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Pan J, Li X, Fu C, Bian J, Wang Z, Yu C, Liu X, Wang G, Tian R, Song X, Li C, Xia H, Zhao S, Hou L, Gao M, Zi H, Bertioli D, Leal-Bertioli S, Pandey MK, Wang X, Zhao C. High-density bin-based genetic map reveals a 530-kb chromosome segment derived from wild peanut contributing to late leaf spot resistance. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:69. [PMID: 38441650 DOI: 10.1007/s00122-024-04580-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
KEY MESSAGE Twenty-eight QTLs for LLS disease resistance were identified using an amphidiploid constructed mapping population, a favorable 530-kb chromosome segment derived from wild species contributes to the LLS resistance. Late leaf spot (LLS) is one of the major foliar diseases of peanut, causing serious yield loss and affecting the quality of kernel and forage. Some wild Arachis species possess higher resistance to LLS as compared with cultivated peanut; however, ploidy level differences restrict utilization of wild species. In this study, a synthetic amphidiploid (Ipadur) of wild peanuts with high LLS resistance was used to cross with Tifrunner to construct TI population. In total, 200 recombinant inbred lines were collected for whole-genome resequencing. A high-density bin-based genetic linkage map was constructed, which includes 4,809 bin markers with an average inter-bin distance of 0.43 cM. The recombination across cultivated and wild species was unevenly distributed, providing a novel recombination landscape for cultivated-wild Arachis species. Using phenotyping data collected across three environments, 28 QTLs for LLS disease resistance were identified, explaining 4.35-20.42% of phenotypic variation. The major QTL located on chromosome 14, qLLS14.1, could be consistently detected in 2021 Jiyang and 2022 Henan with 20.42% and 12.12% PVE, respectively. A favorable 530-kb chromosome segment derived from Ipadur was identified in the region of qLLS14.1, in which 23 disease resistance proteins were located and six of them showed significant sequence variations between Tifrunner and Ipadur. Allelic variation analysis indicating the 530-kb segment of wild species might contribute to the disease resistance of LLS. These associate genomic regions and candidate resistance genes are of great significance for peanut breeding programs for bringing durable resistance through pyramiding such multiple LLS resistance loci into peanut cultivars.
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Affiliation(s)
- Jiaowen Pan
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaojie Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Chun Fu
- Weifang Academy of Agricultural Sciences, Weifang, 261071, People's Republic of China
| | - Jianxin Bian
- Institute of Advanced Agricultural Science, Peking University, Weifang, 261071, People's Republic of China
| | - Zhenyu Wang
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, People's Republic of China
| | - Conghui Yu
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaoqin Liu
- Institute of Advanced Agricultural Science, Peking University, Weifang, 261071, People's Republic of China
| | - Guanghao Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Ruizheng Tian
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Xiaofeng Song
- Weifang Academy of Agricultural Sciences, Weifang, 261071, People's Republic of China
| | - Changsheng Li
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - Han Xia
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Shuzhen Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Lei Hou
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Meng Gao
- Institute of Plant Protection, Henan Academy of Agricultural Sciences, Zhengzhou, 450000, People's Republic of China
| | - Hailing Zi
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
| | - David Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Soraya Leal-Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30602, USA
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Xingjun Wang
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China
| | - Chuanzhi Zhao
- Institute of Crop Germplasm Resources (Institute of Biotechnology), Shandong Academy of Agricultural Sciences, Jinan, 250100, People's Republic of China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, People's Republic of China.
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Chen YJ, Pandey S, Catto M, Leal-Bertioli S, Abney MR, Bag S, Hopkins M, Culbreath A, Srinivasan R. Evaluation of Wild Peanut Species and Their Allotetraploids for Resistance against Thrips and Thrips-Transmitted Tomato Spotted Wilt Orthotospovirus (TSWV). Pathogens 2023; 12:1102. [PMID: 37764910 PMCID: PMC10536083 DOI: 10.3390/pathogens12091102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Thrips-transmitted tomato spotted wilt orthotospovirus (TSWV) causes spotted wilt disease in peanut (Arachis hypogaea L.) and limits yield. Breeding programs have been developing TSWV-resistant cultivars, but availability of sources of resistance against TSWV in cultivated germplasm is extremely limited. Diploid wild Arachis species can serve as important sources of resistance, and despite ploidy barriers (cultivated peanut is tetraploid), their usage in breeding programs is now possible because of the knowledge and development of induced interspecific allotetraploid hybrids. This study screened 10 wild diploid Arachis and six induced allotetraploid genotypes via thrips-mediated TSWV transmission assays and thrips' feeding assays in the greenhouse. Three parameters were evaluated: percent TSWV infection, virus accumulation, and temporal severity of thrips feeding injury. Results indicated that the diploid A. stenosperma accession V10309 and its derivative-induced allotetraploid ValSten1 had the lowest TSWV infection incidences among the evaluated genotypes. Allotetraploid BatDur1 had the lowest thrips-inflicted damage at each week post thrips release, while diploid A. batizocoi accession K9484 and A. duranensis accession V14167 had reduced feeding damage one week post thrips release, and diploids A. valida accession GK30011 and A. batizocoi had reduced feeding damage three weeks post thrips releasethan the others. Overall, plausible TSWV resistance in diploid species and their allotetraploid hybrids was characterized by reduced percent TSWV infection, virus accumulation, and feeding severity. Furthermore, a few diploids and tetraploid hybrids displayed antibiosis against thrips. These results document evidence for resistance against TSWV and thrips in wild diploid Arachis species and peanut-compatible-induced allotetraploids.
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Affiliation(s)
- Yi-Ju Chen
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA; (Y.-J.C.); (S.P.)
| | - Sudeep Pandey
- Department of Entomology, University of Georgia, Griffin, GA 30223, USA; (Y.-J.C.); (S.P.)
| | - Michael Catto
- Department of Entomology, University of Georgia, Athens, GA 30602, USA;
| | - Soraya Leal-Bertioli
- Department of Plant Pathology, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Mark R. Abney
- Department of Entomology, University of Georgia, Tifton, GA 31794, USA;
| | - Sudeep Bag
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.B.); (A.C.)
| | - Mark Hopkins
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA 30602, USA;
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA 31793, USA; (S.B.); (A.C.)
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Ravikiran KT, Thribhuvan R, Sheoran S, Kumar S, Kushwaha AK, Vineeth TV, Saini M. Tailoring crops with superior product quality through genome editing: an update. PLANTA 2023; 257:86. [PMID: 36949234 DOI: 10.1007/s00425-023-04112-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 02/28/2023] [Indexed: 06/18/2023]
Abstract
In this review, using genome editing, the quality trait alterations in important crops have been discussed, along with the challenges encountered to maintain the crop products' quality. The delivery of economic produce with superior quality is as important as high yield since it dictates consumer's acceptance and end use. Improving product quality of various agricultural and horticultural crops is one of the important targets of plant breeders across the globe. Significant achievements have been made in various crops using conventional plant breeding approaches, albeit, at a slower rate. To keep pace with ever-changing consumer tastes and preferences and industry demands, such efforts must be supplemented with biotechnological tools. Fortunately, many of the quality attributes are resultant of well-understood biochemical pathways with characterized genes encoding enzymes at each step. Targeted mutagenesis and transgene transfer have been instrumental in bringing out desired qualitative changes in crops but have suffered from various pitfalls. Genome editing, a technique for methodical and site-specific modification of genes, has revolutionized trait manipulation. With the evolution of versatile and cost effective CRISPR/Cas9 system, genome editing has gained significant traction and is being applied in several crops. The availability of whole genome sequences with the advent of next generation sequencing (NGS) technologies further enhanced the precision of these techniques. CRISPR/Cas9 system has also been utilized for desirable modifications in quality attributes of various crops such as rice, wheat, maize, barley, potato, tomato, etc. The present review summarizes salient findings and achievements of application of genome editing for improving product quality in various crops coupled with pointers for future research endeavors.
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Affiliation(s)
- K T Ravikiran
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Lucknow, Uttar Pradesh, India
| | - R Thribhuvan
- ICAR-Central Research Institute for Jute and Allied Fibres, Barrackpore, West Bengal, India
| | - Seema Sheoran
- ICAR-Indian Agricultural Research Institute, Regional Station, Karnal, Haryana, India.
| | - Sandeep Kumar
- ICAR-Indian Institute of Natural Resins and Gums, Ranchi, Jharkhand, India
| | - Amar Kant Kushwaha
- ICAR-Central Institute for Subtropical Horticulture, Lucknow, Uttar Pradesh, India
| | - T V Vineeth
- ICAR-Central Soil Salinity Research Institute, Regional Research Station, Bharuch, Gujarat, India
- Department of Plant Physiology, College of Agriculture, Kerala Agricultural University, Vellanikkara, Thrissur, Kerala, India
| | - Manisha Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Ariyoshi C, Sant’ana GC, Felicio MS, Sera GH, Nogueira LM, Rodrigues LMR, Ferreira RV, da Silva BSR, de Resende MLV, Destéfano SAL, Domingues DS, Pereira LFP. Genome-wide association study for resistance to Pseudomonas syringae pv. garcae in Coffea arabica. FRONTIERS IN PLANT SCIENCE 2022; 13:989847. [PMID: 36330243 PMCID: PMC9624508 DOI: 10.3389/fpls.2022.989847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
Bacteria halo blight (BHB), a coffee plant disease caused by Pseudomonas syringae pv. garcae, has been gaining importance in producing mountain regions and mild temperatures areas as well as in coffee nurseries. Most Coffea arabica cultivars are susceptible to this disease. In contrast, a great source of genetic diversity and resistance to BHB are found in C. arabica Ethiopian accessions. Aiming to identify quantitative trait nucleotides (QTNs) associated with resistance to BHB and the influence of these genomic regions during the domestication of C. arabica, we conducted an analysis of population structure and a Genome-Wide Association Study (GWAS). For this, we used genotyping by sequencing (GBS) and phenotyping for resistance to BHB of a panel with 120 C. arabica Ethiopian accessions from a historical FAO collection, 11 C. arabica cultivars, and the BA-10 genotype. Population structure analysis based on single-nucleotide polymorphisms (SNPs) markers showed that the 132 accessions are divided into 3 clusters: most wild Ethiopian accessions, domesticated Ethiopian accessions, and cultivars. GWAS, using the single-locus model MLM and the multi-locus models mrMLM, FASTmrMLM, FASTmrEMMA, and ISIS EM-BLASSO, identified 11 QTNs associated with resistance to BHB. Among these QTNs, the four with the highest values of association for resistance to BHB are linked to g000 (Chr_0_434_435) and g010741 genes, which are predicted to encode a serine/threonine-kinase protein and a nucleotide binding site leucine-rich repeat (NBS-LRR), respectively. These genes displayed a similar transcriptional downregulation profile in a C. arabica susceptible cultivar and in a C. arabica cultivar with quantitative resistance, when infected with P. syringae pv. garcae. However, peaks of upregulation were observed in a C. arabica cultivar with qualitative resistance, for both genes. Our results provide SNPs that have potential for application in Marker Assisted Selection (MAS) and expand our understanding about the complex genetic control of the resistance to BHB in C. arabica. In addition, the findings contribute to increasing understanding of the C. arabica domestication history.
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Affiliation(s)
- Caroline Ariyoshi
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | - Mariane Silva Felicio
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
- Programa de pós-graduação em Ciências Biológicas (Genética), Universidade Estadual Paulista “Júlio de Mesquita Filho“ (UNESP), Instituto de Biociências, Campus de Botucatu, Botucatu, Brazil
| | - Gustavo Hiroshi Sera
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | - Livia Maria Nogueira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | - Rafaelle Vecchia Ferreira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | - Bruna Silvestre Rodrigues da Silva
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
| | | | | | - Douglas Silva Domingues
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo (USP), Piracicaba, Brazil
| | - Luiz Filipe Protasio Pereira
- Programa de pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Londrina (UEL), Centro de Ciâncias Biológicas, Londrina, Brazil
- Área de Melhoramento Genético e Propagação Vegetal, Instituto de Desenvolvimento Rural do Paraná (IDR-Paraná), Londrina, Brazil
- Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA-Café), Brasília, Brazil
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Biswas S, Wahl NJ, Thomson MJ, Cason JM, McCutchen BF, Septiningsih EM. Optimization of Protoplast Isolation and Transformation for a Pilot Study of Genome Editing in Peanut by Targeting the Allergen Gene Ara h 2. Int J Mol Sci 2022; 23:837. [PMID: 35055026 PMCID: PMC8775966 DOI: 10.3390/ijms23020837] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/09/2022] [Accepted: 01/10/2022] [Indexed: 12/22/2022] Open
Abstract
The cultivated peanut (Arachis hypogaea L.) is a legume consumed worldwide in the form of oil, nuts, peanut butter, and candy. Improving peanut production and nutrition will require new technologies to enable novel trait development. Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) is a powerful and versatile genome-editing tool for introducing genetic changes for studying gene expression and improving crops, including peanuts. An efficient in vivo transient CRISPR-Cas9- editing system using protoplasts as a testbed could be a versatile platform to optimize this technology. In this study, multiplex CRISPR-Cas9 genome editing was performed in peanut protoplasts to disrupt a major allergen gene with the help of an endogenous tRNA-processing system. In this process, we successfully optimized protoplast isolation and transformation with green fluorescent protein (GFP) plasmid, designed two sgRNAs for an allergen gene, Ara h 2, and tested their efficiency by in vitro digestion with Cas9. Finally, through deep-sequencing analysis, several edits were identified in our target gene after PEG-mediated transformation in protoplasts with a Cas9 and sgRNA-containing vector. These findings demonstrated that a polyethylene glycol (PEG)-mediated protoplast transformation system can serve as a rapid and effective tool for transient expression assays and sgRNA validation in peanut.
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Affiliation(s)
- Sudip Biswas
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
| | - Nancy J. Wahl
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
| | - Michael J. Thomson
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
| | - John M. Cason
- Texas A&M AgriLife Research and Extension Center at Stephenville, Stephenville, TX 76401, USA; (J.M.C.); (B.F.M.)
| | - Bill F. McCutchen
- Texas A&M AgriLife Research and Extension Center at Stephenville, Stephenville, TX 76401, USA; (J.M.C.); (B.F.M.)
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (S.B.); (N.J.W.); (M.J.T.)
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Mota APZ, Brasileiro ACM, Vidigal B, Oliveira TN, da Cunha Quintana Martins A, Saraiva MADP, de Araújo ACG, Togawa RC, Grossi-de-Sá MF, Guimaraes PM. Defining the combined stress response in wild Arachis. Sci Rep 2021; 11:11097. [PMID: 34045561 PMCID: PMC8160017 DOI: 10.1038/s41598-021-90607-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/11/2021] [Indexed: 02/04/2023] Open
Abstract
Nematodes and drought are major constraints in tropical agriculture and often occur simultaneously. Plant responses to these stresses are complex and require crosstalk between biotic and abiotic signaling pathways. In this study, we explored the transcriptome data of wild Arachis species subjected to drought (A-metaDEG) and the root-knot nematode Meloidogyne arenaria (B-metaDEG) via meta-analysis, to identify core-stress responsive genes to each individual and concurrent stresses in these species. Transcriptome analysis of a nematode/drought bioassay (cross-stress) showed that the set of stress responsive DEGs to concurrent stress is distinct from those resulting from overlapping A- and B-metaDEGs, indicating a specialized and unique response to combined stresses in wild Arachis. Whilst individual biotic and abiotic stresses elicit hormone-responsive genes, most notably in the jasmonic and abscisic acid pathways, combined stresses seem to trigger mainly the ethylene hormone pathway. The overexpression of a cross-stress tolerance candidate gene identified here, an endochitinase-encoding gene (AsECHI) from Arachis stenosperma, reduced up to 30% of M. incognita infection and increased post-drought recovery in Arabidopsis plants submitted to both stresses. The elucidation of the network of cross-stress responsive genes in Arachis contributes to better understanding the complex regulation of biotic and abiotic responses in plants facilitating more adequate crop breeding for combined stress tolerance.
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Affiliation(s)
- Ana Paula Zotta Mota
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.8532.c0000 0001 2200 7498Universidade Federal do Rio Grande do Sul, Porto Alegre, RS Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil ,grid.8183.20000 0001 2153 9871Present Address: CIRAD, UMR AGAP, 34398 Montpellier, France ,grid.463758.b0000 0004 0445 8705Present Address: AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Ana Cristina Miranda Brasileiro
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Bruna Vidigal
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Thais Nicolini Oliveira
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Andressa da Cunha Quintana Martins
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Mario Alfredo de Passos Saraiva
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Ana Claudia Guerra de Araújo
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Roberto C. Togawa
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
| | - Maria Fatima Grossi-de-Sá
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil ,grid.411952.a0000 0001 1882 0945Universidade Católica de Brasília (UCB)-Genomic Sciences and Biotechnology, Brasilia, DF Brazil
| | - Patricia Messenberg Guimaraes
- grid.460200.00000 0004 0541 873XEMBRAPA Recursos Geneticos e Biotecnologia, Brasilia, DF Brazil ,grid.468194.6National Institute of Science and Technology-INCT PlantStress Biotech-EMBRAPA, Brasilia, Brazil
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7
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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Mota APZ, Vidigal B, Danchin EGJ, Togawa RC, Leal-Bertioli SCM, Bertioli DJ, Araujo ACG, Brasileiro ACM, Guimaraes PM. Comparative root transcriptome of wild Arachis reveals NBS-LRR genes related to nematode resistance. BMC PLANT BIOLOGY 2018; 18:159. [PMID: 30081841 PMCID: PMC6080386 DOI: 10.1186/s12870-018-1373-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 07/26/2018] [Indexed: 05/08/2023]
Abstract
BACKGROUND The Root-Knot Nematode (RKN), Meloidogyne arenaria, significantly reduces peanut grain quality and yield worldwide. Whilst the cultivated species has low levels of resistance to RKN and other pests and diseases, peanut wild relatives (Arachis spp.) show rich genetic diversity and harbor high levels of resistance to many pathogens and environmental constraints. Comparative transcriptome analysis can be applied to identify candidate resistance genes. RESULTS Transcriptome analysis during the early stages of RKN infection of two peanut wild relatives, the highly RKN resistant Arachis stenosperma and the moderately susceptible A. duranensis, revealed genes related to plant immunity with contrasting expression profiles. These included genes involved in hormone signaling and secondary metabolites production and also members of the NBS-LRR class of plant disease resistance (R) genes. From 345 NBS-LRRs identified in A.duranensis reference genome, 52 were differentially expressed between inoculated and control samples, with the majority occurring in physical clusters unevenly distributed on eight chromosomes with preferential tandem duplication. The majority of these NBS-LRR genes showed contrasting expression behaviour between A. duranensis and A. stenosperma, particularly at 6 days after nematode inoculation, coinciding with the onset of the Hypersensitive Response in the resistant species. The physical clustering of some of these NBS-LRR genes correlated with their expression patterns in the contrasting genotypes. Four NBS-LRR genes exclusively expressed in A. stenosperma are located within clusters on chromosome Aradu. A09, which harbors a QTL for RKN resistance, suggesting a functional role for their physical arrangement and their potential involvement in this defense response. CONCLUSION The identification of functional novel R genes in wild Arachis species responsible for triggering effective defense cascades can contribute to the crop genetic improvement and enhance peanut resilience to RKN.
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Affiliation(s)
- Ana Paula Zotta Mota
- EMBRAPA Genetic Resources and Biotechnology, Brasilia, DF Brazil
- Universidade Federal do Rio Grande do Sul, Campus do Vale, Porto Alegre, RS Brazil
| | - Bruna Vidigal
- EMBRAPA Genetic Resources and Biotechnology, Brasilia, DF Brazil
| | | | | | | | - David John Bertioli
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia USA
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Clevenger J, Chu Y, Chavarro C, Botton S, Culbreath A, Isleib TG, Holbrook CC, Ozias-Akins P. Mapping Late Leaf Spot Resistance in Peanut ( Arachis hypogaea) Using QTL-seq Reveals Markers for Marker-Assisted Selection. FRONTIERS IN PLANT SCIENCE 2018; 9:83. [PMID: 29459876 PMCID: PMC5807350 DOI: 10.3389/fpls.2018.00083] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/15/2018] [Indexed: 05/21/2023]
Abstract
Late leaf spot (LLS; Cercosporidium personatum) is a major fungal disease of cultivated peanut (Arachis hypogaea). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools. Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.
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Affiliation(s)
- Josh Clevenger
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Ye Chu
- Department of Horticulture, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, United States
| | - Carolina Chavarro
- Center for Applied Genetic Technologies, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Stephanie Botton
- Department of Horticulture, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, United States
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
| | - Thomas G. Isleib
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - C. C. Holbrook
- United States Department of Agriculture-Agricultural Research Service, Tifton, GA, United States
| | - Peggy Ozias-Akins
- Department of Horticulture, Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Tifton, GA, United States
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Zhang X, Zhang J, He X, Wang Y, Ma X, Yin D. Genome-Wide Association Study of Major Agronomic Traits Related to Domestication in Peanut. FRONTIERS IN PLANT SCIENCE 2017; 8:1611. [PMID: 29018458 PMCID: PMC5623184 DOI: 10.3389/fpls.2017.01611] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 09/04/2017] [Indexed: 05/04/2023]
Abstract
Peanut (Arachis hypogaea) consists of two subspecies, hypogaea and fastigiata, and has been cultivated worldwide for hundreds of years. Here, 158 peanut accessions were selected to dissect the molecular footprint of agronomic traits related to domestication using specific-locus amplified fragment sequencing (SLAF-seq method). Then, a total of 17,338 high-quality single nucleotide polymorphisms (SNPs) in the whole peanut genome were revealed. Eleven agronomic traits in 158 peanut accessions were subsequently analyzed using genome-wide association studies (GWAS). Candidate genes responsible for corresponding traits were then analyzed in genomic regions surrounding the peak SNPs, and 1,429 genes were found within 200 kb windows centerd on GWAS-identified peak SNPs related to domestication. Highly differentiated genomic regions were observed between hypogaea and fastigiata accessions using FST values and sequence diversity (π) ratios. Among the 1,429 genes, 662 were located on chromosome A3, suggesting the presence of major selective sweeps caused by artificial selection during long domestication. These findings provide a promising insight into the complicated genetic architecture of domestication-related traits in peanut, and reveal whole-genome SNP markers of beneficial candidate genes for marker-assisted selection (MAS) in future breeding programs.
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