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Arévalo-Marín E, Casas A, Alvarado-Sizzo H, Ruiz-Sanchez E, Castellanos-Morales G, Jardón-Barbolla L, Fermin G, Padilla-Ramírez JS, Clement CR. Genetic analyses and dispersal patterns unveil the Amazonian origin of guava domestication. Sci Rep 2024; 14:15755. [PMID: 38977809 PMCID: PMC11231237 DOI: 10.1038/s41598-024-66495-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024] Open
Abstract
Guava (Psidium guajava L.) is a semi-domesticated fruit tree of moderate importance in the Neotropics, utilized for millennia due to its nutritional and medicinal benefits, but its origin of domestication remains unknown. In this study, we examine genetic diversity and population structure in 215 plants from 11 countries in Mesoamerica, the Andes, and Amazonia using 25 nuclear microsatellite loci to propose an origin of domestication. Genetic analyses reveal one gene pool in Mesoamerica (Mexico) and four in South America (Brazilian Amazonia, Peruvian Amazonia and Andes, and Colombia), indicating greater differentiation among localities, possibly due to isolation between guava populations, particularly in the Amazonian and Andean regions. Moreover, Mesoamerican populations show high genetic diversity, with moderate genetic structure due to gene flow from northern South American populations. Dispersal scenarios suggest that Brazilian Amazonia is the probable origin of guava domestication, spreading from there to the Peruvian Andes, northern South America, Central America, and Mexico. These findings present the first evidence of guava domestication in the Americas, contributing to a deeper understanding of its evolutionary history.
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Affiliation(s)
- Edna Arévalo-Marín
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad-IIES, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico.
- Posgrado en Ciencias Biológicas, Unidad de Posgrado, Ciudad Universitaria, Coyoacán, CDMX, Mexico.
| | - Alejandro Casas
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad-IIES, Universidad Nacional Autónoma de México, Morelia, Michoacán, Mexico.
| | - Hernán Alvarado-Sizzo
- Laboratorio de Biogeografía y Sistemática, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, CDMX, Mexico
| | - Eduardo Ruiz-Sanchez
- Departamento de Botánica y Zoología, Centro Universitario de Ciencias Biológicas y Agropecuarias, Universidad de Guadalajara, Zapopan, Jalisco, Mexico
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Unidad Villahermosa (ECOSUR-Villahermosa), Villahermosa, Tabasco, Mexico
| | - Lev Jardón-Barbolla
- Centro de Investigaciones Interdisciplinarias en Ciencias y Humanidades, Universidad Nacional Autónoma de México, Ciudad Universitaria, Coyoacán, CDMX, Mexico
| | - Gustavo Fermin
- Instituto Jardín Botánico de Mérida, Facultad de Ciencias, Universidad de Los Andes, Mérida, Mérida, Venezuela
| | - José S Padilla-Ramírez
- Campo Experimental Pabellón, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Aguascalientes, Mexico
| | - Charles R Clement
- Instituto Nacional de Pesquisas da Amazônia, Manaus, Amazonas, Brazil.
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Mathiazhagan M, Elangovan D, Chinnaiyan V, Shivashankara KS, Sudhakar Rao DV, Ravishankar KV. A high-density linkage map construction in guava ( Psidium guajava L.) using genotyping by sequencing and identification of QTLs for leaf, peel, and pulp color in an intervarietal mapping population. FRONTIERS IN PLANT SCIENCE 2024; 15:1335715. [PMID: 38476683 PMCID: PMC10927721 DOI: 10.3389/fpls.2024.1335715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 02/12/2024] [Indexed: 03/14/2024]
Abstract
Psidium guajava L. is an important fruit crop in the tropical and subtropical regions of the world. The advanced breeding methods are not employed for important commercial traits like peel and pulp color, seed hardiness, fruit size, etc., due to the scarcity of genome-wide molecular markers and high-density linkage maps. In this study, we employed single-nucleotide polymorphism (SNP) markers and identified quantitative trait loci (QTL) regions that are associated with color traits of leaf, peel, and pulp in the guava intervarietal mapping population. The mapping population was developed from the contrasting genotypes of fruit and leaf color. Variations in color among the segregating hybrids were recorded both visually and using a Color reader. A high-density linkage map of guava was constructed using the SNP markers from genotyping by sequencing (GBS) of 150 hybrid individuals of the cross 'Arka Poorna' (green) x 'Purple Local' (purple). The integrated linkage map consisted of 1426 SNPs mapped on 11 linkage groups (LG), spanning a total distance of around 730 cM with an average of 129.6 markers per LG. Through QTL analysis for color traits, a minor QTL region was identified for visually scored leaf color and peel color on LG1, whereas a major QTL was detected for pulp color in LG4. The Hunter color values (L* and, a*) also had major QTLs with overlapping marker intervals for leaf and peel colors, establishing the association of SNP markers to the trait. The QTLs harbored genes and transcription factors involved in lycopene and anthocyanin pigment biosynthesis. This is the first report of a high-density linkage map based on SNP markers in guava and QTL mapping for color characters in leaf, fruit peel and pulp. The genotyping information generated in this study can aid in genetic engineering and marker-assisted breeding in guava.
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Affiliation(s)
- Malarvizhi Mathiazhagan
- Division of Basic Sciences, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
- Centre for Post-graduate Studies, Jain (Deemed-to-be) University, Bengaluru, India
| | - Dayanandhi Elangovan
- Division of Basic Sciences, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | - Vasugi Chinnaiyan
- Division of Fruit Crops, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
| | | | - Darisi Venkata Sudhakar Rao
- Division of Post Harvest Technology and Agricultural Engineering, ICAR-Indian Institute of Horticultural Research, Bengaluru, India
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Tzatzani TT, Michail I, Boutsika A, Sarrou E, Ganopoulos I. Micropropagation of guava ( Psidium guajava) seedlings, a plant with interest in cool subtropics, using an innovative BB culture medium. BIOTECHNOL BIOTEC EQ 2023. [DOI: 10.1080/13102818.2022.2159524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Thiresia-Teresa Tzatzani
- Laboratory of Subtropical Plants and Tissue Culture, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Crete, Chania, Greece
| | - Ioanna Michail
- Laboratory of Subtropical Plants and Tissue Culture, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization DIMITRA, Crete, Chania, Greece
| | - Anastasia Boutsika
- Department of Medicinal and Aromatic Plants, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization – DIMITRA Thermi, Thessaloniki, Greece
| | - Eirini Sarrou
- Department of Medicinal and Aromatic Plants, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization – DIMITRA Thermi, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Department of Medicinal and Aromatic Plants, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization – DIMITRA Thermi – Thessalonikis, Thessaloniki, Greece
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Mbhele Z, Zharare GE, Zimudzi C, Ntuli NR. Assessing Genetic Variation among Strychnos spinosa Lam. Morphotypes Using Simple Sequence Repeat Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:2810. [PMID: 37570964 PMCID: PMC10421500 DOI: 10.3390/plants12152810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 07/26/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023]
Abstract
Strychnos spinosa Lam., commonly known as green monkey orange, is a highly valued indigenous fruit tree in South Africa with potential for domestication and commercialization. However, no study has reported on the molecular diversity of Strychnos spinosa morphotypes. Therefore, this study aimed to determine genetic variation among 32 Strychnos spinosa morphotypes using simple sequence repeat (SSR) markers. Fourteen amplified SSR markers produced 159 alleles, with a mean of 5.68 per locus. The polymorphic information content (PIC) values ranged from 0.22 (Ssp_1) to 0.84 (Ssp_6). Morphotypes were clustered in a biplot based on their genetic distances. The dendrogram chiefly discriminated morphotypes according to variation of pericarp texture. The population structure had the highest delta value K = 3, thus the 32 morphotypes were divided into three subpopulations based on the Bayesian approach. The affinities produced by the population structure agreed with the genetic distance of closely related morphotypes. This study is the first to report on SSR marker development and their successful use for genetic diversity and population structure studies of Strychnos spinosa. It provides insights into the molecular characterisation of Strychnos spinosa. This can lead to breeding programs and crop improvement programs, particularly in varietal developmental programs, which can contribute to alleviating food security challenges.
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Affiliation(s)
- Zoliswa Mbhele
- Department of Botany, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
| | | | - Clemence Zimudzi
- Department of Biological Sciences and Ecology, Faculty of Science, University of Zimbabwe, Harare P.O. Box MP167, Zimbabwe;
| | - Nontuthuko Rosemary Ntuli
- Department of Botany, Faculty of Science, Agriculture and Engineering, University of Zululand, KwaDlangezwa 3886, South Africa;
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Maan SS, Brar JS, Mittal A, Gill MIS, Arora NK, Sohi HS, Chhuneja P, Dhillon GS, Singh N, Thakur S. Construction of a genetic linkage map and QTL mapping of fruit quality traits in guava ( Psidium guajava L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1123274. [PMID: 37426984 PMCID: PMC10324979 DOI: 10.3389/fpls.2023.1123274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/08/2023] [Indexed: 07/11/2023]
Abstract
Guava (Psidium guajava L.) is an important fruit crop of the Indian sub-continent, with potential for improvements in quality and yield. The goal of the present study was to construct a genetic linkage map in an intraspecific cross between the elite cultivar 'Allahabad Safeda' and the Purple Guava landrace to identify the genomic regions responsible for important fruit quality traits, viz., total soluble solids, titratable acidity, vitamin C, and sugars. This population was phenotyped in field trials (as a winter crop) for three consecutive years, and showed moderate-to-high values of heterogeneity coefficients along with higher heritability (60.0%-97.0%) and genetic-advance-over-mean values (13.23%-31.17%), suggesting minimal environmental influence on the expression of fruit-quality traits and indicating that these traits can be improved by phenotypic selection methods. Significant correlations and strong associations were also detected among fruit physico-chemical traits in segregating progeny. The constructed linkage map consisted of 195 markers distributed across 11 chromosomes, spanning a length of 1,604.47 cM (average inter-loci distance of 8.80 markers) and with 88.00% coverage of the guava genome. Fifty-eight quantitative trait loci (QTLs) were detected in three environments with best linear unbiased prediction (BLUP) values using the composite interval mapping algorithm of the BIP (biparental populations) module. The QTLs were distributed on seven different chromosomes, explaining 10.95%-17.77% of phenotypic variance, with the highest LOD score being 5.96 for qTSS.AS.pau-6.2. Thirteen QTLs detected across multiple environments with BLUPs indicate stability and utility in a future breeding program for guava. Furthermore, seven QTL clusters with stable or common individual QTLs affecting two or more different traits were located on six linkage groups (LGs), explaining the correlation among fruit-quality traits. Thus, the multiple environmental evaluations conducted here have increased our understanding of the molecular basis of phenotypic variation, providing the basis for future high-resolution fine-mapping and paving the way for marker-assisted breeding of fruit-quality traits.
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Affiliation(s)
| | | | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Naresh Kumar Arora
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, India
| | - Harjot Singh Sohi
- Krishi Vigyan Kendra, Guru Angad Dev Veterinary and Animal Sciences University, Barnala, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Navdeep Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sujata Thakur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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Fernandes Santos CA, Rodrigues da Costa S, Silva Boiteux L, Grattapaglia D, Silva-Junior OB. Genetic associations with resistance to Meloidogyne enterolobii in guava (Psidium sp.) using cross-genera SNPs and comparative genomics to Eucalyptus highlight evolutionary conservation across the Myrtaceae. PLoS One 2022; 17:e0273959. [PMID: 36322533 PMCID: PMC9629644 DOI: 10.1371/journal.pone.0273959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 10/14/2022] [Indexed: 11/07/2022] Open
Abstract
Tropical fruit tree species constitute a yet untapped supply of outstanding diversity of taste and nutritional value, barely developed from the genetics standpoint, with scarce or no genomic resources to tackle the challenges arising in modern breeding practice. We generated a de novo genome assembly of the Psidium guajava, the super fruit “apple of the tropics”, and successfully transferred 14,268 SNP probesets from Eucalyptus to Psidium at the nucleotide level, to detect genomic loci linked to resistance to the root knot nematode (RKN) Meloidogyne enterolobii derived from the wild relative P. guineense. Significantly associated loci with resistance across alternative analytical frameworks, were detected at two SNPs on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome to determine the order and orientation of the contigs. The P. guineense-derived resistance response to RKN and disease onset is conceivably triggered by mineral nutrients and phytohormone homeostasis or signaling with the involvement of the miRNA pathway. Hotspots of mapped resistance quantitative trait loci and functional annotation in the same genomic region of Eucalyptus provide further indirect support to our results, highlighting the evolutionary conservation of genomes across genera of Myrtaceae in the adaptation to pathogens. Marker assisted introgression of the resistance loci mapped should accelerate the development of improved guava cultivars and hybrid rootstocks.
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Affiliation(s)
| | - Soniane Rodrigues da Costa
- Graduate program in Genetic Resources, Universidade Estadual de Feira de Santana, Feira de Santana, Bahia, Brazil
| | | | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology (CENARGEN), Brasília, Distrito Federal, Brazil
- * E-mail:
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Sohi HS, Gill MIS, Chhuneja P, Arora NK, Maan SS, Singh J. Construction of Genetic Linkage Map and Mapping QTL Specific to Leaf Anthocyanin Colouration in Mapping Population 'Allahabad Safeda' × 'Purple Guava (Local)' of Guava ( Psidium guajava L.). PLANTS (BASEL, SWITZERLAND) 2022; 11:2014. [PMID: 35956491 PMCID: PMC9370526 DOI: 10.3390/plants11152014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 06/15/2023]
Abstract
In the present investigation, F1 hybrids were developed in guava (Psidium guajava L.) by crossing high leaf-anthocyanin reflective-index (ARI1) content cultivars purple guava (local) 'PG', 'CISH G-1' and low leaf-ARI1 content cultivar Seedless 'SL' with Allahabad Safeda 'AS'. On the basis of phenotypic observations, high ARI1 content was observed in the cross 'AS' × 'PG' (0.214). Further, an SSR-markers-based genetic linkage map was developed from a mapping population of 238 F1 individuals derived from cross 'AS' × 'PG'. The linkage map comprised 11 linkage groups (LGs), spanning 1601.7 cM with an average marker interval distance of 29.61 cM between adjacent markers. Five anthocyanin-content related gene-specific markers from apple were tested for parental polymorphism in the genotypes 'AS' and 'PG'. Subsequently, a marker, viz., 'MdMYB10F1', revealed a strong association with leaf anthocyanin content in the guava mapping population. QTL (qARI-6-1) on LG6 explains much of the variation (PVE = 11.51% with LOD = 4.67) in levels of leaf anthocyanin colouration. This is the first report of amplification/utilization of apple anthocyanin-related genes in guava. The genotypic data generated from the genetic map can be further exploited in future for the enrichment of linkage maps and for identification of complex quantitative trait loci (QTLs) governing economically important fruit quality traits in guava.
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Affiliation(s)
- Harjot Singh Sohi
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Manav Indra Singh Gill
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India;
| | - Naresh Kumar Arora
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Sukhjinder Singh Maan
- Department of Fruit Science, College of Horticulture and Forestry Punjab Agricultural University, Ludhiana 141004, India; (M.I.S.G.); (N.K.A.); (S.S.M.)
| | - Jagmohan Singh
- Division of Plant Pathology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India;
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Antunes AM, Nunes Stival JG, Targueta CP, de Campos Telles MP, Soares TN. A Pipeline for the Development of Microsatellite Markers using Next Generation Sequencing Data. Curr Genomics 2022; 23:175-181. [PMID: 36777003 PMCID: PMC9878831 DOI: 10.2174/1389202923666220428101350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/27/2022] [Accepted: 02/14/2022] [Indexed: 11/22/2022] Open
Abstract
Background: Also known as Simple Sequence Repetitions (SSRs), microsatellites are profoundly informative molecular markers and powerful tools in genetics and ecology studies on plants. Objective: This research presents a workflow for developing microsatellite markers using genome skimming. Methods: The pipeline was proposed in several stages that must be performed sequentially: obtaining DNA sequences, identifying microsatellite regions, designing primers, and selecting candidate microsatellite regions to develop the markers. Our pipeline efficiency was analyzed using Illumina sequencing data from the non-model tree species Pterodon emarginatus Vog. Results: The pipeline revealed 4,382 microsatellite regions and drew 7,411 pairs of primers for P. emarginatus. However, a much larger number of microsatellite regions with the potential to develop markers were discovered from our pipeline. We selected 50 microsatellite regions with high potential for developing markers and organized 29 microsatellite regions in sets for multiplex PCR. Conclusion: The proposed pipeline is a powerful tool for fast and efficient development of microsatellite markers on a large scale in several species, especially nonmodel plant species.
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Affiliation(s)
- Adriana Maria Antunes
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil;,Address correspondence to this author at the Department of Genetics, Institute of Biological Sciences, Goias Federal University, Goiânia, Brazil; Tel/Fax: +55 62 981660987; E-mail:
| | - Júlio Gabriel Nunes Stival
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Cíntia Pelegrineti Targueta
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil
| | - Mariana Pires de Campos Telles
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Goiânia, Goiás, Brasil
| | - Thannya Nascimentos Soares
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, Goiás, Brasil;,Programa de Pós Graduação em Genética e Melhoramento de Plantas, Escola de Agronomia, Universidade Federal de Goias, Goiânia, Goiás, Brasil
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Mathiazhagan M, Chidambara B, Hunashikatti LR, Ravishankar KV. Genomic Approaches for Improvement of Tropical Fruits: Fruit Quality, Shelf Life and Nutrient Content. Genes (Basel) 2021; 12:1881. [PMID: 34946829 PMCID: PMC8701245 DOI: 10.3390/genes12121881] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/23/2021] [Accepted: 11/16/2021] [Indexed: 12/17/2022] Open
Abstract
The breeding of tropical fruit trees for improving fruit traits is complicated, due to the long juvenile phase, generation cycle, parthenocarpy, polyploidy, polyembryony, heterozygosity and biotic and abiotic factors, as well as a lack of good genomic resources. Many molecular techniques have recently evolved to assist and hasten conventional breeding efforts. Molecular markers linked to fruit development and fruit quality traits such as fruit shape, size, texture, aroma, peel and pulp colour were identified in tropical fruit crops, facilitating Marker-assisted breeding (MAB). An increase in the availability of genome sequences of tropical fruits further aided in the discovery of SNP variants/Indels, QTLs and genes that can ascertain the genetic determinants of fruit characters. Through multi-omics approaches such as genomics, transcriptomics, metabolomics and proteomics, the identification and quantification of transcripts, including non-coding RNAs, involved in sugar metabolism, fruit development and ripening, shelf life, and the biotic and abiotic stress that impacts fruit quality were made possible. Utilizing genomic assisted breeding methods such as genome wide association (GWAS), genomic selection (GS) and genetic modifications using CRISPR/Cas9 and transgenics has paved the way to studying gene function and developing cultivars with desirable fruit traits by overcoming long breeding cycles. Such comprehensive multi-omics approaches related to fruit characters in tropical fruits and their applications in breeding strategies and crop improvement are reviewed, discussed and presented here.
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Affiliation(s)
| | | | | | - Kundapura V. Ravishankar
- Division of Basic Sciences, ICAR Indian Institute of Horticultural Research, Hessaraghatta Lake Post, Bengaluru 560089, India; (M.M.); (B.C.); (L.R.H.)
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10
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Thakur S, Yadav IS, Jindal M, Sharma PK, Dhillon GS, Boora RS, Arora NK, Gill MIS, Chhuneja P, Mittal A. Development of Genome-Wide Functional Markers Using Draft Genome Assembly of Guava ( Psidium guajava L.) cv. Allahabad Safeda to Expedite Molecular Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:708332. [PMID: 34630458 PMCID: PMC8494772 DOI: 10.3389/fpls.2021.708332] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Abstract
Guava (Psidium guajava L.), a rich source of nutrients, is an important tropical and subtropical fruit of the Myrtaceae family and exhibits magnificent diversity. Genetic diversity analysis is the first step toward the identification of parents for hybridization, genetic mapping, and molecular breeding in any crop species. A diversity analysis based on whole-genome functional markers increases the chances of identifying genetic associations with agronomically important traits. Therefore, here, we sequenced the genome of guava cv. Allahabad Safeda on an Illumina platform and generated a draft assembly of ~304 MB. The assembly of the Allahabad Safeda genome constituted >37.95% repeat sequences, gene prediction with RNA-seq data as evidence identified 14,115 genes, and BLAST n/r, Interproscan, PfamScan, BLAST2GO, and KEGG annotated 13,957 genes. A comparative protein transcript analysis of tree species revealed the close relatedness of guava with Eucalyptus. Comparative transcriptomics-based SSR/InDel/SNP-PCR ready genome-wide markers in greenish-yellow skinned and white fleshed-Allahabad Safeda to four contrasting cultivars viz apple-color-skinned and white-fleshed-Lalima, greenish-yellow-skinned and pink-fleshed-Punjab Pink, purple-black-skinned and purple-fleshed-Purple Local and widely used rootstock-Lucknow-49 were developed. The molecular markers developed here revealed a high level of individual heterozygosity within genotypes in 22 phenotypically diverse guava cultivars. Principal coordinate, STRUCTURE clustering, and neighbor-joining-based genetic diversity analysis identified distinct clusters associated with fruit skin and flesh color. The genome sequencing of guava, functional annotation, comparative transcriptomics-based genome-wide markers, and genetic diversity analysis will expand the knowledge of genomes of climacteric fruits, facilitating trait-based molecular breeding and diversifying the nutritional basket.
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Affiliation(s)
- Sujata Thakur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Inderjit Singh Yadav
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Manish Jindal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Parva Kumar Sharma
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | | | - Rajbir Singh Boora
- Fruit Research Sub-Station, Punjab Agricultural University, Bahadurgarh, India
| | - Naresh Kumar Arora
- Department of Fruit Science, Punjab Agricultural University, Ludhiana, India
| | | | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Amandeep Mittal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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