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Azam MG, Sarker U, Hossain MA, Mahabubul Alam AKM, Islam MR, Hossain N, Alamri S. Phenotypic diversity in qualitative and quantitative traits for selection of high yield potential field pea genotypes. Sci Rep 2024; 14:18561. [PMID: 39122809 PMCID: PMC11316029 DOI: 10.1038/s41598-024-69448-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024] Open
Abstract
Field pea (Pisum sativum L.) needs improvement to increase productivity due to its high price and demand. However, the incidence of powdery mildew (PM) disease limits its production. This study aimed to analyze the diversity of qualitative and quantitative traits against powdery mildew resistance by utilizing cluster and principal component analysis to explore PM resistance high-yield potential field peas. Shannon-Weaver's diversity index (H') displayed high intra-genotype diversity for quantitative and qualitative aspects. Heterogeneity was identified for resistance against powdery mildew infections. Eighty-five genotypes were divided into five groups using Mohalanobis generalized distance (D2) statistics. The highest inter-cluster D2 value was observed between clusters 2 and 3 (11.89) while the lowest value was found between clusters 3 and 4 (2.06). Most of the genotypes had noticeable differences, so these could be employed in a crossing scheme. Twelve genotypes were extremely resistant, 29 genotypes were resistant, 25 genotypes were moderately resistant, 18 genotypes were fairly susceptible, and 1 genotype was susceptible to powdery mildew disease. Among 29 resistant genotypes, BFP77, BFP74, BFP63, BFP62, BFP43, and BFP80 were high yielders and, could be used directly and/or transferred through hybridization to high-yielding disease-susceptible genotypes. Among the 25 moderately resistant genotypes, BFP78, BFP45, BFP79, and BFP48 were found to be high yielders. In principal component analysis (PCA), the first four PCs with Eigen values > 1 accounted for 88.4% variability for quantitative traits. Clustering sorted genotypes into five groups, where groups 1 to 5 assembled 37, 28, 1, 8, and 11 genotypes, respectively. Genotypes of cluster 4 were identified as high yielders with its attributes. Pearson correlation significantly and positively correlated across all traits except for PM. This variation suggested that there is a mechanism to select promising genotypes for field pea breeding. Considering all features, BFP78, BFP77, BFP74, BFP63, BFP62, BFP45, BFP79, and BFP80 could be preferred as high yielders and PM resistance owing to longer pod lengths, seeds per pod and pods per plant.
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Affiliation(s)
- Mohammad Golam Azam
- Pulses Research Centre, Bangladesh Agricultural Research Institute, Ishurdi, Pabna, 6620, Bangladesh
| | - Umakanta Sarker
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur, 1706, Bangladesh.
| | - Mohammad Amir Hossain
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - A K M Mahabubul Alam
- Pulses Research Sub-Station, Bangladesh Agricultural Research Institute, Gazipur, 1701, Bangladesh
| | - Mohammad Rafiqul Islam
- Agronomy Division, Regional Agricultural Research Station, Bangladesh Agricultural Research Institute, Pabna, 6620, Bangladesh
| | - Nazmul Hossain
- Department of Agronomy, Iowa State University, Ames, IA, 50010, USA
| | - Saud Alamri
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia
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Liu N, Lyu X, Zhang X, Zhang G, Zhang Z, Guan X, Chen X, Yang X, Feng Z, Gao Q, Shi W, Deng Y, Sheng K, Ou J, Zhu Y, Wang B, Bu Y, Zhang M, Zhang L, Zhao T, Gong Y. Reference genome sequence and population genomic analysis of peas provide insights into the genetic basis of Mendelian and other agronomic traits. Nat Genet 2024:10.1038/s41588-024-01867-8. [PMID: 39103648 DOI: 10.1038/s41588-024-01867-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/08/2024] [Indexed: 08/07/2024]
Abstract
Peas are essential for human nutrition and played a crucial role in the discovery of Mendelian laws of inheritance. In this study, we assembled the genome of the elite vegetable pea cultivar 'Zhewan No. 1' at the chromosome level and analyzed resequencing data from 314 accessions, creating a comprehensive map of genetic variation in peas. We identified 235 candidate loci associated with 57 important agronomic traits through genome-wide association studies. Notably, we pinpointed the causal gene haplotypes responsible for four Mendelian traits: stem length (Le/le), flower color (A/a), cotyledon color (I/i) and seed shape (R/r). Additionally, we discovered the genes controlling pod form (Mendelian P/p) and hilum color. Our study also involved constructing a gene expression atlas across 22 tissues, highlighting key gene modules related to pod and seed development. These findings provide valuable pea genomic information and will facilitate the future genome-informed improvement of pea crops.
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Affiliation(s)
- Na Liu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Xiaolong Lyu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueying Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guwen Zhang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Ziqian Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xueying Guan
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyang Chen
- Station of Zhejiang Seed Management, Hangzhou, China
| | - Xiaoming Yang
- Crop Research Institute, Gansu Academy of Agricultural Sciences, Lanzhou, China
| | - Zhijuan Feng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qiang Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Wanghong Shi
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Yayuan Deng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Hainan Institute of Zhejiang University, Sanya, China
| | - Kuang Sheng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Jinwen Ou
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yumeng Zhu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bin Wang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yuanpeng Bu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Mingfang Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Sanya, China.
| | - Liangsheng Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Yazhouwan National Laboratory, Sanya, China.
| | - Ting Zhao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
| | - Yaming Gong
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Zhejiang Xianghu Laboratory, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China.
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Burillo E, Ortega R, Vander Schoor JK, Martínez-Fernández I, Weller JL, Bombarely A, Balanzà V, Ferrándiz C. Seed production determines the entrance to dormancy of the inflorescence meristem of Pisum sativum and the end of the flowering period. PHYSIOLOGIA PLANTARUM 2024; 176:e14425. [PMID: 38982330 DOI: 10.1111/ppl.14425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 06/04/2024] [Accepted: 06/23/2024] [Indexed: 07/11/2024]
Abstract
Flowering plants adjust their reproductive period to maximize the success of the offspring. Monocarpic plants, those with a single reproductive cycle that precedes plant senescence and death, tightly regulate both flowering initiation and flowering cessation. The end of the flowering period involves the arrest of the inflorescence meristem activity, known as proliferative arrest, in what has been interpreted as an evolutionary adaptation to maximize the allocation of resources to seed production and the viability of the progeny. Factors influencing proliferative arrest were described for several monocarpic plant species many decades ago, but only in the last few years studies performed in Arabidopsis have allowed to approach proliferative arrest regulation in a comprehensive manner by studying the physiology, hormone dynamics, and genetic factors involved in its regulation. However, these studies remain restricted to Arabidopsis and there is a need to expand our knowledge to other monocarpic species to propose general mechanisms controlling the process. In this work, we have characterized proliferative arrest in Pisum sativum, trying to parallel available studies in Arabidopsis to maximize this comparative framework. We have assessed quantitatively the role of fruits/seeds in the process, the influence of the positional effect of these fruits/seeds in the behavior of the inflorescence meristem, and the transcriptomic changes in the inflorescence associated with the arrested state of the meristem. Our results support a high conservation of the factors triggering arrest in pea and Arabidopsis, but also reveal differences reinforcing the need to perform similar studies in other species.
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Affiliation(s)
- Eduardo Burillo
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia, Valencia, Spain
| | - Raul Ortega
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Jacqueline K Vander Schoor
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Irene Martínez-Fernández
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia, Valencia, Spain
| | - James L Weller
- School of Biological Sciences, University of Tasmania, Hobart, Tasmania, Australia
- ARC Centre of Excellence for Plant Success in Nature and Agriculture, University of Tasmania, Hobart, Tasmania, Australia
| | - Aureliano Bombarely
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia, Valencia, Spain
| | - Vicente Balanzà
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia, Valencia, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universitat Politècnica de Valencia, Valencia, Spain
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Li L, Xu JB, Zhu ZW, Ma R, Wu XZ, Geng YK. Genome-wide identification and expression analysis of the SPL transcription factor family and its response to abiotic stress in Pisum sativum L. BMC Genomics 2024; 25:539. [PMID: 38822248 PMCID: PMC11140923 DOI: 10.1186/s12864-024-10262-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 03/27/2024] [Indexed: 06/02/2024] Open
Abstract
Squamous promoter binding protein-like (SPL) genes encode plant-specific transcription factors (TFs) that play essential roles in modulating plant growth, development, and stress response. Pea (Pisum sativum L.) is a coarse grain crop of great importance in food production, biodiversity conservation and molecular genetic research, providing genetic information and nutritional resources for improving agricultural production and promoting human health. However, only limited researches on the structure and functions of SPL genes exist in pea (PsSPLs). In this study, we identified 22 PsSPLs and conducted a genome-wide analysis of their physical characteristics, chromosome distribution, gene structure, phylogenetic evolution and gene expression patterns. As a result, the PsSPLs were unevenly distributed on the seven chromosomes of pea and harbored the SBP domain, which is composed of approximately 76 amino acid residues. The phylogenetic analysis revealed that the PsSPLs clustered into eight subfamilies and showed high homology with SPL genes in soybean. Further analysis showed the presence of segmental duplications in the PsSPLs. The expression patterns of 22 PsSPLs at different tissues, developmental stages and under various stimulus conditions were evaluated by qRT-PCR method. It was found that the expression patterns of PsSPLs from the same subfamily were similar in different tissues, the transcripts of most PsSPLs reached the maximum peak value at 14 days after anthesis in the pod. Abiotic stresses can cause significantly up-regulated PsSPL19 expression with spatiotemporal specificity, in addition, four plant hormones can cause the up-regulated expression of most PsSPLs including PsSPL19 in a time-dependent manner. Therefore, PsSPL19 could be a key candidate gene for signal transduction during pea growth and development, pod formation, abiotic stress and plant hormone response. Our findings should provide insights for the elucidating of development regulation mechanism and breeding for resistance to abiotic stress pea.
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Affiliation(s)
- Long Li
- Minzu University of China, 100010, Beijing, P.R. China
- College of Agronomy, Hebei Agricultural University, 071001, Baoding, P.R. China
| | - Jian Bo Xu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Zhi Wen Zhu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China
| | - Rui Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, 712100, Yangling, Shaanxi, P.R. China
| | - Xiao Zong Wu
- School of Food and Biological engineering, Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
- Zhengzhou University of Light Industry, 450002, Zhengzhou, P.R. China.
| | - Yu Ke Geng
- Minzu University of China, 100010, Beijing, P.R. China.
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5
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Kälin C, Piombo E, Bourras S, Brantestam AK, Dubey M, Elfstrand M, Karlsson M. Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea. BMC PLANT BIOLOGY 2024; 24:144. [PMID: 38413860 PMCID: PMC10900555 DOI: 10.1186/s12870-024-04817-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 02/12/2024] [Indexed: 02/29/2024]
Abstract
BACKGROUND Aphanomyces euteiches is a soil-borne oomycete that causes root rot in pea and other legume species. Symptoms of Aphanomyces root rot (ARR) include root discoloration and wilting, leading to significant yield losses in pea production. Resistance to ARR is known to be polygenic but the roles of single genes in the pea immune response are still poorly understood. This study uses transcriptomics to elucidate the immune response of two pea genotypes varying in their levels of resistance to A. euteiches. RESULTS In this study, we inoculated roots of the pea (P. sativum L.) genotypes 'Linnea' (susceptible) and 'PI180693' (resistant) with two different A. euteiches strains varying in levels of virulence. The roots were harvested at 6 h post-inoculation (hpi), 20 hpi and 48 hpi, followed by differential gene expression analysis. Our results showed a time- and genotype-dependent immune response towards A. euteiches infection, involving several WRKY and MYB-like transcription factors, along with genes associated with jasmonic acid (JA) and abscisic acid (ABA) signaling. By cross-referencing with genes segregating with partial resistance to ARR, we identified 39 candidate disease resistance genes at the later stage of infection. Among the genes solely upregulated in the resistant genotype 'PI180693', Psat7g091800.1 was polymorphic between the pea genotypes and encoded a Leucine-rich repeat receptor-like kinase reminiscent of the Arabidopsis thaliana FLAGELLIN-SENSITIVE 2 receptor. CONCLUSIONS This study provides new insights into the gene expression dynamics controlling the immune response of resistant and susceptible pea genotypes to A. euteiches infection. We present a set of 39 candidate disease resistance genes for ARR in pea, including the putative immune receptor Psat7g091800.1, for future functional validation.
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Affiliation(s)
- Carol Kälin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Edoardo Piombo
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Salim Bourras
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Mukesh Dubey
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Malin Elfstrand
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Magnus Karlsson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Zorin EA, Sulima AS, Zhernakov AI, Kuzmina DO, Rakova VA, Kliukova MS, Romanyuk DA, Kulaeva OA, Akhtemova GA, Shtark OY, Tikhonovich IA, Zhukov VA. Genomic and Transcriptomic Analysis of Pea ( Pisum sativum L.) Breeding Line 'Triumph' with High Symbiotic Responsivity. PLANTS (BASEL, SWITZERLAND) 2023; 13:78. [PMID: 38202386 PMCID: PMC10781049 DOI: 10.3390/plants13010078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/12/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024]
Abstract
Pea (Pisum sativum L.), like most legumes, forms mutualistic symbioses with nodule bacteria and arbuscular mycorrhizal (AM) fungi. The positive effect of inoculation is partially determined by the plant genotype; thus, pea varieties with high and low symbiotic responsivity have been described, but the molecular genetic basis of this trait remains unknown. Here, we compare the symbiotically responsive breeding line 'Triumph' of grain pea with its parental cultivars 'Vendevil' (a donor of high symbiotic responsivity) and 'Classic' (a donor of agriculturally valuable traits) using genome and transcriptome sequencing. We show that 'Triumph' inherited one-fourth of its genome from 'Vendevil', including the genes related to AM and nodule formation, and reveal that under combined inoculation with nodule bacteria and AM fungi, 'Triumph' and 'Vendevil', in contrast to 'Classic', demonstrate similar up-regulation of the genes related to solute transport, hormonal regulation and flavonoid biosynthesis in their roots. We also identify the gene PsGLP2, whose expression pattern distinguishing 'Triumph' and 'Vendevil' from 'Classic' correlates with difference within the promoter region sequence, making it a promising marker for the symbiotic responsivity trait. The results of this study may be helpful for future molecular breeding programs aimed at creation of symbiotically responsive cultivars of pea.
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Affiliation(s)
- Evgeny A. Zorin
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Aleksandr I. Zhernakov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Daria O. Kuzmina
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Valeria A. Rakova
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
| | - Marina S. Kliukova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Daria A. Romanyuk
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Gulnar A. Akhtemova
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Oksana Y. Shtark
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology (ARRIAM), Pushkin, St. Petersburg 196608, Russia; (E.A.Z.); (A.S.S.); (A.I.Z.); (D.O.K.); (M.S.K.); (D.A.R.); (O.A.K.); (G.A.A.); (O.Y.S.); (I.A.T.)
- Center of Genetics and Life Sciences, Sirius University of Science and Technology, Sirius 354340, Russia;
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Singh A, Mazahar S, Chapadgaonkar SS, Giri P, Shourie A. Phyto-microbiome to mitigate abiotic stress in crop plants. Front Microbiol 2023; 14:1210890. [PMID: 37601386 PMCID: PMC10433232 DOI: 10.3389/fmicb.2023.1210890] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.
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Affiliation(s)
- Anamika Singh
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Samina Mazahar
- Department of Botany, Dyal Singh College, University of Delhi, New Delhi, India
| | - Shilpa Samir Chapadgaonkar
- Department of Biosciences and Technology, Dr. Vishwanath Karad MIT World Peace University, Pune, Maharashtra, India
| | - Priti Giri
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India
| | - Abhilasha Shourie
- Department of Biotechnology, Faculty of Engineering and Technology, Manav Rachna International Institute of Research and Studies, Faridabad, India
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Rispail N, Wohor OZ, Osuna-Caballero S, Barilli E, Rubiales D. Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection. Int J Mol Sci 2023; 24:2470. [PMID: 36768792 PMCID: PMC9916889 DOI: 10.3390/ijms24032470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.
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Affiliation(s)
- Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Osman Zakaria Wohor
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale P.O. Box TL52, Ghana
| | | | - Eleonora Barilli
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
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9
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Wohor OZ, Rispail N, Ojiewo CO, Rubiales D. Pea Breeding for Resistance to Rhizospheric Pathogens. PLANTS (BASEL, SWITZERLAND) 2022; 11:2664. [PMID: 36235530 PMCID: PMC9572552 DOI: 10.3390/plants11192664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 09/30/2022] [Accepted: 10/06/2022] [Indexed: 06/16/2023]
Abstract
Pea (Pisum sativum L.) is a grain legume widely cultivated in temperate climates. It is important in the race for food security owing to its multipurpose low-input requirement and environmental promoting traits. Pea is key in nitrogen fixation, biodiversity preservation, and nutritional functions as food and feed. Unfortunately, like most crops, pea production is constrained by several pests and diseases, of which rhizosphere disease dwellers are the most critical due to their long-term persistence in the soil and difficulty to manage. Understanding the rhizosphere environment can improve host plant root microbial association to increase yield stability and facilitate improved crop performance through breeding. Thus, the use of various germplasm and genomic resources combined with scientific collaborative efforts has contributed to improving pea resistance/cultivation against rhizospheric diseases. This improvement has been achieved through robust phenotyping, genotyping, agronomic practices, and resistance breeding. Nonetheless, resistance to rhizospheric diseases is still limited, while biological and chemical-based control strategies are unrealistic and unfavourable to the environment, respectively. Hence, there is a need to consistently scout for host plant resistance to resolve these bottlenecks. Herein, in view of these challenges, we reflect on pea breeding for resistance to diseases caused by rhizospheric pathogens, including fusarium wilt, root rots, nematode complex, and parasitic broomrape. Here, we will attempt to appraise and harmonise historical and contemporary knowledge that contributes to pea resistance breeding for soilborne disease management and discuss the way forward.
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Affiliation(s)
- Osman Z. Wohor
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale Post TL52, Ghana
| | - Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Chris O. Ojiewo
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue—Gigiri, Nairobi P.O. Box 1041-00621, Kenya
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain
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10
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Yang T, Liu R, Luo Y, Hu S, Wang D, Wang C, Pandey MK, Ge S, Xu Q, Li N, Li G, Huang Y, Saxena RK, Ji Y, Li M, Yan X, He Y, Liu Y, Wang X, Xiang C, Varshney RK, Ding H, Gao S, Zong X. Improved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics. Nat Genet 2022; 54:1553-1563. [PMID: 36138232 PMCID: PMC9534762 DOI: 10.1038/s41588-022-01172-2] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 07/26/2022] [Indexed: 12/21/2022]
Abstract
Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.
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Affiliation(s)
- Tao Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yingfeng Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Dong Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
| | - Chenyu Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Song Ge
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Quanle Xu
- College of Life Sciences, Northwest A&F University, Yangling, China
| | - Nana Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China
- College of Life Science, Shandong Normal University, Jinan, China
| | - Guan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuning Huang
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rachit K Saxena
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yishan Ji
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mengwei Li
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xin Yan
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuhua He
- Institute of Grain Crops, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Yujiao Liu
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining, China
- Qinghai Academy of Agricultural and Forestry Sciences, Xining, China
| | - Xuejun Wang
- Jiangsu Yanjiang Institute of Agricultural Sciences, Nantong, China
| | - Chao Xiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, China
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Murdoch's Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
| | - Hanfeng Ding
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences / Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, China.
- College of Life Science, Shandong Normal University, Jinan, China.
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Xuxiao Zong
- National Key Facility for Crop Gene Resources and Genetic Improvement / Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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11
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Ali A, Altaf MT, Nadeem MA, Karaköy T, Shah AN, Azeem H, Baloch FS, Baran N, Hussain T, Duangpan S, Aasim M, Boo KH, Abdelsalam NR, Hasan ME, Chung YS. Recent advancement in OMICS approaches to enhance abiotic stress tolerance in legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:952759. [PMID: 36247536 PMCID: PMC9554552 DOI: 10.3389/fpls.2022.952759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
The world is facing rapid climate change and a fast-growing global population. It is believed that the world population will be 9.7 billion in 2050. However, recent agriculture production is not enough to feed the current population of 7.9 billion people, which is causing a huge hunger problem. Therefore, feeding the 9.7 billion population in 2050 will be a huge target. Climate change is becoming a huge threat to global agricultural production, and it is expected to become the worst threat to it in the upcoming years. Keeping this in view, it is very important to breed climate-resilient plants. Legumes are considered an important pillar of the agriculture production system and a great source of high-quality protein, minerals, and vitamins. During the last two decades, advancements in OMICs technology revolutionized plant breeding and emerged as a crop-saving tool in wake of the climate change. Various OMICs approaches like Next-Generation sequencing (NGS), Transcriptomics, Proteomics, and Metabolomics have been used in legumes under abiotic stresses. The scientific community successfully utilized these platforms and investigated the Quantitative Trait Loci (QTL), linked markers through genome-wide association studies, and developed KASP markers that can be helpful for the marker-assisted breeding of legumes. Gene-editing techniques have been successfully proven for soybean, cowpea, chickpea, and model legumes such as Medicago truncatula and Lotus japonicus. A number of efforts have been made to perform gene editing in legumes. Moreover, the scientific community did a great job of identifying various genes involved in the metabolic pathways and utilizing the resulted information in the development of climate-resilient legume cultivars at a rapid pace. Keeping in view, this review highlights the contribution of OMICs approaches to abiotic stresses in legumes. We envisage that the presented information will be helpful for the scientific community to develop climate-resilient legume cultivars.
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Affiliation(s)
- Amjad Ali
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Adnan Noor Shah
- Department of Agricultural Engineering, Khwaja Fareed University of Engineering and Information Technology, Rahim Yar Khan, Pakistan
| | - Hajra Azeem
- Department of Plant Pathology, Faculty of Agricultural Sciences & Technology, Bahauddin Zakariya University, Multan, Pakistan
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Nurettin Baran
- Bitkisel Uretim ve Teknolojileri Bolumu, Uygulamali Bilimler Faku Itesi, Mus Alparslan Universitesi, Mus, Turkey
| | - Tajamul Hussain
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Saowapa Duangpan
- Laboratory of Plant Breeding and Climate Resilient Agriculture, Agricultural Innovation and Management Division, Faculty of Natural Resources, Prince of Songkla University, Hat Yai, Thailand
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Kyung-Hwan Boo
- Subtropical/Tropical Organism Gene Bank, Department of Biotechnology, College of Applied Life Science, Jeju National University, Jeju, South Korea
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Mohamed E. Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, South Korea
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12
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Zorin EA, Kliukova MS, Afonin AM, Gribchenko ES, Gordon ML, Sulima AS, Zhernakov AI, Kulaeva OA, Romanyuk DA, Kusakin PG, Tsyganova AV, Tsyganov VE, Tikhonovich IA, Zhukov VA. A variable gene family encoding nodule-specific cysteine-rich peptides in pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:884726. [PMID: 36186063 PMCID: PMC9515463 DOI: 10.3389/fpls.2022.884726] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/08/2022] [Indexed: 06/16/2023]
Abstract
Various legume plants form root nodules in which symbiotic bacteria (rhizobia) fix atmospheric nitrogen after differentiation into a symbiotic form named bacteroids. In some legume species, bacteroid differentiation is promoted by defensin-like nodule-specific cysteine-rich (NCR) peptides. NCR peptides have best been studied in the model legume Medicago truncatula Gaertn., while in many other legumes relevant information is still fragmentary. Here, we characterize the NCR gene family in pea (Pisum sativum L.) using genomic and transcriptomic data. We found 360 genes encoding NCR peptides that are expressed in nodules. The sequences of pea NCR genes and putative peptides are highly variable and differ significantly from NCR sequences of M. truncatula. Indeed, only one pair of orthologs (PsNCR47-MtNCR312) has been identified. The NCR genes in the pea genome are located in clusters, and the expression patterns of NCR genes from one cluster tend to be similar. These data support the idea of independent evolution of NCR genes by duplication and diversification in related legume species. We also described spatiotemporal expression profiles of NCRs and identified specific transcription factor (TF) binding sites in promoters of "early" and "late" NCR genes. Further, we studied the expression of NCR genes in nodules of Fix- mutants and predicted potential regulators of NCR gene expression, one among them being the TF ERN1 involved in the early steps of nodule organogenesis. In general, this study contributes to understanding the functions of NCRs in legume nodules and contributes to understanding the diversity and potential antibiotic properties of pea nodule-specific antimicrobial molecules.
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Affiliation(s)
- Evgeny A. Zorin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Marina S. Kliukova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Alexey M. Afonin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Emma S. Gribchenko
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Mikhail L. Gordon
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | | | - Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Daria A. Romanyuk
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Pyotr G. Kusakin
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Anna V. Tsyganova
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Viktor E. Tsyganov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
- Department of Genetics and Biotechnology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Saint Petersburg, Russia
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13
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Pandey PK, Bhowmik P, Kagale S. Optimized methods for random and targeted mutagenesis in field pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:995542. [PMID: 36160971 PMCID: PMC9498975 DOI: 10.3389/fpls.2022.995542] [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: 07/16/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Field pea is an important pulse crop for its dense nutritional profile and contribution to sustainable agricultural practices. Recently, it has received extensive attention as a potential leading source of plant-based proteins. However, the adoption of peas as a mainstream source of proteins is affected by a relatively moderate protein content, anti-nutritional factors and high levels of off-flavor components that reduce protein quality. Availability of genetic variation for desirable seed quality traits is the foundation for the sustainable development of pea varieties with improved protein content and quality. Mutagenesis has been an important tool in gene functional characterization studies and creating genetic variability for crop breeding. Large-scale mutagenesis of a crop using physical and chemical agents requires diligent selection of the mutagen and optimization of its dose to increase the frequency of mutations. In this study, we present detailed optimized protocols for physical and chemical mutagenesis of pea using gamma irradiation and ethyl methanesulfonate (EMS), respectively. Gamma radiation and EMS titration kill curves were established to identify optimal doses of the two mutagenic agents. Based on germination, survival rate and growth phenotypes, a gamma radiation dose of 225 Gy and EMS concentration of 5 mm were selected as optimal dosages for mutagenesis in field pea. The presented protocol has been modified from previously established mutagenesis protocols in other crop plants. Our results indicate that the optimal mutagen dosage is genotype dependent. CRISPR/Cas-based gene editing provides a precise and rapid method for targeted genetic manipulation in plants. With the recent success of gene editing in pea using CRISPR/Cas, this innovative technology is expected to become an integral component of the gene discovery and crop improvement toolkit in pea. Here, we describe an optimized methods for targeted mutagenesis of pea protoplasts, including mesophyll protoplast extraction, PEG-mediated transformation and gene editing of a LOX gene using CRISPR/Cas system. The general strategies and methods of mutagenesis described here provide an essential resource for mutation breeding and functional genomics studies in pea. These methods also provide a foundation for similar studies in other crops.
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14
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Deng D, Sun S, Wu W, Xiang C, Duan C, Yu D, Wu X, Zhu Z. Disease Resistance and Molecular Variations in Irradiation Induced Mutants of Two Pea Cultivars. Int J Mol Sci 2022; 23:8793. [PMID: 35955926 PMCID: PMC9369183 DOI: 10.3390/ijms23158793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/28/2022] [Accepted: 08/01/2022] [Indexed: 11/21/2022] Open
Abstract
Induced mutation is useful for improving the disease resistance of various crops. Fusarium wilt and powdery mildew are two important diseases which severely influence pea production worldwide. In this study, we first evaluated Fusarium wilt and powdery mildew resistance of mutants derived from two elite vegetable pea cultivars, Shijiadacaiwan 1 (SJ1) and Chengwan 8 (CW8), respectively. Nine SJ1 and five CW8 M3 mutants showed resistant variations in Fusarium wilt, and the same five CW8 mutants in powdery mildew. These resistant variations were confirmed in M4 and M5 mutants as well. Then, we investigated the genetic variations and relationships of mutant lines using simple sequence repeat (SSR) markers. Among the nine effective SSR markers, the genetic diversity index and polymorphism information content (PIC) values were averaged at 0.55 and 0.46, which revealed considerable genetic variations in the mutants. The phylogenetic tree and population structure analyses divided the M3 mutants into two major groups at 0.62 genetic similarity (K = 2), which clearly separated the mutants of the two cultivars and indicated that a great genetic difference existed between the two mutant populations. Further, the two genetic groups were divided into five subgroups at 0.86 genetic similarity (K = 5) and each subgroup associated with resistant phenotypes of the mutants. Finally, the homologous PsMLO1 cDNA of five CW8 mutants that gained resistance to powdery mildew was amplified and cloned. A 129 bp fragment deletion was found in the PsMLO1 gene, which was in accord with er1-2. The findings provide important information on disease resistant and molecular variations of pea mutants, which is useful for pea production, new cultivar breeding, and the identification of resistance genes.
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Affiliation(s)
- Dong Deng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Suli Sun
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Wenqi Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chao Xiang
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Canxing Duan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Dongmei Yu
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Xuehong Wu
- College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhendong Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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15
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Zhao H, Pandey BR, Khansefid M, Khahrood HV, Sudheesh S, Joshi S, Kant S, Kaur S, Rosewarne GM. Combining NDVI and Bacterial Blight Score to Predict Grain Yield in Field Pea. FRONTIERS IN PLANT SCIENCE 2022; 13:923381. [PMID: 35837454 PMCID: PMC9274273 DOI: 10.3389/fpls.2022.923381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Field pea is the most commonly grown temperate pulse crop, with close to 15 million tons produced globally in 2020. Varieties improved through breeding are important to ensure ongoing improvements in yield and disease resistance. Genomic selection (GS) is a modern breeding approach that could substantially improve the rate of genetic gain for grain yield, and its deployment depends on the prediction accuracy (PA) that can be achieved. In our study, four yield trials representing breeding lines' advancement stages of the breeding program (S0, S1, S2, and S3) were assessed with grain yield, aerial high-throughput phenotyping (normalized difference vegetation index, NDVI), and bacterial blight disease scores (BBSC). Low-to-moderate broad-sense heritability (0.31-0.71) and narrow-sense heritability (0.13-0.71) were observed, as the estimated additive and non-additive genetic components for the three traits varied with the different models fitted. The genetic correlations among the three traits were high, particularly in the S0-S2 stages. NDVI and BBSC were combined to investigate the PA for grain yield by univariate and multivariate GS models, and multivariate models showed higher PA than univariate models in both cross-validation and forward prediction methods. A 6-50% improvement in PA was achieved when multivariate models were deployed. The highest PA was indicated in the forward prediction scenario when the training population consisted of early generation breeding stages with the multivariate models. Both NDVI and BBSC are commonly used traits that could be measured in the early growth stage; however, our study suggested that NDVI is a more useful trait to predict grain yield with high accuracy in the field pea breeding program, especially in diseased trials, through its incorporation into multivariate models.
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Affiliation(s)
- Huanhuan Zhao
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Babu R. Pandey
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Majid Khansefid
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Hossein V. Khahrood
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Shimna Sudheesh
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Sameer Joshi
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
| | - Surya Kant
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Garry M. Rosewarne
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC, Australia
- Centre for Agricultural Innovation, The University of Melbourne, Melbourne, VIC, Australia
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16
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Baloglu MC, Celik Altunoglu Y, Baloglu P, Yildiz AB, Türkölmez N, Özden Çiftçi Y. Gene-Editing Technologies and Applications in Legumes: Progress, Evolution, and Future Prospects. Front Genet 2022; 13:859437. [PMID: 35836569 PMCID: PMC9275826 DOI: 10.3389/fgene.2022.859437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 05/13/2022] [Indexed: 12/22/2022] Open
Abstract
Legumes are rich in protein and phytochemicals and have provided a healthy diet for human beings for thousands of years. In recognition of the important role they play in human nutrition and agricultural production, the researchers have made great efforts to gain new genetic traits in legumes such as yield, stress tolerance, and nutritional quality. In recent years, the significant increase in genomic resources for legume plants has prepared the groundwork for applying cutting-edge breeding technologies, such as transgenic technologies, genome editing, and genomic selection for crop improvement. In addition to the different genome editing technologies including the CRISPR/Cas9-based genome editing system, this review article discusses the recent advances in plant-specific gene-editing methods, as well as problems and potential benefits associated with the improvement of legume crops with important agronomic properties. The genome editing technologies have been effectively used in different legume plants including model legumes like alfalfa and lotus, as well as crops like soybean, cowpea, and chickpea. We also discussed gene-editing methods used in legumes and the improvements of agronomic traits in model and recalcitrant legumes. Despite the immense opportunities genome editing can offer to the breeding of legumes, governmental regulatory restrictions present a major concern. In this context, the comparison of the regulatory framework of genome editing strategies in the European Union and the United States of America was also discussed. Gene-editing technologies have opened up new possibilities for the improvement of significant agronomic traits in legume breeding.
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Affiliation(s)
- Mehmet Cengiz Baloglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Yasemin Celik Altunoglu
- Department of Genetics and Bioengineering, Faculty of Engineering and Architecture, Kastamonu University, Kastamonu, Turkey
| | - Pinar Baloglu
- Research and Application Center, Kastamonu University, Kastamonu, Turkey
| | - Ali Burak Yildiz
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Nil Türkölmez
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
| | - Yelda Özden Çiftçi
- Department of Molecular Biology and Genetics, Gebze Technical University, Kocaeli, Turkey
- Smart Agriculture Research and Application Center, Gebze Technical University, Kocaeli, Turkey
- *Correspondence: Yelda Özden Çiftçi,
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Lozada DN, Bosland PW, Barchenger DW, Haghshenas-Jaryani M, Sanogo S, Walker S. Chile Pepper ( Capsicum) Breeding and Improvement in the "Multi-Omics" Era. FRONTIERS IN PLANT SCIENCE 2022; 13:879182. [PMID: 35592583 PMCID: PMC9113053 DOI: 10.3389/fpls.2022.879182] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
Chile pepper (Capsicum spp.) is a major culinary, medicinal, and economic crop in most areas of the world. For more than hundreds of years, chile peppers have "defined" the state of New Mexico, USA. The official state question, "Red or Green?" refers to the preference for either red or the green stage of chile pepper, respectively, reflects the value of these important commodities. The presence of major diseases, low yields, decreased acreages, and costs associated with manual labor limit production in all growing regions of the world. The New Mexico State University (NMSU) Chile Pepper Breeding Program continues to serve as a key player in the development of improved chile pepper varieties for growers and in discoveries that assist plant breeders worldwide. Among the traits of interest for genetic improvement include yield, disease resistance, flavor, and mechanical harvestability. While progress has been made, the use of conventional breeding approaches has yet to fully address producer and consumer demand for these traits in available cultivars. Recent developments in "multi-omics," that is, the simultaneous application of multiple omics approaches to study biological systems, have allowed the genetic dissection of important phenotypes. Given the current needs and production constraints, and the availability of multi-omics tools, it would be relevant to examine the application of these approaches in chile pepper breeding and improvement. In this review, we summarize the major developments in chile pepper breeding and present novel tools that can be implemented to facilitate genetic improvement. In the future, chile pepper improvement is anticipated to be more data and multi-omics driven as more advanced genetics, breeding, and phenotyping tools are developed.
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Affiliation(s)
- Dennis N. Lozada
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | - Paul W. Bosland
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
| | | | - Mahdi Haghshenas-Jaryani
- Department of Mechanical and Aerospace Engineering, New Mexico State University, Las Cruces, NM, United States
| | - Soumaila Sanogo
- Department of Entomology, Plant Pathology and Weed Science, New Mexico State University, Las Cruces, NM, United States
| | - Stephanie Walker
- Chile Pepper Institute, New Mexico State University, Las Cruces, NM, United States
- Department of Extension Plant Sciences, New Mexico State University, Las Cruces, NM, United States
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Rubiales D, Annicchiarico P, Vaz Patto MC, Julier B. Legume Breeding for the Agroecological Transition of Global Agri-Food Systems: A European Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:782574. [PMID: 34868184 PMCID: PMC8637196 DOI: 10.3389/fpls.2021.782574] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Wider and more profitable legume crop cultivation is an indispensable step for the agroecological transition of global agri-food systems but represents a challenge especially in Europe. Plant breeding is pivotal in this context. Research areas of key interest are represented by innovative phenotypic and genome-based selection procedures for crop yield, tolerance to abiotic and biotic stresses enhanced by the changing climate, intercropping, and emerging crop quality traits. We see outmost priority in the exploration of genomic selection (GS) opportunities and limitations, to ease genetic gains and to limit the costs of multi-trait selection. Reducing the profitability gap of legumes relative to major cereals will not be possible in Europe without public funding devoted to crop improvement research, pre-breeding, and, in various circumstances, public breeding. While most of these activities may profit of significant public-private partnerships, all of them can provide substantial benefits to seed companies. A favorable institutional context may comprise some changes to variety registration tests and procedures.
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Affiliation(s)
- Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | | | | | - Bernadette Julier
- Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), URP3F, Lusignan, France
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