide important forage species. This study presents the chromosome number and morphology of eight species of the genus Stylosanthes (S. acuminata, S. gracilis, S. grandifolia, S. guianensis, S. hippocampoides, S. pilosa, S. macrocephala, and S. ruellioides). In addition, staining with CMA and DAPI, in situ hybridization with 5S and 35S rDNA probes, and estimation of DNA content were performed. The interpretation of Stylosanthes chromosome diversification was anchored by a comparison with the sister genus Arachis and a dated molecular phylogeny based on nuclear and plastid loci. Stylosanthes species showed 2n = 20, with low cytomolecular diversification regarding 5S rDNA, 35S rDNA, and genome size. Arachis has a more ancient diversification (~7 Mya in the Pliocene) than the relatively recent Stylosanthes (~2 Mya in the Pleistocene), and it seems more diverse than its sister lineage. Our data support the idea that the cytomolecular stability of Stylosanthes in relation to Arachis could be a result of its recent origin. The recent diversification of Stylosanthes could also be related to the low morphological differentiation among species, and to the recurrent formation of allopolyploid complexes.
Collapse
Affiliation(s)
- Ana Luiza Franco
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Amanda Figueredo
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Lívia de Moraes Pereira
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | - Saulo Marçal de Sousa
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| | - Gustavo Souza
- Universidade Federal de Pernambuco, Departamento de Botânica, Laboratório de Citogenética e Evolução Vegetal, CCB, Recife, PE, Brazil
| | | | - Marcelo F. Simon
- Empresa Brasileira de Pesquisa Agropecuária, Embrapa Recursos Genéticos e Biotecnologia, PqEB, Brasília, DF, Brazil
| | - Lyderson Facio Viccini
- Universidade Federal de Juiz de Fora, Departamento de Biologia, Laboratório de Genética, Juiz de Fora, MG, Brazil
| |
Collapse
|
15
|
Sharma V, Bhattacharyya S, Kumar R, Kumar A, Ibañez F, Wang J, Guo B, Sudini HK, Gopalakrishnan S, DasGupta M, Varshney RK, Pandey MK. Molecular Basis of Root Nodule Symbiosis between Bradyrhizobium and 'Crack-Entry' Legume Groundnut ( Arachis hypogaea L.). PLANTS (BASEL, SWITZERLAND) 2020; 9:E276. [PMID: 32093403 PMCID: PMC7076665 DOI: 10.3390/plants9020276] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/16/2022]
Abstract
Nitrogen is one of the essential plant nutrients and a major factor limiting crop productivity. To meet the requirements of sustainable agriculture, there is a need to maximize biological nitrogen fixation in different crop species. Legumes are able to establish root nodule symbiosis (RNS) with nitrogen-fixing soil bacteria which are collectively called rhizobia. This mutualistic association is highly specific, and each rhizobia species/strain interacts with only a specific group of legumes, and vice versa. Nodulation involves multiple phases of interactions ranging from initial bacterial attachment and infection establishment to late nodule development, characterized by a complex molecular signalling between plants and rhizobia. Characteristically, legumes like groundnut display a bacterial invasion strategy popularly known as "crack-entry'' mechanism, which is reported approximately in 25% of all legumes. This article accommodates critical discussions on the bacterial infection mode, dynamics of nodulation, components of symbiotic signalling pathway, and also the effects of abiotic stresses and phytohormone homeostasis related to the root nodule symbiosis of groundnut and Bradyrhizobium. These parameters can help to understand how groundnut RNS is programmed to recognize and establish symbiotic relationships with rhizobia, adjusting gene expression in response to various regulations. This review further attempts to emphasize the current understanding of advancements regarding RNS research in the groundnut and speculates on prospective improvement possibilities in addition to ways for expanding it to other crops towards achieving sustainable agriculture and overcoming environmental challenges.
Collapse
Affiliation(s)
- Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Samrat Bhattacharyya
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (M.D.)
- Department of Botany, Sister Nibedita Government General Degree College for Girls, Kolkata 700027, India
| | - Rakesh Kumar
- Department of Life Sciences, Central University of Karnataka, Kadaganchi-585367, India
| | - Ashish Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
- DBT-National Agri-food Biotechnology Institute (NABI), Punjab 140308, India
| | - Fernando Ibañez
- Instituto de Investigaciones Agrobiotecnológicas (CONICET-UNRC), Río Cuarto-5800, Córdoba, Argentina
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL 103610, USA;
| | - Baozhu Guo
- Crop Protection and Management Research Unit, United State Department of Agriculture- Agriculture Research Service (USDA-ARS), Tifton, GA 31793, USA;
| | - Hari K. Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Subramaniam Gopalakrishnan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Maitrayee DasGupta
- Department of Biochemistry, University of Calcutta, Kolkata 700019, India (M.D.)
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; (V.S.); (H.K.S.); (S.G.); (R.K.V.)
| |
Collapse
|
16
|
Huisman R, Geurts R. A Roadmap toward Engineered Nitrogen-Fixing Nodule Symbiosis. PLANT COMMUNICATIONS 2020; 1:100019. [PMID: 33404552 PMCID: PMC7748023 DOI: 10.1016/j.xplc.2019.100019] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 11/06/2019] [Accepted: 12/27/2019] [Indexed: 05/26/2023]
Abstract
In the late 19th century, it was discovered that legumes can establish a root nodule endosymbiosis with nitrogen-fixing rhizobia. Soon after, the question was raised whether it is possible to transfer this trait to non-leguminous crops. In the past century, an ever-increasing amount of knowledge provided unique insights into the cellular, molecular, and genetic processes controlling this endosymbiosis. In addition, recent phylogenomic studies uncovered several genes that evolved to function specifically to control nodule formation and bacterial infection. However, despite this massive body of knowledge, the long-standing objective to engineer the nitrogen-fixing nodulation trait on non-leguminous crop plants has not been achieved yet. In this review, the unsolved questions and engineering strategies toward nitrogen-fixing nodulation in non-legume plants are discussed and highlighted.
Collapse
Affiliation(s)
- Rik Huisman
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| | - Rene Geurts
- Wageningen University, Department of Plant Sciences, Laboratory of Molecular Biology, Droevendaalsesteeg 1, Wageningen 6708PB, The Netherlands
| |
Collapse
|
17
|
Sahruzaini NA, Rejab NA, Harikrishna JA, Khairul Ikram NK, Ismail I, Kugan HM, Cheng A. Pulse Crop Genetics for a Sustainable Future: Where We Are Now and Where We Should Be Heading. FRONTIERS IN PLANT SCIENCE 2020; 11:531. [PMID: 32431724 PMCID: PMC7212832 DOI: 10.3389/fpls.2020.00531] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/07/2020] [Indexed: 05/12/2023]
Abstract
The last decade has witnessed dramatic changes in global food consumption patterns mainly because of population growth and economic development. Food substitutions for healthier eating, such as swapping regular servings of meat for protein-rich crops, is an emerging diet trend that may shape the future of food systems and the environment worldwide. To meet the erratic consumer demand in a rapidly changing world where resources become increasingly scarce due largely to anthropogenic activity, the need to develop crops that benefit both human health and the environment has become urgent. Legumes are often considered to be affordable plant-based sources of dietary proteins. Growing legumes provides significant benefits to cropping systems and the environment because of their natural ability to perform symbiotic nitrogen fixation, which enhances both soil fertility and water-use efficiency. In recent years, the focus in legume research has seen a transition from merely improving economically important species such as soybeans to increasingly turning attention to some promising underutilized species whose genetic resources hold the potential to address global challenges such as food security and climate change. Pulse crops have gained in popularity as an affordable source of food or feed; in fact, the United Nations designated 2016 as the International Year of Pulses, proclaiming their critical role in enhancing global food security. Given that many studies have been conducted on numerous underutilized pulse crops across the world, we provide a systematic review of the related literature to identify gaps and opportunities in pulse crop genetics research. We then discuss plausible strategies for developing and using pulse crops to strengthen food and nutrition security in the face of climate and anthropogenic changes.
Collapse
Affiliation(s)
- Nurul Amylia Sahruzaini
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Ardiyana Rejab
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Kusaira Khairul Ikram
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Centre for Research in Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
| | - Ismanizan Ismail
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Hazel Marie Kugan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
| | - Acga Cheng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- *Correspondence: Acga Cheng,
| |
Collapse
|
18
|
Wang J, Qin J, Sun P, Ma X, Yu J, Li Y, Sun S, Lei T, Meng F, Wei C, Li X, Guo H, Liu X, Xia R, Wang L, Ge W, Song X, Zhang L, Guo D, Wang J, Bao S, Jiang S, Feng Y, Li X, Paterson AH, Wang X. Polyploidy Index and Its Implications for the Evolution of Polyploids. Front Genet 2019; 10:807. [PMID: 31552101 PMCID: PMC6746930 DOI: 10.3389/fgene.2019.00807] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/02/2019] [Indexed: 11/13/2022] Open
Abstract
Polyploidy has contributed to the divergence and domestication of plants; however, estimation of the relative roles that different types of polyploidy have played during evolution has been difficult. Unbalanced and balanced gene removal was previously related to allopolyploidies and autopolyploidies, respectively. Here, to infer the types of polyploidies and evaluate their evolutionary effects, we devised a statistic, the Polyploidy-index or P-index, to characterize the degree of divergence between subgenomes of a polyploidy, to find whether there has been a balanced or unbalanced gene removal from the homoeologous regions. Based on a P-index threshold of 0.3 that distinguishes between known or previously inferred allo- or autopolyploidies, we found that 87.5% of 24 angiosperm paleo-polyploidies were likely produced by allopolyploidizations, responsible for establishment of major tribes such as Poaceae and Fabaceae, and large groups such as monocots and eudicots. These findings suggest that >99.7% of plant genomes likely derived directly from allopolyploidies, with autopolyploidies responsible for the establishment of only a few small genera, including Glycine, Malus, and Populus, each containing tens of species. Overall, these findings show that polyploids with high divergence between subgenomes (presumably allopolyploids) established the major plant groups, possibly through secondary contact between previously isolated populations and hybrid vigor associated with their re-joining.
Collapse
Affiliation(s)
- Jinpeng Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Science, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Qin
- Cereal & Oil Crop Institute, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, China
| | - Pengchuan Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xuelian Ma
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Jigao Yu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Yuxian Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Sangrong Sun
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Tianyu Lei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Fanbo Meng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Chendan Wei
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xinyu Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - He Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaojian Liu
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Ruiyan Xia
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Li Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Weina Ge
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Xiaoming Song
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Lan Zhang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Di Guo
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| | - Jinyu Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shoutong Bao
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Shan Jiang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Yishan Feng
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Xueping Li
- School of Life Sciences, North China University of Science and Technology, Tangshan, China
| | - Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Xiyin Wang
- School of Life Sciences, North China University of Science and Technology, Tangshan, China.,Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, China
| |
Collapse
|
19
|
Wu Z, Wang M, Yang S, Chen S, Chen X, Liu C, Wang S, Wang H, Zhang B, Liu H, Qin R, Wang X. A global coexpression network of soybean genes gives insights into the evolution of nodulation in nonlegumes and legumes. THE NEW PHYTOLOGIST 2019; 223:2104-2119. [PMID: 30977533 DOI: 10.1111/nph.15845] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
A coexpression network is a powerful tool for revealing genes' relationship with many biological processes. Mass transcriptomic and genomic data from different plant species provide the foundation for understanding the evolution of nodulation across the Viridiplantae at a systematic level. We used weighted coexpression network analysis (WGCNA) to mine a nodule-related module (NRM) in Glycine max. Comparative genomic analysis of 78 green plant species revealed that NRM genes are recruited from different evolutionary nodes along with gene duplication events. A set of core coexpressed genes within legumes may play vital roles in regulating nodule environments essential for nitrogen fixation, including oxygen concentrations, sulfur transport, and iron homeostasis (such as GmCHY). The regulation of these genes occurred mainly at the transcription level, although some of them, such as sulfate transporters, may also undergo positive selection at protein level. We revealed that ancient orthologs and duplication events before the origin of legumes were preadapted for symbiosis. Conserved coregulated genes found within legumes paved the way for nodule formation and nitrogen fixation. These findings provide significant insights into the evolution of nodulation and indicate promising candidates for identifying other key components of legume nodulation and nitrogen fixation.
Collapse
Affiliation(s)
- Zhihua Wu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Meirong Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Siyu Yang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shengcai Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Xu Chen
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Chang Liu
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Shixiang Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Haijiao Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Bao Zhang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Hong Liu
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Rui Qin
- Hubei Provincial Key Laboratory for Protection and Application of Special Plant Germplasm in Wuling Area of China, South-Central University for Nationalities, Wuhan, Hubei Province, 430074, China
| | - Xuelu Wang
- National Key Laboratory of Crop Genetic Improvement, Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| |
Collapse
|
20
|
Tan S, Debellé F, Gamas P, Frugier F, Brault M. Diversification of cytokinin phosphotransfer signaling genes in Medicago truncatula and other legume genomes. BMC Genomics 2019; 20:373. [PMID: 31088345 PMCID: PMC6518804 DOI: 10.1186/s12864-019-5724-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Accepted: 04/22/2019] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering root cortical cell divisions at the onset of nodule initiation. Cytokinin signaling is based on a Two-Component System (TCS) phosphorelay cascade, involving successively Cytokinin-binding Histidine Kinase receptors, phosphorelay proteins shuttling between the cytoplasm and the nucleus, and Type-B Response Regulator (RRB) transcription factors activating the expression of cytokinin primary response genes. Among those, Type-A Response Regulators (RRA) exert a negative feedback on the TCS signaling. To determine whether the legume plant nodulation capacity is linked to specific features of TCS proteins, a genome-wide identification was performed in six legume genomes (Cajanus cajan, pigeonpea; Cicer arietinum, chickpea; Glycine max, soybean; Phaseolus vulgaris, common bean; Lotus japonicus; Medicago truncatula). The diversity of legume TCS proteins was compared to the one found in two non-nodulating species, Arabidopsis thaliana and Vitis vinifera, which are references for functional analyses of TCS components and phylogenetic analyses, respectively. RESULTS A striking expansion of non-canonical RRBs was identified, notably leading to the emergence of proteins where the conserved phosphor-accepting aspartate residue is replaced by a glutamate or an asparagine. M. truncatula genome-wide expression datasets additionally revealed that only a limited subset of cytokinin-related TCS genes is highly expressed in different organs, namely MtCHK1/MtCRE1, MtHPT1, and MtRRB3, suggesting that this "core" module potentially acts in most plant organs including nodules. CONCLUSIONS Further functional analyses are required to determine the relevance of these numerous non-canonical TCS RRBs in symbiotic nodulation, as well as of canonical MtHPT1 and MtRRB3 core signaling elements.
Collapse
Affiliation(s)
- Sovanna Tan
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Frédéric Debellé
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Pascal Gamas
- LIPM, Université de Toulouse, INRA, CNRS, Castanet-Tolosan, France
| | - Florian Frugier
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| | - Mathias Brault
- IPS2 (Institute of Plant Sciences Paris-Saclay), CNRS, Université Paris-Sud, Université Paris-Diderot, INRA, Université d’Evry, Université Paris-Saclay, Rue de Noetzlin, 91190 Gif-sur-Yvette, France
| |
Collapse
|
21
|
ÇAKIR Ö, UÇARLI C, TARHAN Ç, PEKMEZ M, TURGUT-KARA N. Nutritional and health benefits of legumes and their distinctive genomic properties. FOOD SCIENCE AND TECHNOLOGY 2019. [DOI: 10.1590/fst.42117] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|
22
|
Fudge JB, Lee RH, Laurie RE, Mysore KS, Wen J, Weller JL, Macknight RC. Medicago truncatula SOC1 Genes Are Up-regulated by Environmental Cues That Promote Flowering. FRONTIERS IN PLANT SCIENCE 2018; 9:496. [PMID: 29755488 PMCID: PMC5934494 DOI: 10.3389/fpls.2018.00496] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2017] [Accepted: 04/03/2018] [Indexed: 05/20/2023]
Abstract
Like Arabidopsis thaliana, the flowering of the legume Medicago truncatula is promoted by long day (LD) photoperiod and vernalization. However, there are differences in the molecular mechanisms involved, with orthologs of two key Arabidopsis thaliana regulators, FLOWERING LOCUS C (FLC) and CONSTANS (CO), being absent or not having a role in flowering time function in Medicago. In Arabidopsis, the MADS-box transcription factor gene, SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (AtSOC1), plays a key role in integrating the photoperiodic and vernalization pathways. In this study, we set out to investigate whether the Medicago SOC1 genes play a role in regulating flowering time. Three Medicago SOC1 genes were identified and characterized (MtSOC1a-MtSOC1c). All three MtSOC1 genes, when heterologously expressed, were able to promote earlier flowering of the late-flowering Arabidopsis soc1-2 mutant. The three MtSOC1 genes have different patterns of expression. However, consistent with a potential role in flowering time regulation, all three MtSOC1 genes are expressed in the shoot apex and are up-regulated in the shoot apex of plants in response to LD photoperiods and vernalization. The up-regulation of MtSOC1 genes was reduced in Medicago fta1-1 mutants, indicating that they are downstream of MtFTa1. Insertion mutant alleles of Medicago soc1b do not flower late, suggestive of functional redundancy among Medicago SOC1 genes in promoting flowering.
Collapse
Affiliation(s)
- Jared B. Fudge
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Robyn H. Lee
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Rebecca E. Laurie
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Kirankumar S. Mysore
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - Jiangqi Wen
- Plant Biology Division, Samuel Roberts Noble Foundation, Ardmore, OK, United States
| | - James L. Weller
- School of Biological Sciences, University of Tasmania, Hobart, TAS, Australia
| | - Richard C. Macknight
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
- New Zealand Institute for Plant and Food Research Ltd., University of Otago, Dunedin, New Zealand
- *Correspondence: Richard C. Macknight,
| |
Collapse
|
23
|
Cai F, Watson BS, Meek D, Huhman DV, Wherritt DJ, Ben C, Gentzbittel L, Driscoll BT, Sumner LW, Bede JC. Medicago truncatula Oleanolic-Derived Saponins Are Correlated with Caterpillar Deterrence. J Chem Ecol 2017; 43:712-724. [PMID: 28744732 DOI: 10.1007/s10886-017-0863-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2017] [Revised: 06/06/2017] [Accepted: 06/21/2017] [Indexed: 11/24/2022]
Abstract
Plant resistance mechanisms to insect herbivory can potentially be bred into crops as an important strategy for integrated pest management. Medicago truncatula ecotypes inoculated with the rhizobium Ensifer medicae (Sinorhizobium medica) WSM419 were screened for resistance to herbivory by caterpillars of the beet armyworm, Spodoptera exigua, through leaf and whole plant choice studies; TN1.11 and F83005.5 are identified as the least and most deterrent ecotypes, respectively. In response to caterpillar herbivory, both ecotypes mount a robust burst of plant defensive jasmonate phytohormones. Restriction of caterpillars to either of these ecotypes does not adversely affect pest performance. This argues for an antixenosis (deterrence) resistance mechanism associated with the F83005.5 ecotype. Unbiased metabolomic profiling identified strong ecotype-specific differences in metabolite profile, particularly in the content of oleanolic-derived saponins that may act as antifeedants. Compared to the more susceptible ecotype, F83005.5 has higher levels of oleanolic-type zanhic acid- and medicagenic acid-derived compounds. Together, these data support saponin-mediated deterrence as a resistance mechanism of the F83005.5 ecotype and implicates these compounds as potential antifeedants that could be used in agricultural sustainable pest management strategies.
Collapse
Affiliation(s)
- Fanping Cai
- Department of Plant Science, McGill University, 21,111 Lakeshore, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Bonnie S Watson
- The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - David Meek
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - David V Huhman
- The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA
| | - Daniel J Wherritt
- Department of Chemistry, University of Texas at San Antonio, San Antonio, TX, 78249, USA
| | - Cecile Ben
- EcoLab, Université de Toulouse, Centre National de Recherche Scientifique, Institute National Polytechnique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Laurent Gentzbittel
- EcoLab, Université de Toulouse, Centre National de Recherche Scientifique, Institute National Polytechnique de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Brian T Driscoll
- Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada
| | - Lloyd W Sumner
- The Samuel Roberts Noble Foundation, Ardmore, OK, 73401, USA.,Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Jacqueline C Bede
- Department of Plant Science, McGill University, 21,111 Lakeshore, Ste-Anne-de-Bellevue, QC, H9X 3V9, Canada.
| |
Collapse
|
24
|
Le Signor C, Aimé D, Bordat A, Belghazi M, Labas V, Gouzy J, Young ND, Prosperi JM, Leprince O, Thompson RD, Buitink J, Burstin J, Gallardo K. Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds. THE NEW PHYTOLOGIST 2017; 214:1597-1613. [PMID: 28322451 DOI: 10.1111/nph.14500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/27/2017] [Indexed: 05/25/2023]
Abstract
Improving nutritional seed quality is an important challenge in grain legume breeding. However, the genes controlling the differential accumulation of globulins, which are major contributors to seed nutritional value in legumes, remain largely unknown. We combined a search for protein quantity loci with genome-wide association studies on the abundance of 7S and 11S globulins in seeds of the model legume species Medicago truncatula. Identified genomic regions and genes carrying polymorphisms linked to globulin variations were then cross-compared with pea (Pisum sativum), leading to the identification of candidate genes for the regulation of globulin abundance in this crop. Key candidates identified include genes involved in transcription, chromatin remodeling, post-translational modifications, transport and targeting of proteins to storage vacuoles. Inference of a gene coexpression network of 12 candidate transcription factors and globulin genes revealed the transcription factor ABA-insensitive 5 (ABI5) as a highly connected hub. Characterization of loss-of-function abi5 mutants in pea uncovered a role for ABI5 in controlling the relative abundance of vicilin, a sulfur-poor 7S globulin, in pea seeds. This demonstrates the feasibility of using genome-wide association studies in M. truncatula to reveal genes that can be modulated to improve seed nutritional value.
Collapse
Affiliation(s)
- Christine Le Signor
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Delphine Aimé
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Amandine Bordat
- Unité Mixte de Recherche (UMR) 1332 Biologie du Fruit et Pathologie, INRA, 33882, Villenave d'Ornon, France
| | - Maya Belghazi
- UMR 7286 - CRN2M, Centre d'Analyses Protéomiques de Marseille, CNRS, Aix-Marseille Université, Marseille, France
| | - Valérie Labas
- INRA, UMR85 Physiologie de la Reproduction et des Comportements-Centre National de la Recherche Scientifique (CNRS) UMR 7247-Université François Rabelais-Institut Français du Cheval et de l'Equitation, Laboratoire de Spectrométrie de Masse, Plate-forme d'Analyse Intégrative des Biomolécules, 37380, Nouzilly, France
| | - Jérôme Gouzy
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, INRA, Université de Toulouse, Castanet-Tolosan, France
| | - Nevin D Young
- Department of Plant Pathology, University of Minnesota, St Paul, MN, 55108, USA
| | - Jean-Marie Prosperi
- Genetic Improvement and Adaptation of Mediterranean and Tropical Plants (AGAP), INRA, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier Supagro, 34060, Montpellier, France
| | - Olivier Leprince
- Institut de recherche en horticulture et semences (IRHS), INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Richard D Thompson
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Julia Buitink
- Institut de recherche en horticulture et semences (IRHS), INRA, Agrocampus-Ouest, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Judith Burstin
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| | - Karine Gallardo
- Agroécologie, AgroSup Dijon, Institut National de la Recherche Agronomique (INRA), Université Bourgogne Franche-Comté, 21000, Dijon, France
| |
Collapse
|
25
|
Cullis C, Kunert KJ. Unlocking the potential of orphan legumes. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1895-1903. [PMID: 28003311 DOI: 10.1093/jxb/erw437] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Orphan, or underutilized, legumes are domesticated legumes with useful properties, but with less importance than major world crops due to use and supply constraints. However, they play a significant role in many developing countries, providing food security and nutrition to consumers, as well as income to resource-poor farmers. They have been largely neglected by both researchers and industry due to their limited economic importance in the global market. Orphan legumes are better adapted than the major legume crops to extreme soil and climatic conditions, with high tolerance to abiotic environmental stresses such as drought. As a stress response they can also produce compounds with pharmaceutical value. Orphan legumes are therefore a likely source of important traits for introduction into major crops to aid in combating the stresses associated with global climate change. Modern large-scale genomics techniques are now being applied to many of these previously understudied crops, with the first successes reported in the genomics area. However, greater investment of resources and manpower are necessary if the potential of orphan legumes is to be unlocked and applied in the future.
Collapse
Affiliation(s)
- Christopher Cullis
- Department of Biology, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Karl J Kunert
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| |
Collapse
|
26
|
Zheng F, Wu H, Zhang R, Li S, He W, Wong FL, Li G, Zhao S, Lam HM. Molecular phylogeny and dynamic evolution of disease resistance genes in the legume family. BMC Genomics 2016; 17:402. [PMID: 27229309 PMCID: PMC4881053 DOI: 10.1186/s12864-016-2736-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2015] [Accepted: 05/12/2016] [Indexed: 02/06/2023] Open
Abstract
Background Legumes are the second-most important crop family in agriculture for its economic and nutritional values. Disease resistance (R-) genes play an important role in responding to pathogen infections in plants. To further increase the yield of legume crops, we need a comprehensive understanding of the evolution of R-genes in the legume family. Results In this study, we developed a robust pipeline and identified a total of 4,217 R-genes in the genomes of seven sequenced legume species. A dramatic diversity of R-genes with structural variances indicated a rapid birth-and-death rate during the R-gene evolution in legumes. The number of R-genes transiently expanded and then quickly contracted after whole-genome duplications, which meant that R-genes were sensitive to subsequent diploidization. R proteins with the Coiled-coil (CC) domain are more conserved than others in legumes. Meanwhile, other types of legume R proteins with only one or two typical domains were subjected to higher rates of loss during evolution. Although R-genes evolved quickly in legumes, they tended to undergo purifying selection instead of positive selection during evolution. In addition, domestication events in some legume species preferentially selected for the genes directly involved in the plant-pathogen interaction pathway while suppressing those R-genes with low occurrence rates. Conclusions Our results provide insights into the dynamic evolution of R-genes in the legume family, which will be valuable for facilitating genetic improvements in the disease resistance of legume cultivars. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2736-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Fengya Zheng
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Haiyang Wu
- BGI-Shenzhen, Shenzhen, 518083, China.,HKU-BGI Bioinformatics Laboratory and Department of Computer Science, University of Hong Kong, Pofulam, Hong Kong
| | - Rongzhi Zhang
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | | | | | - Fuk-Ling Wong
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong
| | - Genying Li
- Crop research institution, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Shancen Zhao
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong. .,BGI-Shenzhen, Shenzhen, 518083, China.
| | - Hon-Ming Lam
- Centre for Soybean Research, Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, New Territories, Hong Kong.
| |
Collapse
|
27
|
Wang Z, Cheng K, Wan L, Yan L, Jiang H, Liu S, Lei Y, Liao B. Genome-wide analysis of the basic leucine zipper (bZIP) transcription factor gene family in six legume genomes. BMC Genomics 2015; 16:1053. [PMID: 26651343 PMCID: PMC4676100 DOI: 10.1186/s12864-015-2258-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 11/30/2015] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Plant bZIP proteins characteristically harbor a highly conserved bZIP domain with two structural features: a DNA-binding basic region and a leucine (Leu) zipper dimerization region. They have been shown to be diverse transcriptional regulators, playing crucial roles in plant development, physiological processes, and biotic/abiotic stress responses. Despite the availability of six completely sequenced legume genomes, a comprehensive investigation of bZIP family members in legumes has yet to be presented. RESULTS In this study, we identified 428 bZIP genes encoding 585 distinct proteins in six legumes, Glycine max, Medicago truncatula, Phaseolus vulgaris, Cicer arietinum, Cajanus cajan, and Lotus japonicus. The legume bZIP genes were categorized into 11 groups according to their phylogenetic relationships with genes from Arabidopsis. Four kinds of intron patterns (a-d) within the basic and hinge regions were defined and additional conserved motifs were identified, both presenting high group specificity and supporting the group classification. We predicted the DNA-binding patterns and the dimerization properties, based on the characteristic features in the basic and hinge regions and the Leu zipper, respectively, which indicated that some highly conserved amino acid residues existed across each major group. The chromosome distribution and analysis for WGD-derived duplicated blocks revealed that the legume bZIP genes have expanded mainly by segmental duplication rather than tandem duplication. Expression data further revealed that the legume bZIP genes were expressed constitutively or in an organ-specific, development-dependent manner playing roles in multiple seed developmental stages and tissues. We also detected several key legume bZIP genes involved in drought- and salt-responses by comparing fold changes of expression values in drought-stressed or salt-stressed roots and leaves. CONCLUSIONS In summary, this genome-wide identification, characterization and expression analysis of legume bZIP genes provides valuable information for understanding the molecular functions and evolution of the legume bZIP transcription factor family, and highlights potential legume bZIP genes involved in regulating tissue development and abiotic stress responses.
Collapse
Affiliation(s)
- Zhihui Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Ke Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Liyun Wan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China.
| |
Collapse
|
28
|
Kim TS, Raveendar S, Suresh S, Lee GA, Lee JR, Cho JH, Lee SY, Ma KH, Cho GT, Chung JW. Transcriptome Analysis of Two Vicia sativa Subspecies: Mining Molecular Markers to Enhance Genomic Resources for Vetch Improvement. Genes (Basel) 2015; 6:1164-82. [PMID: 26540077 PMCID: PMC4690033 DOI: 10.3390/genes6041164] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 10/16/2015] [Accepted: 10/19/2015] [Indexed: 11/26/2022] Open
Abstract
The vetch (Vicia sativa) is one of the most important annual forage legumes globally due to its multiple uses and high nutritional content. Despite these agronomical benefits, many drawbacks, including cyano-alanine toxin, has reduced the agronomic value of vetch varieties. Here, we used 454 technology to sequence the two V. sativa subspecies (ssp. sativa and ssp. nigra) to enrich functional information and genetic marker resources for the vetch research community. A total of 86,532 and 47,103 reads produced 35,202 and 18,808 unigenes with average lengths of 735 and 601 bp for V. sativa sativa and V. sativa nigra, respectively. Gene Ontology annotations and the cluster of orthologous gene classes were used to annotate the function of the Vicia transcriptomes. The Vicia transcriptome sequences were then mined for simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers. About 13% and 3% of the Vicia unigenes contained the putative SSR and SNP sequences, respectively. Among those SSRs, 100 were chosen for the validation and the polymorphism test using the Vicia germplasm set. Thus, our approach takes advantage of the utility of transcriptomic data to expedite a vetch breeding program.
Collapse
Affiliation(s)
- Tae-Sung Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 340-702, Korea.
| | - Sebastin Raveendar
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Sundan Suresh
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
- Department of Botany, Directorate of Distance Education, Madurai Kamaraj University, Madurai 625 021, India.
| | - Gi-An Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jung-Ro Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Joon-Hyeong Cho
- Department of Biological and Environmental Science, Dongguk University, Seoul 100-175, Korea.
| | - Sok-Young Lee
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Kyung-Ho Ma
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Gyu-Taek Cho
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| | - Jong-Wook Chung
- National Agrobiodiversity Centre, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Korea.
| |
Collapse
|
29
|
CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea. J Biosci 2015; 40:579-92. [PMID: 26333404 DOI: 10.1007/s12038-015-9545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.
Collapse
|
30
|
Chakraborty S, Salekdeh GH, Yang P, Woo SH, Chin CF, Gehring C, Haynes PA, Mirzaei M, Komatsu S. Proteomics of Important Food Crops in the Asia Oceania Region: Current Status and Future Perspectives. J Proteome Res 2015; 14:2723-44. [DOI: 10.1021/acs.jproteome.5b00211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
| | | | - Pingfang Yang
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Sun Hee Woo
- Chungbuk National University, Cheongju 362-763, Korea
| | - Chiew Foan Chin
- University of Nottingham Malaysia Campus, 43500 Semenyih, Selangor, Malaysia
| | - Chris Gehring
- King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia
| | | | | | - Setsuko Komatsu
- National Institute of Crop Science, Tsukuba, Ibaraki 305-8518, Japan
| |
Collapse
|
31
|
Nepal MP, Benson BV. CNL Disease Resistance Genes in Soybean and Their Evolutionary Divergence. Evol Bioinform Online 2015; 11:49-63. [PMID: 25922568 PMCID: PMC4395141 DOI: 10.4137/ebo.s21782] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 02/01/2015] [Accepted: 02/01/2015] [Indexed: 01/29/2023] Open
Abstract
Disease resistance genes (R-genes) encode proteins involved in detecting pathogen attack and activating downstream defense molecules. Recent availability of soybean genome sequences makes it possible to examine the diversity of gene families including disease-resistant genes. The objectives of this study were to identify coiled-coil NBS-LRR (= CNL) R-genes in soybean, infer their evolutionary relationships, and assess structural as well as functional divergence of the R-genes. Profile hidden Markov models were used for sequence identification and model-based maximum likelihood was used for phylogenetic analysis, and variation in chromosomal positioning, gene clustering, and functional divergence were assessed. We identified 188 soybean CNL genes nested into four clades consistent to their orthologs in Arabidopsis. Gene clustering analysis revealed the presence of 41 gene clusters located on 13 different chromosomes. Analyses of the K s-values and chromosomal positioning suggest duplication events occurring at varying timescales, and an extrapericentromeric positioning may have facilitated their rapid evolution. Each of the four CNL clades exhibited distinct patterns of gene expression. Phylogenetic analysis further supported the extrapericentromeric positioning effect on the divergence and retention of the CNL genes. The results are important for understanding the diversity and divergence of CNL genes in soybean, which would have implication in soybean crop improvement in future.
Collapse
Affiliation(s)
- Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| | - Benjamin V Benson
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
| |
Collapse
|
32
|
Lagunas B, Schäfer P, Gifford ML. Housing helpful invaders: the evolutionary and molecular architecture underlying plant root-mutualist microbe interactions. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:2177-86. [PMID: 25743160 PMCID: PMC4986721 DOI: 10.1093/jxb/erv038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 01/10/2015] [Accepted: 01/16/2015] [Indexed: 05/24/2023]
Abstract
Plant root rhizosphere interactions with mutualistic microbes are diverse and numerous, having evolved over time in response to selective pressures on plants to attain anchorage and nutrients. These relationships can be considered to be formed through a combination of architectural connections: molecular architecture interactions that control root-microbe perception and regulate the balance between host and symbiont and developmental architecture interactions that enable the microbes to be 'housed' in the root and enable the exchange of compounds. Recent findings that help to understand the common architecture that exists between nodulation and mycorrhizal interactions, and how this architecture could be re-tuned to develop new symbioses, are discussed here.
Collapse
Affiliation(s)
- B Lagunas
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - P Schäfer
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| | - M L Gifford
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK
| |
Collapse
|
33
|
Bajaj D, Upadhyaya HD, Khan Y, Das S, Badoni S, Shree T, Kumar V, Tripathi S, Gowda CLL, Singh S, Sharma S, Tyagi AK, Chattopdhyay D, Parida SK. A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Sci Rep 2015; 5:9264. [PMID: 25786576 PMCID: PMC4365403 DOI: 10.1038/srep09264] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 02/13/2015] [Indexed: 01/02/2023] Open
Abstract
High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic potential (82-96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8-25.8% with LOD: 7.0-13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1-171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea.
Collapse
Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Yusuf Khan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tanima Shree
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasis Chattopdhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| |
Collapse
|
34
|
Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH. Chromosome Res 2015; 23:253-66. [PMID: 25634499 DOI: 10.1007/s10577-014-9464-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/22/2022]
Abstract
Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes.
Collapse
|
35
|
Kamphuis LG, Hane JK, Nelson MN, Gao L, Atkins CA, Singh KB. Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:14-25. [PMID: 25060816 PMCID: PMC4309465 DOI: 10.1111/pbi.12229] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/27/2014] [Accepted: 06/12/2014] [Indexed: 05/18/2023]
Abstract
Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome-derived gene-based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome-derived markers and 66 BAC-end sequence-derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map.
Collapse
Affiliation(s)
- Lars G Kamphuis
- CSIRO Plant IndustryWembley, WA, Australia
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
| | | | - Matthew N Nelson
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
- The School of Plant Biology, University of Western AustraliaCrawley, WA, Australia
| | | | - Craig A Atkins
- The School of Plant Biology, University of Western AustraliaCrawley, WA, Australia
| | - Karam B Singh
- CSIRO Plant IndustryWembley, WA, Australia
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
- *Correspondence (Tel +61 8 9333 6320; fax +61 8 9383 9673; email )
| |
Collapse
|
36
|
Weller JL, Ortega R. Genetic control of flowering time in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:207. [PMID: 25914700 PMCID: PMC4391241 DOI: 10.3389/fpls.2015.00207] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 03/15/2015] [Indexed: 05/18/2023]
Abstract
The timing of flowering, and in particular the degree to which it is responsive to the environment, is a key factor in the adaptation of a given species to various eco-geographic locations and agricultural practices. Flowering time variation has been documented in many crop legumes, and selection for specific variants has permitted significant expansion and improvement in cultivation, from prehistoric times to the present day. Recent advances in legume genomics have accelerated the process of gene identification and functional analysis, and opened up new prospects for a molecular understanding of flowering time adaptation in this important crop group. Within the legumes, two species have been prominent in flowering time studies; the vernalization-responsive long-day species pea (Pisum sativum) and the warm-season short-day plant soybean (Glycine max). Analysis of flowering in these species is now being complemented by reverse genetics capabilities in the model legumes Medicago truncatula and Lotus japonicus, and the emergence of genome-scale resources in a range of other legumes. This review will outline the insights gained from detailed forward genetic analysis of flowering time in pea and soybean, highlighting the importance of light perception, the circadian clock and the FT family of flowering integrators. It discusses the current state of knowledge on genetic mechanisms for photoperiod and vernalization response, and concludes with a broader discussion of flowering time adaptation across legumes generally.
Collapse
Affiliation(s)
- James L. Weller
- *Correspondence: James L. Weller, School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart, TAS 7001, Australia
| | | |
Collapse
|
37
|
Brutnell TP, Bennetzen JL, Vogel JP. Brachypodium distachyon and Setaria viridis: Model Genetic Systems for the Grasses. ANNUAL REVIEW OF PLANT BIOLOGY 2015; 66:465-85. [PMID: 25621515 DOI: 10.1146/annurev-arplant-042811-105528] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
The family of grasses encompasses the world's most important food, feed, and bioenergy crops, yet we are only now beginning to develop the genetic resources to explore the diversity of form and function that underlies economically important traits. Two emerging model systems, Brachypodium distachyon and Setaria viridis, promise to greatly accelerate the process of gene discovery in the grasses and to serve as bridges in the exploration of panicoid and pooid grasses, arguably two of the most important clades of plants from a food security perspective. We provide both a historical view of the development of plant model systems and highlight several recent reports that are providing these developing communities with the tools for gene discovery and pathway engineering.
Collapse
|
38
|
Morton JB, Benedito VA, Panaccione DG, Jenks MA. Potential for Industrial Application of Microbes in Symbioses that Influence Plant Productivity and Sustainability in Agricultural, Natural, or Restored Ecosystems. Ind Biotechnol (New Rochelle N Y) 2014. [DOI: 10.1089/ind.2014.0014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Joseph B. Morton
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Vagner A. Benedito
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Daniel G. Panaccione
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| | - Matthew A. Jenks
- Division of Plant and Soil Sciences, Davis College of Agriculture, Natural Resources and Design, West Virginia University, Morgantown, WV
| |
Collapse
|
39
|
Laloum T, Baudin M, Frances L, Lepage A, Billault-Penneteau B, Cerri MR, Ariel F, Jardinaud MF, Gamas P, de Carvalho-Niebel F, Niebel A. Two CCAAT-box-binding transcription factors redundantly regulate early steps of the legume-rhizobia endosymbiosis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:757-68. [PMID: 24930743 DOI: 10.1111/tpj.12587] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 04/30/2014] [Accepted: 06/02/2014] [Indexed: 05/08/2023]
Abstract
During endosymbiotic interactions between legume plants and nitrogen-fixing rhizobia, successful root infection by bacteria and nodule organogenesis requires the perception and transduction of bacterial lipo-chitooligosaccharidic signal called Nod factor (NF). NF perception in legume roots leads to the activation of an early signaling pathway and of a set of symbiotic genes which is controlled by specific early transcription factors (TFs) including CYCLOPS/IPD3, NSP1, NSP2, ERN1 and NIN. In this study, we bring convincing evidence that the Medicago truncatula CCAAT-box-binding NF-YA1 TF, previously associated with later stages of rhizobial infection and nodule meristem formation is, together with its closest homolog NF-YA2, also an essential positive regulator of the NF-signaling pathway. Here we show that NF-YA1 and NF-YA2 are both expressed in epidermal cells responding to NFs and their knock-down by reverse genetic approaches severely affects the NF-induced expression of symbiotic genes and rhizobial infection. Further over-expression, transactivation and ChIP-PCR approaches indicate that NF-YA1 and NF-YA2 function, at least in part, via the direct activation of ERN1. We thus propose a model in which NF-YA1 and NF-YA2 appear as early symbiotic regulators acting downstream of DMI3 and NIN and possibly within the same regulatory complexes as NSP1/2 to directly activate the expression of ERN1.
Collapse
Affiliation(s)
- Tom Laloum
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, F-31326, Castanet-Tolosan, France; Laboratoire des Interactions Plantes-Microorganismes (LIPM), CNRS, UMR2594, F-31326, Castanet-Tolosan, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
40
|
Zielonka S, Ernst AM, Hawat S, Twyman RM, Prüfer D, Noll GA. Characterization of five subgroups of the sieve element occlusion gene family in Glycine max reveals genes encoding non-forisome P-proteins, forisomes and forisome tails. PLANT MOLECULAR BIOLOGY 2014; 86:51-67. [PMID: 24928491 DOI: 10.1007/s11103-014-0211-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Accepted: 06/04/2014] [Indexed: 06/03/2023]
Abstract
P-proteins are structural phloem proteins discussed to be involved in the rapid sealing of injured sieve elements. P-proteins are found in all dicotyledonous and some monocotyledonous plants, but additional crystalloid P-proteins, known as forisomes, have evolved solely in the Fabaceae. Both types are encoded by members of the sieve element occlusion (SEO) gene family, which comprises seven phylogenetic subgroups. The Fabaceae-specific subgroup 1 contains genes encoding forisome subunits in e.g. Medicago truncatula, Vicia faba, Dipteryx panamensis and Canavalia gladiata whereas basal subgroup 5 encodes P-proteins in Nicotiana tabacum (tobacco) and Arabidopsis thaliana. The function of remaining subgroups is still unknown. We chose Glycine max (soybean) as a model to investigate SEO proteins representing different subgroups in one species. We isolated native P-proteins to determine the SEO protein composition and analyzed the expression pattern, localization and structure of the G. max SEO proteins representing five of the subgroups. We found that subgroup 1 GmSEO genes encode forisome subunits, a member of subgroup 5 encodes a non-forisome P-protein and subgroup 2 GmSEO genes encode the components of forisome tails, which are present in a restricted selection of Fabaceaen species. We therefore present the first molecular characterization of a Fabaceae non-forisome P-protein and the first evidence that forisome tails are encoded by a phylogenetically-distinct branch of the SEO gene family.
Collapse
Affiliation(s)
- Sascia Zielonka
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Schlossplatz 8, 48143, Münster, Germany
| | | | | | | | | | | |
Collapse
|
41
|
Serwatowska J, Roque E, Gómez-Mena C, Constantin GD, Wen J, Mysore KS, Lund OS, Johansen E, Beltrán JP, Cañas LA. Two euAGAMOUS genes control C-function in Medicago truncatula. PLoS One 2014; 9:e103770. [PMID: 25105497 PMCID: PMC4126672 DOI: 10.1371/journal.pone.0103770] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 07/02/2014] [Indexed: 02/07/2023] Open
Abstract
C-function MADS-box transcription factors belong to the AGAMOUS (AG) lineage and specify both stamen and carpel identity and floral meristem determinacy. In core eudicots, the AG lineage is further divided into two branches, the euAG and PLE lineages. Functional analyses across flowering plants strongly support the idea that duplicated AG lineage genes have different degrees of subfunctionalization of the C-function. The legume Medicago truncatula contains three C-lineage genes in its genome: two euAG genes (MtAGa and MtAGb) and one PLENA-like gene (MtSHP). This species is therefore a good experimental system to study the effects of gene duplication within the AG subfamily. We have studied the respective functions of each euAG genes in M. truncatula employing expression analyses and reverse genetic approaches. Our results show that the M. truncatula euAG- and PLENA-like genes are an example of subfunctionalization as a result of a change in expression pattern. MtAGa and MtAGb are the only genes showing a full C-function activity, concomitant with their ancestral expression profile, early in the floral meristem, and in the third and fourth floral whorls during floral development. In contrast, MtSHP expression appears late during floral development suggesting it does not contribute significantly to the C-function. Furthermore, the redundant MtAGa and MtAGb paralogs have been retained which provides the overall dosage required to specify the C-function in M. truncatula.
Collapse
Affiliation(s)
- Joanna Serwatowska
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Edelín Roque
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Concepción Gómez-Mena
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Gabriela D. Constantin
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - Jiangqi Wen
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America
| | - Kirankumar S. Mysore
- Plant Biology Division, The Samuel Roberts Noble Foundation, Ardmore, Oklahoma, United States of America
| | - Ole S. Lund
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - Elisabeth Johansen
- Department of Plant Biology, Danish Institute of Agricultural Sciences, Frederiksberg C, Denmark
| | - José Pío Beltrán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
| | - Luis A. Cañas
- Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV). Ciudad Politécnica de la Innovación, Valencia, Spain
- * E-mail:
| |
Collapse
|
42
|
Lin Y, Cheng Y, Jin J, Jin X, Jiang H, Yan H, Cheng B. Genome duplication and gene loss affect the evolution of heat shock transcription factor genes in legumes. PLoS One 2014; 9:e102825. [PMID: 25047803 PMCID: PMC4105503 DOI: 10.1371/journal.pone.0102825] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2013] [Accepted: 06/25/2014] [Indexed: 11/18/2022] Open
Abstract
Whole-genome duplication events (polyploidy events) and gene loss events have played important roles in the evolution of legumes. Here we show that the vast majority of Hsf gene duplications resulted from whole genome duplication events rather than tandem duplication, and significant differences in gene retention exist between species. By searching for intraspecies gene colinearity (microsynteny) and dating the age distributions of duplicated genes, we found that genome duplications accounted for 42 of 46 Hsf-containing segments in Glycine max, while paired segments were rarely identified in Lotus japonicas, Medicago truncatula and Cajanus cajan. However, by comparing interspecies microsynteny, we determined that the great majority of Hsf-containing segments in Lotus japonicas, Medicago truncatula and Cajanus cajan show extensive conservation with the duplicated regions of Glycine max. These segments formed 17 groups of orthologous segments. These results suggest that these regions shared ancient genome duplication with Hsf genes in Glycine max, but more than half of the copies of these genes were lost. On the other hand, the Glycine max Hsf gene family retained approximately 75% and 84% of duplicated genes produced from the ancient genome duplication and recent Glycine-specific genome duplication, respectively. Continuous purifying selection has played a key role in the maintenance of Hsf genes in Glycine max. Expression analysis of the Hsf genes in Lotus japonicus revealed their putative involvement in multiple tissue-/developmental stages and responses to various abiotic stimuli. This study traces the evolution of Hsf genes in legume species and demonstrates that the rates of gene gain and loss are far from equilibrium in different species.
Collapse
Affiliation(s)
- Yongxiang Lin
- Key Lab of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
- Crop Research Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China
| | - Ying Cheng
- Key Lab of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
| | - Jing Jin
- Key Lab of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
| | - Xiaolei Jin
- Key Lab of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
| | - Haiyang Jiang
- Key Lab of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
| | - Hanwei Yan
- Key Lab of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
| | - Beijiu Cheng
- Key Lab of Crop Biology of Anhui Province, School of Life Sciences, Anhui Agricultural University, Hefei, Anhui, China
| |
Collapse
|
43
|
Kroc M, Koczyk G, Święcicki W, Kilian A, Nelson MN. New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1237-1249. [PMID: 24633641 DOI: 10.1007/s00122-014-2294-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2013] [Accepted: 02/21/2014] [Indexed: 06/03/2023]
Abstract
This is the first clear evidence of duplication and/or triplication of large chromosomal regions in a genome of a Genistoid legume, the most basal clade of Papilionoid legumes. Lupinus angustifolius L. (narrow-leafed lupin) is the most widely cultivated species of Genistoid legume, grown for its high-protein grain. As a member of this most basal clade of Papilionoid legumes, L. angustifolius serves as a useful model for exploring legume genome evolution. Here, we report an improved reference genetic map of L. angustifolius comprising 1207 loci, including 299 newly developed Diversity Arrays Technology markers and 54 new gene-based PCR markers. A comparison between the L. angustifolius and Medicago truncatula genomes was performed using 394 sequence-tagged site markers acting as bridging points between the two genomes. The improved L. angustifolius genetic map, the updated M. truncatula genome assembly and the increased number of bridging points between the genomes together substantially enhanced the resolution of synteny and chromosomal colinearity between these genomes compared to previous reports. While a high degree of syntenic fragmentation was observed that was consistent with the large evolutionary distance between the L. angustifolius and M. truncatula genomes, there were striking examples of conserved colinearity of loci between these genomes. Compelling evidence was found of large-scale duplication and/or triplication in the L. angustifolius genome, consistent with one or more ancestral polyploidy events.
Collapse
Affiliation(s)
- Magdalena Kroc
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479, Poznan, Poland
| | | | | | | | | |
Collapse
|
44
|
Kudapa H, Ramalingam A, Nayakoti S, Chen X, Zhuang WJ, Liang X, Kahl G, Edwards D, Varshney RK. Functional genomics to study stress responses in crop legumes: progress and prospects. FUNCTIONAL PLANT BIOLOGY : FPB 2013; 40:1221-1233. [PMID: 32481190 DOI: 10.1071/fp13191] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 08/22/2013] [Indexed: 06/11/2023]
Abstract
Legumes are important food crops worldwide, contributing to more than 33% of human dietary protein. The production of crop legumes is frequently impacted by abiotic and biotic stresses. It is therefore important to identify genes conferring resistance to biotic stresses and tolerance to abiotic stresses that can be used to both understand molecular mechanisms of plant response to the environment and to accelerate crop improvement. Recent advances in genomics offer a range of approaches such as the sequencing of genomes and transcriptomes, gene expression microarray as well as RNA-seq based gene expression profiling, and map-based cloning for the identification and isolation of biotic and abiotic stress-responsive genes in several crop legumes. These candidate stress associated genes should provide insights into the molecular mechanisms of stress tolerance and ultimately help to develop legume varieties with improved stress tolerance and productivity under adverse conditions. This review provides an overview on recent advances in the functional genomics of crop legumes that includes the discovery as well as validation of candidate genes.
Collapse
Affiliation(s)
- Himabindu Kudapa
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Abirami Ramalingam
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Swapna Nayakoti
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| | - Xiaoping Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Wei-Jian Zhuang
- Fujian Provincial Key Laboratory of Plant Molecular and Cell Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, PR China
| | - Xuanqiang Liang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Guenter Kahl
- Goethe University Frankfurt am Main, Institute for Molecular BioSciences, Max-von-Laue-Str. 9, Frankfurt am Main 60438, Germany
| | - David Edwards
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, St Lucia, Qld 4072, Australia
| | - Rajeev K Varshney
- International Crops Research Institute for the Semiarid Tropics (ICRISAT), Patancheru 502324, India
| |
Collapse
|
45
|
Lestari P, Van K, Lee J, Kang YJ, Lee SH. Gene divergence of homeologous regions associated with a major seed protein content QTL in soybean. FRONTIERS IN PLANT SCIENCE 2013; 4:176. [PMID: 23761803 PMCID: PMC3672674 DOI: 10.3389/fpls.2013.00176] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 05/17/2013] [Indexed: 05/28/2023]
Abstract
Understanding several modes of duplication contributing on the present genome structure is getting an attention because it could be related to numerous agronomically important traits. Since soybean serves as a rich protein source for animal feeds and human consumption, breeding efforts in soybean have been directed toward enhancing seed protein content. The publicly available soybean sequences and its genomically featured elements facilitate comprehending of quantitative trait loci (QTL) for seed protein content in concordance with homeologous regions in soybean genome. Although parts of chromosome (Chr) 20 and Chr 10 showed synteny, QTLs for seed protein content present only on Chr 20. Using comparative analysis of gene contents in recently duplicated genomic regions harboring QTL for protein/oil content on Chrs 20 and 10, a total of 27 genes are present in duplicated regions of both Chrs. Notably, 4 tandem duplicates of the putative homeobox protein 22 (HB22) are present only on Chr 20 and this Medicago truncatula homolog expressed in endosperm at seed filling stage. These tandem duplicates could contribute on the protein/oil QTL of Chr 20. Our study suggests that non-shared gene contents within the duplicated genomic regions might lead to absence/presence of QTL related to protein/oil content.
Collapse
Affiliation(s)
- Puji Lestari
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National UniversitySeoul, Korea
- Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and DevelopmentBogor, Indonesia
| | - Kyujung Van
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National UniversitySeoul, Korea
| | - Jayern Lee
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National UniversitySeoul, Korea
| | - Yang Jae Kang
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National UniversitySeoul, Korea
| | - Suk-Ha Lee
- Department of Plant Science, Research Institute for Agriculture and Life Sciences, Seoul National UniversitySeoul, Korea
- Plant Genomics and Breeding Institute, Seoul National UniversitySeoul, Korea
| |
Collapse
|
46
|
Jain M, Misra G, Patel RK, Priya P, Jhanwar S, Khan AW, Shah N, Singh VK, Garg R, Jeena G, Yadav M, Kant C, Sharma P, Yadav G, Bhatia S, Tyagi AK, Chattopadhyay D. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:715-29. [PMID: 23489434 DOI: 10.1111/tpj.12173] [Citation(s) in RCA: 231] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 02/27/2013] [Accepted: 03/04/2013] [Indexed: 05/17/2023]
Abstract
Cicer arietinum L. (chickpea) is the third most important food legume crop. We have generated the draft sequence of a desi-type chickpea genome using next-generation sequencing platforms, bacterial artificial chromosome end sequences and a genetic map. The 520-Mb assembly covers 70% of the predicted 740-Mb genome length, and more than 80% of the gene space. Genome analysis predicts the presence of 27,571 genes and 210 Mb as repeat elements. The gene expression analysis performed using 274 million RNA-Seq reads identified several tissue-specific and stress-responsive genes. Although segmental duplicated blocks are observed, the chickpea genome does not exhibit any indication of recent whole-genome duplication. Nucleotide diversity analysis provides an assessment of a narrow genetic base within the chickpea cultivars. We have developed a resource for genetic markers by comparing the genome sequences of one wild and three cultivated chickpea genotypes. The draft genome sequence is expected to facilitate genetic enhancement and breeding to develop improved chickpea varieties.
Collapse
Affiliation(s)
- Mukesh Jain
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Bellieny-Rabelo D, Oliveira AEA, Venancio TM. Impact of whole-genome and tandem duplications in the expansion and functional diversification of the F-box family in legumes (Fabaceae). PLoS One 2013; 8:e55127. [PMID: 23390519 PMCID: PMC3563651 DOI: 10.1371/journal.pone.0055127] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Accepted: 12/18/2012] [Indexed: 12/16/2022] Open
Abstract
F-box proteins constitute a large gene family that regulates processes from hormone signaling to stress response. F-box proteins are the substrate recognition modules of SCF E3 ubiquitin ligases. Here we report very distinct trends in family size, duplication, synteny and transcription of F-box genes in two nitrogen-fixing legumes, Glycine max (soybean) and Medicago truncatula (alfafa). While the soybean FBX genes emerged mainly through segmental duplications (including whole-genome duplications), M. truncatula genome is dominated by locally-duplicated (tandem) F-box genes. Many of these young FBX genes evolved complex transcriptional patterns, including preferential transcription in different tissues, suggesting that they have probably been recruited to important biochemical pathways (e.g. nodulation and seed development).
Collapse
Affiliation(s)
- Daniel Bellieny-Rabelo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Antônia Elenir Amâncio Oliveira
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Thiago Motta Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, Rio de Janeiro, Brazil
| |
Collapse
|
48
|
Sreenivasulu N, Wobus U. Seed-development programs: a systems biology-based comparison between dicots and monocots. ANNUAL REVIEW OF PLANT BIOLOGY 2013; 64:189-217. [PMID: 23451786 DOI: 10.1146/annurev-arplant-050312-120215] [Citation(s) in RCA: 143] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Seeds develop differently in dicots and monocots, especially with respect to the major storage organs. High-resolution transcriptome data have provided the first insights into the molecular networks and pathway interactions that function during the development of individual seed compartments. Here, we review mainly recent data obtained by systems biology-based approaches, which have allowed researchers to construct and model complex metabolic networks and fluxes and identify key limiting steps in seed development. Comparative coexpression network analyses define evolutionarily conservative (FUS3/ABI3/LEC1) and divergent (LEC2) networks in dicots and monocots. Finally, we discuss the determination of seed size--an important yield-related characteristic--as mediated by a number of processes (maternal and epigenetic factors, fine-tuned regulation of cell death in distinct seed compartments, and endosperm growth) and underlying genes defined through mutant analyses. Altogether, systems approaches can make important contributions toward a more complete and holistic knowledge of seed biology and thus support strategies for knowledge-based molecular breeding.
Collapse
Affiliation(s)
- Nese Sreenivasulu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Gatersleben, Germany.
| | | |
Collapse
|
49
|
Abstract
Sequencing of mRNA using next-generation sequencing (NGS) technologies (RNA-seq) has the potential to reveal unprecedented complexity of the transcriptomes. The transcriptome sequencing of an organism provides quick insights into the gene space, opportunity to isolate genes of interest, development of functional markers, quantitation of gene expression, and comparative genomic studies. Although becoming cheaper, transcriptome sequencing still remains an expensive endeavor. Further, the assembly of millions and billions of RNA-seq reads to construct the complete transcriptome poses great informatics challenges. Here, first we outline various important issues from experimental design to data analysis, including various strategies of transcriptome assembly, which need substantial consideration for a successful RNA-seq experiment. Further, we describe a method for using RNA-seq to characterize the transcriptome of a plant species, taking the example of a legume crop plant chickpea. Our aim is to provide a quick start guide to the nonexpert researchers for NGS-based transcriptome analysis.
Collapse
Affiliation(s)
- Rohini Garg
- National Institute of Plant Genome Research, New Delhi, India
| | | |
Collapse
|