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Dadu RHR, Bar I, Ford R, Sambasivam P, Croser J, Ribalta F, Kaur S, Sudheesh S, Gupta D. Lens orientalis Contributes Quantitative Trait Loci and Candidate Genes Associated With Ascochyta Blight Resistance in Lentil. FRONTIERS IN PLANT SCIENCE 2021; 12:703283. [PMID: 34539696 PMCID: PMC8442733 DOI: 10.3389/fpls.2021.703283] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/28/2021] [Indexed: 05/24/2023]
Abstract
Australian lentil production is affected by several major biotic constraints including Ascochyta blight (AB), caused by Ascochyta lentis, a devastating fungal disease. Cultivation of AB resistant cultivars, alongside agronomic management including fungicide application, is the current most economically viable control strategy. However, the breakdown of AB resistance in cultivars, such as Northfield and Nipper, suggests the need for introgression of new and diverse resistance genes. Successful introgression entails an understanding of the genetic basis of resistance. In this context, a biparental mapping population derived from a cross between a recently identified AB resistant accession ILWL 180 (Lens orientalis) and a susceptible cultivar ILL 6002 was produced. A genetic linkage map was constructed from single-nucleotide polymorphism markers generated using a genotyping-by-sequencing transcript approach. Genetic dissection of the mapping population revealed a major quantitative trait loci (QTL) region nested with three QTLs on linkage group 5 and explained 9.5-11.5 percent (%) of phenotypic variance for AB resistance. Another QTL was identified on LG2 with phenotypic variance of 9.6%. The identified QTL regions harbored putative candidate genes potentially associated with defense responses to A. lentis infection. The QTL analysis and the candidate gene information are expected to contribute to the development of diagnostic markers and enable marker-assisted resistance selection in lentil breeding programmes.
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Affiliation(s)
- Rama Harinath Reddy Dadu
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, Dookie College, The University of Melbourne, Dookie, VIC, Australia
- Grains Innovation Park, Agriculture Victoria, DJPR, Horsham, VIC, Australia
| | - Ido Bar
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Rebecca Ford
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Prabhakaran Sambasivam
- Centre for Planetary Health and Food Security, Griffith University, Nathan, QLD, Australia
| | - Janine Croser
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Federico Ribalta
- Centre for Plant Genetics and Breeding, School of Agriculture and Environment, The University of Western Australia, Crawley, WA, Australia
| | - Sukhjiwan Kaur
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Shimna Sudheesh
- Agriculture Victoria, AgriBio, Centre for Agri Bioscience, Bundoora, VIC, Australia
| | - Dorin Gupta
- School of Agriculture and Food, Faculty of Veterinary and Agriculture Sciences, Dookie College, The University of Melbourne, Dookie, VIC, Australia
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Guerra-García A, Gioia T, von Wettberg E, Logozzo G, Papa R, Bitocchi E, Bett KE. Intelligent Characterization of Lentil Genetic Resources: Evolutionary History, Genetic Diversity of Germplasm, and the Need for Well-Represented Collections. Curr Protoc 2021; 1:e134. [PMID: 34004055 DOI: 10.1002/cpz1.134] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
The genetic and phenotypic characterization of crops allows us to elucidate their evolutionary and domestication history, the genetic basis of important traits, and the use of variation present in landraces and wild relatives to enhance resilience. In this context, we aim to provide an overview of the main genetic resources developed for lentil and their main outcomes, and to suggest protocols for continued work on this important crop. Lens culinaris is the third-most-important cool-season grain and its use is increasing as a quick-cooking, nutritious, plant-based source of protein. L. culinaris was domesticated in the Fertile Crescent, and six additional wild taxa (L. orientalis, L. tomentosus, L. odemensis, L. lamottei, L. ervoides, and L. nigricans) are recognized. Numerous genetic diversity studies have shown that wild relatives present high levels of genetic variation and provide a reservoir of alleles that can be used for breeding programs. Furthermore, the integration of genetics/genomics and breeding techniques has resulted in identification of quantitative trait loci and genes related to attributes of interest. Genetic maps, massive genotyping, marker-assisted selection, and genomic selection are some of the genetic resources generated and applied in lentil. In addition, despite its size (∼4 Gbp) and complexity, the L. culinaris genome has been assembled, allowing a deeper understanding of its architecture. Still, major knowledge gaps exist in lentil, and a deeper understanding and characterization of germplasm resources, including wild relatives, is critical to lentil breeding and improvement. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Recording of lentil seed descriptors Basic Protocol 2: Lentil seed imaging Basic Protocol 3: Lentil seed increase Basic Protocol 4: Recording of primary lentil seed INCREASE descriptors.
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Affiliation(s)
- Azalea Guerra-García
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Tania Gioia
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Eric von Wettberg
- Department of Plant and Soil Sciences and Gund Institute for the Environment, University of Vermont, Burlington, Vermont
| | - Giuseppina Logozzo
- School of Agriculture, Forestry, Food and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Roberto Papa
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Vishnyakova MA, Aleksandrova TG, Buravtseva TV, Burlyaeva MO, Egorova GP, Semenova EV, Seferova IV, Suvorova GN. SPECIES DIVERSITY OF THE VIR COLLECTION OF GRAIN LEGUME GENETIC RESOURCES AND ITS USE IN DOMESTIC BREEDING. PROCEEDINGS ON APPLIED BOTANY, GENETICS AND BREEDING 2019. [DOI: 10.30901/2227-8834-2019-2-109-123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The world’s genebanks hold 7.5 million germplasm accessions of plant genetic resources (PGR). One of the qualitative characteristics of the PGR collections is the species diversity, in particular, the presence of crop wild relatives (CWR), which makes it possible to widen the use of gene pools in the breeding process. The collection of the Vavilov Institute (VIR) is one of the most diverse holdings in the number of plant species. A survey is provided here of the species diversity in VIR’s grain legume collection, and its use in domestic breeding practice is analyzed. Comparison of this diversity with the state of PGR exploitation in the world makes it possible to assess the prospects of more efficient utilization of gene pool potential, especially for species that are unjustifiably cultivated on a too small scale or even neglected as crops in this country. The VIR collection of grain legumes incorporates 196 species from 9 genera of the family Fabaceae. This number includes cultigens and CWR. The cultivars of 21 species of grain legumes listed in the State Register of Breeding Achievements (2018) are adapted to the soil and climate conditions of this country. However, the species diversity of the collection could be used more efficiently in domestic plant breeding and crop production. This concerns both underutilized crops in Russia (broad beans, lima beans and grass pea) and those whose adaptive potential is adjusted only to certain and limited areas of the Russian Federation (Tepary beans and Vigna spp.). It is also necessary to exploit more efficiently species of the wild flora, both for direct utilization as pastures, green manure or phytoremediation crops and for introgressive breeding and domestication (Vicia benghalensis L., V. narbonensis L., Lathyrus sylvestris L., Lupinus hartwegii Lindl., etc.). Incorporation of crop wild relatives into the breeding process is promising for crop improvement in a number of aspects: for example, to increase resistance to diseases, pests, abiotic stressors, etc.
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Affiliation(s)
- M. A. Vishnyakova
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | | | - T. V. Buravtseva
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - M. O. Burlyaeva
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - G. P. Egorova
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - E. V. Semenova
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - I. V. Seferova
- N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR)
| | - G. N. Suvorova
- Federal Scientific Center of Grain Legumes and Groat Crops
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Zhang H, Yasmin F, Song BH. Neglected treasures in the wild - legume wild relatives in food security and human health. CURRENT OPINION IN PLANT BIOLOGY 2019; 49:17-26. [PMID: 31085425 PMCID: PMC6817337 DOI: 10.1016/j.pbi.2019.04.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 05/08/2023]
Abstract
The legume family (Fabaceae) is the third-largest flowering family with over 18 000 species worldwide that are rich in proteins, oils, and nutrients. However, the production potential of legume-derived food cannot meet increasing global demand. Wild legumes represent a large group of wild species adaptive to diverse habitats and harbor rich genetic diversity for the improvement of the agronomic, nutritional, and medicinal values of the domesticated legumes. Accumulating evidence suggests that the genetic variation retained in these under-exploited leguminous wild relatives can be used to improve crop yield, nutrient contents, and resistance/tolerance to environmental stresses via the integration of omics, genetics, and genome-editing technologies.
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Affiliation(s)
- Hengyou Zhang
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Farida Yasmin
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Bao-Hua Song
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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Zhou Z, Bar I, Sambasivam PT, Ford R. Determination of the Key Resistance Gene Analogs Involved in Ascochyta rabiei Recognition in Chickpea. FRONTIERS IN PLANT SCIENCE 2019; 10:644. [PMID: 31191572 PMCID: PMC6546118 DOI: 10.3389/fpls.2019.00644] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 04/29/2019] [Indexed: 05/21/2023]
Abstract
Chickpea (Cicer arietinum L.) is an important cool season food legume, however, its production is severely constrained by the foliar disease Ascochyta blight caused by the fungus Ascochyta rabiei (syn. Phoma rabiei). Several disease management options have been developed to control the pathogen, including breeding for host plant resistance. However, the pathogen population is evolving to produce more aggressive isolates. For host resistance to be effective, the plant must quickly recognize the pathogen and instigate initial defense mechanisms, optimally at the point of contact. Given that the most resistant host genotypes display rapid pathogen recognition and response, the approach taken was to assess the type, speed and pattern of recognition via Resistance Gene Analog (RGA) transcription among resistant and susceptible cultivated chickpea varieties. RGAs are key factors in the recognition of plant pathogens and the signaling of inducible defenses. In this study, a suite of RGA loci were chosen for further investigation from both published literature and from newly mined homologous sequences within the National Center for Biotechnology Information (NCBI) database. Following their validation in the chickpea genome, 10 target RGAs were selected for differential expression analysis in response to A. rabiei infection. This was performed in a set of four chickpea varieties including two resistant cultivars (ICC3996 and PBA Seamer), one moderately resistant cultivar (PBA HatTrick) and one susceptible cultivar (Kyabra). Gene expression at each RGA locus was assessed via qPCR at 2, 6, and 24 h after A. rabiei inoculation with a previously characterized highly aggressive isolate. As a result, all loci were differentially transcribed in response to pathogen infection in at least one genotype and at least one time point after inoculation. Among these, the differential expression of four RGAs was significant and consistently increased in the most resistant genotype ICC3996 immediately following inoculation, when spore germination began and ahead of penetration into the plant's epidermal tissues. Further in silico analyses indicated that the differentially transcribed RGAs function through ADP-binding within the pathogen recognition pathway. These represent clear targets for future functional validation and potential for selective resistance breeding for introgression into elite cultivars.
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Affiliation(s)
| | | | | | - Rebecca Ford
- Environmental Futures Research Institute, School of Environment and Science, Griffith University, Nathan, QLD, Australia
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Polanco C, Sáenz de Miera LE, González AI, García P, Fratini R, Vaquero F, Vences FJ, Pérez de la Vega M. Construction of a high-density interspecific (Lens culinaris x L. odemensis) genetic map based on functional markers for mapping morphological and agronomical traits, and QTLs affecting resistance to Ascochyta in lentil. PLoS One 2019; 14:e0214409. [PMID: 30917174 PMCID: PMC6436743 DOI: 10.1371/journal.pone.0214409] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 03/12/2019] [Indexed: 01/13/2023] Open
Abstract
Usage of high-throughput sequencing approaches allow for the generation and characterization of reference transcriptome datasets that support gene-based marker discovery, which in turn can be used to build genetic maps among other purposes. We have obtained a transcriptome assembly including 49,453 genes for the lentil (Lens culinaris Medik.) cultivar Alpo using RNAseq methodology. This transcriptome was used as reference to obtain 6,306 quality polymorphic markers (SNPs and short indels) analyzing genotype data from a RIL population at F7 generation derived from the interspecific cross between L. culinaris cv. Alpo and L. odemensis accession ILWL235. L. odemensis is a wild species included in the secondary gene pool and can be used as a source for gene introgression in lentil breeding programs. Marker data were used to construct the first genetic interspecific map between these two species. This linkage map has been used to precisely identify regions of the CDC-Redberry lentil draft genome in which the candidate genes for some qualitative traits (seed coat spotting pattern, flower color, and stem pigmentation) could be located. The genome regions corresponding to a significant single quantitative trait locus (QTL) controlling "time to flowering" located in chromosome 6 and three QTLs regulating seed size and positioned in chromosomes 1 and 5 (two QTLs) were also identified. Significant QTLs for Ascochyta blight resistance in lentil were mapped to chromosome 6 in the genome region or close to it where QTLs for Ascochyta blight resistance have previously been reported.
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Affiliation(s)
- Carlos Polanco
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
- * E-mail:
| | | | - Ana Isabel González
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Pedro García
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Richard Fratini
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Francisca Vaquero
- Área de Genética, Departamento de Biología Molecular, Universidad de León, León, Spain
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