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Thomas WJW, Amas JC, Dolatabadian A, Huang S, Zhang F, Zandberg JD, Neik TX, Edwards D, Batley J. Recent advances in the improvement of genetic resistance against disease in vegetable crops. PLANT PHYSIOLOGY 2024; 196:32-46. [PMID: 38796840 PMCID: PMC11376385 DOI: 10.1093/plphys/kiae302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Revised: 04/10/2024] [Accepted: 05/15/2024] [Indexed: 05/29/2024]
Affiliation(s)
- William J W Thomas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Junrey C Amas
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Aria Dolatabadian
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Shuanglong Huang
- Department of Plant Science, University of Manitoba, Winnipeg, R3T 2N2, Canada
| | - Fangning Zhang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Jaco D Zandberg
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
| | - Ting Xiang Neik
- Department of Biological Sciences, National University of Singapore, Singapore, 117543, Republic of Singapore
- NUS Agritech Centre, National University of Singapore, Singapore, 118258, Republic of Singapore
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
- Centre for Applied Bioinformatics, The University of Western Australia, Perth, 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Perth, 6009, Australia
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Gurina AA, Gancheva MS, Alpatieva NV, Rogozina EV. In silico search for and analysis of R gene variation in primitive cultivated potato species. Vavilovskii Zhurnal Genet Selektsii 2024; 28:175-184. [PMID: 38680181 PMCID: PMC11043503 DOI: 10.18699/vjgb-24-21] [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: 07/16/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 05/01/2024] Open
Abstract
Pathogen recognition receptors encoded by R genes play a key role in plant protection. Nowadays, R genes are a basis for breeding many crops, including potato. Many potato R genes have been discovered and found suitable for breeding thanks to the studies of a wide variety of wild potato species. The use of primitive cultivated potato species (PCPS) as representatives of the primary gene pool can also be promising in this respect. PCPS are the closest to the early domesticated forms of potato; therefore, their investigation could help understand the evolution of R genes. The present study was aimed at identifying and analyzing R genes in PCPS listed in the open database of NCBI and Solomics DB. In total, the study involved 27 accessions belonging to three species: Solanum phureja Juz. & Bukasov, S. stenotomum Juz. & Bukasov and S. goniocalyx Juz. & Bukasov Materials for the analysis were the sequencing data for the said three species from the PRJNA394943 and PRJCA006011 projects. An in silico search was carried out for sequences homologous to 26 R genes identified in potato species differing in phylogenetic distance from PCPS, namely nightshade (S. americanum), North- (S. bulbocastanum, S. demissum) and South-American (S. venturii, S. berthaultii) wild potato species, as well as the cultivated potato species S. tuberosum and S. andigenum. Homologs of all investigated protein-coding sequences were discovered in PCPS with a relatively high degree of similarity (85-100 %). Homologs of the Rpi-R3b, Rpi-amr3 and Rpi-ber1 genes have been identified in PCPS for the first time. An analysis of polymorphism of nucleotide and amino acid sequences has been carried out for 15 R genes. The differences in frequencies of substitutions in PCPS have been demonstrated by analysis of R genes, the reference sequences of which have been identified in different species. For all the studied NBS-LRR genes, the proportion of substituted amino acids in the LRR domain exceeds this figure for the NBS domain. The potential prospects of using PCPS as sources of resistance to Verticillium wilt have been shown.
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Affiliation(s)
- A A Gurina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - M S Gancheva
- St. Petersburg State University, St. Petersburg, Russia
| | - N V Alpatieva
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - E V Rogozina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
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Martina M, De Rosa V, Magon G, Acquadro A, Barchi L, Barcaccia G, De Paoli E, Vannozzi A, Portis E. Revitalizing agriculture: next-generation genotyping and -omics technologies enabling molecular prediction of resilient traits in the Solanaceae family. FRONTIERS IN PLANT SCIENCE 2024; 15:1278760. [PMID: 38375087 PMCID: PMC10875072 DOI: 10.3389/fpls.2024.1278760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 01/22/2024] [Indexed: 02/21/2024]
Abstract
This review highlights -omics research in Solanaceae family, with a particular focus on resilient traits. Extensive research has enriched our understanding of Solanaceae genomics and genetics, with historical varietal development mainly focusing on disease resistance and cultivar improvement but shifting the emphasis towards unveiling resilience mechanisms in genebank-preserved germplasm is nowadays crucial. Collecting such information, might help researchers and breeders developing new experimental design, providing an overview of the state of the art of the most advanced approaches for the identification of the genetic elements laying behind resilience. Building this starting point, we aim at providing a useful tool for tackling the global agricultural resilience goals in these crops.
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Affiliation(s)
- Matteo Martina
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Valeria De Rosa
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Gabriele Magon
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Emanuele De Paoli
- Department of Agricultural, Food, Environmental and Animal Sciences (DI4A), University of Udine, Udine, Italy
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), Laboratory of Plant Genetics and Breeding, University of Padua, Legnaro, Italy
| | - Ezio Portis
- Department of Agricultural, Forest and Food Sciences (DISAFA), Plant Genetics, University of Torino, Grugliasco, Italy
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