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Lateef I, Katoch S, Katoch A, Badiyal A, Pathania A, Dhiman S, Nisa Q, Bashir A, Nabi A, Nabi N, Fayaz T, Gulzar G, Shah MD, Shikari AB, Dar ZA, Itoo H, Shah RA, Sofi TA, Sharma V, Sharma MK, Rathour R, Sharma PN, Padder BA. Fine mapping of a new common bean anthracnose resistance gene (Co-18) to the proximal end of Pv10 in Indian landrace KRC-5. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:32. [PMID: 38270625 DOI: 10.1007/s00122-023-04539-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 12/27/2023] [Indexed: 01/26/2024]
Abstract
KEY MESSAGE Mapping and fine mapping of bean anthracnose resistance genes is a continuous process. We report fine mapping of anthracnose resistance gene Co-18 which is the first anthracnose gene mapped to Pv10. The discovery of resistance gene is a major gain in the bean anthracnose pathosystem research. Among the Indian common bean landraces, KRC-5 exhibit high levels of resistance to the bean anthracnose pathogen Colletotrichum lindemuthianum. To precisely map the anthracnose resistance gene, we used a Recombinant Inbred Line (F2:9 RIL) population (KRC-5 × Jawala). The inheritance test revealed that KRC-5 carries a dominant resistance gene temporarily designated as Co-18. We discovered two RAPD markers linked to Co-18 among 287 RAPD markers. These RAPD markers were eventually developed into SCARs (Sc-OPR15 and Sc-OPF6) and flank Co-18 on chromosome Pv10 at a distance of 5.3 and 4.2 cM, respectively. At 4.0-4.1 Mb on Pv10, we detected a SNP (single-nucleotide polymorphism) signal. We synthesized 58 SSRs and 83 InDels from a pool of 135 SSRs and 1134 InDels, respectively. Five SSRs, four InDels, and two SCARs were used to generate the high-density linkage map, which led to the identification of two SSRs (SSR24 and SSR36) that are tightly linked to Co-18. These two SSRs flank the Co-18 to 178 kb genomic region with 13 candidate genes including five NLR (nucleotide-binding and leucine-rich repeat) genes. The closely linked markers SSR24 and SSR36 will be used in cloning and pyramiding of the Co-18 gene with other R genes to develop durable resistant bean varieties.
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Affiliation(s)
- Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Shabnam Katoch
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Abhishek Katoch
- University Institute of Agricultural Sciences, Chandigarh University, Ajitgarh, India
| | - Anila Badiyal
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Anju Pathania
- Faculty of Agriculture, DAV University, Jalandhar, Punjab, 144001, India
| | - Shiwali Dhiman
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Adfar Bashir
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Naziya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Tabia Fayaz
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Gazala Gulzar
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Mehraj D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Asif B Shikari
- Division of Plant Breeding and Genetics, SKUAST-K, FoA, Wadura, Baramulla, Sopore, India
| | | | - Hamidullah Itoo
- Ambri Apple Research Center, Pahanoo, SKUAST-K, Shopian, 192303, India
| | - Rafiq A Shah
- Ambri Apple Research Center, Pahanoo, SKUAST-K, Shopian, 192303, India
| | - Tariq A Sofi
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Vivek Sharma
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - M K Sharma
- Division of Fruit Science, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rajeev Rathour
- Department of Agricultural Biotechnology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - P N Sharma
- Department of Plant Pathology, CSK HP Agricultural University, Palampur, HP, 176062, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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Pan J, Yang X, Hu C, Fu T, Zhang X, Liu Z, Wang Y, Zhang F, He X, Yu JH. Functional, transcriptomic, and lipidomic studies of the choC gene encoding a phospholipid methyltransferase in Aspergillus fumigatus. Microbiol Spectr 2024; 12:e0216823. [PMID: 38009944 PMCID: PMC10783049 DOI: 10.1128/spectrum.02168-23] [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: 06/06/2023] [Accepted: 10/02/2023] [Indexed: 11/29/2023] Open
Abstract
IMPORTANCE This study explored the phospholipid metabolic pathway in A. fumigatus and its relationship with fungal growth, metabolism, and pathogenicity. ChoC, based on its critical roles in many aspects of the fungus and relatively conserved characteristics in filamentous fungi with low similarity with mammalian ones, can be a novel target of new antifungal drugs.
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Affiliation(s)
- Jiao Pan
- Institute for Cultural Heritage and History of Science and Technology, University of Science and Technology Beijing, Beijing, China
| | - Xinyu Yang
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Cuiting Hu
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Tongtong Fu
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiuyan Zhang
- College of Food Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Zijun Liu
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Yu Wang
- Institute for Cultural Heritage and History of Science and Technology, University of Science and Technology Beijing, Beijing, China
| | - Fengyu Zhang
- Department of Microbiology, College of Life Sciences, Nankai University, Tianjin, China
| | - Xiaoyuan He
- Department of Hematology, Tianjin First Central Hospital, Tianjin, China
| | - Jae-Hyuk Yu
- Department of Bacteriology, Food Research Institute, University of Wisconsin, Madison, Wisconsin, USA
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Tomlekova N, Idziak-Helmcke D, Franke P, Rojek-Jelonek M, Kwasniewska J. Phaseolus vulgaris mutants reveal variation in the nuclear genome. FRONTIERS IN PLANT SCIENCE 2024; 14:1308830. [PMID: 38239224 PMCID: PMC10794375 DOI: 10.3389/fpls.2023.1308830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 12/08/2023] [Indexed: 01/22/2024]
Abstract
Phaseolus vulgaris L. (common bean) is an essential source of proteins in the human diet worldwide. Bean breeding programs to increase genetic diversity based on induced mutagenesis have a long tradition in Bulgaria. Common bean varieties with high productivity, wide environmental adaptability, good nutritional properties, and improved disease resistance have been successfully developed. In this study, we aimed to investigate selected nuclear genome features, such as the genome size, the number and chromosomal distribution of 5S and 35S rDNA loci by using the fluorescence in situ hybridization (FISH), as well as the level of DNA damage in some local Bulgarian accessions and mutants of P. vulgaris. Flow cytometry analyses revealed no significant differences in genome size between analyzed lines except for one of the analyzed mutants, M19. The value of genome size 2C DNA is about 1.37 pg2C -1 for all lines, whereas it is 1.42 pg2C-1 for M19. The chromosome number remains the same (2n=22) for all analyzed lines. Results of FISH analyses showed that the number of 5S rDNA was stable among accessions and mutant lines (four loci), while the number of 35S rDNA loci was shown as highly polymorphic, varying between ten and sixteen, and displaying differences in the size and location of 35S rDNA loci between analyzed genotypes. The cell cycle profile was different for the analyzed genotypes. The results revealed that wide variation in genome organization and size as well as DNA damage characterizes the analyzed genetic resources of the common bean.
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Affiliation(s)
- Nasya Tomlekova
- Laboratory of Molecular Biology, Department of Breeding, Marisa Vegetable Crops Research Institute, Plovdiv, Agricultural Academy, Sofia, Bulgaria
| | - Dominika Idziak-Helmcke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Paula Franke
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Magdalena Rojek-Jelonek
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jolanta Kwasniewska
- Plant Cytogenetics and Molecular Biology Group, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
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Fang P, Li M, Guo Q, Wu X, Hu Y, Cheng Y, Xu P. Genome-wide analysis of the SMXL gene family in common bean and identification of karrikin-responsive PvSMXL2 as a negative regulator of PEG-induced drought stress. Gene 2023; 887:147741. [PMID: 37634881 DOI: 10.1016/j.gene.2023.147741] [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: 06/19/2023] [Revised: 08/05/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is a major legume crop worldwide, but its growth and development frequently face challenges due to abiotic stresses, particularly drought. Proper supplement of copper could mitigate the adverse effects of drought, but excessive accumulation of this metal in plants can be harmful. The suppressor of MAX2 1-like (SMXL) gene family, which plays important roles in various plant processes, including stress responses, remains poorly understood in common bean. In this study, we identified nine orthologues of SMXL genes in common bean, which are located on six chromosomes and classified into four subgroups. Basic molecular properties, including theoretical isoelectric point (PI), molecular weight (MW), grand average of hydropathicity (GVIO), gene structure, and conserved motifs were characterized, and numerous cis-elements in promoters were predicted. The expression patterns of PvSMXL genes were found to be distinct under 10% polyethylene glycol (PEG)-induced drought stress and 200 μM Cu treatments. Most PvSMXLs showed reduced expression in response to Cu treatment, whereas nearly half PvSMXLs exhibited inducible expression under drought stress. PvSMXL2, which exhibited a rapid response to karrikin 1 (KAR1), an active form of the plant growth regulators newly found in the smoke of burning plant material, was down-regulated by both PEG-induced drought and Cu stresses. Transient silencing of PvSMXL2 resulted in enhanced drought stress tolerance without conferring Cu tolerance. These findings provide valuable insights into the functions of SMXL genes in common bean under abiotic stress conditions.
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Affiliation(s)
- Pingping Fang
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Minxuan Li
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Qinwei Guo
- Quzhou Key Laboratory for Germplasm Innovation and Utilization of Crop, Institute of Vegetables, Quzhou Academy of Agricultural and Forestry Sciences, Quzhou 324000, PR China
| | - Xinyang Wu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Yannan Hu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Yusu Cheng
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China
| | - Pei Xu
- Key Laboratory of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang, College of Life Sciences, China Jiliang University, Hangzhou 310018, PR China.
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Meziadi C, Alvarez-Diaz JC, Thareau V, Gratias A, Marande W, Soler-Garzon A, Miklas PN, Pflieger S, Geffroy V. Fine-mapping and evolutionary history of R-BPMV, a dominant resistance gene to Bean pod mottle virus in Phaseolus vulgaris L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:8. [PMID: 38092992 DOI: 10.1007/s00122-023-04513-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/21/2023] [Indexed: 12/18/2023]
Abstract
KEY MESSAGE R-BPMV is located within a recently expanded TNL cluster in the Phaseolus genus with suppressed recombination and known for resistance to multiple pathogens including potyviruses controlled by the I gene. Bean pod mottle virus (BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the R-BPMV resistance gene conferring resistance to BPMV and linked with the I resistance gene. To fine map R-BPMV, 182 recombinant inbred lines (RILs) derived from the cross BAT93 × JaloEEP558 were genotyped with polymerase chain reaction (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned R-BPMV to a target region containing at least 16 TIR-NB-LRR (TNL) sequences in BAT93. Because the I cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as R-BPMV candidate gene. The evolutionary history of the TNLs for the I cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family. A single I TNL was present in Medicago truncatula and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the I cluster predates the divergence of the Phaseolus species, in agreement with the emergence of R-BPMV before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of R-BPMV resistance gene in order to transfer the resistance into soybean.
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Affiliation(s)
- Chouaïb Meziadi
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Juan-Camilo Alvarez-Diaz
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Vincent Thareau
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Ariane Gratias
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | | | - Alvaro Soler-Garzon
- Irrigated Agriculture Research and Extension Center, Washington State Univ, Prosser, WA, USA
| | - Phillip N Miklas
- Grain Legume Genetics and Physiology Research Unit, USDA ARS, Prosser, WA, USA
| | - Stéphanie Pflieger
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France
| | - Valérie Geffroy
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Université Evry, 91190, Gif Sur Yvette, France.
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Cité, CNRS, INRAE, 91190, Gif Sur Yvette, Rue Noetzlin, 91405, Orsay, France.
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Ferraz ME, Ribeiro T, Sader M, Nascimento T, Pedrosa-Harand A. Comparative analysis of repetitive DNA in dysploid and non-dysploid Phaseolus beans. Chromosome Res 2023; 31:30. [PMID: 37812264 DOI: 10.1007/s10577-023-09739-3] [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: 07/11/2023] [Revised: 08/31/2023] [Accepted: 09/15/2023] [Indexed: 10/10/2023]
Abstract
Structural karyotype changes result from ectopic recombination events frequently associated with repetitive DNA. Although most Phaseolus species present relatively stable karyotypes with 2n = 22 chromosomes, the karyotypes of species of the Leptostachyus group show high rates of structural rearrangements, including a nested chromosome fusion that led to the dysploid chromosome number of the group (2n = 20). We examined the roles of repetitive landscapes in the rearrangements of species of the Leptostachyus group using genome-skimming data to characterize the repeatome in a range of Phaseolus species and compared them to species of that group (P. leptostachyus and P. macvaughii). LTR retrotransposons, especially the Ty3/gypsy lineage Chromovirus, were the most abundant elements in the genomes. Differences in the abundance of Tekay, Retand, and SIRE elements between P. macvaughii and P. leptostachyus were reflected in their total amounts of Ty3/gypsy and Ty1/copia. The satellite DNA fraction was the most divergent among the species, varying both in abundance and distribution, even between P. leptostachyus and P. macvaughii. The rapid turnover of repeats in the Leptostachyus group may be associated with the several rearrangements observed.
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Affiliation(s)
- Maria Eduarda Ferraz
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Tiago Ribeiro
- Integrative Plant Research Lab, Department of Botany and Ecology, Institute of Biosciences, Federal University of Mato Grosso, Cuiabá, MT, Brazil
| | - Mariela Sader
- Multidisciplinary Institute of Plant Biology, National Council for Scientific and Technical Research, National University of Córdoba, Córdoba, Argentina
| | - Thiago Nascimento
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plant Cytogenetics and Evolution, Department of Botany, Biosciences Centre, Federal University of Pernambuco, Recife, PE, Brazil.
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Nascimento T, Pedrosa-Harand A. High rates of structural rearrangements have shaped the chromosome evolution in dysploid Phaseolus beans. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:215. [PMID: 37751069 DOI: 10.1007/s00122-023-04462-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/09/2023] [Indexed: 09/27/2023]
Abstract
KEY MESSAGE Karyotypes evolve through numerical and structural chromosome rearrangements. We show that Phaseolus leptostachyus, a wild bean, underwent a rapid genome reshuffling associated with the reduction from 11 to 10 chromosome pairs, but without whole genome duplication, the highest chromosome evolution rate known for plants. Plant karyotypes evolve through structural rearrangements often associated with polyploidy or dysploidy. The genus Phaseolus comprises ~ 90 species, five of them domesticated due to their nutritional relevance. Most of the species have 2n = 22 karyotypes and are highly syntenic, except for three dysploid karyotypes of species from the Leptostachyus group (2n = 20) that have accumulated several rearrangements. Here, we investigated the degrees of structural rearrangements among Leptostachyus and other Phaseolus groups by estimating their chromosomal evolution rates (CER). For this, we combined our oligo-FISH barcode system for beans and chromosome-specific painting probes for chromosomes 2 and 3, with rDNA and a centromeric probe to establish chromosome orthologies and identify structural rearrangements across nine Phaseolus species. We also integrated the detected rearrangements with a phylogenomic approach to estimate the CERs for each Phaseolus lineage. Our data allowed us to identify translocations, inversions, duplications and deletions, mostly in species belonging to the Leptostachyus group. Phaseolus leptostachyus showed the highest CER (12.31 rearrangements/My), a tenfold increase in contrast to the 2n = 22 species analysed. This is the highest rate known yet for plants, making it a model species for investigating the mechanisms behind rapid genome reshuffling in early species diversification.
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Affiliation(s)
- Thiago Nascimento
- Laboratory of Plants Cytogenetics and Evolution, Department of Botany, Biosciences Center, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil
| | - Andrea Pedrosa-Harand
- Laboratory of Plants Cytogenetics and Evolution, Department of Botany, Biosciences Center, Federal University of Pernambuco, Recife, PE, 50670-901, Brazil.
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de Souza IP, de Azevedo BR, Coelho ASG, de Souza TLPO, Valdisser PAMR, Gomes-Messias LM, Funicheli BO, Brondani C, Vianello RP. Whole-genome resequencing of common bean elite breeding lines. Sci Rep 2023; 13:12721. [PMID: 37543642 PMCID: PMC10404220 DOI: 10.1038/s41598-023-39399-6] [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: 03/15/2023] [Accepted: 07/25/2023] [Indexed: 08/07/2023] Open
Abstract
The expansion of bean genome technologies has prompted new perspectives on generating resources and knowledge essential to research and implementing biotechnological tools for the practical operations of plant breeding programs. This study aimed to resequence the entire genome (whole genome sequencing-WGS) of 40 bean genotypes selected based on their significance in breeding programs worldwide, with the objective of generating an extensive database for the identification of single nucleotide polymorphisms (SNPs). Over 6 million SNPs were identified, distributed across the 11 bean chromosomes. After quality variant filtering, 420,509 high-quality SNPs were established, with an average of 38,228 SNPs per chromosome. These variants were categorized based on their predicted effects, revealing that the majority exerted a modifier impact on non-coding genome regions (94.68%). Notably, a significant proportion of SNPs occurred in intergenic regions (62.89%) and at least one SNP was identified in 58.63% of the genes annotated in the bean genome. Of particular interest, 7841 SNPs were identified in 85% of the putative plant disease defense-related genes, presenting a valuable resource for crop breeding efforts. These findings provide a foundation for the development of innovative and broadly applicable technologies for the routine selection of superior genotypes in global bean improvement and germplasm characterization programs.
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Affiliation(s)
- Isabela Pavanelli de Souza
- Genetics and Plant Breeding, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil.
| | - Beatriz Rosa de Azevedo
- Biotechnology, Scientific Initiation Scholarship, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil
| | | | | | | | | | | | - Claudio Brondani
- Molecular Biology, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil
| | - Rosana Pereira Vianello
- Molecular Biology, Brazilian Agricultural Research Corporation, Santo Antônio de Goiás, GO, Brazil
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de Koning R, Wils GE, Kiekens R, De Vuyst L, Angenon G. Impact of drought and salt stress on galactinol and raffinose family oligosaccharides in common bean ( Phaseolus vulgaris). AOB PLANTS 2023; 15:plad038. [PMID: 37426172 PMCID: PMC10327629 DOI: 10.1093/aobpla/plad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
Due to climate change, farmers will face more extreme weather conditions and hence will need crops that are better adapted to these challenges. The raffinose family oligosaccharides (RFOs) could play a role in the tolerance of crops towards abiotic stress. To investigate this, we determined for the first time the importance of galactinol and RFOs in the roots and leaves of common bean under drought and salt stress conditions. Initially, the physiological characteristics of common bean under agronomically relevant abiotic stress conditions were investigated by measuring the growth rate, transpiration rate, chlorophyll concentration and membrane stability, allowing to establish relevant sampling points. Subsequently, the differential gene expression profiles of the galactinol and RFO biosynthetic genes and the amount of galactinol and RFO molecules were measured in the primary leaves and roots of Phaseolus vulgaris cv. CIAP7247F at these sampling points, using RT-qPCR and HPAEC-PAD, respectively. Under drought stress, the genes galactinol synthase 1, galactinol synthase 3 and stachyose synthase were significantly upregulated in the leaves and had a high transcript level in comparison with the other galactinol and RFO biosynthetic genes. This was in accordance with the significantly higher amount of galactinol and raffinose detected in the leaves. Under salt stress, raffinose was also present in a significantly higher quantity in the leaves. In the roots, transcript levels of the RFO biosynthetic genes were generally low and no galactinol, raffinose or stachyose could be detected. These results suggest that in the leaves, both galactinol and raffinose could play a role in the protection of common bean against abiotic stresses. Especially, the isoform galactinol synthase 3 could have a specific role during drought stress and forms an interesting candidate to improve the abiotic stress resistance of common bean or other plant species.
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Affiliation(s)
- Ramon de Koning
- Research Group of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
| | - Gertjan E Wils
- Research Group of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
| | - Raphaël Kiekens
- Research Group of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
| | - Luc De Vuyst
- Research Group of Industrial Microbiology and Food Biotechnology, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
| | - Geert Angenon
- Research Group of Plant Genetics, Faculty of Sciences and Bioengineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, Belgium
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Yang EJ, Maranas CJ, Nemhauser JL. A comparative analysis of stably expressed genes across diverse angiosperms exposes flexibility in underlying promoter architecture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.12.544596. [PMID: 37398445 PMCID: PMC10312641 DOI: 10.1101/2023.06.12.544596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Promoters regulate both the amplitude and pattern of gene expression-key factors needed for optimization of many synthetic biology applications. Previous work in Arabidopsis found that promoters that contain a TATA-box element tend to be expressed only under specific conditions or in particular tissues, while promoters which lack any known promoter elements, thus designated as Coreless, tend to be expressed more ubiquitously. To test whether this trend represents a conserved promoter design rule, we identified stably expressed genes across multiple angiosperm species using publicly available RNA-seq data. Comparisons between core promoter architectures and gene expression stability revealed differences in core promoter usage in monocots and eudicots. Furthermore, when tracing the evolution of a given promoter across species, we found that core promoter type was not a strong predictor of expression stability. Our analysis suggests that core promoter types are correlative rather than causative in promoter expression patterns and highlights the challenges in finding or building constitutive promoters that will work across diverse plant species.
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Affiliation(s)
- Eric J.Y. Yang
- University of Washington, Department of Biology, Seattle, WA 98105-1800, USA
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11
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Reyero-Saavedra R, Fuentes SI, Leija A, Jiménez-Nopala G, Peláez P, Ramírez M, Girard L, Porch TG, Hernández G. Identification and Characterization of Common Bean ( Phaseolus vulgaris) Non-Nodulating Mutants Altered in Rhizobial Infection. PLANTS (BASEL, SWITZERLAND) 2023; 12:1310. [PMID: 36986997 PMCID: PMC10059843 DOI: 10.3390/plants12061310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 06/19/2023]
Abstract
The symbiotic N2-fixation process in the legume-rhizobia interaction is relevant for sustainable agriculture. The characterization of symbiotic mutants, mainly in model legumes, has been instrumental for the discovery of symbiotic genes, but similar studies in crop legumes are scant. To isolate and characterize common bean (Phaseolus vulgaris) symbiotic mutants, an ethyl methanesulphonate-induced mutant population from the BAT 93 genotype was analyzed. Our initial screening of Rhizobium etli CE3-inoculated mutant plants revealed different alterations in nodulation. We proceeded with the characterization of three non-nodulating (nnod), apparently monogenic/recessive mutants: nnod(1895), nnod(2353) and nnod(2114). Their reduced growth in a symbiotic condition was restored when the nitrate was added. A similar nnod phenotype was observed upon inoculation with other efficient rhizobia species. A microscopic analysis revealed a different impairment for each mutant in an early symbiotic step. nnod(1895) formed decreased root hair curling but had increased non-effective root hair deformation and no rhizobia infection. nnod(2353) produced normal root hair curling and rhizobia entrapment to form infection chambers, but the development of the latter was blocked. nnod(2114) formed infection threads that did not elongate and thus did not reach the root cortex level; it occasionally formed non-infected pseudo-nodules. The current research is aimed at mapping the responsible mutated gene for a better understanding of SNF in this critical food crop.
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Affiliation(s)
- Rocío Reyero-Saavedra
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Sara Isabel Fuentes
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Alfonso Leija
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Gladys Jiménez-Nopala
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Pablo Peláez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Mario Ramírez
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Lourdes Girard
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
| | - Timothy G. Porch
- USDA-ARS, Tropical Agriculture Research Station, 2200 P.A. Campos Avenue, Suite 201, Mayaguez 00680, Puerto Rico;
| | - Georgina Hernández
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Cuernavaca 62210, Morelos, Mexico; (R.R.-S.); (S.I.F.); (A.L.); (G.J.-N.); (P.P.); (M.R.); (L.G.)
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12
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Gayacharan, Parida SK, Mondal N, Yadav R, Vishwakarma H, Rana JC. Mining legume germplasm for genetic gains: An Indian perspective. Front Genet 2023; 14:996828. [PMID: 36816034 PMCID: PMC9933516 DOI: 10.3389/fgene.2023.996828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023] Open
Abstract
Legumes play a significant role in food and nutritional security and contribute to environmental sustainability. Although legumes are highly beneficial crops, it has not yet been possible to enhance their yield and production to a satisfactory level. Amid a rising population and low yield levels, per capita average legume consumption in India has fallen by 71% over the last 50 years, and this has led to protein-related malnutrition in a large segment of the Indian population, especially women and children. Several factors have hindered attempts to achieve yield enhancement in grain legumes, including biotic and abiotic pressures, a lack of good ideotypes, less amenability to mechanization, poorer responsiveness to fertilizer input, and a poor genetic base. Therefore, there is a need to mine the approximately 0.4 million ex situ collections of legumes that are being conserved in gene banks globally for identification of ideal donors for various traits. The Indian National Gene Bank conserves over 63,000 accessions of legumes belonging to 61 species. Recent initiatives have been undertaken in consortia mode with the aim of unlocking the genetic potential of ex situ collections and conducting large-scale germplasm characterization and evaluation analyses. We assume that large-scale phenotyping integrated with omics-based science will aid the identification of target traits and their use to enhance genetic gains. Additionally, in cases where the genetic base of major legumes is narrow, wild relatives have been evaluated, and these are being exploited through pre-breeding. Thus far, >200 accessions of various legumes have been registered as unique donors for various traits of interest.
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Affiliation(s)
- Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Swarup K. Parida
- DBT-National Institute of Plant Genome Research, New Delhi, India
| | - Nupur Mondal
- Shivaji College, University of Delhi, New Delhi, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Jai C. Rana
- Alliance of Bioversity International and CIAT, India Office, National Agricultural Science Complex, New Delhi, India
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13
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Subramani M, Urrea CA, Habib R, Bhide K, Thimmapuram J, Kalavacharla V. Comparative Transcriptome Analysis of Tolerant and Sensitive Genotypes of Common Bean ( Phaseolus vulgaris L.) in Response to Terminal Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12010210. [PMID: 36616341 PMCID: PMC9824821 DOI: 10.3390/plants12010210] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 06/10/2023]
Abstract
We conducted a genome-wide transcriptomic analysis of three drought tolerant and sensitive genotypes of common bean to examine their transcriptional responses to terminal drought stress. We then conducted pairwise comparisons between the root and leaf transcriptomes from the resulting tissue based on combined transcriptomic data from the tolerant and sensitive genotypes. Our transcriptomic data revealed that 491 (6.4%) DEGs (differentially expressed genes) were upregulated in tolerant genotypes, whereas they were downregulated in sensitive genotypes; likewise, 396 (5.1%) DEGs upregulated in sensitive genotypes were downregulated in tolerant genotypes. Several transcription factors, heat shock proteins, and chaperones were identified in the study. Several DEGs in drought DB (data Base) overlapped between genotypes. The GO (gene ontology) terms for biological processes showed upregulation of DEGs in tolerant genotypes for sulfate and drug transmembrane transport when compared to sensitive genotypes. A GO term for cellular components enriched with upregulated DEGs for the apoplast in tolerant genotypes. These results substantiated the temporal pattern of root growth (elongation and initiation of root growth), and ABA-mediated drought response in tolerant genotypes. KEGG (kyoto encyclopedia of genes and genomes) analysis revealed an upregulation of MAPK (mitogen activated protein kinase) signaling pathways and plant hormone signaling pathways in tolerant genotypes. As a result of this study, it will be possible to uncover the molecular mechanisms of drought tolerance in response to terminal drought stress in the field. Further, genome-wide transcriptomic analysis of both tolerant and sensitive genotypes will assist us in identifying potential genes that may contribute to improving drought tolerance in the common bean.
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Affiliation(s)
- Mayavan Subramani
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Carlos A. Urrea
- Panhandle Research and Extension Center, University of Nebraska, 4502 Avenue I, Scottsbluff, NE 69361, USA
| | - Rasheed Habib
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
| | - Ketaki Bhide
- Bioinformatics Core, Purdue University, West Lafayette, IN 47907, USA
| | | | - Venu Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, College of Agriculture, Science and Technology (CAST), Delaware State University, Dover, DE 19901, USA
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14
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Wang G, Chen Q, Yang Y, Duan Y, Yang Y. Exchanges of economic plants along the land silk road. BMC PLANT BIOLOGY 2022; 22:619. [PMID: 36581803 PMCID: PMC9801618 DOI: 10.1186/s12870-022-04022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUD The greatest contribution of the Silk Road is to communicate among different countries and nationalities, and promote two-way cultural exchanges between the East and the West. We now have clearer understanding about how material civilization and religious culture of Central Asia and West Asia spread eastward along the Land Silk Road. However, there is controversial about how crops migrate along the Land Silk Road. RESULTS We summarize archaeology, genetics, and genomics data to explore crop migration patterns. Of the 207 crops that were domesticated along the Land Silk Road, 19 for which genomic evidence was available were selected for discussion. CONCLUSIONS There were conflicting lines of evidence for the domestication of Tibetan barley, mustard, lettuce, buckwheat, and chickpea. The main reasons for the conflicting results may include incomplete early knowledge, record differences in different period, sample sizes, and data analysis techniques. There was strong evidence that Tibetan barley, barley, wheat, and jujube were introduced into China before the existence of the Land Silk Road; and mustard, lettuce, buckwheat, chickpea, alfalfa, walnut, cauliflower, grape, spinach, apple, cucumber, mulberry, and pea spread to China via trade and human migration along the Land Silk Road.
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Affiliation(s)
- Guangyan Wang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650201, China
| | - Qian Chen
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650201, China
| | - Ya Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yuanwen Duan
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650201, China.
| | - Yongping Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China.
- Institute of Tibetan Plateau Research at Kunming, Chinese Academy of Sciences, Kunming, 650201, China.
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15
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Zhang H, Mascher M, Abbo S, Jayakodi M. Advancing Grain Legumes Domestication and Evolution Studies with Genomics. PLANT & CELL PHYSIOLOGY 2022; 63:1540-1553. [PMID: 35534441 PMCID: PMC9680859 DOI: 10.1093/pcp/pcac062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 06/14/2023]
Abstract
Grain legumes were domesticated in parallel with cereals in several regions of the world and formed the economic basis of early farming cultures. Since then, legumes have played a vital role in human and animal diets and in fostering agrobiodiversity. Increasing grain legume cultivation will be crucial to safeguard nutritional security and the resilience of agricultural ecosystems across the globe. A better understanding of the molecular underpinnings of domestication and crop evolution of grain legumes may be translated into practical approaches in modern breeding programs to stabilize yield, which is threatened by evolving pathogens and changing climates. During recent decades, domestication research in all crops has greatly benefited from the fast progress in genomic technologies. Yet still, many questions surrounding the domestication and diversification of legumes remain unanswered. In this review, we assess the potential of genomic approaches in grain legume research. We describe the centers of origin and the crucial domestication traits of grain legumes. In addition, we survey the effect of domestication on both above-ground and below-ground traits that have economic importance. Finally, we discuss open questions in grain legume domestication and diversification and outline how to bridge the gap between the preservation of historic crop diversity and their utilization in modern plant breeding.
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Affiliation(s)
- Hailin Zhang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, Seeland 06466, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, Leipzig 04103, Germany
| | - Shahal Abbo
- The Levi Eshkol School of Agriculture, The Hebrew University of Jerusalem, POB 12, Rehovot 7610001, Israel
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16
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Singh N, Jain P, Ujinwal M, Langyan S. Escalate protein plates from legumes for sustainable human nutrition. Front Nutr 2022; 9:977986. [PMID: 36407518 PMCID: PMC9672682 DOI: 10.3389/fnut.2022.977986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 09/22/2022] [Indexed: 11/06/2022] Open
Abstract
Protein is one of the most important, foremost, and versatile nutrients in food. The quantity and quality of protein are determinants of its nutritional values. Therefore, adequate consumption of high-quality protein is essential for optimal growth, development, and health of humans. Based on short-term nitrogen balance studies, the Recommended Dietary Allowance of protein for the healthy adult with minimal physical activity is 0.8 g protein/kg body weight (BW) per day. Proteins are present in good quantities in not only animals but also in plants, especially in legumes. With the growing demand for protein, interest in plant proteins is also rising due to their comparative low cost as well as the increase in consumers' demand originating from health and environmental concerns. Legumes are nutrient-dense foods, comprising components identified as "antinutritional factors" that can reduce the bioavailability of macro and micronutrients. Other than nutritive value, the physiochemical and behavioral properties of proteins during processing plays a significant role in determining the end quality of food. The term "complete protein" refers to when all nine essential amino acids are present in the correct proportion in our bodies. To have a balanced diet, the right percentage of protein is required for our body. The consumption of these high protein-containing foods will lead to protein sustainability and eradicate malnutrition. Here, we shed light on major opportunities to strengthen the contribution of diversity in legume crops products to sustainable diets. This review will boost awareness and knowledge on underutilized proteinous foods into national nutritional security programs.
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Affiliation(s)
- Nisha Singh
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Priyanka Jain
- National Institute of Plant Genome Research, New Delhi, India
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University, Noida, Uttar Pradesh, India
| | - Megha Ujinwal
- Department of Bioinformatics, Gujarat Biotechnology University, Gandhinagar, Gujarat, India
| | - Sapna Langyan
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
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17
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Taboada G, Abán CL, Mercado Cárdenas G, Spedaletti Y, Aparicio González M, Maita E, Ortega-Baes P, Galván M. Characterization of fungal pathogens and germplasm screening for disease resistance in the main production area of the common bean in Argentina. FRONTIERS IN PLANT SCIENCE 2022; 13:986247. [PMID: 36161011 PMCID: PMC9490223 DOI: 10.3389/fpls.2022.986247] [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: 07/04/2022] [Accepted: 08/04/2022] [Indexed: 06/16/2023]
Abstract
The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet, mainly in Africa and Latin America. Argentina is one of the five major producers of the common bean in the world, and the main cultivation areas are concentrated in the northwestern provinces of this country. Crop production of the common bean is often affected by biotic factors like some endemic fungal diseases, which exert a major economic impact on the region. The most important fungal diseases affecting the common bean in Argentina are white mold caused by Sclerotinia sclerotiorum, angular leaf spot caused by Pseudocercospora griseola, web blight and root rot caused by Rhizoctonia solani, which can cause production losses of up to 100% in the region. At the present, the most effective strategy for controlling these diseases is the use of genetic resistance. In this sense, population study and characterization of fungal pathogens are essential for developing cultivars with durable resistance. In this review we report diversity studies carried out on these three fungal pathogens affecting the common bean in northwestern Argentina, analyzing more than 200 isolates by means of molecular, morphological and pathogenic approaches. Also, the screening of physiological resistance in several common bean commercial lines and wild native germplasm is reviewed. This review contributes to the development of sustainable management strategies and cultural practices in bean production aimed to minimize yield losses due to fungal diseases in the common bean.
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Affiliation(s)
- Gisel Taboada
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Carla L. Abán
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | | | - Yamila Spedaletti
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Mónica Aparicio González
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
| | - Efrain Maita
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Laboratorio de Investigaciones Botánicas (LABIBO), Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Pablo Ortega-Baes
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Laboratorio de Investigaciones Botánicas (LABIBO), Facultad de Ciencias Naturales, Universidad Nacional de Salta, Salta, Argentina
| | - Marta Galván
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) CCT-Salta, Salta, Argentina
- Instituto Nacional de Tecnología Agropecuaria (INTA) EEA Salta, Salta, Argentina
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18
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Boubakri H, Najjar E, Jihnaoui N, Chihaoui SA, Barhoumi F, Jebara M. Genome-wide identification, characterization and expression analysis of glutaredoxin gene family (Grxs) in Phaseolus vulgaris. Gene 2022; 833:146591. [PMID: 35597531 DOI: 10.1016/j.gene.2022.146591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 04/19/2022] [Accepted: 05/16/2022] [Indexed: 01/29/2023]
Abstract
Glutaredoxins (Grxs) are ubiquitous oxidoreductase proteins implicated in development and abiotic stress response mainly through maintaining redox homoeostasis. Here, we conducted the first systematic analysis of the Grx gene family (PvGrx) in the most popular legume Phaseolus vulgaris (common bean). A total of 50 PvGrx genes were identified, and divided into four classes (CC-type, CGFS-type, CPYC-type and Grl-type) based on the phylogenetic analysis. The different classes have different introns-exons structures and conserved motifs, indicating functional divergence in the PvGrx family. Both tandem and segmental duplications were found to be involved in the expansion of PvGrx family that underwent a purifying selection by excluding the deleterious loss-of-function mutations. Cis-acting regulatory elements and gene ontology analyses predicted their role of distinctive members in abiotic stress response and hormonal signalling. RNA-seq based expression analysis revealed their differential expression pattern during plant development. On the other hand, RT q-PCR analysis revealed that target PvGrx isoforms were associated with nodule organogenesis and symbiosis based on their expression profiles. In addition, a battery of PvGrx candidates were markedly upregulated by different abiotic stressors suggesting their broad spectrum of functions. These findings serve as a reference for functional analysis and genetic improvement in P. vulgaris and related legume species.
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Affiliation(s)
- Hatem Boubakri
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia.
| | - Eya Najjar
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Nada Jihnaoui
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Saif-Allah Chihaoui
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Fathi Barhoumi
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, BP 901, 2050 Hammam-Lif, Tunisia
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Salgotra RK, Stewart CN. Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security. PLANTS 2022; 11:plants11141866. [PMID: 35890499 PMCID: PMC9325189 DOI: 10.3390/plants11141866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in next generation sequencing (NGS) technologies have led the surge of genomic resources for the improvement legume crops. Advances in high throughput genotyping (HTG) and high throughput phenotyping (HTP) enable legume breeders to improve legume crops more precisely and efficiently. Now, the legume breeder can reshuffle the natural gene combinations of their choice to enhance the genetic potential of crops. These genomic resources are efficiently deployed through molecular breeding approaches for genetic augmentation of important legume crops, such as chickpea, cowpea, pigeonpea, groundnut, common bean, lentil, pea, as well as other underutilized legume crops. In the future, advances in NGS, HTG, and HTP technologies will help in the identification and assembly of superior haplotypes to tailor the legume crop varieties through haplotype-based breeding. This review article focuses on the recent development of genomic resource databases and their deployment in legume molecular breeding programmes to secure global food security.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
- Correspondence: (R.K.S.); (C.N.S.J.)
| | - Charles Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (R.K.S.); (C.N.S.J.)
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20
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Zia B, Shi A, Olaoye D, Xiong H, Ravelombola W, Gepts P, Schwartz HF, Brick MA, Otto K, Ogg B, Chen S. Genome-Wide Association Study and Genomic Prediction for Bacterial Wilt Resistance in Common Bean ( Phaseolus vulgaris) Core Collection. Front Genet 2022; 13:853114. [PMID: 35711938 PMCID: PMC9197503 DOI: 10.3389/fgene.2022.853114] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 04/14/2022] [Indexed: 11/30/2022] Open
Abstract
Common bean (Phaseolus vulgaris) is one of the major legume crops cultivated worldwide. Bacterial wilt (BW) of common bean (Curtobacterium flaccumfaciens pv. flaccumfaciens), being a seed-borne disease, has been a challenge in common bean producing regions. A genome-wide association study (GWAS) was conducted to identify SNP markers associated with BW resistance in the USDA common bean core collection. A total of 168 accessions were evaluated for resistance against three different isolates of BW. Our study identified a total of 14 single nucleotide polymorphism (SNP) markers associated with the resistance to BW isolates 528, 557, and 597 using mixed linear models (MLMs) in BLINK, FarmCPU, GAPIT, and TASSEL 5. These SNPs were located on chromosomes Phaseolus vulgaris [Pv]02, Pv04, Pv08, and Pv09 for isolate 528; Pv07, Pv10, and Pv11 for isolate 557; and Pv04, Pv08, and Pv10 for isolate 597. The genomic prediction accuracy was assessed by utilizing seven GP models with 1) all the 4,568 SNPs and 2) the 14 SNP markers. The overall prediction accuracy (PA) ranged from 0.30 to 0.56 for resistance against the three BW isolates. A total of 14 candidate genes were discovered for BW resistance located on chromosomes Pv02, Pv04, Pv07, Pv08, and Pv09. This study revealed vital information for developing genetic resistance against the BW pathogen in common bean. Accordingly, the identified SNP markers and candidate genes can be utilized in common bean molecular breeding programs to develop novel resistant cultivars.
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Affiliation(s)
- Bazgha Zia
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Dotun Olaoye
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR, United States
| | - Waltram Ravelombola
- Organic & Specialty Crop Breeding, Texas A&M AgriLife Research, Vernon, TX, United States
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, Davis, Davis, CA, United States
| | - Howard F Schwartz
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Kristen Otto
- Department of Agricultural Biology, Colorado State University, Fort Collins, CO, United States
| | - Barry Ogg
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Senyu Chen
- Department of Plant Pathology, University of Minnesota, Minneapolis, MN, United States
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21
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Guerra‐García A, Rojas‐Barrera IC, Ross‐Ibarra J, Papa R, Piñero D. The genomic signature of wild‐to‐crop introgression during the domestication of scarlet runner bean (
Phaseolus coccineus
L.). Evol Lett 2022; 6:295-307. [PMID: 35937471 PMCID: PMC9346085 DOI: 10.1002/evl3.285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 03/06/2022] [Accepted: 05/15/2022] [Indexed: 11/23/2022] Open
Abstract
The scarlet runner bean (Phaseolus coccineus) is one of the five domesticated Phaseolus species. It is cultivated in small‐scale agriculture in the highlands of Mesoamerica for its dry seeds and immature pods, and unlike the other domesticated beans, P. coccineus is an open‐pollinated legume. Contrasting with its close relative, the common bean, few studies focusing on its domestication history have been conducted. Demographic bottlenecks associated with domestication might reduce genetic diversity and facilitate the accumulation of deleterious mutations. Conversely, introgression from wild relatives could be a source of variation. Using Genotyping by Sequencing data (79,286 single‐nucleotide variants) from 237 cultivated and wild samples, we evaluated the demographic history of traditional varieties from different regions of Mexico and looked for evidence of introgression between sympatric wild and cultivated populations. Traditional varieties have high levels of diversity, even though there is evidence of a severe initial genetic bottleneck followed by a population expansion. Introgression from wild to domesticated populations was detected, which might contribute to the recovery of the genetic variation. Introgression has occurred at different times: constantly in the center of Mexico; recently in the North West; and anciently in the South. Several factors are acting together to increase and maintain genetic diversity in P. coccineus cultivars, such as demographic expansion and introgression. Wild relatives represent a valuable genetic resource and have played a key role in scarlet runner bean evolution via introgression into traditional varieties.
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Affiliation(s)
- Azalea Guerra‐García
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Department of Plant Sciences University of Saskatchewan Saskatoon SK S7N 5A2 Canada
| | - Idalia C. Rojas‐Barrera
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
- Environmental Genomics Max Planck Institute for Evolutionary Biology 24306 Plön Germany
| | - Jeffrey Ross‐Ibarra
- Department of Evolution and Ecology, Center for Population Biology, and Genome Center University of California, Davis Davis California 95616
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali Università Politecnica delle Marche Ancona 60131 Italy
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología Universidad Nacional Autónoma de México Ciudad de México 04510 México
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22
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Feng S, Shi J, Hu Y, Li D, Guo L, Zhao Z, Lee GS, Qiao Y. Genome-Wide Analysis of Soybean Lateral Organ Boundaries Domain Gene Family Reveals the Role in Phytophthora Root and Stem Rot. FRONTIERS IN PLANT SCIENCE 2022; 13:865165. [PMID: 35599907 PMCID: PMC9116278 DOI: 10.3389/fpls.2022.865165] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 03/16/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific lateral organ boundaries (LOB) domain (LBD) proteins, a family of transcription factors, play important roles in plant growth and development, as well as in responses to various stresses. However, little is known about the functions of LBD genes in soybean (Glycine max). In this study, we investigated the evolution and classification of the LBD family in soybean by a phylogenetic tree of the LBD gene family from 16 species. Phylogenetic analysis categorized these proteins into two classes (Class I and Class II) with seven subgroups. Moreover, we found that all the 18 LBD ancestors in angiosperm were kept in soybean, common bean genomes, and genome-wide duplication, suggesting the main force for the expansion of LBD from common bean to soybean. Analysis of gene expression profiling data indicated that 16 GmLBD genes were significantly induced at different time points after inoculation of soybean plants (cv. Huachun 6) with Phytophthora sojae (P. sojae). We further assessed the role of four highly upregulated genes, GmLBD9, GmLBD16, GmLBD23, and GmLBD88, in plant defense in soybean hairy roots using the transient overexpression and knockdown assays. The results showed that GmLBD9 and GmLBD23 negatively regulate plant immunity against P. sojae, whereas GmLBD16 and GmLBD88 positively manipulate plant immunity against P. sojae. Collectively, our findings expand our knowledge of the origin and evolution of the GmLBD gene family in soybean and promote the potential application of these genes in soybean genetic improvement.
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Affiliation(s)
- Siqi Feng
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jinxia Shi
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yongkang Hu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Die Li
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Liang Guo
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhibo Zhao
- Department of Plant Pathology, College of Agriculture, Guizhou University, Guiyang, China
| | - Gang-Seob Lee
- National Institute of Agricultural Science, Jeonju, South Korea
| | - Yongli Qiao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
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23
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Sofi PA, Mir RR, Zargar SM, Rani S, Fatima S, Shafi S, Zaffar A. What makes the beans (Phaseolus vulgaris L.) soft: insights into the delayed cooking and hard to cook trait. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2022. [DOI: 10.1007/s43538-022-00075-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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Castaingts M, Kirolinko C, Rivero C, Artunian J, Mancini Villagra U, Blanco FA, Zanetti ME. Identification of conserved and new miRNAs that affect nodulation and strain selectivity in the Phaseolus vulgaris-Rhizobium etli symbiosis through differential analysis of host small RNAs. THE NEW PHYTOLOGIST 2022; 234:1430-1447. [PMID: 35203109 DOI: 10.1111/nph.18055] [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: 01/15/2022] [Accepted: 02/07/2022] [Indexed: 06/14/2023]
Abstract
Phaseolus vulgaris plants from the Mesoamerican centre of genetic diversification establish a preferential and more efficient root nodule symbiosis with sympatric Rhizobium etli strains. This is mediated by changes in host gene expression, which might occur either at the transcriptional or at the post-transcriptional level. However, the implication of small RNA (sRNA)-mediated control of gene expression in strain selectivity has remained elusive. sRNA sequencing was used to identify host microRNAs (miRNAs) differentially regulated in roots at an early stage of the symbiotic interaction, which were further characterized by applying a reverse genetic approach. In silico analysis identified known and new miRNAs that accumulated to a greater extent in the preferential and more efficient interaction. One of them, designated as Pvu-miR5924, participates in the mechanisms that determine the selection of R. etli strains that will colonize the nodules. In addition, the functional analysis of Pvu-miR390b verified that this miRNA is a negative modulator of nodule formation and bacterial infection. This study not only extended the list of miRNAs identified in P. vulgaris but also enabled the identification of miRNAs that play relevant functions in nodule formation, rhizobial infection and the selection of the rhizobial strains that will occupy the nodule.
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Affiliation(s)
- Melisse Castaingts
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Cristina Kirolinko
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Claudio Rivero
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Jennifer Artunian
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Ulises Mancini Villagra
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - Flavio Antonio Blanco
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
| | - María Eugenia Zanetti
- Facultad de Ciencias Exactas, Instituto de Biotecnología y Biología Molecular, Universidad Nacional de La Plata, Centro Científico y Tecnológico-La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, La Plata, 1900, Argentina
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25
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Wang W, Xie Y, Liu L, King GJ, White P, Ding G, Wang S, Cai H, Wang C, Xu F, Shi L. Genetic Control of Seed Phytate Accumulation and the Development of Low-Phytate Crops: A Review and Perspective. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3375-3390. [PMID: 35275483 DOI: 10.1021/acs.jafc.1c06831] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Breeding low phytic acid (lpa) crops is a strategy that has potential to both improve the nutritional quality of food and feed and contribute to the sustainability of agriculture. Here, we review the lipid-independent and -dependent pathways of phytate synthesis and their regulatory mechanisms in plants. We compare the genetic variation of the phytate concentration and distribution in seeds between dicot and monocot species as well as the associated temporal and spatial expression patterns of the genes involved in phytate synthesis and transport. Quantitative trait loci or significant single nucleotide polymorphisms for the seed phytate concentration have been identified in different plant species by linkage and association mapping, and some genes have been cloned from lpa mutants. We summarize the effects of various lpa mutations on important agronomic traits in crop plants and propose SULTR3;3 and SULTR3;4 as optimal target genes for lpa crop breeding.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Yiwen Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross University, Lismore New South Wales 2480, Australia
| | - Graham J King
- Southern Cross Plant Science, Southern Cross University, Lismore New South Wales 2480, Australia
| | - Philip White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- The James Hutton Institute, Invergowrie, Dundee DD2 5DA, United Kingdom
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Sheliang Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Hongmei Cai
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Chuang Wang
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
- Microelement Research Center, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, Hubei 430070, People's Republic of China
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26
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Aguilar OM, Collavino MM, Mancini U. Nodulation competitiveness and diversification of symbiosis genes in common beans from the American centers of domestication. Sci Rep 2022; 12:4591. [PMID: 35301409 PMCID: PMC8931114 DOI: 10.1038/s41598-022-08720-0] [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: 08/17/2021] [Accepted: 02/24/2022] [Indexed: 11/09/2022] Open
Abstract
Phaseolus vulgaris (common bean), having a proposed Mexican origin within the Americas, comprises three centers of diversification: Mesoamerica, the southern Andes, and the Amotape-Huancabamba Depression in Peru-Ecuador. Rhizobium etli is the predominant rhizobium found symbiotically associated with beans in the Americasalthough closely related Rhizobium phylotypes have also been detected. To investigate if symbiosis between bean varieties and rhizobia evolved affinity, firstly nodulation competitiveness was studied after inoculation with a mixture of sympatric and allopatric rhizobial strains isolated from the respective geographical regions. Rhizobia strains harboring nodC types α and \documentclass[12pt]{minimal}
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\begin{document}$$\upgamma$$\end{document}γ, which were found predominant in Mexico and Ecuador, were comparable in nodule occupancy at 50% of each in beans from the Mesoamerican and Andean gene pools, but it is one of those two nodC types which clearly predominated in Ecuadorian-Peruvian beans as well as in Andean beans nodC type \documentclass[12pt]{minimal}
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\begin{document}$$\upgamma$$\end{document}γ predominated the sympatric nodC type δ. The results indicated that those beans from Ecuador-Peru and Andean region, respectively exhibited no affinity for nodulation by the sympatric rhizobial lineages that were found to be predominant in bean nodules formed in those respective areas. Unlike the strains isolated from Ecuador, Rhizobium etli isolated from Mexico as well from the southern Andes was highly competitive for nodulation in beans from Ecuador-Peru, and quite similarly competitive in Mesoamerican and Andean beans. Finally, five gene products associated with symbiosis were examined to analyze variations that could be correlated with nodulation competitiveness. A small GTPase RabA2, transcriptional factors NIN and ASTRAY, and nodulation factor receptors NFR1 and NFR5- indicated high conservation but NIN, NFR1 and NFR5 of beans representative of the Ecuador-Peru genetic pool clustered separated from the Mesoamerican and Andean showing diversification and possible different interaction. These results indicated that both host and bacterial genetics are important for mutual affinity, and that symbiosis is another trait of legumes that could be sensitive to evolutionary influences and local adaptation.
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Affiliation(s)
- O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina.
| | - Mónica M Collavino
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
| | - Ulises Mancini
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina
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27
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Transcriptomic analysis of Mesoamerican and Andean Phaseolus vulgaris accessions revealed mRNAs and lncRNAs associated with strain selectivity during symbiosis. Sci Rep 2022; 12:2614. [PMID: 35173231 PMCID: PMC8850587 DOI: 10.1038/s41598-022-06566-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 01/28/2022] [Indexed: 12/29/2022] Open
Abstract
Legume plants establish a nitrogen-fixing symbiosis with soil bacteria known as rhizobia. Compatibility between legumes and rhizobia is determined at species-specific level, but variations in the outcome of the symbiotic process are also influenced by the capacity of the plant to discriminate and select specific strains that are better partners. We compared the transcriptional response of two genetically diverse accessions of Phaseolus vulgaris from Mesoamerica and South Andes to Rhizobium etli strains that exhibit variable degrees of symbiotic affinities. Our results indicate that the plant genotype is the major determinant of the transcriptional reprogramming occurring in roots at early stages of the symbiotic interaction. Differentially expressed genes (DEGs) regulated in the Mesoamerican and the Andean accessions in response to specific strains are different, but they belong to the same functional categories. The common and strain-specific transcriptional responses to rhizobia involve distinct transcription factors and cis-elements present in the promoters of DEGs in each accession, showing that diversification and domestication of common bean at different geographic regions influenced the evolution of symbiosis differently in each genetic pool. Quantitative PCR analysis validated our transcriptional datasets, which constitute a valuable source of coding and non-coding candidate genes to further unravel the molecular determinants governing the mechanisms by which plants select bacterial strains that produce a better symbiotic outcome.
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28
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Zhou R, Yang S, Zhang B, Qi Z, Xin D, Su A, Li S, Cheng P, Bai Y, Yin Z, Zhang B, Zhao Y, Zhao Y, Chen Q, Wu X. Analysis of the genetic diversity of grain legume germplasm resources in China and the development of universal SSR primers. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2021.2006784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Runnan Zhou
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Siqi Yang
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Bo Zhang
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhaoming Qi
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Dawei Xin
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Anyu Su
- Department of Land Remediation Engineering, College of Public Administration and Law, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Sinan Li
- Key Lab of Maize Genetics and Breeding, Department of National Corn Engineering Laboratory, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, PR China
| | - Peng Cheng
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Yunqi Bai
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Zhengong Yin
- Crop Resources Institute of Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, PR China
| | - Binshuo Zhang
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Yujing Zhao
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Ying Zhao
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Qingshan Chen
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
| | - Xiaoxia Wu
- Department of Agronomy, College of Agriculture, Northeast Agricultural University, Harbin, Heilongjiang, PR China
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29
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Nabi A, Lateef I, Nisa Q, Banoo A, Rasool RS, Shah MD, Ahmad M, Padder BA. Phaseolus vulgaris-Colletotrichum lindemuthianum Pathosystem in the Post-Genomic Era: An Update. Curr Microbiol 2022; 79:36. [PMID: 34982236 DOI: 10.1007/s00284-021-02711-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022]
Abstract
Phaseolus vulgaris-Colletotrichum lindemuthianum is one among the oldest host and pathogen interface. Researchers have taken painstaking efforts across the world for understanding the dialogue during early and late phases of interaction. Collectively, these efforts resulted in the deluge of information that helped the researchers to underpin the interface. The latest molecular biology techniques furnished novel detection methods for the anthracnose pathogen, refined the understanding of pathogen population dynamics, and provided the insights on co-evolutionary common bean resistance and C. lindemuthianum virulence dynamics. One of the important breakthroughs came when the Phaseolus vulgaris and its corresponding anthracnose pathogen (C. lindemuthianum) genomes were decoded in 2014 and 2017, respectively. Availability of both the genomes yielded a significant genomic information that helped bean communities to fine map the economically important traits and to identify the pathogenicity determinants and effector molecules. The interface is in a continuous development as knowledge of the anthracnose resistance genes, their precise physical locations, and the identification of effector proteins; the fungus arsenals are being routinely updated. Hence, we revisited the interface and tried to provide an overview of host pathogen dialogue in the genomic era. Additionally, we compiled the sporadic information on this pathosystem from India and provided its futuristic road map to shape its research in the world and northern India, the major dry bean area in the country.
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Affiliation(s)
- Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aqleema Banoo
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rovidha S Rasool
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - M D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Mushtaq Ahmad
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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Tello-Ruiz MK, Jaiswal P, Ware D. Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways. Methods Mol Biol 2022; 2443:101-131. [PMID: 35037202 DOI: 10.1007/978-1-0716-2067-0_5] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gramene is an integrated bioinformatics resource for accessing, visualizing, and comparing plant genomes and biological pathways. Originally targeting grasses, Gramene has grown to host annotations for over 90 plant genomes including agronomically important cereals (e.g., maize, sorghum, wheat, teff), fruits and vegetables (e.g., apple, watermelon, clementine, tomato, cassava), specialty crops (e.g., coffee, olive tree, pistachio, almond), and plants of special or emerging interest (e.g., cotton, tobacco, cannabis, or hemp). For some species, the resource includes multiple varieties of the same species, which has paved the road for the creation of species-specific pan-genome browsers. The resource also features plant research models, including Arabidopsis and C4 warm-season grasses and brassicas, as well as other species that fill phylogenetic gaps for plant evolution studies. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies to integrate structural and functional annotation data. This chapter outlines system requirements for end-users and database hosting, data types and basic navigation within Gramene, and provides examples of how to (1) explore Gramene's search results, (2) explore gene-centric comparative genomics data visualizations in Gramene, and (3) explore genetic variation associated with a gene locus. This is the first publication describing in detail Gramene's integrated search interface-intended to provide a simplified entry portal for the resource's main data categories (genomic location, phylogeny, gene expression, pathways, and external references) to the most complete and up-to-date set of plant genome and pathway annotations.
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Affiliation(s)
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
- USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit, Cornell University, Ithaca, NY, USA.
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Liu C, Tai Y, Luo J, Wu Y, Zhao X, Dong R, Ding X, Zhao S, Luo L, Liu P, Liu G. Integrated multi-omics analysis provides insights into genome evolution and phosphorus deficiency adaptation in pigeonpea ( Cajanus cajan). HORTICULTURE RESEARCH 2022; 9:uhac107. [PMID: 35795392 PMCID: PMC9251600 DOI: 10.1093/hr/uhac107] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/23/2022] [Indexed: 05/12/2023]
Abstract
Pigeonpea (Cajanus cajan) is an important legume food crop and plays a crucial role in a secure food supply in many developing countries. Several previous studies have suggested that pigeonpea has great potential for phosphorus (P) deficiency tolerance, but little is known about the underlying mechanism. In this study, the physiological and molecular responses of pigeonpea roots to phosphate (Pi) starvation were investigated through integrating phenotypic, genomic, transcriptomic, metabolomic, and lipidomic analyses. The results showed that low-Pi treatment increased total root length, root surface area, and root acid phosphatase activity, and promoted the secretion of organic acids (e.g. citric acids, piscidic acids, and protocatechuic acids) and the degradation of phospholipids and other P-containing metabolites in the roots of pigeonpea. Consistent with the morphological, physiological, and biochemical changes, a large number of genes involved in these Pi-starvation responses were significantly upregulated in Pi-deficient pigeonpea roots. Among these Pi-starvation response genes upregulated by low-Pi treatment, four gene families were expanded through recent tandem duplication in the pigeonpea genome, namely phosphate transporter 1 (PHT1), phosphoethanolamine/phosphocholine phosphatase (PECP), fasciclin-like arabinogalactan protein (FLA), and glutamate decarboxylase (GAD). These gene families may be associated with Pi uptake from the soil, phospholipid recycling, root morphological remodeling, and regulation of organic acid exudation. Taken together, our results suggest that pigeonpea employs complex Pi-starvation responses to strengthen P acquisition and utilization during low-Pi stress. This study provides new insights into the genome evolution and P deficiency adaptation mechanism of pigeonpea.
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Affiliation(s)
| | | | - Jiajia Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Yuanhang Wu
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Xingkun Zhao
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Rongshu Dong
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Xipeng Ding
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Shancen Zhao
- BGI Institute of Applied Agriculture, BGI-Shenzhen, Shenzhen 518120, China
| | - Lijuan Luo
- College of Forestry & College of Tropical Crops, Hainan University, Haikou 570228, China
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Han Y, Gao Y, Li M, Du Y, Zhang Y, Zhang W, Du J. The molecular events underpinning cultivar differences in melatonin counteracting salt damage in Phaseolus vulgaris. FUNCTIONAL PLANT BIOLOGY : FPB 2022; 49:201-217. [PMID: 34871542 DOI: 10.1071/fp21126] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
Melatonin (N -acetyl-5-methoxytryptamine) plays important roles in multiple stress responses, especially under salt stress. However, cultivar differences in melatonin mediated salt stress tolerance are unclear. Phaseolus vulgaris L. (common bean) cultivars Jiyin 1 (JY, salt-tolerant) and Xuliyabai (XL, salt-sensitive) were used in this study. Exogenous melatonin significantly improved root growth under salt stress in JY, but had little effect on XL. Physiology analysis showed significant differences in activities of antioxidant enzymes (superoxide, SOD; and catalase, CAT) and malondialdehyde content between JY and XL. Meanwhile, the change of ABA content in JY and XL root was opposite in salt plus melatonin treatment. Comparative root transcriptomes of JY and XL revealed 3505 and 668 differentially expressed genes (DEGs) regulated by salt stress and melatonin. The most enriched melatonin-responsive genes under salt stress are mainly involved in regulation of transcription, oxidation-reduction process, transcription factor activity, oxidoreductase activity. In addition, melatonin induced more obvious changes of DEGs in JY than that in XL under salt condition. Melatonin also significantly induced 41 DEGs only in JY, including signal transduction genes, transcription factors, ubiquitin protein ligases, ion homeostasis and osmotic adjustment genes etc. This study uncovered the molecular mechanism of cultivar difference of melatonin response under salt stress in common bean.
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Affiliation(s)
- Yiqiang Han
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China; and National Coarse Cereals Engineering Research Center, Daqing 163319, Heilongjiang Province, P. R. China
| | - Yamei Gao
- College of Life Science and Technology, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China; and Heilongjiang Provincial Key Laboratory of Environmental Microbiology and Recycling of Argo-Waste in the Cold Region, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China
| | - Ming Li
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China
| | - Yanli Du
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China
| | - Yuxian Zhang
- National Coarse Cereals Engineering Research Center, Daqing 163319, Heilongjiang Province, P. R. China; and College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China
| | - Wenhui Zhang
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China
| | - Jidao Du
- National Coarse Cereals Engineering Research Center, Daqing 163319, Heilongjiang Province, P. R. China; and College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163319, Heilongjiang Province, P. R. China
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Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes. Int J Mol Sci 2021; 23:ijms23010399. [PMID: 35008831 PMCID: PMC8745526 DOI: 10.3390/ijms23010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.
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Alvarez-Diaz JC, Richard MMS, Thareau V, Teano G, Paysant-Le-Roux C, Rigaill G, Pflieger S, Gratias A, Geffroy V. Genome-Wide Identification of Key Components of RNA Silencing in Two Phaseolus vulgaris Genotypes of Contrasting Origin and Their Expression Analyses in Response to Fungal Infection. Genes (Basel) 2021; 13:genes13010064. [PMID: 35052407 PMCID: PMC8774654 DOI: 10.3390/genes13010064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 12/13/2022] Open
Abstract
RNA silencing serves key roles in a multitude of cellular processes, including development, stress responses, metabolism, and maintenance of genome integrity. Dicer, Argonaute (AGO), double-stranded RNA binding (DRB) proteins, RNA-dependent RNA polymerase (RDR), and DNA-dependent RNA polymerases known as Pol IV and Pol V form core components to trigger RNA silencing. Common bean (Phaseolus vulgaris) is an important staple crop worldwide. In this study, we aimed to unravel the components of the RNA-guided silencing pathway in this non-model plant, taking advantage of the availability of two genome assemblies of Andean and Meso-American origin. We identified six PvDCLs, thirteen PvAGOs, 10 PvDRBs, 5 PvRDRs, in both genotypes, suggesting no recent gene amplification or deletion after the gene pool separation. In addition, we identified one PvNRPD1 and one PvNRPE1 encoding the largest subunits of Pol IV and Pol V, respectively. These genes were categorized into subgroups based on phylogenetic analyses. Comprehensive analyses of gene structure, genomic localization, and similarity among these genes were performed. Their expression patterns were investigated by means of expression models in different organs using online data and quantitative RT-PCR after pathogen infection. Several of the candidate genes were up-regulated after infection with the fungus Colletotrichum lindemuthianum.
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Affiliation(s)
- Juan C. Alvarez-Diaz
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Manon M. S. Richard
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Vincent Thareau
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Gianluca Teano
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Christine Paysant-Le-Roux
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Guillem Rigaill
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Laboratoire de Mathématiques et Modélisation d’Evry, Université Paris-Saclay, CNRS, Université Evry, INRAE, 91037 Evry, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France; (J.C.A.-D.); (M.M.S.R.); (V.T.); (G.T.); (C.P.-L.-R.); (G.R.); (S.P.); (A.G.)
- Université de Paris, Institute of Plant Sciences Paris Saclay (IPS2), 91405 Orsay, France
- Correspondence: ; Tel.: +33-1-69-15-33-65
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Losa A, Vorster J, Cominelli E, Sparvoli F, Paolo D, Sala T, Ferrari M, Carbonaro M, Marconi S, Camilli E, Reboul E, Waswa B, Ekesa B, Aragão F, Kunert K. Drought and heat affect common bean minerals and human diet—What we know and where to go. Food Energy Secur 2021. [DOI: 10.1002/fes3.351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Alessia Losa
- Council for Research in Agriculture and Economics Research Centre for Genomics and Bioinformatics (CREA‐GB) Montanaso Italy
| | - Juan Vorster
- Department Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa
| | - Eleonora Cominelli
- National Research Council Institute of Agricultural Biology and Biotechnology (CNR‐IBBA) Milan Italy
| | - Francesca Sparvoli
- National Research Council Institute of Agricultural Biology and Biotechnology (CNR‐IBBA) Milan Italy
| | - Dario Paolo
- National Research Council Institute of Agricultural Biology and Biotechnology (CNR‐IBBA) Milan Italy
| | - Tea Sala
- Council for Research in Agriculture and Economics Research Centre for Genomics and Bioinformatics (CREA‐GB) Montanaso Italy
| | - Marika Ferrari
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | - Marina Carbonaro
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | - Stefania Marconi
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | - Emanuela Camilli
- Council for Agricultural Research and Economics Research Centre for Food and Nutrition (CREA‐AN) Rome Italy
| | | | - Boaz Waswa
- International Center for Tropical Agriculture (CIAT) CIAT Regional Office for Africa Nairobi Kenya
| | - Beatrice Ekesa
- International Center for Tropical Agriculture (CIAT) CIAT Regional Office for Africa Nairobi Kenya
| | | | - Karl Kunert
- Department Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute University of Pretoria Pretoria South Africa
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Chen NWG, Ruh M, Darrasse A, Foucher J, Briand M, Costa J, Studholme DJ, Jacques M. Common bacterial blight of bean: a model of seed transmission and pathological convergence. MOLECULAR PLANT PATHOLOGY 2021; 22:1464-1480. [PMID: 33942466 PMCID: PMC8578827 DOI: 10.1111/mpp.13067] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 05/31/2023]
Abstract
BACKGROUND Xanthomonas citri pv. fuscans (Xcf) and Xanthomonas phaseoli pv. phaseoli (Xpp) are the causal agents of common bacterial blight of bean (CBB), an important disease worldwide that remains difficult to control. These pathogens belong to distinct species within the Xanthomonas genus and have undergone a dynamic evolutionary history including the horizontal transfer of genes encoding factors probably involved in adaptation to and pathogenicity on common bean. Seed transmission is a key point of the CBB disease cycle, favouring both vertical transmission of the pathogen and worldwide distribution of the disease through global seed trade. TAXONOMY Kingdom: Bacteria; phylum: Proteobacteria; class: Gammaproteobacteria; order: Lysobacterales (also known as Xanthomonadales); family: Lysobacteraceae (also known as Xanthomonadaceae); genus: Xanthomonas; species: X. citri pv. fuscans and X. phaseoli pv. phaseoli (Xcf-Xpp). HOST RANGE The main host of Xcf-Xpp is the common bean (Phaseolus vulgaris). Lima bean (Phaseolus lunatus) and members of the Vigna genus (Vigna aconitifolia, Vigna angularis, Vigna mungo, Vigna radiata, and Vigna umbellata) are also natural hosts of Xcf-Xpp. Natural occurrence of Xcf-Xpp has been reported for a handful of other legumes such as Calopogonium sp., Pueraria sp., pea (Pisum sativum), Lablab purpureus, Macroptilium lathyroides, and Strophostyles helvola. There are conflicting reports concerning the natural occurrence of CBB agents on tepary bean (Phaseolus acutifolius) and cowpea (Vigna unguiculata subsp. unguiculata). SYMPTOMS CBB symptoms occur on all aerial parts of beans, that is, seedlings, leaves, stems, pods, and seeds. Symptoms initially appear as water-soaked spots evolving into necrosis on leaves, pustules on pods, and cankers on twigs. In severe infections, defoliation and wilting may occur. DISTRIBUTION CBB is distributed worldwide, meaning that it is frequently encountered in most places where bean is cultivated in the Americas, Asia, Africa, and Oceania, except for arid tropical areas. Xcf-Xpp are regulated nonquarantine pathogens in Europe and are listed in the A2 list by the European and Mediterranean Plant Protection Organization (EPPO). GENOME The genome consists of a single circular chromosome plus one to four extrachromosomal plasmids of various sizes, for a total mean size of 5.27 Mb with 64.7% GC content and an average predicted number of 4,181 coding sequences. DISEASE CONTROL Management of CBB is based on integrated approaches that comprise measures aimed at avoiding Xcf-Xpp introduction through infected seeds, cultural practices to limit Xcf-Xpp survival between host crops, whenever possible the use of tolerant or resistant bean genotypes, and chemical treatments, mainly restricted to copper compounds. The use of pathogen-free seeds is essential in an effective management strategy and requires appropriate sampling, detection, and identification methods. USEFUL WEBSITES: https://gd.eppo.int/taxon/XANTPH, https://gd.eppo.int/taxon/XANTFF, and http://www.cost.eu/COST_Actions/ca/CA16107.
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Affiliation(s)
- Nicolas W. G. Chen
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Mylène Ruh
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Armelle Darrasse
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Justine Foucher
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Martial Briand
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F‐49000 Angers, France
| | - Joana Costa
- University of Coimbra, Centre for Functional Ecology ‐ Science for People & the Planet, Department of Life SciencesCoimbraPortugal
| | - David J. Studholme
- Biosciences, College of Life and Environmental SciencesUniversity of ExeterExeterUK
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Chromosome-length genome assemblies of six legume species provide insights into genome organization, evolution, and agronomic traits for crop improvement. J Adv Res 2021; 42:315-329. [PMID: 36513421 PMCID: PMC9788938 DOI: 10.1016/j.jare.2021.10.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 10/20/2021] [Accepted: 10/24/2021] [Indexed: 12/27/2022] Open
Abstract
INTRODUCTION Legume crops are an important source of protein and oil for human health and in fixing atmospheric N2 for soil enrichment. With an objective to accelerate much-needed genetic analyses and breeding applications, draft genome assemblies were generated in several legume crops; many of them are not high quality because they are mainly based on short reads. However, the superior quality of genome assembly is crucial for a detailed understanding of genomic architecture, genome evolution, and crop improvement. OBJECTIVES Present study was undertaken with an objective of developing improved chromosome-length genome assemblies in six different legumes followed by their systematic investigation to unravel different aspects of genome organization and legume evolution. METHODS We employed in situ Hi-C data to improve the existing draft genomes and performed different evolutionary and comparative analyses using improved genome assemblies. RESULTS We have developed chromosome-length genome assemblies in chickpea, pigeonpea, soybean, subterranean clover, and two wild progenitor species of cultivated groundnut (A. duranensis and A. ipaensis). A comprehensive comparative analysis of these genome assemblies offered improved insights into various evolutionary events that shaped the present-day legume species. We highlighted the expansion of gene families contributing to unique traits such as nodulation in legumes, gravitropism in groundnut, and oil biosynthesis in oilseed legume crops such as groundnut and soybean. As examples, we have demonstrated the utility of improved genome assemblies for enhancing the resolution of "QTL-hotspot" identification for drought tolerance in chickpea and marker-trait associations for agronomic traits in pigeonpea through genome-wide association study. Genomic resources developed in this study are publicly available through an online repository, 'Legumepedia'. CONCLUSION This study reports chromosome-length genome assemblies of six legume species and demonstrates the utility of these assemblies in crop improvement. The genomic resources developed here will have significant role in accelerating genetic improvement applications of legume crops.
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Bodrug-Schepers A, Stralis-Pavese N, Buerstmayr H, Dohm JC, Himmelbauer H. Quinoa genome assembly employing genomic variation for guided scaffolding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3577-3594. [PMID: 34365519 PMCID: PMC8519820 DOI: 10.1007/s00122-021-03915-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
We propose to use the natural variation between individuals of a population for genome assembly scaffolding. In today's genome projects, multiple accessions get sequenced, leading to variant catalogs. Using such information to improve genome assemblies is attractive both cost-wise as well as scientifically, because the value of an assembly increases with its contiguity. We conclude that haplotype information is a valuable resource to group and order contigs toward the generation of pseudomolecules. Quinoa (Chenopodium quinoa) has been under cultivation in Latin America for more than 7500 years. Recently, quinoa has gained increasing attention due to its stress resistance and its nutritional value. We generated a novel quinoa genome assembly for the Bolivian accession CHEN125 using PacBio long-read sequencing data (assembly size 1.32 Gbp, initial N50 size 608 kbp). Next, we re-sequenced 50 quinoa accessions from Peru and Bolivia. This set of accessions differed at 4.4 million single-nucleotide variant (SNV) positions compared to CHEN125 (1.4 million SNV positions on average per accession). We show how to exploit variation in accessions that are distantly related to establish a genome-wide ordered set of contigs for guided scaffolding of a reference assembly. The method is based on detecting shared haplotypes and their expected continuity throughout the genome (i.e., the effect of linkage disequilibrium), as an extension of what is expected in mapping populations where only a few haplotypes are present. We test the approach using Arabidopsis thaliana data from different populations. After applying the method on our CHEN125 quinoa assembly we validated the results with mate-pairs, genetic markers, and another quinoa assembly originating from a Chilean cultivar. We show consistency between these information sources and the haplotype-based relations as determined by us and obtain an improved assembly with an N50 size of 1079 kbp and ordered contig groups of up to 39.7 Mbp. We conclude that haplotype information in distantly related individuals of the same species is a valuable resource to group and order contigs according to their adjacency in the genome toward the generation of pseudomolecules.
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Affiliation(s)
- Alexandrina Bodrug-Schepers
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria
| | - Nancy Stralis-Pavese
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria
| | - Hermann Buerstmayr
- Institute of Biotechnology in Plant Production, Department of Agrobiotechnology and Department of Crop Sciences, Universität für Bodenkultur, Tulln, Austria
| | - Juliane C Dohm
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria.
| | - Heinz Himmelbauer
- Institute of Computational Biology, Department of Biotechnology, Universität für Bodenkultur, Vienna, Austria.
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Fuentes D, Molina M, Chorostecki U, Capella-Gutiérrez S, Marcet-Houben M, Gabaldón T. PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. Nucleic Acids Res 2021; 50:D1062-D1068. [PMID: 34718760 PMCID: PMC8728271 DOI: 10.1093/nar/gkab966] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/02/2021] [Accepted: 10/05/2021] [Indexed: 12/20/2022] Open
Abstract
PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.
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Affiliation(s)
- Diego Fuentes
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Manuel Molina
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Uciel Chorostecki
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | | | - Marina Marcet-Houben
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS). Jordi Girona 29, 08034 Barcelona, Spain.,Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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Vlasova A, Hermoso Pulido T, Camara F, Ponomarenko J, Guigó R. FA-nf: A Functional Annotation Pipeline for Proteins from Non-Model Organisms Implemented in Nextflow. Genes (Basel) 2021; 12:genes12101645. [PMID: 34681040 PMCID: PMC8535801 DOI: 10.3390/genes12101645] [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: 09/24/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022] Open
Abstract
Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for proofreading and improving gene structural annotation. Here, we introduce FA-nf, a pipeline implemented in Nextflow, a versatile computational workflow management engine. The pipeline integrates different annotation approaches, such as NCBI BLAST+, DIAMOND, InterProScan, and KEGG. It starts from a protein sequence FASTA file and, optionally, a structural annotation file in GFF format, and produces several files, such as GO assignments, output summaries of the abovementioned programs and final annotation reports. The pipeline can be broken easily into smaller processes for the purpose of parallelization and easily deployed in a Linux computational environment, thanks to software containerization, thus helping to ensure full reproducibility.
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Affiliation(s)
- Anna Vlasova
- Barcelona Supercomputing Centre (BSC-CNS), Jordi Girona, 29, 08034 Barcelona, Spain;
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028 Barcelona, Spain
| | - Toni Hermoso Pulido
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (F.C.); (J.P.); (R.G.)
- Correspondence:
| | - Francisco Camara
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (F.C.); (J.P.); (R.G.)
| | - Julia Ponomarenko
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (F.C.); (J.P.); (R.G.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Roderic Guigó
- Centre for Genomic Regulation (CRG), The Barcelona Institute for Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain; (F.C.); (J.P.); (R.G.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
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Aslam MM, Waseem M, Zhang Q, Ke W, Zhang J, Xu W. Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use. BMC Genomics 2021; 22:723. [PMID: 34615466 PMCID: PMC8495970 DOI: 10.1186/s12864-021-08015-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 08/23/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND White lupin (Lupinus albus) is a leguminous crop with elite adaptive ability in phosphorus-deficient soil and used as a model plant for studying phosphorus (P) use. However, the genetic basis of its adaptation to low P (LP) remains unclear. ATPase binding cassette (ABC) transports G subfamily play a crucial role in the transportation of biological molecules across the membrane. To date, identification of this subfamily has been analyzed in some plants, but no systematic analysis of these transporters in phosphorus acquisition is available for white lupin. RESULTS This study identified 66 ABCG gene family members in the white lupin genome using comprehensive approaches. Phylogenetic analysis of white lupin ABCG transporters revealed six subclades based on their counterparts in Arabidopsis, displaying distinct gene structure and motif distribution in each cluster. Influences of the whole genome duplication on the evolution of L.albABCGs were investigated in detail. Segmental duplications appear to be the major driving force for the expansion of ABCGs in white lupin. Analysis of the Ka/Ks ratios indicated that the paralogs of the L.albABCG subfamily members principally underwent purifying selection. However, it was found that L.albABCG29 was a result of both tandem and segmental duplications. Overexpression of L.albABCG29 in white lupin hairy root enhanced P accumulation in cluster root under LP and improved plant growth. Histochemical GUS staining indicated that L.albABCG29 expression increased under LP in white lupin roots. Further, overexpression of L.albABCG29 in rice significantly improved P use under combined soil drying and LP by improving root growth associated with increased rhizosheath formation. CONCLUSION Through systematic and comprehensive genome-wide bioinformatics analysis, including conserved domain, gene structures, chromosomal distribution, phylogenetic relationships, and gene duplication analysis, the L.albABCG subfamily was identified in white lupin, and L.albABCG29 characterized in detail. In summary, our results provide deep insight into the characterization of the L.albABCG subfamily and the role of L.albABCG29 in improving P use.
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Affiliation(s)
- Mehtab Muhammad Aslam
- College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muhammad Waseem
- College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Qian Zhang
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wang Ke
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jianhua Zhang
- College of Agriculture, Yangzhou University, Yangzhou, 225009, China
- Department of Biology, Hong Kong Baptist University, Stake Key Laboratory of Agrobiotechnology and Chinese University of Hong Kong, Kowloon Tong, Hong Kong
| | - Weifeng Xu
- Joint International Research Laboratory of Water and Nutrient in Crops, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Kandpal M, Dhaka N, Sharma R. Genome-wide in silico analysis of long intergenic non-coding RNAs from rice peduncles at the heading stage. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2389-2406. [PMID: 34744373 PMCID: PMC8526681 DOI: 10.1007/s12298-021-01059-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/21/2021] [Accepted: 08/26/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Long intergenic non-coding RNAs (lincRNAs) belong to the category of long non-coding RNAs (lncRNAs), originated from intergenic regions, which do not code for proteins. LincRNAs perform prominent role in regulation of gene expression during plant development and stress response by directly interacting with DNA, RNA, or proteins, or triggering production of small RNA regulatory molecules. Here, we identified 2973 lincRNAs and investigated their expression dynamics during peduncle elongation in two Indian rice cultivars, Pokkali and Swarna, at the time of heading. Differential expression analysis revealed common and cultivar-specific expression patterns, which we utilized to infer the lincRNA candidates with potential involvement in peduncle elongation and panicle exsertion. Their putative targets were identified using in silico prediction methods followed by pathway mapping and literature-survey based functional analysis. Further, to infer the mechanism of action, we identified the lincRNAs which potentially act as miRNA precursors or target mimics. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01059-2.
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Affiliation(s)
- Manu Kandpal
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Namrata Dhaka
- Department of Biotechnology, School of Interdisciplinary and Applied Sciences, Central University of Haryana, Mahendergarh, Haryana India
| | - Rita Sharma
- Grass Genetics and Informatics Group, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
- Department of Biological Sciences, Birla Institute of Technology and Science (BITS), Pilani Campus, Pilani, Rajasthan 333031 India
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Wang X, Liu S, Zuo H, Zheng W, Zhang S, Huang Y, Pingcuo G, Ying H, Zhao F, Li Y, Liu J, Yi TS, Zan Y, Larkin RM, Deng X, Zeng X, Xu Q. Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees. Curr Biol 2021; 31:3848-3860.e8. [PMID: 34314676 DOI: 10.1016/j.cub.2021.06.062] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 02/25/2021] [Accepted: 06/22/2021] [Indexed: 01/03/2023]
Abstract
The Great Himalayan Mountains and their foothills are believed to be the place of origin and development of many plant species. The genetic basis of adaptation to high plateaus is a fascinating topic that is poorly understood at the population level. We comprehensively collected and sequenced 377 accessions of Prunus germplasm along altitude gradients ranging from 2,067 to 4,492 m in the Himalayas. We de novo assembled three high-quality genomes of Tibetan Prunus species. A comparative analysis of Prunus genomes indicated a remarkable expansion of the SINE retrotransposons occurred in the genomes of Tibetan species. We observed genetic differentiation between Tibetan peaches from high and low altitudes and that genes associated with light stress signaling, especially UV stress signaling, were enriched in the differentiated regions. By profiling the metabolomes of Tibetan peach fruit, we determined 379 metabolites had significant genetic correlations with altitudes and that in particular phenylpropanoids were positively correlated with altitudes. We identified 62 Tibetan peach-specific SINEs that colocalized with metabolites differentially accumualted in Tibetan relative to cultivated peach. We demonstrated that two SINEs were inserted in a locus controlling the accumulation of 3-O-feruloyl quinic acid. SINE1 was specific to Tibetan peach. SINE2 was predominant in high altitudes and associated with the accumulation of 3-O-feruloyl quinic acid. These genomic and metabolic data for Prunus populations native to the Himalayan region indicate that the expansion of SINE retrotransposons helped Tibetan Prunus species adapt to the harsh environment of the Himalayan plateau by promoting the accumulation of beneficial metabolites.
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Affiliation(s)
- Xia Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shengjun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Hao Zuo
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Weikang Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Shanshan Zhang
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yue Huang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Gesang Pingcuo
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Hong Ying
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Fan Zhao
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Yuanrong Li
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
| | - Junwei Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yanjun Zan
- Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, Umeå 90736, Sweden
| | - Robert M Larkin
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China
| | - Xiuli Zeng
- Qinghai-Tibet Plateau Fruit Trees Scientific Observation Test Station (Ministry of Agriculture and Rural Affairs), Lhasa, Tibet 850032, China; Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China.
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China; Key Laboratory of Horticultural Crop (Fruit trees) Biology and Genetic Improvement (Ministry of Agriculture and Rural Affairs), Huazhong Agricultural University, Wuhan 430070, China.
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de Koning R, Kiekens R, Toili MEM, Angenon G. Identification and Expression Analysis of the Genes Involved in the Raffinose Family Oligosaccharides Pathway of Phaseolus vulgaris and Glycine max. PLANTS (BASEL, SWITZERLAND) 2021; 10:1465. [PMID: 34371668 PMCID: PMC8309293 DOI: 10.3390/plants10071465] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 11/17/2022]
Abstract
Raffinose family oligosaccharides (RFO) play an important role in plants but are also considered to be antinutritional factors. A profound understanding of the galactinol and RFO biosynthetic gene families and the expression patterns of the individual genes is a prerequisite for the sustainable reduction of the RFO content in the seeds, without compromising normal plant development and functioning. In this paper, an overview of the annotation and genetic structure of all galactinol- and RFO biosynthesis genes is given for soybean and common bean. In common bean, three galactinol synthase genes, two raffinose synthase genes and one stachyose synthase gene were identified for the first time. To discover the expression patterns of these genes in different tissues, two expression atlases have been created through re-analysis of publicly available RNA-seq data. De novo expression analysis through an RNA-seq study during seed development of three varieties of common bean gave more insight into the expression patterns of these genes during the seed development. The results of the expression analysis suggest that different classes of galactinol- and RFO synthase genes have tissue-specific expression patterns in soybean and common bean. With the obtained knowledge, important galactinol- and RFO synthase genes that specifically play a key role in the accumulation of RFOs in the seeds are identified. These candidate genes may play a pivotal role in reducing the RFO content in the seeds of important legumes which could improve the nutritional quality of these beans and would solve the discomforts associated with their consumption.
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Affiliation(s)
- Ramon de Koning
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
| | - Raphaël Kiekens
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
| | - Mary Esther Muyoka Toili
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
- Department of Horticulture, Jomo Kenyatta University of Agriculture and Technology, Juja 01001, Kiambu County, Kenya
| | - Geert Angenon
- Research Group Plant Genetics, Vrije Universiteit Brussel, 1050 Brussels, Belgium; (R.d.K.); (R.K.); (M.E.M.T.)
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Chand Jha U, Nayyar H, Mantri N, Siddique KHM. Non-Coding RNAs in Legumes: Their Emerging Roles in Regulating Biotic/Abiotic Stress Responses and Plant Growth and Development. Cells 2021; 10:cells10071674. [PMID: 34359842 PMCID: PMC8306516 DOI: 10.3390/cells10071674] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/24/2021] [Accepted: 06/28/2021] [Indexed: 12/28/2022] Open
Abstract
Noncoding RNAs, including microRNAs (miRNAs), small interference RNAs (siRNAs), circular RNA (circRNA), and long noncoding RNAs (lncRNAs), control gene expression at the transcription, post-transcription, and translation levels. Apart from protein-coding genes, accumulating evidence supports ncRNAs playing a critical role in shaping plant growth and development and biotic and abiotic stress responses in various species, including legume crops. Noncoding RNAs (ncRNAs) interact with DNA, RNA, and proteins, modulating their target genes. However, the regulatory mechanisms controlling these cellular processes are not well understood. Here, we discuss the features of various ncRNAs, including their emerging role in contributing to biotic/abiotic stress response and plant growth and development, in addition to the molecular mechanisms involved, focusing on legume crops. Unravelling the underlying molecular mechanisms and functional implications of ncRNAs will enhance our understanding of the coordinated regulation of plant defences against various biotic and abiotic stresses and for key growth and development processes to better design various legume crops for global food security.
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MESH Headings
- Fabaceae/genetics
- Fabaceae/growth & development
- Fabaceae/metabolism
- Food Security
- Gene Expression Regulation, Developmental
- Gene Expression Regulation, Plant
- Humans
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Organ Specificity
- Protein Biosynthesis
- RNA, Circular/classification
- RNA, Circular/genetics
- RNA, Circular/metabolism
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Plant/classification
- RNA, Plant/genetics
- RNA, Plant/metabolism
- RNA, Small Interfering/classification
- RNA, Small Interfering/genetics
- RNA, Small Interfering/metabolism
- Species Specificity
- Stress, Physiological/genetics
- Transcription, Genetic
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Affiliation(s)
- Uday Chand Jha
- ICAR—Indian Institute of Pulses Research (IIPR), Kanpur 208024, India
- Correspondence: (U.C.J.); (K.H.M.S.)
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh 160014, India;
| | - Nitin Mantri
- School of Science, RMIT University, Melbourne 3083, Australia;
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth 6001, Australia
- Correspondence: (U.C.J.); (K.H.M.S.)
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Ayra L, Reyero-Saavedra MDR, Isidra-Arellano MC, Lozano L, Ramírez M, Leija A, Fuentes SI, Girard L, Valdés-López O, Hernández G. Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors. FRONTIERS IN PLANT SCIENCE 2021; 12:679463. [PMID: 34163511 PMCID: PMC8216239 DOI: 10.3389/fpls.2021.679463] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/10/2021] [Indexed: 05/25/2023]
Abstract
Plants MADS-domain/AGL proteins constitute a large transcription factor (TF) family that controls the development of almost every plant organ. We performed a phylogeny of (ca. 500) MADS-domain proteins from Arabidopsis and four legume species. We identified clades with Arabidopsis MADS-domain proteins known to participate in root development that grouped legume MADS-proteins with similar high expression in roots and nodules. In this work, we analyzed the role of AGL transcription factors in the common bean (Phaseolus vulgaris) - Rhizobium etli N-fixing symbiosis. Sixteen P. vulgaris AGL genes (PvAGL), out of 93 family members, are expressed - at different levels - in roots and nodules. From there, we selected the PvAGL gene denominated PvFUL-like for overexpression or silencing in composite plants, with transgenic roots and nodules, that were used for phenotypic analysis upon inoculation with Rhizobium etli. Because of sequence identity in the DNA sequence used for RNAi-FUL-like construct, roots, and nodules expressing this construct -referred to as RNAi_AGL- showed lower expression of other five PvAGL genes highly expressed in roots/nodules. Contrasting with PvFUL-like overexpressing plants, rhizobia-inoculated plants expressing the RNAi_AGL silencing construct presented affection in the generation and growth of transgenic roots from composite plants, both under non-inoculated or rhizobia-inoculated condition. Furthermore, the rhizobia-inoculated plants showed decreased rhizobial infection concomitant with the lower expression level of early symbiotic genes and increased number of small, ineffective nodules that indicate an alteration in the autoregulation of the nodulation symbiotic process. We propose that the positive effects of PvAGL TF in the rhizobia symbiotic processes result from its potential interplay with NIN, the master symbiotic TF regulator, that showed a CArG-box consensus DNA sequence recognized for DNA binding of AGL TF and presented an increased or decreased expression level in roots from non-inoculated plants transformed with OE_FUL or RNAi_AGL construct, respectively. Our work contributes to defining novel transcriptional regulators for the common bean - rhizobia N-fixing symbiosis, a relevant process for sustainable agriculture.
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Affiliation(s)
- Litzy Ayra
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - María del Rocio Reyero-Saavedra
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Mariel C. Isidra-Arellano
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Luis Lozano
- Unidad de Análisis Bioinformáticos, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Mario Ramírez
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Alfonso Leija
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Sara-Isabel Fuentes
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Lourdes Girard
- Programa de Biología de Sistemas y Biología Sintética, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Oswaldo Valdés-López
- Laboratorio de Genómica Funcional de Leguminosas, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlalnepantla de Baz, Mexico
| | - Georgina Hernández
- Programa de Genómica Funcional de Eukaryotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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Shi A, Gepts P, Song Q, Xiong H, Michaels TE, Chen S. Genome-Wide Association Study and Genomic Prediction for Soybean Cyst Nematode Resistance in USDA Common Bean ( Phaseolus vulgaris) Core Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:624156. [PMID: 34163495 PMCID: PMC8215670 DOI: 10.3389/fpls.2021.624156] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 05/14/2021] [Indexed: 05/16/2023]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) has become the major yield-limiting biological factor in soybean production. Common bean is also a good host of SCN, and its production is challenged by this emerging pest in many regions such as the upper Midwest USA. The use of host genetic resistance has been the most effective and environmentally friendly method to manage SCN. The objectives of this study were to evaluate the SCN resistance in the USDA common bean core collection and conduct a genome-wide association study (GWAS) of single nucleotide polymorphism (SNP) markers with SCN resistance. A total of 315 accessions of the USDA common bean core collection were evaluated for resistance to SCN HG Type 0 (race 6). The common bean core set was genotyped with the BARCBean6K_3 Infinium BeadChips, consisting of 4,654 SNPs. Results showed that 15 accessions were resistant to SCN with a Female Index (FI) at 4.8 to 9.4, and 62 accessions were moderately resistant (10 < FI < 30) to HG Type 0. The association study showed that 11 SNP markers, located on chromosomes Pv04, 07, 09, and 11, were strongly associated with resistance to HG Type 0. GWAS was also conducted for resistance to HG Type 2.5.7 and HG Type 1.2.3.5.6.7 based on the public dataset (N = 276), consisting of a diverse set of common bean accessions genotyped with the BARCBean6K_3 chip. Six SNPs associated with HG Type 2.5.7 resistance on Pv 01, 02, 03, and 07, and 12 SNPs with HG Type 1.2.3.5.6.7 resistance on Pv 01, 03, 06, 07, 09, 10, and 11 were detected. The accuracy of genomic prediction (GP) was 0.36 to 0.49 for resistance to the three SCN HG types, indicating that genomic selection (GS) of SCN resistance is feasible. This study provides basic information for developing SCN-resistant common bean cultivars, using the USDA core germ plasm accessions. The SNP markers can be used in molecular breeding in common beans through marker-assisted selection (MAS) and GS.
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Affiliation(s)
- Ainong Shi
- Department of Horticulture, PTSC316, University of Arkansas, Fayetteville, AR, United States
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, Davis, CA, United States
| | - Qijian Song
- United States Department of Agriculture, Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, MD, United States
| | - Haizheng Xiong
- Department of Horticulture, PTSC316, University of Arkansas, Fayetteville, AR, United States
| | - Thomas E. Michaels
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
| | - Senyu Chen
- Southern Research and Outreach Center, University of Minnesota, Waseca, MN, United States
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Chacón-Sánchez MI, Martínez-Castillo J, Duitama J, Debouck DG. Gene Flow in Phaseolus Beans and Its Role as a Plausible Driver of Ecological Fitness and Expansion of Cultigens. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.618709] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The genus Phaseolus, native to the Americas, is composed of more than eighty wild species, five of which were domesticated in pre-Columbian times. Since the beginning of domestication events in this genus, ample opportunities for gene flow with wild relatives have existed. The present work reviews the extent of gene flow in the genus Phaseolus in primary and secondary areas of domestication with the aim of illustrating how this evolutionary force may have conditioned ecological fitness and the widespread adoption of cultigens. We focus on the biological bases of gene flow in the genus Phaseolus from a spatial and time perspective, the dynamics of wild-weedy-crop complexes in the common bean and the Lima bean, the two most important domesticated species of the genus, and the usefulness of genomic tools to detect inter and intraspecific introgression events. In this review we discuss the reproductive strategies of several Phaseolus species, the factors that may favor outcrossing rates and evidence suggesting that interspecific gene flow may increase ecological fitness of wild populations. We also show that wild-weedy-crop complexes generate genetic diversity over which farmers are able to select and expand their cultigens outside primary areas of domestication. Ultimately, we argue that more studies are needed on the reproductive biology of the genus Phaseolus since for most species breeding systems are largely unknown. We also argue that there is an urgent need to preserve wild-weedy-crop complexes and characterize the genetic diversity generated by them, in particular the genome-wide effects of introgressions and their value for breeding programs. Recent technological advances in genomics, coupled with agronomic characterizations, may make a large contribution.
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Nadeem MA, Yeken MZ, Shahid MQ, Habyarimana E, Yılmaz H, Alsaleh A, Hatipoğlu R, Çilesiz Y, Khawar KM, Ludidi N, Ercişli S, Aasim M, Karaköy T, Baloch FS. Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1920462] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, PR China
| | | | - Hilal Yılmaz
- Department of Plant and Animal Production, Izmit Vocational School, Kocaeli University, Kocaeli, Turkey
| | - Ahmad Alsaleh
- Department of Food and Agriculture, Insitutue of Hemp Research, Yozgat Bozok University, 66200, Yozgat, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Khalid Mahmood Khawar
- Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Ndiko Ludidi
- Department of Biotechnology and DSI-NRF Center of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Muhammad Aasim
- 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
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
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Richard MMS, Gratias A, Alvarez Diaz JC, Thareau V, Pflieger S, Meziadi C, Blanchet S, Marande W, Bitocchi E, Papa R, Miklas PN, Geffroy V. A common bean truncated CRINKLY4 kinase controls gene-for-gene resistance to the fungus Colletotrichum lindemuthianum. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:3569-3581. [PMID: 33693665 DOI: 10.1093/jxb/erab082] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 03/05/2021] [Indexed: 05/27/2023]
Abstract
Identifying the molecular basis of resistance to pathogens is critical to promote a chemical-free cropping system. In plants, nucleotide-binding leucine-rich repeat constitute the largest family of disease resistance (R) genes, but this resistance can be rapidly overcome by the pathogen, prompting research into alternative sources of resistance. Anthracnose, caused by the fungus Colletotrichum lindemuthianum, is one of the most important diseases of common bean. This study aimed to identify the molecular basis of Co-x, an anthracnose R gene conferring total resistance to the extremely virulent C. lindemuthianum strain 100. To that end, we sequenced the Co-x 58 kb target region in the resistant JaloEEP558 (Co-x) common bean and identified KTR2/3, an additional gene encoding a truncated and chimeric CRINKLY4 kinase, located within a CRINKLY4 kinase cluster. The presence of KTR2/3 is strictly correlated with resistance to strain 100 in a diversity panel of common beans. Furthermore, KTR2/3 expression is up-regulated 24 hours post-inoculation and its transient expression in a susceptible genotype increases resistance to strain 100. Our results provide evidence that Co-x encodes a truncated and chimeric CRINKLY4 kinase probably resulting from an unequal recombination event that occurred recently in the Andean domesticated gene pool. This atypical R gene may act as a decoy involved in indirect recognition of a fungal effector.
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Affiliation(s)
- Manon M S Richard
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
- Molecular Plant Pathology, Swammerdam Institute for Life Sciences (SILS), University of Amsterdam, Amsterdam, The Netherlands
| | - Ariane Gratias
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Juan C Alvarez Diaz
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Vincent Thareau
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Stéphanie Pflieger
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Chouaib Meziadi
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | - Sophie Blanchet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Phillip N Miklas
- USDA ARS, Grain Legume Genet & Physiol Res Unit, Prosser, WA, USA
| | - Valérie Geffroy
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), Orsay, France
- Université de Paris, CNRS, INRAE, Institute of Plant Sciences Paris Saclay (IPS2), Orsay, France
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