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Itoo H, Shah RA, Qurat S, Jeelani A, Khursheed S, Bhat ZA, Mir MA, Rather GH, Zargar SM, Shah MD, Padder BA. Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut ( Juglans regia L.). 3 Biotech 2023; 13:136. [PMID: 37124992 PMCID: PMC10130282 DOI: 10.1007/s13205-023-03563-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 04/15/2023] [Indexed: 05/02/2023] Open
Abstract
In the present study, we designed and validated genome-wide polymorphic SSR markers (110 SSRs) by mining the walnut genome. A total of 198,924 SSR loci were identified. Among these, successful primers were designed for 162,594 (81.73%) SSR loci. Dinucleotides were the most predominant accounting for 88.40% (175,075) of total SSRs. The SSR frequency was 377.312 SSR/Mb and it showed a decreasing trend from dinucleotide to octanucleotide motifs. We identified 20 highly polymorphic SSR markers and used them to genotype 72 walnut accessions. Over all, we obtained 118 alleles that ranged from 2 to 12 with an average value of 5.9. The higher SSR PIC values indicate their robustness in discriminating walnut genotypes. Heat map, PCA, and population structure categorized 72 walnut genotypes into 2 distinct clusters. The genetic variation within population was higher than among population as inferred by analysis of molecular variance (AMOVA). For walnut improvement, it is necessary to have a large repository of SSRs with high discriminative power. The present study reports 150,000 SSRs, which is the largest SSR repository for this important nut crop. Scientific communities may use this repository for walnut improvement such as QTL mapping, genetic studies, linkage map construction, and marker-assisted selection. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03563-6.
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Affiliation(s)
- H. Itoo
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Rafiq Ahmad Shah
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - S. Qurat
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Afnan Jeelani
- Division of Fruit Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - Sheikh Khursheed
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Zahoor A. Bhat
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - M. A. Mir
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - G. H. Rather
- Ambri Apple Research Centre, Pahnoo Shopian, Sheri-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, J&K 192303 India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Faculty of Horticulture, Shalimar, Kashmir, Srinagar, J&K 190 025 India
| | - M. D. Shah
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
| | - Bilal A. Padder
- Plant Virology and Molecular Plant Pathology Laboratory, Division of Plant Pathology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Kashmir, 190 025 Srinagar, J&K India
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Gupta C, Salgotra RK, Damm U, Rajeshkumar KC. Phylogeny and pathogenicity of Colletotrichum lindemuthianum causing anthracnose of Phaseolus vulgaris cv. Bhaderwah-Rajmash from northern Himalayas, India. 3 Biotech 2022; 12:169. [PMID: 35845112 PMCID: PMC9279525 DOI: 10.1007/s13205-022-03216-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 05/27/2022] [Indexed: 11/24/2022] Open
Abstract
With an annual loss of up to 100%, anthracnose caused by Colletotrichum is one of the most devastating diseases of common beans (Phaseolus vulgaris L.). Due to few distinctive morphological characters, Colletotrichum species are frequently misidentified. In India, several Colletotrichum species have been reported as pathogens of Phaseolus species, but none had previously been validated by means of molecular tools. In this study, we studied Colletotrichum strains from common beans cv. Bhaderwah-Rajmash from the northern Himalayas of India based on both morphological and DNA sequence data of six loci, namely ITS, gapdh, chs-1, his3, act, tub2. The strains were identified as C. lindemuthianum that belongs to the C. orbiculare species complex. Representative C. lindemuthianum strains tested on Phaseolus vulgaris cv. Bhaderwah-Rajmash were pathogenic and exhibited variation in symptomology and disease progression. By identifying the causal agent, we provided substantial information to develop the best control strategies for anthracnose of Phaseolus vulgaris from the northern Himalayas of India. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03216-0.
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Nabi A, Lateef I, Nisa Q, Banoo A, Rasool RS, Shah MD, Ahmad M, Padder BA. Phaseolus vulgaris-Colletotrichum lindemuthianum Pathosystem in the Post-Genomic Era: An Update. Curr Microbiol 2022; 79:36. [PMID: 34982236 DOI: 10.1007/s00284-021-02711-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Accepted: 10/27/2021] [Indexed: 11/24/2022]
Abstract
Phaseolus vulgaris-Colletotrichum lindemuthianum is one among the oldest host and pathogen interface. Researchers have taken painstaking efforts across the world for understanding the dialogue during early and late phases of interaction. Collectively, these efforts resulted in the deluge of information that helped the researchers to underpin the interface. The latest molecular biology techniques furnished novel detection methods for the anthracnose pathogen, refined the understanding of pathogen population dynamics, and provided the insights on co-evolutionary common bean resistance and C. lindemuthianum virulence dynamics. One of the important breakthroughs came when the Phaseolus vulgaris and its corresponding anthracnose pathogen (C. lindemuthianum) genomes were decoded in 2014 and 2017, respectively. Availability of both the genomes yielded a significant genomic information that helped bean communities to fine map the economically important traits and to identify the pathogenicity determinants and effector molecules. The interface is in a continuous development as knowledge of the anthracnose resistance genes, their precise physical locations, and the identification of effector proteins; the fungus arsenals are being routinely updated. Hence, we revisited the interface and tried to provide an overview of host pathogen dialogue in the genomic era. Additionally, we compiled the sporadic information on this pathosystem from India and provided its futuristic road map to shape its research in the world and northern India, the major dry bean area in the country.
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Affiliation(s)
- Aasiya Nabi
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Irtifa Lateef
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Qadrul Nisa
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Aqleema Banoo
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Rovidha S Rasool
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - M D Shah
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Mushtaq Ahmad
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India
| | - Bilal A Padder
- Plant Virology and Molecular Plant Pathology Laboratory, SKUAST-Kashmir, Shalimar, Srinagar, 190025, India.
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Nagel JH, Cruywagen EM, Machua J, Wingfield MJ, Slippers B. Highly transferable microsatellite markers for the genera Lasiodiplodia and Neofusicoccum. FUNGAL ECOL 2020. [DOI: 10.1016/j.funeco.2019.100903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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