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Anuradha C, Chandrasekar A, Backiyarani S, Uma S. MusaRgeneDB: an online comprehensive database for disease resistance genes in Musa spp. 3 Biotech 2022; 12:222. [PMID: 35971335 PMCID: PMC9374869 DOI: 10.1007/s13205-022-03285-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 07/28/2022] [Indexed: 02/05/2023] Open
Abstract
Banana is one of the major food crops and its production is subject to many pests and diseases. Banana breeding exploits wild relatives and progenitor species for the introgression of resistant genes (R) into cultivated varieties to overcome these hurdles. With advances in sequencing technologies, whole-genome sequences are available for many Musa spp. and many of them are potential donors of disease resistance genes. Considering their potential role, R genes from these species were explored to develop an user-friendly open-access database that will be useful for studying and implementing disease resistance in bananas. MusaRgene database is complemented with complete details of 3598 R genes identified from eight Musa spp. and rice, Arabidopsis, sorghum along with its classification and separate modules on its expression under various stresses in resistant and susceptible cultivars and corresponding SSRs are also provided. This database can be regarded as the primary resource of information on R genes from bananas and their relatives. R genes from other allele mining studies are also incorporated which will enable the identification of its homolog in related Musa spp. MusaRgene database will aid in the identification of genes and markers associated, cloning of full-length R genes, and genetic transformation or gene editing of the R genes in susceptible cultivars. Multiple R genes can also be identified for pyramiding the genes to increase the level of resistance and durability. Overall, this database will facilitate the understanding of defense mechanisms in bananas against biotic or abiotic stresses leading to the development of promising disease-resistant varieties.
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Affiliation(s)
- Chelliah Anuradha
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Arumugam Chandrasekar
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Suthanthiram Backiyarani
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
| | - Subbaraya Uma
- ICAR-National Research Centre for Banana, Thogamalai Road, Thayanur Post, Tiruchirappalli, Tamil Nadu 620 102 India
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Biswas MK, Bagchi M, Biswas D, Harikrishna JA, Liu Y, Li C, Sheng O, Mayer C, Yi G, Deng G. Genome-Wide Novel Genic Microsatellite Marker Resource Development and Validation for Genetic Diversity and Population Structure Analysis of Banana. Genes (Basel) 2020; 11:genes11121479. [PMID: 33317074 PMCID: PMC7763637 DOI: 10.3390/genes11121479] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/20/2020] [Accepted: 11/20/2020] [Indexed: 11/17/2022] Open
Abstract
Trait tagging through molecular markers is an important molecular breeding tool for crop improvement. SSR markers encoded by functionally relevant parts of a genome are well suited for this task because they may be directly related to traits. However, a limited number of these markers are known for Musa spp. Here, we report 35136 novel functionally relevant SSR markers (FRSMs). Among these, 17,561, 15,373 and 16,286 FRSMs were mapped in-silico to the genomes of Musa acuminata, M. balbisiana and M. schizocarpa, respectively. A set of 273 markers was validated using eight accessions of Musa spp., from which 259 markers (95%) produced a PCR product of the expected size and 203 (74%) were polymorphic. In-silico comparative mapping of FRSMs onto Musa and related species indicated sequence-based orthology and synteny relationships among the chromosomes of Musa and other plant species. Fifteen FRSMs were used to estimate the phylogenetic relationships among 50 banana accessions, and the results revealed that all banana accessions group into two major clusters according to their genomic background. Here, we report the first large-scale development and characterization of functionally relevant Musa SSR markers. We demonstrate their utility for germplasm characterization, genetic diversity studies, and comparative mapping in Musa spp. and other monocot species. The sequences for these novel markers are freely available via a searchable web interface called Musa Marker Database.
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Affiliation(s)
- Manosh Kumar Biswas
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- Correspondence: (M.K.B.); (G.D.)
| | - Mita Bagchi
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- The College of Economics and Managements, South China Agricultural University, Guangzhou 510640, China
| | - Dhiman Biswas
- Department of Computer Science and Engineering, Maulana Abul Kalam Azad University of Technology, West Bengal 700064, India;
| | - Jennifer Ann Harikrishna
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK; (M.B.); (J.A.H.)
- University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yuxuan Liu
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Chunyu Li
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Ou Sheng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany;
| | - Ganjun Yi
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
| | - Guiming Deng
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Tianhe District, Guangzhou 510640, China; (Y.L.); (C.L.); (O.S.); (G.Y.)
- Correspondence: (M.K.B.); (G.D.)
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MusatransSSRDB (a transcriptome derived SSR database) – An advanced tool for banana improvement. J Biosci 2019. [DOI: 10.1007/s12038-018-9819-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Awasthi P, Singh A, Sheikh G, Mahajan V, Gupta AP, Gupta S, Bedi YS, Gandhi SG. Mining and characterization of EST-SSR markers for Zingiber officinale Roscoe with transferability to other species of Zingiberaceae. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:925-931. [PMID: 29158639 PMCID: PMC5671454 DOI: 10.1007/s12298-017-0472-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 07/13/2017] [Accepted: 09/19/2017] [Indexed: 05/11/2023]
Abstract
Zingiber officinale is a model spice herb, well known for its medicinal value. It is primarily a vegetatively propagated commercial crop. However, considerable diversity in its morphology, fiber content and chemoprofiles has been reported. The present study explores the utility of EST-derived markers in studying genetic diversity in different accessions of Z. officinale and their cross transferability within the Zingiberaceae family. A total of 38,115 ESTs sequences were assembled to generate 7850 contigs and 10,762 singletons. SSRs were searched in the unigenes and 515 SSR-containing ESTs were identified with a frequency of 1 SSR per 25.21 kb of the genome. These ESTs were also annotated using BLAST2GO. Primers were designed for 349 EST-SSRs and 25 primer pairs were randomly picked for EST SSR study. Out of these, 16 primer pairs could be optimized for amplification in different accessions of Z. officinale as well as other species belonging to Zingiberaceae. GES454, GES466, GES480 and GES486 markers were found to exhibit 100% cross-transferability among different members of Zingiberaceae.
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Affiliation(s)
- Praveen Awasthi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Ashish Singh
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Gulfam Sheikh
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Vidushi Mahajan
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Ajai Prakash Gupta
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
| | - Suphla Gupta
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Yashbir S. Bedi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
| | - Sumit G. Gandhi
- Indian Institute of Integrative Medicine (CSIR-IIIM), Council of Scientific and Industrial Research, Canal Road, Jammu Tawi, 180001 India
- Division of Biosciences, Faculty of Sciences, Academy of Scientific and Innovative Research, Kolkata, India
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da Costa ZP, Munhoz CDF, Vieira MLC. Report on the development of putative functional SSR and SNP markers in passion fruits. BMC Res Notes 2017; 10:445. [PMID: 28874179 PMCID: PMC5585897 DOI: 10.1186/s13104-017-2771-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). RESULTS A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. CONCLUSIONS Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.
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Affiliation(s)
- Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Carla de Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
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Dash PK, Rai R. Translating the "Banana Genome" to Delineate Stress Resistance, Dwarfing, Parthenocarpy and Mechanisms of Fruit Ripening. FRONTIERS IN PLANT SCIENCE 2016; 7:1543. [PMID: 27833619 PMCID: PMC5080353 DOI: 10.3389/fpls.2016.01543] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2016] [Accepted: 09/30/2016] [Indexed: 05/07/2023]
Abstract
Evolutionary frozen, genetically sterile and globally iconic fruit "Banana" remained untouched by the green revolution and, as of today, researchers face intrinsic impediments for its varietal improvement. Recently, this wonder crop entered the genomics era with decoding of structural genome of double haploid Pahang (AA genome constitution) genotype of Musa acuminata. Its complex genome decoded by hybrid sequencing strategies revealed panoply of genes and transcription factors involved in the process of sucrose conversion that imparts sweetness to its fruit. Historically, banana has faced the wrath of pandemic bacterial, fungal, and viral diseases and multitude of abiotic stresses that has ruined the livelihood of small/marginal farmers' and destroyed commercial plantations. Decoding structural genome of this climacteric fruit has given impetus to a deeper understanding of the repertoire of genes involved in disease resistance, understanding the mechanism of dwarfing to develop an ideal plant type, unraveling the process of parthenocarpy, and fruit ripening for better fruit quality. Further, injunction of comparative genomics will usher in integration of information from its decoded genome and other monocots into field applications in banana related but not limited to yield enhancement, food security, livelihood assurance, and energy sustainability. In this mini review, we discuss pre- and post-genomic discoveries and highlight accomplishments in structural genomics, genetic engineering and forward genetic accomplishments with an aim to target genes and transcription factors for translational research in banana.
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Affiliation(s)
- Prasanta K. Dash
- ICAR-National Research Centre on Plant BiotechnologyNew Delhi, India
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Ferraz dos Santos L, Moreira Fregapani R, Falcão LL, Togawa RC, Costa MMDC, Lopes UV, Peres Gramacho K, Alves RM, Micheli F, Marcellino LH. First Microsatellite Markers Developed from Cupuassu ESTs: Application in Diversity Analysis and Cross-Species Transferability to Cacao. PLoS One 2016; 11:e0151074. [PMID: 26949967 PMCID: PMC4780773 DOI: 10.1371/journal.pone.0151074] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2015] [Accepted: 02/23/2016] [Indexed: 01/25/2023] Open
Abstract
The cupuassu tree (Theobroma grandiflorum) (Willd. ex Spreng.) Schum. is a fruitful species from the Amazon with great economical potential, due to the multiple uses of its fruit´s pulp and seeds in the food and cosmetic industries, including the production of cupulate, an alternative to chocolate. In order to support the cupuassu breeding program and to select plants presenting both pulp/seed quality and fungal disease resistance, SSRs from Next Generation Sequencing ESTs were obtained and used in diversity analysis. From 8,330 ESTs, 1,517 contained one or more SSRs (1,899 SSRs identified). The most abundant motifs identified in the EST-SSRs were hepta- and trinucleotides, and they were found with a minimum and maximum of 2 and 19 repeats, respectively. From the 1,517 ESTs containing SSRs, 70 ESTs were selected based on their functional annotation, focusing on pulp and seed quality, as well as resistance to pathogens. The 70 ESTs selected contained 77 SSRs, and among which, 11 were polymorphic in cupuassu genotypes. These EST-SSRs were able to discriminate the cupuassu genotype in relation to resistance/susceptibility to witches’ broom disease, as well as to pulp quality (SST/ATT values). Finally, we showed that these markers were transferable to cacao genotypes, and that genome availability might be used as a predictive tool for polymorphism detection and primer design useful for both Theobroma species. To our knowledge, this is the first report involving EST-SSRs from cupuassu and is also a pioneer in the analysis of marker transferability from cupuassu to cacao. Moreover, these markers might contribute to develop or saturate the cupuassu and cacao genetic maps, respectively.
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Affiliation(s)
- Lucas Ferraz dos Santos
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662–900 Ilhéus-BA, Brazil
- Embrapa Recursos Genéticos e Biotecnologia, Brasília-DF, 70770–917, Brazil
| | | | - Loeni Ludke Falcão
- Embrapa Recursos Genéticos e Biotecnologia, Brasília-DF, 70770–917, Brazil
| | | | | | | | | | | | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662–900 Ilhéus-BA, Brazil
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- * E-mail:
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Biswas MK, Liu Y, Li C, Sheng O, Mayer C, Yi G. Genome-Wide Computational Analysis of Musa Microsatellites: Classification, Cross-Taxon Transferability, Functional Annotation, Association with Transposons & miRNAs, and Genetic Marker Potential. PLoS One 2015; 10:e0131312. [PMID: 26121637 PMCID: PMC4488140 DOI: 10.1371/journal.pone.0131312] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/01/2015] [Indexed: 01/14/2023] Open
Abstract
The development of organized, informative, robust, user-friendly, and freely accessible molecular markers is imperative to the Musa marker assisted breeding program. Although several hundred SSR markers have already been developed, the number of informative, robust, and freely accessible Musa markers remains inadequate for some breeding applications. In view of this issue, we surveyed SSRs in four different data sets, developed large-scale non-redundant highly informative therapeutic SSR markers, and classified them according to their attributes, as well as analyzed their cross-taxon transferability and utility for the genetic study of Musa and its relatives. A high SSR frequency (177 per Mbp) was found in the Musa genome. AT-rich dinucleotide repeats are predominant, and trinucleotide repeats are the most abundant in transcribed regions. A significant number of Musa SSRs are associated with pre-miRNAs, and 83% of these SSRs are promising candidates for the development of therapeutic SSR markers. Overall, 74% of the SSR markers were polymorphic, and 94% were transferable to at least one Musa spp. Two hundred forty-three markers generated a total of 1047 alleles, with 2-8 alleles each and an average of 4.38 alleles per locus. The PIC values ranged from 0.31 to 0.89 and averaged 0.71. We report the largest set of non-redundant, polymorphic, new SSR markers to be developed in Musa. These additional markers could be a valuable resource for marker-assisted breeding, genetic diversity and genomic studies of Musa and related species.
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Affiliation(s)
- Manosh Kumar Biswas
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- The College of Life Science, South China Agricultural University, Guangzhou, China
| | - Yuxuan Liu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chunyu Li
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Ou Sheng
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
| | - Christoph Mayer
- Forschungsmuseum Alexander Koenig, Bonn, Adenauerallee 160, 53113 Bonn, Germany
| | - Ganjun Yi
- Institution of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong Province, China
- Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture, Guangzhou, China
- * E-mail:
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