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Delvento C, Arcieri F, Marcotrigiano AR, Guerriero M, Fanelli V, Dellino M, Curci PL, Bouwmeester H, Lotti C, Ricciardi L, Pavan S. High-density linkage mapping and genetic dissection of resistance to broomrape ( Orobanche crenata Forsk.) in pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1216297. [PMID: 37492777 PMCID: PMC10364127 DOI: 10.3389/fpls.2023.1216297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 06/21/2023] [Indexed: 07/27/2023]
Abstract
Pea (Pisum sativum L.) is a widely cultivated legume of major importance for global food security and agricultural sustainability. Crenate broomrape (Orobanche crenata Forsk.) (Oc) is a parasitic weed severely affecting legumes, including pea, in the Mediterranean Basin and the Middle East. Previously, the identification of the pea line "ROR12", displaying resistance to Oc, was reported. Two-year field trials on a segregant population of 148 F7 recombinant inbred lines (RILs), originating from a cross between "ROR12" and the susceptible cultivar "Sprinter", revealed high heritability (0.84) of the "ROR12" resistance source. Genotyping-by-sequencing (GBS) on the same RIL population allowed the construction of a high-density pea linkage map, which was compared with the pea reference genome and used for quantitative trait locus (QTL) mapping. Three QTLs associated with the response to Oc infection, named PsOcr-1, PsOcr-2, and PsOcr-3, were identified, with PsOcr-1 explaining 69.3% of the genotypic variance. Evaluation of the effects of different genotypic combinations indicated additivity between PsOcr-1 and PsOcr-2, and between PsOcr-1 and PsOcr-3, and epistasis between PsOcr-2 and PsOcr-3. Finally, three Kompetitive Allele Specific PCR (KASP) marker assays were designed on the single-nucleotide polymorphisms (SNPs) associated with the QTL significance peaks. Besides contributing to the development of pea genomic resources, this work lays the foundation for the obtainment of pea cultivars resistant to Oc and the identification of genes involved in resistance to parasitic Orobanchaceae.
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Affiliation(s)
- Chiara Delvento
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Arcieri
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Marzia Guerriero
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Maria Dellino
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Luca Curci
- Institute of Biosciences and Bioresources, National Research Council (CNR), Bari, Italy
| | - Harro Bouwmeester
- Plant Hormone Biology Group, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, Section of Plant Genetics and Breeding, University of Bari Aldo Moro, Bari, Italy
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Odesola KA, Olawuyi OJ, Paliwal R, Oyatomi OA, Abberton MT. Genome-Wide association analysis of phenotypic traits in Bambara groundnut under drought-stressed and non-stressed conditions based on DArTseq SNP. FRONTIERS IN PLANT SCIENCE 2023; 14:1104417. [PMID: 36866383 PMCID: PMC9972976 DOI: 10.3389/fpls.2023.1104417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/05/2023] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Bambara groundnut (BG) (Vigna subterranea [L.] Verdc) is an indigenous, resilient, but underutilized leguminous crop that occurs mostly as genetically heterogeneous landraces with limited information on the drought tolerant attributes. This study elucidates the associations between sequencing-based diversity array technology (DArTseq) and phenotypic character as well as differing indices related to drought tolerance in one hundred accessions of Bambara groundnut. METHODS The field experiments were conducted at IITA research stations in Kano and Ibadan between 2016 and 2018 planting seasons. The experiments were arranged in randomised complete block design with three replications, under the different water regimes. The phenotypic traits evaluated was further to construct the dendrogram. Genome-wide association mapping was conducted based on 5927 DArTs loci with < 20% missing data. RESULTS AND DISCUSSIONS The genome wide association study predicted drought tolerance in Bambara accessions for geometric mean productivity (GMP) and stress tolerance index (STI). TVSu-423 had the highest GMP and STI values (28.50, 2.40), while TVSu-2017 had the lowest at GMP (1.74) and STI (0.01) respectively. The relative water content (%) was significantly higher for accessions; TVSu-266 (60.35, 61.49), TVSu-2 (58.29, 53.94), and TVSu-411 (55.17, 58.92) in 2016/2017 and 2017/2018, respectively. The phenotypic characters studied delineated the accessions into two major clusters and five distinct sub-clusters, indicating variations across all the geographical locations. The 5,927 DArTseq genomic markers in association with STI further grouped the 100 accessions into two main clusters. TVSu-1897 from Botswana (Southern Africa) was in the first cluster, while the remaining 99 accessions from Western, Central, and Eastern Africa made up the second cluster. The eight significant Quantitative Trait Loci (QTLs) (24346377|F|0-22:A>G-22:A>G, 24384105|F|0-56:A>G33 :A> G, 24385643|F|0-53:G>C-53:G>C, 24385696|F|0-43:A>G-43:A>G, 4177257|F|0-44:A>T-44:A>T, 4182070|F|0-66:G>A-66:G>A, 4183483|F|0-24:G>A-24:G>A, 4183904|F|0-11:C>T-11:C>T) identified with Bonferroni threshold was in association with STI, indicative of variations under the drought-stressed condition. The observation of consistent SNPs in the 2016 and 2017 planting seasons, as well as in combination with the 2016 and 2017 planting seasons, led to the designation of these QTLs as significant. The drought selected accessions could form basis for hybridization breeding. The identified quantitative trait loci could be useful in marker-assisted selection in drought molecular breeding programs.
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Affiliation(s)
- Kafilat Abiodun Odesola
- Department of Biological Sciences, Bells University of Technology, Sango Otta, Ogun State, Nigeria
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
- Department of Botany, University of Ibadan, Ibadan, Oyo State, Nigeria
| | | | - Rajneesh Paliwal
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
| | - Olaniyi Ajewole Oyatomi
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
| | - Michael T. Abberton
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Oyo State, Nigeria
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Lee RC, Grime CR, O'Driscoll K, Khentry Y, Farfan-Caceres LM, Tahghighi H, Kamphuis LG. Field Pea ( Pisum sativum) Germplasm Screening for Seedling Ascochyta Blight Resistance and Genome-Wide Association Studies Reveal Loci Associated with Resistance to Peyronellaea pinodes and Ascochyta koolunga. PHYTOPATHOLOGY 2023; 113:265-276. [PMID: 35984372 DOI: 10.1094/phyto-02-22-0051-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Ascochyta blight is a damaging disease that affects the stems, leaves, and pods of field pea (Pisum sativum) and impacts yield and grain quality. In Australia, field pea Ascochyta blight is primarily caused by the necrotrophic fungal species Peyronellaea pinodes and Ascochyta koolunga. In this study, we screened 1,276 Pisum spp. germplasm accessions in seedling disease assays with a mix of three isolates of P. pinodes and 641 accessions with three mixed isolates of A. koolunga (513 accessions were screened with both species). A selection of three P. sativum accessions with low disease scores for either pathogen, or in some cases both, were crossed with Australian field pea varieties PBA Gunyah and PBA Oura, and recombinant inbred line populations were made. Populations at the F3:4 and F4:5 generation were phenotyped for their disease response to P. pinodes and A. koolunga, and genotypes were determined using the diversity arrays technology genotyping method. Marker-trait associations were identified using a genome-wide association study approach. Trait-associated loci were mapped to the published P. sativum genome assembly, and candidate resistance gene analogues were identified in the corresponding genomic regions. One locus on chromosome 2 (LG1) was associated with resistance to P. pinodes, and the 8 Mb genomic region contains 156 genes, two of which are serine/threonine protein kinases, putatively contributing to the resistance trait. A second locus on chromosome 5 (LG3) was associated with resistance to A. koolunga, and the 35 Mb region contains 488 genes, of which five are potential candidate resistance genes, including protein kinases, a mitogen-activated protein kinase, and an ethylene-responsive protein kinase homolog.
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Affiliation(s)
- Robert C Lee
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102 Australia
| | - Christina R Grime
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102 Australia
| | - Kane O'Driscoll
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102 Australia
| | - Yuphin Khentry
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102 Australia
| | - Lina M Farfan-Caceres
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102 Australia
| | - Hediyeh Tahghighi
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102 Australia
| | - Lars G Kamphuis
- Centre for Crop and Disease Management, School of Molecular and Life Sciences, Curtin University, Bentley, WA, 6102 Australia
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Rispail N, Wohor OZ, Osuna-Caballero S, Barilli E, Rubiales D. Genetic Diversity and Population Structure of a Wide Pisum spp. Core Collection. Int J Mol Sci 2023; 24:2470. [PMID: 36768792 PMCID: PMC9916889 DOI: 10.3390/ijms24032470] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/19/2023] [Accepted: 01/25/2023] [Indexed: 02/03/2023] Open
Abstract
Peas (Pisum sativum) are the fourth most cultivated pulses worldwide and a critical source of protein in animal feed and human food. Developing pea core collections improves our understanding of pea evolution and may ease the exploitation of their genetic diversity in breeding programs. We carefully selected a highly diverse pea core collection of 325 accessions and established their genetic diversity and population structure. DArTSeq genotyping provided 35,790 polymorphic DArTseq markers, of which 24,279 were SilicoDArT and 11,511 SNP markers. More than 90% of these markers mapped onto the pea reference genome, with an average of 2787 SilicoDArT and 1644 SNP markers per chromosome, and an average LD50 distance of 0.48 and 1.38 Mbp, respectively. The pea core collection clustered in three or six subpopulations depending on the pea subspecies. Many admixed accessions were also detected, confirming the frequent genetic exchange between populations. Our results support the classification of Pisum genus into two species, P. fulvum and P. sativum (including subsp. sativum, arvense, elatius, humile, jomardii and abyssinicum). In addition, the study showed that wild alleles were incorporated into the cultivated pea through the intermediate P. sativum subsp. jomardii and P. sativum subsp. arvense during pea domestication, which have important implications for breeding programs. The high genetic diversity found in the collection and the high marker coverage are also expected to improve trait discovery and the efficient implementation of advanced breeding approaches.
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Affiliation(s)
- Nicolas Rispail
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Osman Zakaria Wohor
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
- Savanna Agriculture Research Institute, CSIR, Nyankpala, Tamale P.O. Box TL52, Ghana
| | | | - Eleonora Barilli
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
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Chromosomal Location of Pm12-A Novel Powdery Mildew Resistance Gene from Avena sterilis. Genes (Basel) 2022; 13:genes13122409. [PMID: 36553676 PMCID: PMC9778159 DOI: 10.3390/genes13122409] [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: 11/05/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Identification of new, effective disease resistance genes is a very important aspect of plant breeding. Also important is the precise location of individual loci and tagging them with DNA markers for marker assisted selection. The aim of the present study was identification of the molecular markers linked with Pm12, a new effective resistance gene to powdery mildew, and their location in the oat genome. The analysis was performed on 167 F2 individuals from a hybrid of Fuchs × CN67383, with the status of the locus in each individual verified by progeny test in F3. Segregation ratios confirmed the monogenic nature of resistance. Making use of the sequence data of DNA markers and the oat OT3098 v2 genome reference assembly, Pm12 is located on chromosome 7C. A comparison was also made with the reference consensus map, to which there are more reports of mapped genes to date. The mapping results suggest that Pm12 is located in the interval 103.8-111.7 cM on this map. No powdery mildew resistance locus has been identified in this region so far, suggesting that Avena sterilis CN67383 carries a novel locus offering effective resistance in oat breeding. The information included in the oat genome annotation allowed for the identification of candidate genes in the close region of the marker cluster for Pm12. This information may provide an interesting source of further analysis of the pathways of various genes in response to the stress of powdery mildew infection.
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Osuna-Caballero S, Rispail N, Barilli E, Rubiales D. Identification and Characterization of Novel Sources of Resistance to Rust Caused by Uromyces pisi in Pisum spp. PLANTS (BASEL, SWITZERLAND) 2022; 11:2268. [PMID: 36079654 PMCID: PMC9460634 DOI: 10.3390/plants11172268] [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: 08/01/2022] [Revised: 08/26/2022] [Accepted: 08/29/2022] [Indexed: 06/15/2023]
Abstract
Pea rust is a major disease worldwide caused by Uromyces pisi in temperate climates. Only moderate levels of partial resistance against U. pisi have been identified so far in pea, urging for enlarging the levels of resistance available for breeding. Herein, we describe the responses to U. pisi of 320 Pisum spp. accessions, including cultivated pea and wild relatives, both under field and controlled conditions. Large variations for U. pisi infection response for most traits were observed between pea accessions under both field and controlled conditions, allowing the detection of genotypes with partial resistance. Simultaneous multi-trait indexes were applied to the datasets allowing the identification of partial resistance, particularly in accessions JI224, BGE004710, JI198, JI199, CGN10205, and CGN10206. Macroscopic observations were complemented with histological observations on the nine most resistant accessions and compared with three intermediates and three susceptible ones. This study confirmed that the reduced infection of resistant accessions was associated with smaller rust colonies due to a reduction in the number of haustoria and hyphal tips per colony. Additionally, a late acting hypersensitive response was identified for the first time in a pea accession (PI273209). These findings demonstrate that screening pea collections continues to be a necessary method in the search for complete resistance against U. pisi. In addition, the large phenotypic diversity contained in the studied collection will be useful for further association analysis and breeding perspectives.
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Parihar AK, Kumar J, Gupta DS, Lamichaney A, Naik SJ S, Singh AK, Dixit GP, Gupta S, Toklu F. Genomics Enabled Breeding Strategies for Major Biotic Stresses in Pea ( Pisum sativum L.). FRONTIERS IN PLANT SCIENCE 2022; 13:861191. [PMID: 35665148 PMCID: PMC9158573 DOI: 10.3389/fpls.2022.861191] [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: 01/24/2022] [Accepted: 03/28/2022] [Indexed: 06/15/2023]
Abstract
Pea (Pisum sativum L.) is one of the most important and productive cool season pulse crops grown throughout the world. Biotic stresses are the crucial constraints in harnessing the potential productivity of pea and warrant dedicated research and developmental efforts to utilize omics resources and advanced breeding techniques to assist rapid and timely development of high-yielding multiple stress-tolerant-resistant varieties. Recently, the pea researcher's community has made notable achievements in conventional and molecular breeding to accelerate its genetic gain. Several quantitative trait loci (QTLs) or markers associated with genes controlling resistance for fusarium wilt, fusarium root rot, powdery mildew, ascochyta blight, rust, common root rot, broomrape, pea enation, and pea seed borne mosaic virus are available for the marker-assisted breeding. The advanced genomic tools such as the availability of comprehensive genetic maps and linked reliable DNA markers hold great promise toward the introgression of resistance genes from different sources to speed up the genetic gain in pea. This review provides a brief account of the achievements made in the recent past regarding genetic and genomic resources' development, inheritance of genes controlling various biotic stress responses and genes controlling pathogenesis in disease causing organisms, genes/QTLs mapping, and transcriptomic and proteomic advances. Moreover, the emerging new breeding approaches such as transgenics, genome editing, genomic selection, epigenetic breeding, and speed breeding hold great promise to transform pea breeding. Overall, the judicious amalgamation of conventional and modern omics-enabled breeding strategies will augment the genetic gain and could hasten the development of biotic stress-resistant cultivars to sustain pea production under changing climate. The present review encompasses at one platform the research accomplishment made so far in pea improvement with respect to major biotic stresses and the way forward to enhance pea productivity through advanced genomic tools and technologies.
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Affiliation(s)
- Ashok Kumar Parihar
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Jitendra Kumar
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Debjyoti Sen Gupta
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Amrit Lamichaney
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Satheesh Naik SJ
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Anil K. Singh
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, India
| | - Girish P. Dixit
- All India Coordinated Research Project on Chickpea, ICAR-IIPR, Kanpur, India
| | - Sanjeev Gupta
- Indian Council of Agricultural Research, New Delhi, India
| | - Faruk Toklu
- Department of Field Crops, Faculty of Agricultural, Cukurova University, Adana, Turkey
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Ollivier R, Glory I, Cloteau R, Le Gallic JF, Denis G, Morlière S, Miteul H, Rivière JP, Lesné A, Klein A, Aubert G, Kreplak J, Burstin J, Pilet-Nayel ML, Simon JC, Sugio A. A major-effect genetic locus, ApRVII, controlling resistance against both adapted and non-adapted aphid biotypes in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1511-1528. [PMID: 35192006 DOI: 10.1007/s00122-022-04050-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
KEY MESSAGE A genome-wide association study for pea resistance against a pea-adapted biotype and a non-adapted biotype of the aphid, Acyrthosiphon pisum, identified a genomic region conferring resistance to both biotypes. In a context of reduced insecticide use, the development of cultivars resistant to insect pests is crucial for an integrated pest management. Pea (Pisum sativum) is a crop of major importance among cultivated legumes, for the supply of dietary proteins and nitrogen in low-input cropping systems. However, yields of the pea crop have become unstable due to plant parasites. The pea aphid (Acyrthosiphon pisum) is an insect pest species forming a complex of biotypes, each one adapted to feed on one or a few related legume species. This study aimed to identify resistance to A. pisum and the underlying genetic determinism by examining a collection of 240 pea genotypes. The collection was screened against a pea-adapted biotype and a non-adapted biotype of A. pisum to characterize their resistant phenotype. Partial resistance was observed in some pea genotypes exposed to the pea-adapted biotype. Many pea genotypes were completely resistant to non-adapted biotype, but some exhibited partial susceptibility. A genome-wide association study, using pea exome-capture sequencing data, enabled the identification of the major-effect quantitative trait locus ApRVII on the chromosome 7. ApRVII includes linkage disequilibrium blocks significantly associated with resistance to one or both of the two aphid biotypes studied. Finally, we identified candidate genes underlying ApRVII that are potentially involved in plant-aphid interactions and marker haplotypes linked with aphid resistance. This study sets the ground for the functional characterization of molecular pathways involved in pea defence to the aphids but also is a step forward for breeding aphid-resistant cultivars.
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Affiliation(s)
- Rémi Ollivier
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Isabelle Glory
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Romuald Cloteau
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Gaëtan Denis
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Henri Miteul
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | | | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Anthony Klein
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Grégoire Aubert
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Jonathan Kreplak
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | - Judith Burstin
- Agroécologie, INRAE, AgroSup Dijon, Univ Bourgogne-Franche-Comté, 21065, Dijon, France
| | | | | | - Akiko Sugio
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France.
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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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Shitta NS, Unachukwu N, Edemodu AC, Abebe AT, Oselebe HO, Abtew WG. Genetic diversity and population structure of an African yam bean (Sphenostylis stenocarpa) collection from IITA GenBank. Sci Rep 2022; 12:4437. [PMID: 35292678 PMCID: PMC8924269 DOI: 10.1038/s41598-022-08271-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 03/04/2022] [Indexed: 11/30/2022] Open
Abstract
African yam bean, AYB (Sphenostylisstenocarpa), is an underutilized legume of tropical Africa. AYB can boost food and nutritional security in sub-Saharan Africa through its nutrient-rich seeds and tubers. However, inadequate information on germplasm with desirable agro-morphological traits, including insufficient data at the genomic level, has prevented the full exploitation of its food and breeding potentials. Notably, assessing the genetic diversity and population structure in a species is a prerequisite for improvement and eventual successful exploitation. The present study evaluated the population structure and genetic diversity of 169 accessions from the International Institute of Tropical Agriculture (IITA) collection using 26 phenotypic characters and 1789 single nucleotide polymorphism (SNP) markers. The phenotypic traits and SNP markers revealed their usefulness in uniquely distinguishing each AYB accession. The hierarchical cluster of phenotypes grouped accessions into three sub-populations; SNPs analysis also clustered the accessions into three sub-populations. The genetic differentiation (FST) among the three sub-populations was sufficiently high (0.14–0.39) and significant at P = 0.001. The combined analysis revealed three sub-populations; accessions in sub-population 1 were high yielding, members in sub-population 2 showed high polymorphic loci and heterozygosity. This study provides essential information for the breeding and genetic improvement of AYB.
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Affiliation(s)
| | - Nnanna Unachukwu
- International Institute of Tropical Agriculture, Ibadan, Nigeria
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Genomic Variations and Mutational Events Associated with Plant-Pathogen Interactions. BIOLOGY 2022; 11:biology11030421. [PMID: 35336795 PMCID: PMC8945218 DOI: 10.3390/biology11030421] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 12/23/2022]
Abstract
Simple Summary Plants, unlike animals, do not have defender cells or an adaptive immune system. Instead, plants rely on each cell’s innate immunity and systemic signals emitted from infection sites. On the other hand, not all plants, even within the same species, are genetically identical, and their genetic backgrounds determine how well they respond to stress factors. Through evolution, plants have acquired various defense mechanisms that play important roles in the never-ending fight between plants and pathogens. Genetic variation in relation to plant disease resistance can thus be contextualized to provide new insights into these defense mechanisms and evolutionary processes that lead to resistance to pathogens. By focusing on genetic variations and mutational events linked with plant–pathogen interactions, the paper explores how genome compartments facilitate plant and pathogen evolutionary processes. Abstract Phytopathologists are actively researching the molecular basis of plant–pathogen interactions. The mechanisms of responses to pathogens have been studied extensively in model crop plant species and natural populations. Today, with the rapid expansion of genomic technologies such as DNA sequencing, transcriptomics, proteomics, and metabolomics, as well as the development of new methods and protocols, data analysis, and bioinformatics, it is now possible to assess the role of genetic variation in plant–microbe interactions and to understand the underlying molecular mechanisms of plant defense and microbe pathogenicity with ever-greater resolution and accuracy. Genetic variation is an important force in evolution that enables organisms to survive in stressful environments. Moreover, understanding the role of genetic variation and mutational events is essential for crop breeders to produce improved cultivars. This review focuses on genetic variations and mutational events associated with plant–pathogen interactions and discusses how these genome compartments enhance plants’ and pathogens’ evolutionary processes.
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Martins DC, Rubiales D, Vaz Patto MC. Association Mapping of Lathyrus sativus Disease Response to Uromyces pisi Reveals Novel Loci Underlying Partial Resistance. FRONTIERS IN PLANT SCIENCE 2022; 13:842545. [PMID: 35401593 PMCID: PMC8988034 DOI: 10.3389/fpls.2022.842545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/27/2022] [Indexed: 05/17/2023]
Abstract
Uromyces pisi ([Pers.] D.C.) Wint. is an important foliar biotrophic pathogen infecting grass pea (Lathyrus sativus L.), compromising their yield stability. To date, few efforts have been made to assess the natural variation in grass pea resistance and to identify the resistance loci operating against this pathogen, limiting its efficient breeding exploitation. To overcome this knowledge gap, the genetic architecture of grass pea resistance to U. pisi was investigated using a worldwide collection of 182 accessions through a genome-wide association approach. The response of the grass pea collection to rust infection under controlled conditions and at the seedling stage did not reveal any hypersensitive response but a continuous variation for disease severity, with the identification of promising sources of partial resistance. A panel of 5,651 high-quality single-nucleotide polymorphism (SNP) markers previously generated was used to test for SNP-trait associations, based on a mixed linear model accounting for population structure. We detected seven SNP markers significantly associated with U. pisi disease severity, suggesting that partial resistance is oligogenic. Six of the associated SNP markers were located in chromosomes 4 and 6, while the remaining SNP markers had no known chromosomal position. Through comparative mapping with the pea reference genome, a total of 19 candidate genes were proposed, encoding for leucine-rich repeat, NB-ARC domain, and TGA transcription factor family, among others. Results presented in this study provided information on the availability of partial resistance in grass pea germplasm and advanced our understanding of the molecular mechanisms of quantitative resistance to rust in grass pea. Moreover, the detected associated SNP markers constitute promising genomic targets for the development of molecular tools to assist disease resistance precision breeding.
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Affiliation(s)
- Davide Coelho Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- *Correspondence: Davide Coelho Martins,
| | - Diego Rubiales
- Instituto de Agricultura Sostenible, 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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Thant AA, Zaw H, Kalousova M, Singh RK, Lojka B. Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers. PLANTS 2021; 10:plants10122564. [PMID: 34961035 PMCID: PMC8707408 DOI: 10.3390/plants10122564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 11/25/2022]
Abstract
Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.
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Affiliation(s)
- Aye Aye Thant
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech Republic;
- Correspondence: (A.A.T.); (B.L.); Tel.: +420-773495976 (A.A.T.); +420-224382171 or +420-734170763 (B.L.)
| | - Hein Zaw
- Plant Biotechnology Center, Pale Myothit, Shwe Nanthar, Mingaladon, Yangon 110 23, Myanmar;
| | - Marie Kalousova
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech Republic;
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Crop Diversification and Genetics, Al Rwayyah 2, Academic City, Dubai P.O. Box 14660, United Arab Emirates;
| | - Bohdan Lojka
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech Republic;
- Correspondence: (A.A.T.); (B.L.); Tel.: +420-773495976 (A.A.T.); +420-224382171 or +420-734170763 (B.L.)
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Genetic diversity and population structure of ridge gourd (Luffa acutangula) accessions in a Thailand collection using SNP markers. Sci Rep 2021; 11:15311. [PMID: 34321535 PMCID: PMC8319206 DOI: 10.1038/s41598-021-94802-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Accepted: 07/16/2021] [Indexed: 11/23/2022] Open
Abstract
This study explored a germplasm collection consisting of 112 Luffa acutangula (ridge gourd) accessions, mainly from Thailand. A total of 2834 SNPs were used to establish population structure and underlying genetic diversity while exploring the fruit characteristics together with genetic information which would help in the selection of parental lines for a breeding program. The study found that the average polymorphism information content value of 0.288 which indicates a moderate genetic diversity for this L. acutangula germplasm. STRUCTURE analysis (ΔK at K = 6) allowed us to group the accessions into six subpopulations that corresponded well with the unrooted phylogenetic tree and principal coordinate analyses. When plotted, the STRUCTURE bars to the area of collection, we observed an admixed genotype from surrounding accessions and a geneflow confirmed by the value of FST = 0.137. AMOVA based on STRUCTURE clustering showed a low 12.83% variation between subpopulations that correspond well with the negative inbreeding coefficient value (FIS = − 0.092) and low total fixation index (FIT = 0.057). There were distinguishing fruit shapes and length characteristics in specific accessions for each subpopulation. The genetic diversity and different fruit shapes in the L. acutangula germplasm could benefit the ridge gourd breeding programs to meet the demands and needs of consumers, farmers, and vegetable exporters such as increasing the yield of fruit by the fruit width but not by the fruit length to solve the problem of fruit breakage during exportation.
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Balderston S, Taulbee JJ, Celaya E, Fung K, Jiao A, Smith K, Hajian R, Gasiunas G, Kutanovas S, Kim D, Parkinson J, Dickerson K, Ripoll JJ, Peytavi R, Lu HW, Barron F, Goldsmith BR, Collins PG, Conboy IM, Siksnys V, Aran K. Discrimination of single-point mutations in unamplified genomic DNA via Cas9 immobilized on a graphene field-effect transistor. Nat Biomed Eng 2021; 5:713-725. [PMID: 33820980 DOI: 10.1038/s41551-021-00706-z] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Accepted: 02/23/2021] [Indexed: 02/02/2023]
Abstract
Simple and fast methods for the detection of target genes with single-nucleotide specificity could open up genetic research and diagnostics beyond laboratory settings. We recently reported a biosensor for the electronic detection of unamplified target genes using liquid-gated graphene field-effect transistors employing an RNA-guided catalytically deactivated CRISPR-associated protein 9 (Cas9) anchored to a graphene monolayer. Here, using unamplified genomic samples from patients and by measuring multiple types of electrical response, we show that the biosensors can discriminate within one hour between wild-type and homozygous mutant alleles differing by a single nucleotide. We also show that biosensors using a guide RNA-Cas9 orthologue complex targeting genes within the protospacer-adjacent motif discriminated between homozygous and heterozygous DNA samples from patients with sickle cell disease, and that the biosensors can also be used to rapidly screen for guide RNA-Cas9 complexes that maximize gene-targeting efficiency.
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Affiliation(s)
- Sarah Balderston
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | | | | | - Kandace Fung
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | | | - Kasey Smith
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
| | - Reza Hajian
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | - Giedrius Gasiunas
- CasZyme, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | | | - Daehwan Kim
- University of California, Berkeley, Berkeley, CA, USA
| | | | | | | | | | - Hsiang-Wei Lu
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA
- Cardea, San Diego, CA, USA
| | | | | | | | | | - Virginijus Siksnys
- CasZyme, Vilnius, Lithuania
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Kiana Aran
- Keck Graduate Institute, The Claremont Colleges, Claremont, CA, USA.
- Cardea, San Diego, CA, USA.
- University of California, Berkeley, Berkeley, CA, USA.
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16
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Uba CU, Oselebe HO, Tesfaye AA, Abtew WG. Genetic diversity and population structure analysis of bambara groundnut (Vigna subterrenea L) landraces using DArT SNP markers. PLoS One 2021; 16:e0253600. [PMID: 34197522 PMCID: PMC8248626 DOI: 10.1371/journal.pone.0253600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 06/09/2021] [Indexed: 11/18/2022] Open
Abstract
Understanding the genetic structure and diversity of crops facilitates progress in plant breeding. A collection of 270 bambara groundnut (Vigna subterrenea L) landraces sourced from different geographical regions (Nigeria/Cameroon, West, Central, Southern and East Africa) and unknown origin (sourced from United Kingdom) was used to assess genetic diversity, relationship and population structure using DArT SNP markers. The major allele frequency ranged from 0.57 for unknown origin to 0.91 for West Africa region. The total gene diversity (0.482) and Shannon diversity index (0.787) was higher in West African accessions. The genetic distance between pairs of regions varied from 0.002 to 0.028 with higher similarity between Nigeria/Cameroon-West Africa accessions and East-Southern Africa accessions. The analysis of molecular variance (AMOVA) revealed 89% of genetic variation within population, 8% among regions and 3% among population. The genetic relatedness among the collections was evaluated using neighbor joining tree analysis, which grouped all the geographic regions into three major clusters. Three major subgroups of bambara groundnut were identified using the ADMIXTURE model program and confirmed by discriminant analysis of principal components (DAPC). These subgroups were West Africa, Nigeria/Cameroon and unknown origin that gave rise to sub-population one, and Central Africa was sub-population two, while Southern and East Africa were sub-population three. In general, the results of all the different analytical methods used in this study confirmed the existence of high level of diversity among the germplasm used in this study that might be utilized for future genetic improvement of bambara groundnut. The finding also provides new insight on the population structure of African bambara groundnut germplasm which will help in conservation strategy and management of the crop.
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Affiliation(s)
- Charles U. Uba
- Department of Horticulture and Plant Science, Jimma University, Jimma, Ethiopia
- * E-mail:
| | | | - Abush A. Tesfaye
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Wosene G. Abtew
- Department of Horticulture and Plant Science, Jimma University, Jimma, Ethiopia
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Bambara Groundnut (Vigna subterranea L. Verdc): A Crop for the New Millennium, Its Genetic Diversity, and Improvements to Mitigate Future Food and Nutritional Challenges. SUSTAINABILITY 2021. [DOI: 10.3390/su13105530] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The world’s food and agricultural schemes have gradually fallen into an alarming state due to challenges such as high population birth rates, diverse agro-climatic zones, a lack of measures to counter global warming, severe practices of sole-culture cultivation, and asset reduction. A very high dependency on limited staple food crops is associated with repetitious diets, deprivation of food, and shortages of trace minerals, which often causes dietary sicknesses. To ensure nutritious diets worldwide, a real-world and justifiable scheme is provided to garner extra attention towards variation in both agriculture/farming approaches and food habits. The EAT-Lancet statement emphasized an increase in agri-based diets as a way of attaining global generational health. Enlarging neglected crops with plenty of genomic stocks and potentially profitable attributes is a solution that could address food and nutritional security concerns. Bambara groundnut is one such imperative and neglected legume crop that contributes positively to improving global food and nutrient safety. As a “complete food”, this crop has recently been treated as a new millennium crop, and furthermore, it is more adjusted to poor soil and climatic conditions than other dominant crops. Bambara groundnut is a repository of vital nutrients that provides carbohydrates, crucial amino acids, proteins, and energy as well as minerals and vitamins to developed and low-income countries where animal proteins are not readily available. This review explores the potential of Bambara groundnut in ensuring food and nutrient security; its variables, production, processing, nutrient values, role in reducing the nutritional gap, and diverse uses; and attempts in improving its traits. To strengthen food production, an agricultural revolution is required for underutilized crop species to feed the ever-expanding population in the world. Henceforth, advanced plant-breeding procedures, such as next-generation breeding techniques, various molecular tools, TILLING, Eco-TILLING, proteomics, genomics, and transcriptomics (which has been used for major crops), also need to be practiced to intensify production. To boost productivity and to feed the most starved and malnourished populations of the world, it is assumed that the application of modern techniques will play a vital role in the advancement of the underutilized Bambara groundnut.
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Pandey AK, Rubiales D, Wang Y, Fang P, Sun T, Liu N, Xu P. Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:755-776. [PMID: 33433637 DOI: 10.1007/s00122-020-03751-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/10/2020] [Indexed: 05/09/2023]
Abstract
Pea (Pisum sativum L.), a cool-season legume crop grown in more than 85 countries, is the second most important grain legume and one of the major green vegetables in the world. While pea was historically studied as the genetic model leading to the discovery of the laws of genetics, pea research has lagged behind that of other major legumes in the genomics era, due to its large and complex genome. The evolving climate change and growing population have posed grand challenges to the objective of feeding the world, making it essential to invest research efforts to develop multi-omics resources and advanced breeding tools to support fast and continuous development of improved pea varieties. Recently, the pea researchers have achieved key milestones in omics and molecular breeding. The present review provides an overview of the recent important progress including the development of genetic resource databases, high-throughput genotyping assays, reference genome, genes/QTLs responsible for important traits, transcriptomic, proteomic, and phenomic atlases of various tissues under different conditions. These multi-faceted resources have enabled the successful implementation of various markers for monitoring early-generation populations as in marker-assisted backcrossing breeding programs. The emerging new breeding approaches such as CRISPR, speed breeding, and genomic selection are starting to change the paradigm of pea breeding. Collectively, the rich omics resources and omics-enable breeding approaches will enhance genetic gain in pea breeding and accelerate the release of novel pea varieties to meet the elevating demands on productivity and quality.
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Affiliation(s)
- Arun K Pandey
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
| | - Yonggang Wang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Pingping Fang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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Allan V, Vetriventhan M, Senthil R, Geetha S, Deshpande S, Rathore A, Kumar V, Singh P, Reddymalla S, Azevedo VCR. Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces. FRONTIERS IN PLANT SCIENCE 2020; 11:587426. [PMID: 33381130 PMCID: PMC7768014 DOI: 10.3389/fpls.2020.587426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/05/2020] [Indexed: 05/30/2023]
Abstract
Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.
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Affiliation(s)
- Victor Allan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramachandran Senthil
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - S. Geetha
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinod Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prabhat Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surender Reddymalla
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vânia C. R. Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Santos C, Martins D, Rubiales D, Vaz Patto MC. Partial Resistance Against Erysiphe pisi and E. trifolii Under Different Genetic Control in Lathyrus cicera: Outcomes from a Linkage Mapping Approach. PLANT DISEASE 2020; 104:2875-2884. [PMID: 32954987 DOI: 10.1094/pdis-03-20-0513-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Powdery mildew infections are among the most severe foliar biotrophic fungal diseases in grain legumes. Several accessions of Lathyrus cicera (chickling pea) show levels of partial resistance to Erysiphe pisi, the causal agent of pea powdery mildew, and to E. trifolii, a powdery mildew pathogen recently confirmed to infect pea and Lathyrus spp. Nevertheless, the underlying L. cicera resistance mechanisms against powdery mildews are poorly understood. To unveil the genetic control of resistance against powdery mildews in L. cicera, a recombinant inbred line population segregating for response to both species was used in resistance linkage analysis. An improved L. cicera genetic linkage map was used in this analysis. The new higher-density linkage map contains 1,468 polymorphic loci mapped on seven major and two minor linkage groups, covering a total of 712.4 cM. The percentage of the leaf area affected by either E. pisi or E. trifolii was recorded in independent screenings of the recombinant inbred line population, identifying a continuous range of resistance-susceptibility responses. Distinct quantitative trait loci (QTLs) for partial resistance against each pathogen were identified, suggesting different genetic bases are involved in the response to E. pisi and E. trifolii in L. cicera. Moreover, through comparative mapping of L. cicera QTL regions with the pea reference genome, candidate genes and pathways involved in resistance against powdery mildews were identified. This study extended the previously available genetic and genomic tools in Lathyrus species, providing clues about diverse powdery mildew resistance mechanisms useful for future resistance breeding of L. cicera and related species.
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Affiliation(s)
- Carmen Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Davide Martins
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal
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21
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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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van Deventer R, Rhode C, Marx M, Roodt-Wilding R. The development of genome-wide single nucleotide polymorphisms in blue wildebeest using the DArTseq platform. Genomics 2020; 112:3455-3464. [PMID: 32574831 DOI: 10.1016/j.ygeno.2020.04.032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/24/2020] [Accepted: 04/17/2020] [Indexed: 12/30/2022]
Abstract
Blue wildebeest (Connochaetes taurinus taurinus) are economically important antelope that are widely utilised in the South African wildlife industry. However, very few genomic resources are available for blue wildebeest that can assist in breeding management and facilitate research. This study aimed to develop a set of genome-wide single nucleotide polymorphism (SNP) markers for blue wildebeest. The DArTseq genotyping platform, commonly used in polyploid plant species, was selected for SNP discovery. A limited number of published articles have described the use of the DArTseq platform in animals and, therefore, this study also provided a unique opportunity to assess the performance of the DArTseq platform in an animal species. A total of 20,563 SNPs, each located within a 69 bp sequence, were generated. The developed SNP markers had a high average scoring reproducibility (>99%) and a low percentage missing data (~9.21%) compared to other reduced representation sequencing approaches that have been used in animal studies. Furthermore, the number of candidate SNPs per nucleotide position decreased towards the 3' end of sequence reads, and the ratio of transitions (Ts) to transversions (Tv) remained similar for each read position. These observations indicate that there was no read position bias, such as the identification of false SNPs due to low sequencing quality, towards the tail-end of sequencing reads. The DArTseq platform was also successful in identifying a large number of informative SNPs with desirable polymorphism parameters such as a high minor allele frequency (MAF). The Bos taurus genome was used for the in silico mapping of the marker sequences and a total of 6020 (29.28%) sequences were successfully mapped against the bovine genome. The marker sequences mapped to all of the bovine chromosomes establishing the genome-wide distribution of the SNPs. Moreover, the high observed Ts:Tv ratio (2.84:1) indicate that the DArTseq platform targeted gene-rich regions of the blue wildebeest genome. Finally, functional annotation of the marker sequences revealed a wide range of different putative functions indicating that these SNP markers can be useful in functional gene studies. The DArTseq platform, therefore, represents a high-throughput, robust and cost-effective genotyping platform, which may find adoption in several other African antelope and animal species.
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Affiliation(s)
- Riana van Deventer
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa; Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Clint Rhode
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
| | - Munro Marx
- Unistel Medical Laboratories (Pty) Ltd, Parow North 7500, South Africa.
| | - Rouvay Roodt-Wilding
- Department of Genetics, Stellenbosch University, Stellenbosch 7602, South Africa.
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Rivera-Colón AG, Rochette NC, Catchen JM. Simulation with RADinitio improves RADseq experimental design and sheds light on sources of missing data. Mol Ecol Resour 2020; 21:363-378. [PMID: 32275349 DOI: 10.1111/1755-0998.13163] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/25/2020] [Indexed: 12/20/2022]
Abstract
Restriction-site associated DNA sequencing (RADseq) has become a powerful and versatile tool in modern population genomics, enabling large-scale evolutionary and genomic analyses in otherwise inaccessible biological systems. With its widespread use, different variants on the protocol have been developed to suit specific experimental needs. Researchers face the challenge of choosing the optimal molecular and sequencing protocols for their reduced representation experimental design, an often-complicated process. Strategic errors can lead to biased data generation that has reduced power to answer biological questions. Here, we present RADinitio, simulation software for the selection and optimization of RADseq experiments via the generation of sequencing data that behave similarly to empirical sources. RADinitio provides an evolutionary simulation of populations, implementation of various RADseq protocols with customizable parameters, and thorough assessment of missing data. We test the efficacy of the software using different RAD protocols across several organisms, highlighting the importance of protocol selection on the magnitude and quality of data acquired. Additionally, we test the effects of RAD library preparation and sequencing on allelic dropout, observing that library preparation and sequencing often contributes more to missing alleles than population-level variation.
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Affiliation(s)
- Angel G Rivera-Colón
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
| | - Nicolas C Rochette
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
| | - Julian M Catchen
- Department of Evolution, Ecology and Behavior, University of Illinois, Urbana, Illinois, USA
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Barilli E, Carrillo-Perdomo E, Cobos MJ, Kilian A, Carling J, Rubiales D. Identification of potential candidate genes controlling pea aphid tolerance in a Pisum fulvum high-density integrated DArTseq SNP-based genetic map. PEST MANAGEMENT SCIENCE 2020; 76:1731-1742. [PMID: 31758624 DOI: 10.1002/ps.5696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/08/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Pea (Pisum sativum) is one of the most important temperate grain legumes in the world, and its production is severely constrained by the pea aphid (Acyrthosiphon pisum). Wild relatives, such as P. fulvum, are valuable sources of allelic diversity to improve the genetic resistance of cultivated pea species against A. pisum attack. To unravel the genetic control underlying resistance to the pea aphid attack, a quantitative trait loci (QTL) analysis was performed using the previously developed high density integrated genetic linkage map originated from an intraspecific recombinant inbred line (RIL) population (P. fulvum: IFPI3260 × IFPI3251). RESULTS We accurately evaluated specific resistance responses to pea aphid that allowed the identification, for the first time, of genomic regions that control plant damage and aphid reproduction. Eight QTLs associated with tolerance to pea aphid were identified in LGs I, II, III, IV and V, which individually explained from 17.0% to 51.2% of the phenotypic variation depending on the trait scored, and as a whole from 17.0% to 88.6%. The high density integrated genetic linkage map also allowed the identification of potential candidate genes co-located with the QTLs identified. CONCLUSIONS Our work shows how the survival of P. fulvum after the pea aphid attack depends on the triggering of a multi-component protection strategy that implies a quantitative tolerance. The genomic regions associated with the tolerance responses of P. fulvum during A. pisum infestation have provided six potential candidate genes that could be useful in marker-assisted selection (MAS) and genomic assisted breeding (GAB) after functional validation in the future. © 2019 Society of Chemical Industry.
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Affiliation(s)
| | - Estefanía Carrillo-Perdomo
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
- Current address: Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | | | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
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Maximising recombination across macadamia populations to generate linkage maps for genome anchoring. Sci Rep 2020; 10:5048. [PMID: 32193408 PMCID: PMC7081209 DOI: 10.1038/s41598-020-61708-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/24/2020] [Indexed: 01/02/2023] Open
Abstract
The Proteaceae genus Macadamia has a recent history of domestication as a commercial nut crop. We aimed to establish the first sequence-based haploid-correlated reference genetic linkage maps for this primarily outcrossing perennial tree crop, with marker density suitable for genome anchoring. Four first generation populations were used to maximise the segregation patterns available within full-sib, biparental and self-pollinated progeny. This allowed us to combine segregation data from overlapping subsets of >4,000 informative sequence-tagged markers to increase the effective coverage of the karyotype represented by the recombinant crossover events detected. All maps had 14 linkage groups, corresponding to the Macadamia haploid chromosome number, and enabled the anchoring and orientation of sequence scaffolds to construct a pseudo-chromosomal genome assembly for macadamia. Comparison of individual maps indicated a high level of congruence, with minor discrepancies satisfactorily resolved within the integrated maps. The combined set of maps significantly improved marker density and the proportion (70%) of the genome sequence assembly anchored. Overall, increasing our understanding of the genetic landscape and genome for this nut crop represents a substantial advance in macadamia genetics and genomics. The set of maps, large number of sequence-based markers and the reconstructed genome provide a toolkit to underpin future breeding that should help to extend the macadamia industry as well as provide resources for the long term conservation of natural populations in eastern Australia of this unique genus.
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26
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Aznar-Fernández T, Barilli E, Cobos MJ, Kilian A, Carling J, Rubiales D. Identification of quantitative trait loci (QTL) controlling resistance to pea weevil (Bruchus pisorum) in a high-density integrated DArTseq SNP-based genetic map of pea. Sci Rep 2020; 10:33. [PMID: 31913335 PMCID: PMC6949260 DOI: 10.1038/s41598-019-56987-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 12/19/2019] [Indexed: 12/22/2022] Open
Abstract
Pea weevil (Bruchus pisorum) is a damaging insect pest affecting pea (Pisum sativum) production worldwide. No resistant cultivars are available, although some levels of incomplete resistance have been identified in Pisum germplasm. To decipher the genetic control underlying the resistance previously identify in P. sativum ssp. syriacum, a recombinant inbred line (RIL F8:9) population was developed. The RIL was genotyped through Diversity Arrays Technology PL's DArTseq platform and screened under field conditions for weevil seed infestation and larval development along 5 environments. A newly integrated genetic linkage map was generated with a subset of 6,540 markers, assembled into seven linkage groups, equivalent to the number of haploid pea chromosomes. An accumulated distance of 2,503 cM was covered with an average density of 2.61 markers cM-1. The linkage map allowed the identification of three QTLs associated to reduced seed infestation along LGs I, II and IV. In addition, a QTL for reduced larval development was also identified in LGIV. Expression of these QTLs varied with the environment, being particularly interesting QTL BpSI.III that was detected in most of the environments studied. This high-saturated pea genetic map has also allowed the identification of seven potential candidate genes co-located with QTLs for marker-assisted selection, providing an opportunity for breeders to generate effective and sustainable strategies for weevil control.
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Affiliation(s)
| | - Eleonora Barilli
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain.
| | - María J Cobos
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain
| | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari St. Bruce, ACT2617, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Kirinari St. Bruce, ACT2617, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, E-14004, Spain
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Pratap A, Das A, Kumar S, Gupta S. Current Perspectives on Introgression Breeding in Food Legumes. FRONTIERS IN PLANT SCIENCE 2020; 11:589189. [PMID: 33552095 PMCID: PMC7858677 DOI: 10.3389/fpls.2020.589189] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/03/2020] [Indexed: 05/22/2023]
Abstract
Food legumes are important for defeating malnutrition and sustaining agri-food systems globally. Breeding efforts in legume crops have been largely confined to the exploitation of genetic variation available within the primary genepool, resulting in narrow genetic base. Introgression as a breeding scheme has been remarkably successful for an array of inheritance and molecular studies in food legumes. Crop wild relatives (CWRs), landraces, and exotic germplasm offer great potential for introgression of novel variation not only to widen the genetic base of the elite genepool for continuous incremental gains over breeding cycles but also to discover the cryptic genetic variation hitherto unexpressed. CWRs also harbor positive quantitative trait loci (QTLs) for improving agronomic traits. However, for transferring polygenic traits, "specialized population concept" has been advocated for transferring QTLs from CWR into elite backgrounds. Recently, introgression breeding has been successful in developing improved cultivars in chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), peanut (Arachis hypogaea), lentil (Lens culinaris), mungbean (Vigna radiata), urdbean (Vigna mungo), and common bean (Phaseolus vulgaris). Successful examples indicated that the usable genetic variation could be exploited by unleashing new gene recombination and hidden variability even in late filial generations. In mungbean alone, distant hybridization has been deployed to develop seven improved commercial cultivars, whereas in urdbean, three such cultivars have been reported. Similarly, in chickpea, three superior cultivars have been developed from crosses between C. arietinum and Cicer reticulatum. Pigeonpea has benefited the most where different cytoplasmic male sterility genes have been transferred from CWRs, whereas a number of disease-resistant germplasm have also been developed in Phaseolus. As vertical gene transfer has resulted in most of the useful gene introgressions of practical importance in food legumes, the horizontal gene transfer through transgenic technology, somatic hybridization, and, more recently, intragenesis also offer promise. The gains through introgression breeding are significant and underline the need of bringing it in the purview of mainstream breeding while deploying tools and techniques to increase the recombination rate in wide crosses and reduce the linkage drag. The resurgence of interest in introgression breeding needs to be capitalized for development of commercial food legume cultivars.
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Affiliation(s)
- Aditya Pratap
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Arpita Das
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Shiv Kumar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Office, Rabat, Morocco
- *Correspondence: Sanjeev Gupta,
| | - Sanjeev Gupta
- ICAR-Indian Institute of Pulses Research, Kanpur, India
- Shiv Kumar,
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Kankanala P, Nandety RS, Mysore KS. Genomics of Plant Disease Resistance in Legumes. FRONTIERS IN PLANT SCIENCE 2019; 10:1345. [PMID: 31749817 PMCID: PMC6842968 DOI: 10.3389/fpls.2019.01345] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/27/2019] [Indexed: 05/15/2023]
Abstract
The constant interactions between plants and pathogens in the environment and the resulting outcomes are of significant importance for agriculture and agricultural scientists. Disease resistance genes in plant cultivars can break down in the field due to the evolution of pathogens under high selection pressure. Thus, the protection of crop plants against pathogens is a continuous arms race. Like any other type of crop plant, legumes are susceptible to many pathogens. The dawn of the genomic era, in which high-throughput and cost-effective genomic tools have become available, has revolutionized our understanding of the complex interactions between legumes and pathogens. Genomic tools have enabled a global view of transcriptome changes during these interactions, from which several key players in both the resistant and susceptible interactions have been identified. This review summarizes some of the large-scale genomic studies that have clarified the host transcriptional changes during interactions between legumes and their plant pathogens while highlighting some of the molecular breeding tools that are available to introgress the traits into breeding programs. These studies provide valuable insights into the molecular basis of different levels of host defenses in resistant and susceptible interactions.
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29
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Mayes S, Ho WK, Chai HH, Gao X, Kundy AC, Mateva KI, Zahrulakmal M, Hahiree MKIM, Kendabie P, Licea LCS, Massawe F, Mabhaudhi T, Modi AT, Berchie JN, Amoah S, Faloye B, Abberton M, Olaniyi O, Azam-Ali SN. Bambara groundnut: an exemplar underutilised legume for resilience under climate change. PLANTA 2019; 250:803-820. [PMID: 31267230 DOI: 10.1007/s00425-019-03191-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 05/16/2019] [Indexed: 05/18/2023]
Abstract
Bambara groundnut has the potential to be used to contribute more the climate change ready agriculture. The requirement for nitrogen fixing, stress tolerant legumes is clear, particularly in low input agriculture. However, ensuring that existing negative traits are tackled and demand is stimulated through the development of markets and products still represents a challenge to making greater use of this legume. World agriculture is currently based on very limited numbers of crops, representing a significant risk to food supplies, particularly in the face of climate change which is expected to increase the frequency of extreme events. Minor and underutilised crops can help to develop a more resilient and nutritionally dense future agriculture. Bambara groundnut [Vigna subterranea (L.) Verdc.[, as a drought resistant, nitrogen-fixing, legume has a role to play. However, as with most underutilised crops, there are significant gaps in knowledge and also negative traits such as 'hard-to-cook' and 'photoperiod sensitivity to pod filling' associated with the crop which future breeding programmes and processing methods need to tackle, to allow it to make a significant contribution to the well-being of future generations. The current review assesses these factors and also considers what are the next steps towards realising the potential of this crop.
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Affiliation(s)
- Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK.
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia.
| | - Wai Kuan Ho
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Hui Hui Chai
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Xiuqing Gao
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Aloyce C Kundy
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Kumbirai I Mateva
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | | | | | - Presidor Kendabie
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Luis C S Licea
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
| | - Festo Massawe
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
| | - Tafadzwanashe Mabhaudhi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Albert T Modi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Private Bag X01, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Joseph N Berchie
- CSIR-Crop Research Institute, P.O. Box 3785, Fumesua, Kumasi, Ghana
| | - Stephen Amoah
- CSIR-Crop Research Institute, P.O. Box 3785, Fumesua, Kumasi, Ghana
| | - Ben Faloye
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- School of Biosciences, University of Nottingham Malaysia, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
- Genetic Resources Centre, International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Michael Abberton
- Genetic Resources Centre, International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Oyatomi Olaniyi
- Genetic Resources Centre, International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Sayed N Azam-Ali
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire, LE12 5RD, UK
- Crops For the Future, Jalan Broga, 43500, Semenyih, Selangor, Malaysia
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Raggi L, Caproni L, Carboni A, Negri V. Genome-Wide Association Study Reveals Candidate Genes for Flowering Time Variation in Common Bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2019; 10:962. [PMID: 31428109 PMCID: PMC6689981 DOI: 10.3389/fpls.2019.00962] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/10/2019] [Indexed: 05/13/2023]
Abstract
The common bean is one of the most important staples in many areas of the world. Extensive phenotypic and genetic characterization of unexplored bean germplasm are still needed to unlock the breeding potential of this crop. Dissecting genetic control of flowering time is of pivotal importance to foster common bean breeding and to develop new varieties able to adapt to changing climatic conditions. Indeed, flowering time strongly affects yield and plant adaptation ability. The aim of this study was to investigate the genetic control of days to flowering using a whole genome association approach on a panel of 192 highly homozygous common bean genotypes purposely developed from landraces using Single Seed Descent. The phenotypic characterization was carried out at two experimental sites throughout two growing seasons, using a randomized partially replicated experimental design. The same plant material was genotyped using double digest Restriction-site Associated DNA sequencing producing, after a strict quality control, a dataset of about 50 k Single Nucleotide Polymorphisms (SNPs). The Genome-Wide Association Study revealed significant and meaningful associations between days to flowering and several SNP markers; seven genes are proposed as the best candidates to explain the detected associations.
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Affiliation(s)
- Lorenzo Raggi
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Leonardo Caproni
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
| | - Andrea Carboni
- CREA Research Centre for Cereal and Industrial Crops, Bologna, Italy
| | - Valeria Negri
- Dipartimento di Scienze Agrarie, Alimentari e Ambientali (DSA3), Università degli Studi di Perugia, Perugia, Italy
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31
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Coyne CJ, Porter LD, Boutet G, Ma Y, McGee RJ, Lesné A, Baranger A, Pilet-Nayel ML. Confirmation of Fusarium root rot resistance QTL Fsp-Ps 2.1 of pea under controlled conditions. BMC PLANT BIOLOGY 2019; 19:98. [PMID: 30866817 PMCID: PMC6417171 DOI: 10.1186/s12870-019-1699-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/28/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Dry pea production has increased substantially in North America over the last few decades. With this expansion, significant yield losses have been attributed to an escalation in Fusarium root rots in pea fields. Among the most significant rot rotting pathogenic fungal species, Fusarium solani fsp. pisi (Fsp) is one of the main causal agents of root rot of pea. High levels of partial resistance to Fsp has been identified in plant genetic resources. Genetic resistance offers one of the best solutions to control this root rotting fungus. A recombinant inbred population segregating for high levels of partial resistance, previously single nucleotide polymorphism (SNP) genotyped using genotyping-by-sequencing, was phenotyped for disease reaction in replicated and repeated greenhouse trials. Composite interval mapping was deployed to identify resistance-associated quantitative trait loci (QTL). RESULTS Three QTL were identified using three disease reaction criteria: root disease severity, ratios of diseased vs. healthy shoot heights and dry plant weights under controlled conditions using pure cultures of Fusarium solani fsp. pisi. One QTL Fsp-Ps 2.1 explains 44.4-53.4% of the variance with a narrow confidence interval of 1.2 cM. The second and third QTL Fsp-Ps3.2 and Fsp-Ps3.3 are closely linked and explain only 3.6-4.6% of the variance. All of the alleles are contributed by the resistant parent PI 180693. CONCLUSION With the confirmation of Fsp-Ps 2.1 now in two RIL populations, SNPs associated with this region make a good target for marker-assisted selection in pea breeding programs to obtain high levels of partial resistance to Fusarium root rot caused by Fusarium solani fsp. pisi.
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Affiliation(s)
- Clarice J. Coyne
- USDA-ARS Plant Germplasm Introduction & Testing Research, Washington State University, Pullman, WA 99164 USA
| | - Lyndon D. Porter
- USDA-ARS Grain Legume Genetics & Physiology Research, 24106 N. Bunn Road, Prosser, WA 99350 USA
| | - Gilles Boutet
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
| | - Yu Ma
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Rebecca J. McGee
- USDA-ARS, Grain Legume Genetics & Physiology Research, Pullman, WA 99164 USA
| | - Angélique Lesné
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
| | - Alain Baranger
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
| | - Marie-Laure Pilet-Nayel
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
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Zheng Y, Xu F, Li Q, Wang G, Liu N, Gong Y, Li L, Chen ZH, Xu S. QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing. Front Genet 2018; 9:615. [PMID: 30568674 PMCID: PMC6290080 DOI: 10.3389/fgene.2018.00615] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 11/23/2018] [Indexed: 12/04/2022] Open
Abstract
Leaf shape is an important trait that influences the utilization rate of light, and affects quality and yield of pea (Pisum sativum). In the present study, a joint method of high-density genetic mapping using specific locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was applied to rapidly detect loci with leaf shape traits. A total of 7,146 polymorphic SLAFs containing 12,213 SNP markers were employed to construct a high-density genetic map for pea. We conducted quantitative trait locus (QTL) mapping on an F2 population to identify QTLs associated with leaf shape traits. Moreover, SLAF-BSA was conducted on the same F2 population to identify the single nucleotide polymorphism (SNP) markers linked to leaf shape in pea. Two QTLs (qLeaf_or-1, qLeaf_or-2) were mapped on linkage group 7 (LG7) for pea leaf shape. Through alignment of SLAF markers with Cicer arietinum, Medicago truncatula, and Glycine max, the pea LGs were assigned to their corresponding homologous chromosomal groups. The comparative genetic analysis showed that pea is more closely related to M. truncatula. Based on the sequencing results of two pools with different leaf shape, 179 associated markers were obtained after association analysis. The joint analysis of SLAF-seq and BSA showed that the QTLs obtained from mapping on a high-density genetic map are convincing due to the closely associated map region with the BSA results, which provided more potential markers related to leaf shape. Thus, the identified QTLs could be used in marker-assisted selection for pea breeding in the future. Our study revealed that joint analysis of QTL mapping on a high-density genetic map and BSA-seq is a cost-effective and accurate method to reveal genetic architecture of target traits in plant species without a reference genome.
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Affiliation(s)
- Yuanting Zheng
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Fei Xu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qikai Li
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Gangjun Wang
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Na Liu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Yaming Gong
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Lulu Li
- College of Agriculture & Biotechnology, Zhejiang University, Hangzhou, China
| | - Zhong-Hua Chen
- School of Science and Health, Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, Australia
| | - Shengchun Xu
- Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou, China
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