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Construction of A GBS-Based High-Density Genetic Map and Flower Color-Related Loci Mapping in Grasspea (Lathyrus sativus L.). PLANTS 2022; 11:plants11162172. [PMID: 36015475 PMCID: PMC9414002 DOI: 10.3390/plants11162172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 08/17/2022] [Accepted: 08/18/2022] [Indexed: 11/17/2022]
Abstract
Grasspea (Lathyrus sativus L.), a legume crop with excellent resistance to a broad array of environmental stressors, has, to this point, been poorly genetically characterized. High-density genetic linkage maps are critical for draft genome assembly, quantitative trait loci (QTLs) analysis, and gene mining. The lack of a high-density genetic linkage map has limited both genomic studies and selective breeding in grasspea. Here, we developed a high-density genetic linkage map of grasspea using genotyping-by-sequencing (GBS) to sequence 154 grasspea plants, comprising 2 parents and 152 F2 progeny. In all, 307.74 Gb of data was produced, including 2,108,910,938 paired-end reads, as well as 3536 SNPs mapped to seven linkage groups (LG1–LG7). With an average length of 996.52 cM per LG, the overall genetic distance was 6975.68 cM. Both the χ2 test and QTL analysis, based on the Kruskal–Wallis (KW) test and interval mapping (IM) analysis, revealed the monogenic inheritance of flower color in grasspea, with the responsible QTL located between 308.437 cM and 311.346 cM in LG4. The results can aid grasspea genome assembly and accelerate the selective breeding of new grasspea germplasm resources.
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Santos C, Martins DC, González-Bernal MJ, Rubiales D, Vaz Patto MC. Integrating Phenotypic and Gene Expression Linkage Mapping to Dissect Rust Resistance in Chickling Pea. FRONTIERS IN PLANT SCIENCE 2022; 13:837613. [PMID: 35463408 PMCID: PMC9021875 DOI: 10.3389/fpls.2022.837613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 02/23/2022] [Indexed: 06/14/2023]
Abstract
Rusts are among the most important foliar biotrophic fungal diseases in legumes. Lathyrus cicera crop can be severely damaged by Uromyces pisi, to which partial resistance has been identified. Nevertheless, the underlying genetic basis and molecular mechanisms of this resistance are poorly understood in L. cicera. To prioritise the causative variants controlling partial resistance to rust in L. cicera, a recombinant inbred line (RIL) population, segregating for response to this pathogen, was used to combine the detection of related phenotypic- and expression-quantitative trait loci (pQTLs and eQTLs, respectively). RILs' U. pisi disease severity (DS) was recorded in three independent screenings at seedling (growth chamber) and in one season of exploratory screening at adult plant stage (semi-controlled field conditions). A continuous DS range was observed in both conditions and used for pQTL mapping. Different pQTLs were identified under the growth chamber and semi-controlled field conditions, indicating a distinct genetic basis depending on the plant developmental stage and/or the environment. Additionally, the expression of nine genes related to U. pisi resistance in L. cicera was quantified for each RIL individual and used for eQTL mapping. One cis-eQTL and one trans-eQTL were identified controlling the expression variation of one gene related to rust resistance - a member of glycosyl hydrolase family 17. Integrating phenotyping, gene expression and linkage mapping allowed prioritising four candidate genes relevant for disease-resistance precision breeding involved in adaptation to biotic stress, cellular, and organelle homeostasis, and proteins directly involved in plant defence.
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Affiliation(s)
- Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Davide Coelho Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | | | - Diego Rubiales
- Institute for Sustainable Agriculture, Consejo Superior de Investigaciones Científicas, Córdoba, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Sampaio AM, Alves ML, Pereira P, Valiollahi E, Santos C, Šatović Z, Rubiales D, Araújo SDS, van Eeuwijk F, Vaz Patto MC. Grass pea natural variation reveals oligogenic resistance to Fusarium oxysporum f. sp. pisi. THE PLANT GENOME 2021; 14:e20154. [PMID: 34617677 DOI: 10.1002/tpg2.20154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/03/2021] [Indexed: 05/28/2023]
Abstract
Grass pea (Lathyrus sativus L.) is an annual legume species, phylogenetically close to pea (Pisum sativum L.), that may be infected by Fusarium oxysporum f. sp. pisi (Fop), the causal agent of fusarium wilt in peas with vast worldwide yield losses. A range of responses varying from high resistance to susceptibility to this pathogen has been reported in grass pea germplasm. Nevertheless, the genetic basis of that diversity of responses is still unknown, hampering its breeding exploitation. To identify genomic regions controlling grass pea resistance to fusarium wilt, a genome-wide association study approach was applied on a grass pea worldwide collection of accessions inoculated with Fop race 2. Disease responses were scored in this collection that was also subjected to high-throughput based single nucleotide polymorphisms (SNP) screening through genotyping-by-sequencing. A total of 5,651 high-quality SNPs were considered for association mapping analysis, performed using mixed linear models accounting for population structure. Because of the absence of a fully assembled grass pea reference genome, SNP markers' genomic positions were retrieved from the pea's reference genome v1a. In total, 17 genomic regions were associated with three fusarium wilt response traits in grass pea, anticipating an oligogenic control. Seven of these regions were located on pea chromosomes 1, 6, and 7. The candidate genes underlying these regions were putatively involved in secondary and amino acid metabolism, RNA (regulation of transcription), transport, and development. This study revealed important fusarium wilt resistance favorable grass pea SNP alleles, allowing the development of molecular tools for precision disease resistance breeding.
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Affiliation(s)
- Ana Margarida Sampaio
- Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Mara Lisa Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Priscila Pereira
- Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Ehsan Valiollahi
- Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
- Current address: Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad Univ. of Medical Sciences, Mashhad, Iran
| | - Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
| | - Zlatko Šatović
- Faculty of Agriculture, Univ. of Zagreb, Svetošimunska 25, 10000, Zagreb, Croatia
- Center of Excellence for Biodiversity and Molecular Plant Breeding, Svetošimunska 25, 10000, Zagreb, Croatia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Avda. Menéndez Pidal s/n, 14004, Córdoba, Spain
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
- Association BLC3, Technology and Innovation Campus, Centre Bio R&D Unit, Rua Comendador Emílio Augusto Pires, 14, Edifício SIDE UP, 5340-257, Macedo de Cavaleiros, Portugal
| | - Fred van Eeuwijk
- Wageningen Univ. & Research, Biometrics, Applied Statistics, Droevendaalsesteeg 1 6708PB, Wageningen, The Netherlands
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Univ. Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157, Oeiras, Portugal
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Martins D, Araújo SDS, Rubiales D, Vaz Patto MC. Legume Crops and Biotrophic Pathogen Interactions: A Continuous Cross-Talk of a Multilayered Array of Defense Mechanisms. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1460. [PMID: 33137969 PMCID: PMC7692723 DOI: 10.3390/plants9111460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 10/23/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022]
Abstract
Legume species are recognized for their nutritional benefits and contribution to the sustainability of agricultural systems. However, their production is threatened by biotic constraints with devastating impacts on crop yield. A deep understanding of the molecular and genetic architecture of resistance sources culminating in immunity is critical to assist new biotechnological approaches for plant protection. In this review, the current knowledge regarding the major plant immune system components of grain and forage legumes challenged with obligate airborne biotrophic fungi will be comprehensively evaluated and discussed while identifying future directions of research. To achieve this, we will address the multi-layered defense strategies deployed by legume crops at the biochemical, molecular, and physiological levels, leading to rapid pathogen recognition and carrying the necessary information to sub-cellular components, on-setting a dynamic and organized defense. Emphasis will be given to recent approaches such as the identification of critical components of host decentralized immune response negatively regulated by pathogens while targeting the loss-of-function of susceptibility genes. We conclude that advances in gene expression analysis in both host and pathogen, protocols for effectoromics pipelines, and high-throughput disease phenomics platforms are rapidly leading to a deeper understanding of the intricate host-pathogen interaction, crucial for efficient disease resistance breeding initiatives.
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Affiliation(s)
- Davide Martins
- Instituto de Tecnologia Química e Biologia António Xavier, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal; (S.d.S.A.); (M.C.V.P.)
| | - Susana de Sousa Araújo
- Instituto de Tecnologia Química e Biologia António Xavier, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal; (S.d.S.A.); (M.C.V.P.)
- Association BLC3—Technology and Innovation Campus, Centre Bio R&D Unit, Rua Nossa Senhora da Conceição, 2, Lagares, 3405-155 Oliveira do Hospital, Portugal
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, Avenida Menéndez Pidal s/n, 14004 Córdoba, Spain;
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biologia António Xavier, Universidade Nova de Lisboa, Avenida da República, Estação Agronómica Nacional, 2780-157 Oeiras, Portugal; (S.d.S.A.); (M.C.V.P.)
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