1
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Gilding EK, Jackson MA, Nguyen LTT, Hamilton BR, Farquharson KA, Ho WL, Yap K, Hogg CJ, Belov K, Craik DJ. Hijacking of N-fixing legume albumin-1 genes enables the cyclization and stabilization of defense peptides. Nat Commun 2024; 15:6565. [PMID: 39095373 DOI: 10.1038/s41467-024-50742-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
The legume albumin-1 gene family, arising after nodulation, encodes linear a- and b-chain peptides for nutrient storage and defense. Intriguingly, in one prominent legume, Clitoria ternatea, the b-chains are replaced by domains producing ultra-stable cyclic peptides called cyclotides. The mechanism of this gene hijacking is until now unknown. Cyclotides require recruitment of ligase-type asparaginyl endopeptidases (AEPs) for maturation (cyclization), necessitating co-evolution of two gene families. Here we compare a chromosome-level C. ternatea genome with grain legumes to reveal an 8 to 40-fold expansion of the albumin-1 gene family, enabling the additional loci to undergo diversification. Iterative rounds of albumin-1 duplication and diversification create four albumin-1 enriched genomic islands encoding cyclotides, where they are physically grouped by similar pI and net charge values. We identify an ancestral hydrolytic AEP that exhibits neofunctionalization and multiple duplication events to yield two ligase-type AEPs. We propose cyclotides arise by convergence in C. ternatea where their presence enhances defense from biotic attack, thus increasing fitness compared to lineages with linear b-chains and ultimately driving the replacement of b-chains with cyclotides.
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Affiliation(s)
- Edward K Gilding
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Mark A Jackson
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Linh T T Nguyen
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Brett R Hamilton
- Centre for Microscopy and Microanalysis, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Katherine A Farquharson
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Wing L Ho
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Kuok Yap
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Carolyn J Hogg
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Katherine Belov
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia.
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2
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Peña Barrena LE, Mats L, Earl HJ, Bozzo GG. Phenylpropanoid Metabolism in Phaseolus vulgaris during Growth under Severe Drought. Metabolites 2024; 14:319. [PMID: 38921454 PMCID: PMC11205357 DOI: 10.3390/metabo14060319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/27/2024] Open
Abstract
Drought limits the growth and development of Phaseolus vulgaris L. (known as common bean). Common bean plants contain various phenylpropanoids, but it is not known whether the levels of these metabolites are altered by drought. Here, BT6 and BT44, two white bean recombinant inbred lines (RILs), were cultivated under severe drought. Their respective growth and phenylpropanoid profiles were compared to those of well-irrigated plants. Both RILs accumulated much less biomass in their vegetative parts with severe drought, which was associated with more phaseollin and phaseollinisoflavan in their roots relative to well-irrigated plants. A sustained accumulation of coumestrol was evident in BT44 roots with drought. Transient alterations in the leaf profiles of various phenolic acids occurred in drought-stressed BT6 and BT44 plants, including the respective accumulation of two separate caftaric acid isomers and coutaric acid (isomer 1) relative to well-irrigated plants. A sustained rise in fertaric acid was observed in BT44 with drought stress, whereas the greater amount relative to well-watered plants was transient in BT6. Apart from kaempferol diglucoside (isomer 2), the concentrations of most leaf flavonol glycosides were not altered with drought. Overall, fine tuning of leaf and root phenylpropanoid profiles occurs in white bean plants subjected to severe drought.
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Affiliation(s)
- Luis Eduardo Peña Barrena
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.E.P.B.); (H.J.E.)
| | - Lili Mats
- Guelph Research and Development Centre, Agriculture and Agri-Food Canada, 93 Stone Road West, Guelph, ON N1G 5C9, Canada;
| | - Hugh J. Earl
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.E.P.B.); (H.J.E.)
| | - Gale G. Bozzo
- Department of Plant Agriculture, University of Guelph, 50 Stone Road East, Guelph, ON N1G 2W1, Canada; (L.E.P.B.); (H.J.E.)
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Ho WK, Tanzi AS, Sang F, Tsoutsoura N, Shah N, Moore C, Bhosale R, Wright V, Massawe F, Mayes S. A genomic toolkit for winged bean Psophocarpus tetragonolobus. Nat Commun 2024; 15:1901. [PMID: 38429275 PMCID: PMC10907731 DOI: 10.1038/s41467-024-45048-x] [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: 02/13/2022] [Accepted: 01/12/2024] [Indexed: 03/03/2024] Open
Abstract
A sustainable supply of plant protein is critical for future generations and needs to be achieved while reducing green house gas emissions from agriculture and increasing agricultural resilience in the face of climate volatility. Agricultural diversification with more nutrient-rich and stress tolerant crops could provide the solution. However, this is often hampered by the limited availability of genomic resources and the lack of understanding of the genetic structure of breeding germplasm and the inheritance of important traits. One such crop with potential is winged bean (Psophocarpus tetragonolobus), a high seed protein tropical legume which has been termed 'the soybean for the tropics'. Here, we present a chromosome level winged bean genome assembly, an investigation of the genetic diversity of 130 worldwide accessions, together with two linked genetic maps and a trait QTL analysis (and expression studies) for regions of the genome with desirable ideotype traits for breeding, namely architecture, protein content and phytonutrients.
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Affiliation(s)
- Wai Kuan Ho
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Alberto Stefano Tanzi
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Fei Sang
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Niki Tsoutsoura
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Niraj Shah
- Digital and Technology Services, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Christopher Moore
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Rahul Bhosale
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Victoria Wright
- Deep Seq, Centre for Genetics and Genomics, University of Nottingham, Queen's Medical Centre, Nottingham, NG7 2UH, UK
| | - Festo Massawe
- Future Food Beacon, School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Sean Mayes
- Crops for the Future (UK) CIC, NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK.
- Future Food Beacon, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- International Centre for Research in the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, 502324, India.
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Shorinola O, Marks R, Emmrich P, Jones C, Odeny D, Chapman MA. Integrative and inclusive genomics to promote the use of underutilised crops. Nat Commun 2024; 15:320. [PMID: 38191605 PMCID: PMC10774273 DOI: 10.1038/s41467-023-44535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.
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Affiliation(s)
- Oluwaseyi Shorinola
- International Livestock Research Institute, Naivasha Road, Nairobi, Kenya.
- School of Bioscience, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Rose Marks
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Peter Emmrich
- Norwich Institute for Sustainable Development, School of Global Development, University of East Anglia, England, NR4 7TJ, UK
| | - Chris Jones
- International Livestock Research Institute, Naivasha Road, Nairobi, Kenya
| | - Damaris Odeny
- Center of Excellence in Genomics and Systems Biology, ICRISAT, Patancheru, 502324, Telangana, India
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
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Junaid A, Singh B, Bhatia S. Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungo. Life Sci Alliance 2024; 7:e202302074. [PMID: 37923361 PMCID: PMC10624639 DOI: 10.26508/lsa.202302074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 10/17/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023] Open
Abstract
Eukaryotic genomes show an intricate three-dimensional (3D) organization within the nucleus that regulates multiple biological processes including gene expression. Contrary to animals, understanding of 3D genome organization in plants remains at a nascent stage. Here, we investigate the evolution of 3D chromatin architecture in legumes. By using cutting-edge PacBio, Illumina, and Hi-C contact reads, we report a gap-free, chromosome-scale reference genome assembly of Vigna mungo, an important minor legume cultivated in Southeast Asia. We spatially resolved V. mungo chromosomes into euchromatic, transcriptionally active A compartment and heterochromatic, transcriptionally-dormant B compartment. We report the presence of TAD-like-regions throughout the diagonal of the HiC matrix that resembled transcriptional quiescent centers based on their genomic and epigenomic features. We observed high syntenic breakpoints but also high coverage of syntenic sequences and conserved blocks in boundary regions than in the TAD-like region domains. Our findings present unprecedented evolutionary insights into spatial 3D genome organization and epigenetic patterns and their interaction within the V. mungo genome. This will aid future genomics and epigenomics research and breeding programs of V. mungo.
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Affiliation(s)
- Alim Junaid
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Baljinder Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Mwale SE, Shimelis H, Abincha W, Nkhata W, Sefasi A, Mashilo J. Genetic differentiation of a southern Africa tepary bean (Phaseolus acutifolius A Gray) germplasm collection using high-density DArTseq SNP markers. PLoS One 2023; 18:e0295773. [PMID: 38096255 PMCID: PMC10721083 DOI: 10.1371/journal.pone.0295773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023] Open
Abstract
Genetic resources of tepary bean (Phaseolus acutifolius A. Gray) germplasm collections are not well characterized due to a lack of dedicated genomic resources. There is a need to assemble genomic resources specific to tepary bean for germplasm characterization, heterotic grouping, and breeding. Therefore, the objectives of this study were to deduce the genetic groups in tepary bean germplasm collection using high-density Diversity Array Technology (DArT) based single nucleotide polymorphism (SNP) markers and select contrasting genotypes for breeding. Seventy-eight tepary bean accessions were genotyped using 10527 SNPs markers, and genetic parameters were estimated. Population structure was delineated using principal component and admixture analyses. A mean polymorphic information content (PIC) of 0.27 was recorded, indicating a relatively low genetic resolution of the developed SNPs markers. Low genetic variation (with a genetic distance [GD] = 0.32) existed in the assessed tepary bean germplasm collection. Population structure analysis identified five sub-populations through sparse non-negative matrix factorization (snmf) with high admixtures. Analysis of molecular variance indicated high genetic differentiation within populations (61.88%) and low between populations (38.12%), indicating high gene exchange. The five sub-populations exhibited variable fixation index (FST). The following genetically distant accessions were selected: Cluster 1:Tars-Tep 112, Tars-Tep 10, Tars-Tep 23, Tars-Tep-86, Tars-Tep-83, and Tars-Tep 85; Cluster 3: G40022, Tars-Tep-93, and Tars-Tep-100; Cluster 5: Zimbabwe landrace, G40017, G40143, and G40150. The distantly related and contrasting accessions are useful to initiate crosses to enhance genetic variation and for the selection of economic traits in tepary bean.
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Affiliation(s)
- Saul Eric Mwale
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Biological Sciences Department, The African Centre of Excellence in Neglected and Underutilized Biodiversity (ACENUB), Mzuzu University, Luwinga, Mzuzu, Malawi
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Wilfred Abincha
- Kenya Agricultural and Livestock Research Organization (KALRO), Non-Ruminant Research Institute, Kakamega, Kenya
| | - Wilson Nkhata
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
- Alliance of Bioversity International Institute of Tropical Agriculture (CIAT), Chitedze Agricultural Station, Lilongwe, Malawi
| | - Abel Sefasi
- Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
| | - Jacob Mashilo
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement (ACCI), University of KwaZulu-Natal, Pietermaritzburg, South Africa
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7
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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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8
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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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9
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Kitavi M, Gemenet DC, Wood JC, Hamilton JP, Wu S, Fei Z, Khan A, Buell CR. Identification of genes associated with abiotic stress tolerance in sweetpotato using weighted gene co-expression network analysis. PLANT DIRECT 2023; 7:e532. [PMID: 37794882 PMCID: PMC10546384 DOI: 10.1002/pld3.532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 04/22/2023] [Accepted: 08/31/2023] [Indexed: 10/06/2023]
Abstract
Sweetpotato, Ipomoea batatas (L.), a key food security crop, is negatively impacted by heat, drought, and salinity stress. The orange-fleshed sweetpotato cultivar "Beauregard" was exposed to heat, salt, and drought treatments for 24 and 48 h to identify genes responding to each stress condition in leaves. Analysis revealed both common (35 up regulated, 259 down regulated genes in the three stress conditions) and unique sets of up regulated (1337 genes by drought, 516 genes by heat, and 97 genes by salt stress) and down regulated (2445 genes by drought, 678 genes by heat, and 204 genes by salt stress) differentially expressed genes (DEGs) suggesting common, yet stress-specific transcriptional responses to these three abiotic stressors. Gene Ontology analysis of down regulated DEGs common to both heat and salt stress revealed enrichment of terms associated with "cell population proliferation" suggestive of an impact on the cell cycle by the two stress conditions. To identify shared and unique gene co-expression networks under multiple abiotic stress conditions, weighted gene co-expression network analysis was performed using gene expression profiles from heat, salt, and drought stress treated 'Beauregard' leaves yielding 18 co-expression modules. One module was enriched for "response to water deprivation," "response to abscisic acid," and "nitrate transport" indicating synergetic crosstalk between nitrogen, water, and phytohormones with genes encoding osmotin, cell expansion, and cell wall modification proteins present as key hub genes in this drought-associated module. This research lays the groundwork for exploring to a further degree, mechanisms for abiotic stress tolerance in sweetpotato.
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Affiliation(s)
- Mercy Kitavi
- Research Technology Support Facility (RTSF)Michigan State UniversityEast LansingMichiganUSA
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - Dorcus C. Gemenet
- International Potato CenterLimaPeru
- International Maize and Wheat Improvement Center (CIMMYT), ICRAF HouseNairobiKenya
| | - Joshua C. Wood
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
| | - John P. Hamilton
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
| | - Shan Wu
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Zhangjun Fei
- Boyce Thompson InstituteCornell UniversityIthacaNew YorkUSA
| | - Awais Khan
- International Potato CenterLimaPeru
- Present address:
Plant Pathology and Plant‐Microbe Biology Section, School of Integrative Plant ScienceCornell UniversityGenevaNew YorkUSA
| | - C. Robin Buell
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGeorgiaUSA
- Department of Crop & Soil SciencesUniversity of GeorgiaAthensGeorgiaUSA
- Institute of Plant Breeding, Genetics, & GenomicsUniversity of GeorgiaAthensGeorgiaUSA
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10
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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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Lozano-Arce D, García T, Gonzalez-Garcia LN, Guyot R, Chacón-Sánchez MI, Duitama J. Selection signatures and population dynamics of transposable elements in lima bean. Commun Biol 2023; 6:803. [PMID: 37532823 PMCID: PMC10397206 DOI: 10.1038/s42003-023-05144-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 07/13/2023] [Indexed: 08/04/2023] Open
Abstract
The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Previous genetic analyses in lima bean have relied on Single Nucleotide Polymorphism (SNP) loci, and have ignored transposable elements (TEs). Here we show the analysis of whole-genome sequencing data from 61 lima bean accessions to characterize a genomic variation database including TEs and SNPs, to associate selective sweeps with variable TEs and to predict candidate domestication genes. A small percentage of genes under selection are shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. About 75% of TEs are located close to genes, which shows their potential to affect gene functions. The genetic structure inferred from variable TEs is consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated lima bean and its adaptive processes, in particular selection processes during domestication.
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Affiliation(s)
- Daniela Lozano-Arce
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Tatiana García
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Laura Natalia Gonzalez-Garcia
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, CIRAD, 34394, Montpellier, France
| | - Romain Guyot
- Institut de Recherche pour le Développement (IRD), UMR DIADE, Université de Montpellier, CIRAD, 34394, Montpellier, France
| | - Maria Isabel Chacón-Sánchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Jorge Duitama
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia.
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Rose T, Lowe C, Miret JA, Walpole H, Halsey K, Venter E, Urban MO, Buendia HF, Kurup S, O'Sullivan DM, Beebe S, Heuer S. High Temperature Tolerance in a Novel, High-Quality Phaseolus vulgaris Breeding Line Is Due to Maintenance of Pollen Viability and Successful Germination on the Stigma. PLANTS (BASEL, SWITZERLAND) 2023; 12:2491. [PMID: 37447054 DOI: 10.3390/plants12132491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023]
Abstract
The common bean (Phaseolus vulgaris L.) is an important nutritional source globally but is sensitive to high temperatures and thus particularly vulnerable to climate change. Derived from a breeding program at CIAT (Colombia), a heat-tolerant breeding line, named heat-tolerant Andean-type 4 (HTA4), was developed by a series of crosses of parents with a small-bean tepary genotype (Phaseolus acutifolius L.) in their pedigree, which might be the donor of heat stress (HS) tolerance. Importantly, in HTA4, the large, commercially desirable Andean-type beans was restored. To assess underlying tolerance mechanisms, HTA4, together with a heat-sensitive Colombian variety (Calima), was exposed to HS (31 °C/24 °C HS vs. 26 °C/19 °C day/night) under controlled environment conditions. Vegetative growth and photosynthetic performance were not negatively impacted by HS in either genotype, although senescence was delayed in Calima. HS during the reproductive stage caused an increase in pod number in Calima but with few fully developed seeds and many pods aborted and/or abscised. In contrast, HTA4 maintained a similar filled pod number under HS and a higher seed weight per plant. Pollen showed high sterility in Calima, with many non-viable pollen grains (24.9% viability compared to 98.4% in control) with a thicker exine and fewer starch granules under HS. Calima pollen failed to adhere to the stigma and germinate under HS. In HTA4, pollen viability was significantly higher than in Calima (71.1% viability compared to 95.4% under control), and pollen successfully germinated and formed pollen tubes in the style under HS. It is concluded that HTA4 is heat tolerant and maintains a high level of reproductive output due to its ability to produce healthy pollen that is able to adhere to the stigma.
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Affiliation(s)
| | | | - Javier A Miret
- Department of Crop Science, University of Reading, Whiteknights P.O. Box 217, Reading, Berkshire RG6 6AH, UK
| | | | | | | | - Milan O Urban
- Centro Internacional de Agricultura Tropical (CIAT), Kilometro 17, Recta Cali-Palmira, Apartado Aereo, Cali 6713, Colombia
| | - Hector Fabio Buendia
- Centro Internacional de Agricultura Tropical (CIAT), Kilometro 17, Recta Cali-Palmira, Apartado Aereo, Cali 6713, Colombia
| | | | - Donal Martin O'Sullivan
- Department of Crop Science, University of Reading, Whiteknights P.O. Box 217, Reading, Berkshire RG6 6AH, UK
| | - Steve Beebe
- Centro Internacional de Agricultura Tropical (CIAT), Kilometro 17, Recta Cali-Palmira, Apartado Aereo, Cali 6713, Colombia
| | - Sigrid Heuer
- National Institute of Agricultural Botany (NIAB), Lawrence Weaver Road, Cambridge CB3 0LE, UK
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Dwivedi SL, Chapman MA, Abberton MT, Akpojotor UL, Ortiz R. Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses. Front Genet 2023; 14:1193780. [PMID: 37396035 PMCID: PMC10311922 DOI: 10.3389/fgene.2023.1193780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/07/2023] [Indexed: 07/04/2023] Open
Abstract
Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted.
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Affiliation(s)
| | - Mark A. Chapman
- Biological Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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Samal I, Bhoi TK, Raj MN, Majhi PK, Murmu S, Pradhan AK, Kumar D, Paschapur AU, Joshi DC, Guru PN. Underutilized legumes: nutrient status and advanced breeding approaches for qualitative and quantitative enhancement. Front Nutr 2023; 10:1110750. [PMID: 37275642 PMCID: PMC10232757 DOI: 10.3389/fnut.2023.1110750] [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: 11/29/2022] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Underutilized/orphan legumes provide food and nutritional security to resource-poor rural populations during periods of drought and extreme hunger, thus, saving millions of lives. The Leguminaceae, which is the third largest flowering plant family, has approximately 650 genera and 20,000 species and are distributed globally. There are various protein-rich accessible and edible legumes, such as soybean, cowpea, and others; nevertheless, their consumption rate is far higher than production, owing to ever-increasing demand. The growing global urge to switch from an animal-based protein diet to a vegetarian-based protein diet has also accelerated their demand. In this context, underutilized legumes offer significant potential for food security, nutritional requirements, and agricultural development. Many of the known legumes like Mucuna spp., Canavalia spp., Sesbania spp., Phaseolus spp., and others are reported to contain comparable amounts of protein, essential amino acids, polyunsaturated fatty acids (PUFAs), dietary fiber, essential minerals and vitamins along with other bioactive compounds. Keeping this in mind, the current review focuses on the potential of discovering underutilized legumes as a source of food, feed and pharmaceutically valuable chemicals, in order to provide baseline data for addressing malnutrition-related problems and sustaining pulse needs across the globe. There is a scarcity of information about underutilized legumes and is restricted to specific geographical zones with local or traditional significance. Around 700 genera and 20,000 species remain for domestication, improvement, and mainstreaming. Significant efforts in research, breeding, and development are required to transform existing local landraces of carefully selected, promising crops into types with broad adaptability and economic viability. Different breeding efforts and the use of biotechnological methods such as micro-propagation, molecular markers research and genetic transformation for the development of underutilized crops are offered to popularize lesser-known legume crops and help farmers diversify their agricultural systems and boost their profitability.
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Affiliation(s)
- Ipsita Samal
- Department of Entomology, Faculty of Agriculture, Sri Sri University, Cuttack, Odisha, India
| | - Tanmaya Kumar Bhoi
- Forest Protection Division, ICFRE-Arid Forest Research Institute, Jodhpur, India
| | - M. Nikhil Raj
- Division of Entomology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Prasanta Kumar Majhi
- Regional Research and Technology Transfer Station, Odisha University of Agriculture and Technology, Keonjhar, Odisha, India
| | - Sneha Murmu
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Dilip Kumar
- ICAR-National Institute of Agricultural Economics and Policy Research, New Delhi, India
| | | | | | - P. N. Guru
- ICAR-Central Institute of Post-Harvest Engineering and Technology, Ludhiana, India
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15
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An X, Li N, Zhang S, Han Y, Zhang Q. Integration of proteome and metabolome profiling to reveal heat stress response and tolerance mechanisms of Serratia sp. AXJ-M for the bioremediation of papermaking black liquor. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131092. [PMID: 36857821 DOI: 10.1016/j.jhazmat.2023.131092] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/12/2023] [Accepted: 02/24/2023] [Indexed: 05/20/2023]
Abstract
The use of thermophilic bacteria for treating paper black liquor seems to be an efficient bioremediation strategy. In our previous work, the lignin-degrading bacterium Serratia sp. AXJ-M exhibited excellent heat tolerance ability. However, the molecular mechanism of its response to heat stress is unknown. Therefore, the heat stress response of AXJ-M was investigated using morphological and analytical methods. A comparative genomics analysis revealed interesting insights into the adaptability of the genetic basis of AXJ-M to harsh environments. Moreover, TMT quantitative proteomic analysis and parallel reaction monitoring (PRM) assays revealed that proteins related to both component systems, ABC transporters, carbohydrate, and amino metabolism, energy metabolism, etc., were differentially expressed. The non-targeted metabolome analysis revealed that the metabolic pathways associated with the fatty acid and amino acid biosynthesis and metabolism, together with the TCA cycle were most significantly enriched. Furthermore, integrated omics suggested that AXJ-M made metabolic adaptations to compensate for the increased energy demand caused by adverse environmental stimuli. The dominant heat regulator HspQ mediated heat adaptation of AXJ-M at high temperatures and modulated DyP expression. To summarize, the present study sheds light on the effect of high temperature on the lignin-degrading bacterium and its tolerance and underlying regulatory mechanisms.
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Affiliation(s)
- Xuejiao An
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China.
| | - Ningjian Li
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Shulin Zhang
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Yanyan Han
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
| | - Qinghua Zhang
- College of Bioscience and Biotechnology, Jiangxi Agricultural University, Nanchang 330045, PR China
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16
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Parakkunnel R, Naik K B, Vanishree G, C S, Purru S, Bhaskar K U, Bhat KV, Kumar S. Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome. FRONTIERS IN PLANT SCIENCE 2022; 13:1076229. [PMID: 36618639 PMCID: PMC9817154 DOI: 10.3389/fpls.2022.1076229] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.
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Affiliation(s)
- Ramya Parakkunnel
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Bhojaraja Naik K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Girimalla Vanishree
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - Susmita C
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
| | - Supriya Purru
- ICAR- National Academy of Agricultural Research Management, Hyderabad, Telengana, India
| | - Udaya Bhaskar K
- ICAR- Indian Institute of Seed Science, Regional Station, Gandhi Krishi Vigyana Kendra (GKVK) Campus, Bengaluru, India
| | - KV. Bhat
- Division of Genomic Resources, ICAR- National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, Mau, Uttar Pradesh, India
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17
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Liang L, Zhang J, Xiao J, Li X, Xie Y, Tan H, Song X, Zhu L, Xue X, Xu L, Zhou P, Ran J, Sun B, Huang Z, Tang Y, Lin L, Sun G, Lai Y, Li H. Genome and pan-genome assembly of asparagus bean ( Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation. FRONTIERS IN PLANT SCIENCE 2022; 13:1059804. [PMID: 36589110 PMCID: PMC9802904 DOI: 10.3389/fpls.2022.1059804] [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: 10/02/2022] [Accepted: 11/28/2022] [Indexed: 06/17/2023]
Abstract
Asparagus bean (Vigna unguiculata ssp. sesquipedialis) is an important cowpea subspecies. We assembled the genomes of Ningjiang 3 (NJ, 550.31 Mb) and Dubai bean (DB, 564.12 Mb) for comparative genomics analysis. The whole-genome duplication events of DB and NJ occurred at 64.55 and 64.81 Mya, respectively, while the divergence between soybean and Vigna occurred in the Paleogene period. NJ genes underwent positive selection and amplification in response to temperature and abiotic stress. In species-specific gene families, NJ is mainly enriched in response to abiotic stress, while DB is primarily enriched in respiration and photosynthesis. We established the pan-genomes of four accessions (NJ, DB, IT97K-499-35 and Xiabao II) and identified 20,336 (70.5%) core genes present in all the accessions, 6,507 (55.56%) variable genes in two individuals, and 2,004 (6.95%) unique genes. The final pan genome is 616.35 Mb, and the core genome is 399.78 Mb. The variable genes are manifested mainly in stress response functions, ABC transporters, seed storage, and dormancy control. In the pan-genome sequence variation analysis, genes affected by presence/absence variants were enriched in biological processes associated with defense responses, immune system processes, signal transduction, and agronomic traits. The results of the present study provide genetic data that could facilitate efficient asparagus bean genetic improvement, especially in producing cold-adapted asparagus bean.
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Affiliation(s)
- Le Liang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianwei Zhang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jiachang Xiao
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiaomei Li
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
- Vegetable Germplasm Innovation and Variety Improvement Key Laboratory of Sichuan, Chengdu, China
| | - Yongdong Xie
- Institute for Processing and Storage of Agricultural Products, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Huaqiang Tan
- Horticulture Research Institute, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Xueping Song
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Li Zhu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xinru Xue
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Linyu Xu
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Peihan Zhou
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jianzhao Ran
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhi Huang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yi Tang
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lijin Lin
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guochao Sun
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunsun Lai
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huanxiu Li
- Institute of Pomology and Olericulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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18
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Barrera S, Berny Mier y Teran JC, Lobaton JD, Escobar R, Gepts P, Beebe S, Urrea CA. Large genomic introgression blocks of Phaseolus parvifolius Freytag bean into the common bean enhance the crossability between tepary and common beans. PLANT DIRECT 2022; 6:e470. [PMID: 36523608 PMCID: PMC9745863 DOI: 10.1002/pld3.470] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/04/2022] [Accepted: 11/11/2022] [Indexed: 06/10/2023]
Abstract
The production of the common bean (Phaseolus vulgaris L.), one of the most important sources of protein and minerals and one of the most consumed grain legumes globally, is highly affected by heat and drought constraints. In contrast, the tepary bean (Phaseolus acutifolius A. Gray), a common bean-related species, is adapted to hot and dry climates. Hybridization to introduce complex traits from the tepary bean into the common bean has been challenging, as embryo rescue is required. In this study, we report three novel interspecific lines that were obtained by crossing lines from prior common bean × tepary bean hybridization with Phaseolus parvifolius Freytag in order to increase the male gametic diversity to facilitate interspecific crosses. These interspecific lines enhanced the crossability of the common bean and tepary bean species while avoiding the embryo rescue process. Crossing these three interspecific lines with tepary beans resulted in 12-fold more hybrid plants than crossing traditional common beans with tepary beans. Whole-genome sequencing analysis of these three interspecific lines shows large introgressions of genomic regions corresponding to P. parvifolius on chromosomes that presumably contribute to reproductive barriers between both species. The development of these lines opens up the possibility of increasing the introgression of desirable tepary bean traits into the common bean to address constraints driven by climate change.
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Affiliation(s)
- Santos Barrera
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNebraskaUSA
| | | | - Juan David Lobaton
- Department of Evolutionary BiologyNational Australian UniversityCanberraAustralia
| | | | - Paul Gepts
- Department of Plant SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Steve Beebe
- International Center for Tropical Agriculture (CIAT)PalmiraColombia
| | - Carlos A. Urrea
- Department of Agronomy and HorticultureUniversity of NebraskaLincolnNebraskaUSA
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19
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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: 3] [Impact Index Per Article: 1.5] [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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Irshad A, Rehman RNU, Dubey S, Khan MA, Yang P, Hu T. Rhizobium inoculation and exogenous melatonin synergistically increased thermotolerance by improving antioxidant defense, photosynthetic efficiency, and nitro-oxidative homeostasis in Medicago truncatula. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.945695] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Global warming negatively affects plant growth due to the detrimental effects of high temperature-induced heat stress. Rhizobium inoculation (RI) and exogenous melatonin (MT) have shown a positive role in resisting abiotic stress. However, their synergistic effect on avoiding heat-induced damages in Medicago truncatula has not been studied yet. Hence, the objective of the present study was to evaluate the impact of these amendments (RI and MT) to ameliorate the heat damages in Medicago truncatula. The study was comprised of two factors: (1) heat-induced stress: (i) optimum temperature (26 ± 1°C): (23 ± 1°C) (day: night), (ii) moderate heat (35 ± 1°C): (28 ± 1°C), and (iii) severe heat (41 ± 1°C): (35 ± 1°C) for 72 h, and (2) amendments: (i) no RI + no MT (NRI + NMT), (ii) Rhizobium inoculation (RI), (iii) 60 μM melatonin (MT), and (iii) RI + MT. Results showed that the combined application of RI and MT was better than their individual applications, as it prevented heat-induced membrane damages by declining the hydrogen peroxide (34.22% and 29.78%), superoxide anion radical (29.49% and 26.71%), malondialdehyde contents (26.43% and 21.96%), and lipoxygenase activity (44.75% and 25.51%) at both heat stress levels as compared to NRI + NMT. Moreover, RI + MT treated plants showed higher antioxidative and methylglyoxal detoxification enzymes (Gly I and Gly II) activities under heat stress. While, NRI + NMT treated plants showed a higher level of methylglyoxal contents (47.99% and 46.71%) under both levels of heat stress. Relative to NRI + NMT plants, RI + MT pretreated plants exhibited improved heat tolerance as indicated by higher chlorophyll (37.42% and 43.52%), carotenoid contents (32.41% and 47.08%), and photosynthetic rate (42.62% and 64.63%), under moderate and severe heat stress, respectively. Furthermore, RI + MT pretreated plants had considerably higher indole-3 acetic acid and abscisic acid concentrations under moderate (54.02% and 53.92%) and severe (68.36% and 64.61%) heat stress conditions. Similarly, plant dry biomass, NPK uptake, nitric oxide, and nitrate reductase activity were high in RI + MT treated plants, under both levels of stress. Therefore, this study advocates the positive synergistic effect of RI and MT pretreatment against moderate and severe heat-induced stress and for possible maintenance of plant growth under changing scenarios of global warming.
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Chongtham SK, Devi EL, Samantara K, Yasin JK, Wani SH, Mukherjee S, Razzaq A, Bhupenchandra I, Jat AL, Singh LK, Kumar A. Orphan legumes: harnessing their potential for food, nutritional and health security through genetic approaches. PLANTA 2022; 256:24. [PMID: 35767119 DOI: 10.1007/s00425-022-03923-1] [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: 07/16/2021] [Accepted: 05/21/2022] [Indexed: 06/15/2023]
Abstract
Legumes, being angiosperm's third-largest family as well as the second major crop family, contributes beyond 33% of human dietary proteins. The advent of the global food crisis owing to major climatic concerns leads to nutritional deprivation, hunger and hidden hunger especially in developing and underdeveloped nations. Hence, in the wake of promoting sustainable agriculture and nutritional security, apart from the popular legumes, the inclusion of lesser-known and understudied local crop legumes called orphan legumes in the farming systems of various tropical and sub-tropical parts of the world is indeed a need of the hour. Despite possessing tremendous potentialities, wide adaptability under diverse environmental conditions, and rich in nutritional and nutraceutical values, these species are still in a neglected and devalued state. Therefore, a major re-focusing of legume genetics, genomics, and biology is much crucial in pursuance of understanding the yield constraints, and endorsing underutilized legume breeding programs. Varying degrees of importance to these crops do exist among researchers of developing countries in establishing the role of orphan legumes as future crops. Under such circumstances, this article assembles a comprehensive note on the necessity of promoting these crops for further investigations and sustainable legume production, the exploitation of various orphan legume species and their potencies. In addition, an attempt has been made to highlight various novel genetic, molecular, and omics approaches for the improvement of such legumes for enhancing yield, minimizing the level of several anti-nutritional factors, and imparting biotic and abiotic stress tolerance. A significant genetic enhancement through extensive research in 'omics' areas is the absolute necessity to transform them into befitting candidates for large-scale popularization around the globe.
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Affiliation(s)
- Sunil Kumar Chongtham
- Multi Technology Testing Centre and Vocational Training Centre, CAEPHT, CAU, Ranipool, Gangtok, Sikkim, 737135, India
| | | | - Kajal Samantara
- Department of Genetics and Plant Breeding, Centurion University of Technology and Management, Odisha, 761211, India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR-National Bureau Plant Genetic Resources, PUSA Campus, New Delhi, 110012, India
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops, Khudwani, Sher-E-Kashmir University of Agricultural Sciences and Technology, Srinagar, 192101, Jammu and Kashmir, India.
| | - Soumya Mukherjee
- Department of Botany, Jangipur College, University of Kalyani, West Bengal, 742213, India
| | - Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture Faisalabad, Faisalabad, 38040, Pakistan
| | - Ingudam Bhupenchandra
- ICAR-KVK Tamenglong, ICAR RC for NEH Region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Aanandi Lal Jat
- Castor-Mustard Research Station, SDAU, S.K. Nagar, Banaskantha, Gujarat, 385 506, India
| | - Laishram Kanta Singh
- ICAR-KVK Imphal West, ICAR RC for NEH region, Manipur Centre, Lamphelpat, Imphal, Manipur, 795 004, India
| | - Amit Kumar
- ICAR Research Complex for NEH Region, Tadong, Sikkim Centre, 737102, India
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22
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Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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23
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McClean PE, Lee R, Howe K, Osborne C, Grimwood J, Levy S, Haugrud AP, Plott C, Robinson M, Skiba RM, Tanha T, Zamani M, Thannhauser TW, Glahn RP, Schmutz J, Osorno JM, Miklas PN. The Common Bean V Gene Encodes Flavonoid 3'5' Hydroxylase: A Major Mutational Target for Flavonoid Diversity in Angiosperms. FRONTIERS IN PLANT SCIENCE 2022; 13:869582. [PMID: 35432409 PMCID: PMC9009181 DOI: 10.3389/fpls.2022.869582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The classic V (violet, purple) gene of common bean (Phaseolus vulgaris) functions in a complex genetic network that controls seed coat and flower color and flavonoid content. V was cloned to understand its role in the network and the evolution of its orthologs in the Viridiplantae. V mapped genetically to a narrow interval on chromosome Pv06. A candidate gene was selected based on flavonoid analysis and confirmed by recombinational mapping. Protein and domain modeling determined V encodes flavonoid 3'5' hydroxylase (F3'5'H), a P450 enzyme required for the expression of dihydromyricetin-derived flavonoids in the flavonoid pathway. Eight recessive haplotypes, defined by mutations of key functional domains required for P450 activities, evolved independently in the two bean gene pools from a common ancestral gene. V homologs were identified in Viridiplantae orders by functional domain searches. A phylogenetic analysis determined F3'5'H first appeared in the Streptophyta and is present in only 41% of Angiosperm reference genomes. The evolutionarily related flavonoid pathway gene flavonoid 3' hydroxylase (F3'H) is found nearly universally in all Angiosperms. F3'H may be conserved because of its role in abiotic stress, while F3'5'H evolved as a major target gene for the evolution of flower and seed coat color in plants.
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Affiliation(s)
- Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Kevin Howe
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Caroline Osborne
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Shawn Levy
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Amanda Peters Haugrud
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Melanie Robinson
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Ryan M. Skiba
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Tabassum Tanha
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Mariam Zamani
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Theodore W. Thannhauser
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Raymond P. Glahn
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip N. Miklas
- USDA-ARS, Grain Legumes Genetics and Physiology Research Unit, Prosser, WA, United States
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24
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Bickhart DM, Koch LM, Smith TPL, Riday H, Sullivan ML. Chromosome-scale assembly of the highly heterozygous genome of red clover ( Trifolium pratense L.), an allogamous forage crop species. GIGABYTE 2022; 2022:gigabyte42. [PMID: 36824517 PMCID: PMC9650271 DOI: 10.46471/gigabyte.42] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/14/2022] [Indexed: 11/09/2022] Open
Abstract
Relative to other crops, red clover (Trifolium pratense L.) has various favorable traits making it an ideal forage crop. Conventional breeding has improved varieties, but modern genomic methods could accelerate progress and facilitate gene discovery. Existing short-read-based genome assemblies of the ∼420 megabase pair (Mbp) genome are fragmented into >135,000 contigs, with numerous order and orientation errors within scaffolds, probably associated with the plant's biology, which displays gametophytic self-incompatibility resulting in inherent high heterozygosity. Here, we present a high-quality long-read-based assembly of red clover with a more than 500-fold reduction in contigs, improved per-base quality, and increased contig N50 by three orders of magnitude. The 413.5 Mbp assembly is nearly 20% longer than the 350 Mbp short-read assembly, closer to the predicted genome size. We also present quality measures and full-length isoform RNA transcript sequences for assessing accuracy and future genome annotation. The assembly accurately represents the seven main linkage groups in an allogamous (outcrossing), highly heterozygous plant genome.
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Affiliation(s)
- Derek M. Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA, Corresponding authors. E-mail: ;
| | - Lisa M. Koch
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA
| | - Timothy P. L. Smith
- US Meat Animal Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Clay Center, NE, USA
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA
| | - Michael L. Sullivan
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), Madison, WI, USA, Corresponding authors. E-mail: ;
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25
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Wu D, Shen E, Jiang B, Feng Y, Tang W, Lao S, Jia L, Lin HY, Xie L, Weng X, Dong C, Qian Q, Lin F, Xu H, Lu H, Cutti L, Chen H, Deng S, Guo L, Chuah TS, Song BK, Scarabel L, Qiu J, Zhu QH, Yu Q, Timko MP, Yamaguchi H, Merotto A, Qiu Y, Olsen KM, Fan L, Ye CY. Genomic insights into the evolution of Echinochloa species as weed and orphan crop. Nat Commun 2022; 13:689. [PMID: 35115514 PMCID: PMC8814039 DOI: 10.1038/s41467-022-28359-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 01/20/2022] [Indexed: 12/20/2022] Open
Abstract
As one of the great survivors of the plant kingdom, barnyard grasses (Echinochloa spp.) are the most noxious and common weeds in paddy ecosystems. Meanwhile, at least two Echinochloa species have been domesticated and cultivated as millets. In order to better understand the genomic forces driving the evolution of Echinochloa species toward weed and crop characteristics, we assemble genomes of three Echinochloa species (allohexaploid E. crus-galli and E. colona, and allotetraploid E. oryzicola) and re-sequence 737 accessions of barnyard grasses and millets from 16 rice-producing countries. Phylogenomic and comparative genomic analyses reveal the complex and reticulate evolution in the speciation of Echinochloa polyploids and provide evidence of constrained disease-related gene copy numbers in Echinochloa. A population-level investigation uncovers deep population differentiation for local adaptation, multiple target-site herbicide resistance mutations of barnyard grasses, and limited domestication of barnyard millets. Our results provide genomic insights into the dual roles of Echinochloa species as weeds and crops as well as essential resources for studying plant polyploidization, adaptation, precision weed control and millet improvements.
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Affiliation(s)
- Dongya Wu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Enhui Shen
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China
| | - Bowen Jiang
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Yu Feng
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Wei Tang
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Sangting Lao
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Lei Jia
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Han-Yang Lin
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
| | - Lingjuan Xie
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Xifang Weng
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Chenfeng Dong
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Qinghong Qian
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Feng Lin
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Haiming Xu
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
| | - Huabing Lu
- Institute of Maize and Upland Grain, Zhejiang Academy of Agricultural Sciences, Dongyang, 322105, China
| | - Luan Cutti
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Huajun Chen
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Shuiguang Deng
- College of Computer Science and Technology, Zhejiang University, Hangzhou, 310058, China
| | - Longbiao Guo
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China
| | - Tse-Seng Chuah
- Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA, 02600, Arau, Perlis, Malaysia
| | - Beng-Kah Song
- School of Science, Monash University Malaysia, 46150, Bandar Sunway, Selangor, Malaysia
| | - Laura Scarabel
- Istituto per la Protezione Sostenibile delle Piante (IPSP), CNR, Viale dell'Università, 16, 35020, Legnaro (PD), Italy
| | - Jie Qiu
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, 200235, China
| | - Qian-Hao Zhu
- CSIRO Agriculture and Food, GPO Box 1700, Canberra, ACT, 2601, Australia
| | - Qin Yu
- Australian Herbicide Resistance Initiative, School of Agriculture and Environment, University of Western Australia, Crawley, WA, 6009, Australia
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, 22904, USA
| | | | - Aldo Merotto
- Department of Crop Sciences, Agricultural School, Federal University of Rio Grande do Sul, Porto Alegre, RS, 91540-000, Brazil
| | - Yingxiong Qiu
- Institute of Ecology, Zhejiang University, Hangzhou, 310058, China
| | - Kenneth M Olsen
- Department of Biology, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Longjiang Fan
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China
- Zhejiang University Zhongyuan Institute, Zhengzhou, 450000, China
| | - Chu-Yu Ye
- Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou, 310058, China.
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26
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Jiang X, Zhang W, Fernie AR, Wen W. Combining novel technologies with interdisciplinary basic research to enhance horticultural crops. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:35-46. [PMID: 34699639 DOI: 10.1111/tpj.15553] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/17/2021] [Accepted: 10/22/2021] [Indexed: 06/13/2023]
Abstract
Horticultural crops mainly include fruits, vegetables, ornamental trees and flowers, and tea trees (Melaleuca alternifolia). They produce a variety of nutrients for the daily human diet in addition to the nutrition provided by staple crops, and some of them additionally possess ornamental and medicinal features. As such, horticultural crops make unique and important contributions to both food security and a colorful lifestyle. Under the current climate change scenario, the growing population and limited arable land means that agriculture, and especially horticulture, has been facing unprecedented challenges to meet the diverse demands of human daily life. Breeding horticultural crops with high quality and adaptability and establishing an effective system that combines cultivation, post-harvest handling, and sales becomes increasingly imperative for horticultural production. This review discusses characteristic and recent research highlights in horticultural crops, focusing on the breeding of quality traits and the mechanisms that underpin them. It additionally addresses challenges and potential solutions in horticultural production and post-harvest practices. Finally, we provide a prospective as to how emerging technologies can be implemented alongside interdisciplinary basic research to enhance our understanding and exploitation of horticultural crops.
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Affiliation(s)
- Xiaohui Jiang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Guangdong Provincial Key Laboratory of Tea Plant Resources Innovation and Utilization, Tea Research Institute, Guangdong Provincial Academy of Agricultural Sciences, Guangzhou, Guangdong, 510640, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Weiyi Zhang
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Muehlenberg 1, Potsdam-Golm, 14476, Germany
| | - Weiwei Wen
- Key Laboratory of Horticultural Plant Biology (MOE), College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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27
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Suárez JC, Contreras AT, Anzola JA, Vanegas JI, Rao IM. Physiological Characteristics of Cultivated Tepary Bean (Phaseolus acutifolius A. Gray) and Its Wild Relatives Grown at High Temperature and Acid Soil Stress Conditions in the Amazon Region of Colombia. PLANTS 2021; 11:plants11010116. [PMID: 35009119 PMCID: PMC8747739 DOI: 10.3390/plants11010116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/12/2021] [Accepted: 12/18/2021] [Indexed: 11/30/2022]
Abstract
Common bean (Phaseolus vulgaris L.) is sensitive to different types of abiotic stresses (drought, high temperature, low soil fertility, and acid soil), and this may limit its adaptation and consequently to its yield under stress. Because of this, a sister species, tepary bean (Phaseolus acutifolius A. Gray), has recently gained attention in breeding for improved abiotic stress tolerance in common bean. In this study, we evaluated the adaptation of 302 accessions of tepary bean (Phaseolus acutifolius A. Gray) and its wild relatives (grouped in four types of tepary bean genetic resource: cultivated, acutifolius regressive, acutifolius wild, tenuifolius wild) when grown under high temperature and acid soil conditions with aluminum toxicity in the Amazon region of Colombia. Our objective was to determine differences among four types of tepary bean genetic resource in their morpho-phenological, agronomic, and physiological responses to combined high temperature and acid soil stress conditions. We found that cultivated P. acutifolius var acutifolius presented a greater number of pods per plant, as well as larger seeds and a greater number of seeds per pod. Some traits, such as root biomass, days to flowering and physiological maturity, specific leaf area, and stomatal density, showed significant differences between types of tepary bean genetic resource, probably contributing to difference in adaptation to combined stress conditions of high temperature and acid soil conditions. The photochemical quenching (qP) was higher in cultivated P. acutifolius var. acutifolius, while energy dissipation by non-photochemical quenching (NPQ) in the form of heat and the coefficient of non-photochemical dissipation (qN) were higher in acutifolius regressive and tenuifolius wild accessions. We have identified 6 accessions of cultivated and 19 accessions of tenuifolius wild that exhibited grain yields above 1800 kg ha−1. These accessions could be suitable to use as parents to improve dry seed production of tepary bean under combined stress conditions of high temperature and acid soil.
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Affiliation(s)
- Juan Carlos Suárez
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
- Programa de Maestría en Sistemas Sostenibles de Producción, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia
- Grupo de Investigaciones Agroecosistemas y Conservación en Bosques Amazónicos-GAIA, Centro de Investigaciones Amazónicas CIMAZ Macagual César Augusto Estrada González, Florencia 180001, Colombia
- Correspondence: ; Tel.: +57-320-280-4455
| | - Amara Tatiana Contreras
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
- Programa de Maestría en Sistemas Sostenibles de Producción, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia
| | - José Alexander Anzola
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
| | - José Iván Vanegas
- Programa de Ingeniería Agroecológica, Facultad de Ingeniería, Universidad de la Amazonia, Florencia 180001, Colombia; (A.T.C.); (J.A.A.); (J.I.V.)
| | - Idupulapati M. Rao
- International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Cali 763537, Colombia;
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