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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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Rosa-Martínez E, Bovy A, Plazas M, Tikunov Y, Prohens J, Pereira-Dias L. Genetics and breeding of phenolic content in tomato, eggplant and pepper fruits. FRONTIERS IN PLANT SCIENCE 2023; 14:1135237. [PMID: 37025131 PMCID: PMC10070870 DOI: 10.3389/fpls.2023.1135237] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Phenolic acids and flavonoids are large groups of secondary metabolites ubiquitous in the plant kingdom. They are currently in the spotlight due to the numerous health benefits associated with their consumption, as well as for their vital roles in plant biological processes and in plant-environment interaction. Tomato, eggplant and pepper are in the top ten most consumed vegetables in the world, and their fruit accumulation profiles have been extensively characterized, showing substantial differences. A broad array of genetic and genomic tools has helped to identify QTLs and candidate genes associated with the fruit biosynthesis of phenolic acids and flavonoids. The aim of this review was to synthesize the available information making it easily available for researchers and breeders. The phenylpropanoid pathway is tightly regulated by structural genes, which are conserved across species, along with a complex network of regulatory elements like transcription factors, especially of MYB family, and cellular transporters. Moreover, phenolic compounds accumulate in tissue-specific and developmental-dependent ways, as different paths of the metabolic pathway are activated/deactivated along with fruit development. We retrieved 104 annotated putative orthologues encoding for key enzymes of the phenylpropanoid pathway in tomato (37), eggplant (29) and pepper (38) and compiled 267 QTLs (217 for tomato, 16 for eggplant and 34 for pepper) linked to fruit phenolic acids, flavonoids and total phenolics content. Combining molecular tools and genetic variability, through both conventional and genetic engineering strategies, is a feasible approach to improve phenolics content in tomato, eggplant and pepper. Finally, although the phenylpropanoid biosynthetic pathway has been well-studied in the Solanaceae, more research is needed on the identification of the candidate genes behind many QTLs, as well as their interactions with other QTLs and genes.
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Affiliation(s)
- Elena Rosa-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Arnaud Bovy
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Yury Tikunov
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Valencia, Spain
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
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Gaccione L, Martina M, Barchi L, Portis E. A Compendium for Novel Marker-Based Breeding Strategies in Eggplant. PLANTS (BASEL, SWITZERLAND) 2023; 12:1016. [PMID: 36903876 PMCID: PMC10005326 DOI: 10.3390/plants12051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The worldwide production of eggplant is estimated at about 58 Mt, with China, India and Egypt being the major producing countries. Breeding efforts in the species have mainly focused on increasing productivity, abiotic and biotic tolerance/resistance, shelf-life, the content of health-promoting metabolites in the fruit rather than decreasing the content of anti-nutritional compounds in the fruit. From the literature, we collected information on mapping quantitative trait loci (QTLs) affecting eggplant's traits following a biparental or multi-parent approach as well as genome-wide association (GWA) studies. The positions of QTLs were lifted according to the eggplant reference line (v4.1) and more than 700 QTLs were identified, here organized into 180 quantitative genomic regions (QGRs). Our findings thus provide a tool to: (i) determine the best donor genotypes for specific traits; (ii) narrow down QTL regions affecting a trait by combining information from different populations; (iii) pinpoint potential candidate genes.
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Martina M, Acquadro A, Gulino D, Brusco F, Rabaglio M, Portis E, Lanteri S. First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq. FRONTIERS IN PLANT SCIENCE 2022; 13:1009206. [PMID: 36212343 PMCID: PMC9539318 DOI: 10.3389/fpls.2022.1009206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F1 mapping populations, whose female parents were a genotype of a so called 'ponpon' and of a 'double flower' varieties, while the common male parental ('Cipro') was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F1 population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.
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Affiliation(s)
- Matteo Martina
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Davide Gulino
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | | | | | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
| | - Sergio Lanteri
- Dipartimento di Scienze Agrarie, Forestali e Alimentari (DISAFA), Plant Genetics and Breeding, University of Torino, Grugliasco, Italy
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Lee JH, Venkatesh J, Jo J, Jang S, Kim GW, Kim JM, Han K, Ro N, Lee HY, Kwon JK, Kim YM, Lee TH, Choi D, Van Deynze A, Hill T, Kfir N, Freiman A, Davila Olivas NH, Elkind Y, Paran I, Kang BC. High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers. HORTICULTURE RESEARCH 2022; 9:uhac210. [PMID: 36467270 PMCID: PMC9715575 DOI: 10.1093/hr/uhac210] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar 'Dempsey' and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.
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Affiliation(s)
| | | | - Jinkwan Jo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Siyoung Jang
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Geon Woo Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jung-Min Kim
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Koeun Han
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Hea-Young Lee
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jin-Kyung Kwon
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Min Kim
- Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea
| | - Tae-Ho Lee
- Genomics Division, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Doil Choi
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Plant Genomics Breeding Institute, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Allen Van Deynze
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Nir Kfir
- NRGene, 5 Golda Meir St., Ness Ziona 7403649, Israel
| | - Aviad Freiman
- Top Seeds International Ltd. Moshav Sharona, 1523200, Israel
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Barboza GE, García CC, Bianchetti LDB, Romero MV, Scaldaferro M. Monograph of wild and cultivated chili peppers ( Capsicum L., Solanaceae). PHYTOKEYS 2022; 200:1-423. [PMID: 36762372 PMCID: PMC9881532 DOI: 10.3897/phytokeys.200.71667] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 04/27/2022] [Indexed: 06/01/2023]
Abstract
Capsicum L. (tribe Capsiceae, Solanaceae) is an American genus distributed ranging from the southern United States of America to central Argentina and Brazil. The genus includes chili peppers, bell peppers, ajíes, habaneros, jalapeños, ulupicas and pimientos, well known for their economic importance around the globe. Within the Solanaceae, the genus can be recognised by its shrubby habit, actinomorphic flowers, distinctive truncate calyx with or without appendages, anthers opening by longitudinal slits, nectaries at the base of the ovary and the variously coloured and usually pungent fruits. The highest diversity of this genus is located along the northern and central Andes. Although Capsicum has been extensively studied and great advances have been made in the understanding of its taxonomy and the relationships amongst species, there is no monographic treatment of the genus as a whole. Based on morphological and molecular evidence studied from field and herbarium specimens, we present here a comprehensive taxonomic treatment for the genus, including updated information about morphology, anatomy, karyology, phylogeny and distribution. We recognise 43 species and five varieties, including C.mirum Barboza, sp. nov. from São Paulo State, Brazil and a new combination C.muticum (Sendtn.) Barboza, comb. nov.; five of these taxa are cultivated worldwide (C.annuumL.var.annuum, C.baccatumL.var.pendulum (Willd.) Eshbaugh, C.baccatumL.var.umbilicatum (Vell.) Hunz. & Barboza, C.chinense Jacq. and C.frutescens L.). Nomenclatural revision of the 265 names attributed to chili peppers resulted in 89 new lectotypifications and five new neotypifications. Identification keys and detailed descriptions, maps and illustrations for all taxa are provided.
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Affiliation(s)
- Gloria E. Barboza
- Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Casilla de Correo 495, 5000 Córdoba, ArgentinaInstituto Multidisciplinario de Biología VegetalCórdobaArgentina
| | - Carolina Carrizo García
- Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Casilla de Correo 495, 5000 Córdoba, ArgentinaInstituto Multidisciplinario de Biología VegetalCórdobaArgentina
| | - Luciano de Bem Bianchetti
- Empresa Brasileira de Pesquisa Agropecuária—Centro Nacional de Pesquisa de Recursos Genéticos e Biotecnologia (EMBRAPA—Recursos Genéticos e Biotecnologia), PqEB Parque Estação Biológica, Av. W/5 final, Brasília-DF, CEP 70770–917, Caixa Postal 02372, BrazilCentro Nacional de Pesquisa de Recursos Genéticos e BiotecnologiaBrasíliaBrazil
| | - María V. Romero
- Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Casilla de Correo 495, 5000 Córdoba, ArgentinaInstituto Multidisciplinario de Biología VegetalCórdobaArgentina
| | - Marisel Scaldaferro
- Instituto Multidisciplinario de Biología Vegetal (CONICET-Universidad Nacional de Córdoba), Casilla de Correo 495, 5000 Córdoba, ArgentinaInstituto Multidisciplinario de Biología VegetalCórdobaArgentina
- Facultad de Ciencias Exactas, Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba, ArgentinaUniversidad Nacional de CórdobaCórdobaArgentina
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Esposito S, Aiese Cigliano R, Cardi T, Tripodi P. Whole-genome resequencing reveals genomic footprints of Italian sweet and hot pepper heirlooms giving insight into genes underlying key agronomic and qualitative traits. BMC Genom Data 2022; 23:21. [PMID: 35337259 PMCID: PMC8957157 DOI: 10.1186/s12863-022-01039-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Pepper is a major crop species of the Solanaceae family, largely appreciated for its high nutritional and healthy contribution to human diets. In the Mediterranean basin, the favorable pedoclimatic conditions enhanced the selection of several diversified landraces cultivated pepper (Capsicum annuum), for whom Italy can be considered a main pole of diversification. Hence, a survey of traditional C. annuum genetic resources is essential for deep understanding of such diversity and for applications in genomics assisted breeding. Here, we report whole-genome resequencing analyses of two sweet and two pungent genotypes highly diffused in South Italy and representative of the variability for shape, colour and nutritional properties. RESULTS The four genomes were reconstructed at a chromosomal scale using a reference-guided approach, based on a dataset of 2.6 billion paired-end reads, corresponding to 20× genome coverage and a mapping rate above 99% for a final genomes size of approximately 3 Gb. After five iterations of variant calling, a total of 29,258,818 single nucleotide polymorphisms (SNPs) and 1,879,112 InDels, were identified. Substantial differences were observed among the four genomes based on geographical origin, with chromosomes 9 and 11 showing more polymorphisms in the accessions with higher fruit weight and absence of pungency. Among the identified variants, a small private indel (T - > TA) shared between sweet and big fruits accessions induces a frameshift with the generation of a new stop codon in a gene annotated as extensin, whereas two private SNPs within hot types were identified in 1-aminocyclopropane-1-carboxylate oxidase (ACO), a key gene involved in fruit ripening. The estimation of repetitive elements highlights a preponderant presence of Long Terminal Repeats (LTRs), the majority of which belonged to Gypsy superfamily. By comparing the four genomes with publicly available references including 'CM334' and Zunla-1 highlight the presence of 49,475 shared gene families. CONCLUSIONS The new genomic sequences aim to enrich the whole genome information of pepper local varieties, providing a valuable tool for precision gene mapping, marker discovery, comparative studies. Such knowledge widens the frontiers to understand the selection history of Italian pepper landraces toward the recognition of specificity local agri-food products marks.
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Affiliation(s)
- Salvatore Esposito
- CREA Research Centre for Cereal and Industrial Crops, S.S. 673, km 25.200, 71122, Foggia, Italy
| | | | - Teodoro Cardi
- CNR-IBBR, Institute of Biosciences and Bioresources, via Università 133, 80055, Portici, Italy
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy.
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Genome-Wide Survey and Development of the First Microsatellite Markers Database ( AnCorDB) in Anemone coronaria L. Int J Mol Sci 2022; 23:ijms23063126. [PMID: 35328546 PMCID: PMC8949970 DOI: 10.3390/ijms23063126] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/31/2022] Open
Abstract
Anemone coronaria L. (2n = 2x = 16) is a perennial, allogamous, highly heterozygous plant marketed as a cut flower or in gardens. Due to its large genome size, limited efforts have been made in order to develop species-specific molecular markers. We obtained the first draft genome of the species by Illumina sequencing an androgenetic haploid plant of the commercial line “MISTRAL® Magenta”. The genome assembly was obtained by applying the MEGAHIT pipeline and consisted of 2 × 106 scaffolds. The SciRoKo SSR (Simple Sequence Repeats)-search module identified 401.822 perfect and 188.987 imperfect microsatellites motifs. Following, we developed a user-friendly “Anemone coronaria Microsatellite DataBase” (AnCorDB), which incorporates the Primer3 script, making it possible to design couples of primers for downstream application of the identified SSR markers. Eight genotypes belonging to eight cultivars were used to validate 62 SSRs and a subset of markers was applied for fingerprinting each cultivar, as well as to assess their intra-cultivar variability. The newly developed microsatellite markers will find application in Breeding Rights disputes, developing genetic maps, marker assisted breeding (MAS) strategies, as well as phylogenetic studies.
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Borràs D, Barchi L, Schulz K, Moglia A, Acquadro A, Kamranfar I, Balazadeh S, Lanteri S. Transcriptome-Based Identification and Functional Characterization of NAC Transcription Factors Responsive to Drought Stress in Capsicum annuum L. Front Genet 2021; 12:743902. [PMID: 34745217 PMCID: PMC8570119 DOI: 10.3389/fgene.2021.743902] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/28/2021] [Indexed: 11/13/2022] Open
Abstract
Capsicum annuum L. is one of the most cultivated Solanaceae species, and in the open field, water limitation leading to drought stress affects its fruit quality, fruit setting, fruit size and ultimately yield. We identified stage-specific and a common core set of differentially expressed genes, following RNA-seq transcriptome analyses of a breeding line subjected to acute drought stress followed by recovery (rewatering), at three stages of plant development. Among them, two NAC transcription factor (TF) genes, i.e., CaNAC072 and CaNAC104, were always upregulated after drought stress and downregulated after recovery. The two TF proteins were observed to be localized in the nucleus following their transient expression in Nicotiana benthamiana leaves. The expression of the two NACs was also induced by NaCl, polyethylene glycol (PEG) and abscisic acid (ABA) treatments, suggesting that CaNAC072 is an early, while CaNAC104 is a late abiotic stress-responsive gene. Virus-induced gene silencing (VIGS) of CaNAC104 did not affect the pepper plantlet’s tolerance to drought stress, while VIGS of CaNAC072 increased drought tolerance. Heterologous expression of CaNAC072 in Arabidopsis thaliana as well as in plants mutated for its homolog ANAC072 did not increase drought stress tolerance. This highlights a different role of the two NAC homologs in the two species. Here, we discuss the complex role of NACs as transcriptional switches in the response to drought stress in bell pepper.
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Affiliation(s)
- Dionis Borràs
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Lorenzo Barchi
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Karina Schulz
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Andrea Moglia
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Alberto Acquadro
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
| | - Iman Kamranfar
- Department Molecular Biology, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Salma Balazadeh
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany.,Plant Sciences and Natural Products, Institute of Biology Leiden (IBL), Leiden University, Leiden, Netherlands
| | - Sergio Lanteri
- Department of Agricultural, Forest and Food Sciences, Plant Genetics and Breeding, University of Torino, Turin, Italy
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Mehdi SMM, Krishnamoorthy S, Szczesniak MW, Ludwików A. Identification of Novel miRNAs and Their Target Genes in the Response to Abscisic Acid in Arabidopsis. Int J Mol Sci 2021; 22:7153. [PMID: 34281207 PMCID: PMC8268864 DOI: 10.3390/ijms22137153] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 06/23/2021] [Accepted: 06/28/2021] [Indexed: 12/12/2022] Open
Abstract
miRNAs are involved in various biological processes, including adaptive responses to abiotic stress. To understand the role of miRNAs in the response to ABA, ABA-responsive miRNAs were identified by small RNA sequencing in wild-type Arabidopsis, as well as in abi1td, mkkk17, and mkkk18 mutants. We identified 10 novel miRNAs in WT after ABA treatment, while in abi1td, mkkk17, and mkkk18 mutants, three, seven, and nine known miRNAs, respectively, were differentially expressed after ABA treatment. One novel miRNA (miRn-8) was differentially expressed in the mkkk17 mutant. Potential target genes of the miRNA panel were identified using psRNATarget. Sequencing results were validated by quantitative RT-PCR of several known and novel miRNAs in all genotypes. Of the predicted targets of novel miRNAs, seven target genes of six novel miRNAs were further validated by 5' RLM-RACE. Gene ontology analyses showed the potential target genes of ABA-responsive known and novel miRNAs to be involved in diverse cellular processes in plants, including development and stomatal movement. These outcomes suggest that a number of the identified miRNAs have crucial roles in plant responses to environmental stress, as well as in plant development, and might have common regulatory roles in the core ABA signaling pathway.
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Affiliation(s)
- Syed Muhammad Muntazir Mehdi
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Sivakumar Krishnamoorthy
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
| | - Michal Wojciech Szczesniak
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland;
| | - Agnieszka Ludwików
- Laboratory of Biotechnology, Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University in Poznan, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (S.M.M.M.); (S.K.)
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Barchi L, Rabanus‐Wallace MT, Prohens J, Toppino L, Padmarasu S, Portis E, Rotino GL, Stein N, Lanteri S, Giuliano G. Improved genome assembly and pan-genome provide key insights into eggplant domestication and breeding. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 107:579-596. [PMID: 33964091 PMCID: PMC8453987 DOI: 10.1111/tpj.15313] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/30/2021] [Accepted: 05/04/2021] [Indexed: 05/20/2023]
Abstract
Eggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non-anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant '67/3' reference line, by Hi-C retrofitting of a previously released short read- and optical mapping-based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome-level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan-genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan-plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present-day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
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Affiliation(s)
- Lorenzo Barchi
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | | | - Jaime Prohens
- COMAVUniversitat Politècnica de ValènciaCamino de Vera 14Valencia46022Spain
| | - Laura Toppino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Sudharsan Padmarasu
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
| | - Ezio Portis
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
| | - Giuseppe Leonardo Rotino
- CREA Research Centre for Genomics and BioinformaticsVia Paullese 28Montanaso LombardoLO26836Italy
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)Corrensstr. 3Seeland06466Germany
- Department of Crop SciencesCenter for Integrated Breeding Research (CiBreed)Georg‐August‐UniversityVon Siebold Str. 8Göttingen37075Germany
| | - Sergio Lanteri
- DISAFA – Plant geneticsUniversity of TurinGrugliasco (TO)10095Italy
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Pavese V, Cavalet Giorsa E, Barchi L, Acquadro A, Torello Marinoni D, Portis E, James Lucas S, Botta R. Whole-genome assembly of Corylus avellana cv'Tonda Gentile delle Langhe' using linked-reads (10X Genomics). G3-GENES GENOMES GENETICS 2021; 11:6272584. [PMID: 33964151 PMCID: PMC8495946 DOI: 10.1093/g3journal/jkab152] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 04/20/2021] [Indexed: 01/01/2023]
Abstract
The European hazelnut (Corylus avellana L.; 2n = 2x = 22) is a worldwide economically important tree nut that is cross-pollinated due to sporophytic incompatibility. Therefore, any individual plant is highly heterozygous. Cultivars are clonally propagated using mound layering, rooted suckers, and micropropagation. In recent years, the interest in this crop has increased, due to a growing demand related to the recognized health benefits of nut consumption. C. avellana cv “Tonda Gentile delle Langhe” (“TGdL”) is well-known for its high kernel quality, and the premium price paid for this cultivar is an economic benefit for producers in northern Italy. Assembly of a high-quality genome is a difficult task in many plant species because of the high level of heterozygosity. We assembled a chromosome-level genome sequence of “TGdL” with a two-step approach. First, 10X Genomics Chromium Technology was used to create a high-quality sequence, which was then assembled into scaffolds with cv “Tombul” genome as the reference. Eleven pseudomolecules were obtained, corresponding to 11 chromosomes. A total of 11,046 scaffolds remained unplaced, representing 11% of the genome (46,504,161 bp). Gene prediction, performed with Maker-P software, identified 27,791 genes (AED ≤0.4 and 92% of BUSCO completeness), whose function was analyzed with BlastP and InterProScan software. To characterize “TGdL” specific genetic mechanisms, Orthofinder was used to detect orthologs between hazelnut and closely related species. The “TGdL” genome sequence is expected to be a powerful tool to understand hazelnut genetics and allow detection of markers/genes for important traits to be used in targeted breeding programs.
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Affiliation(s)
- Vera Pavese
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Emile Cavalet Giorsa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Lorenzo Barchi
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Daniela Torello Marinoni
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
| | - Stuart James Lucas
- Sabanci University SUNUM Nanotechnology Research and Application Centre, Istanbul, Turkey
| | - Roberto Botta
- Dipartimento di Scienze Agrarie, Forestali e Alimentari-DISAFA, Università degli Studi di Torino, Largo Paolo Braccini 2, Grugliasco, 10095 Torino, Italy
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Tamburino R, Sannino L, Cafasso D, Cantarella C, Orrù L, Cardi T, Cozzolino S, D’Agostino N, Scotti N. Cultivated Tomato ( Solanum lycopersicum L.) Suffered a Severe Cytoplasmic Bottleneck during Domestication: Implications from Chloroplast Genomes. PLANTS 2020; 9:plants9111443. [PMID: 33114641 PMCID: PMC7692331 DOI: 10.3390/plants9111443] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/13/2022]
Abstract
In various crops, genetic bottlenecks occurring through domestication can limit crop resilience to biotic and abiotic stresses. In the present study, we investigated nucleotide diversity in tomato chloroplast genome through sequencing seven plastomes of cultivated accessions from the Campania region (Southern Italy) and two wild species among the closest (Solanum pimpinellifolium) and most distantly related (S. neorickii) species to cultivated tomatoes. Comparative analyses among the chloroplast genomes sequenced in this work and those available in GenBank allowed evaluating the variability of plastomes and defining phylogenetic relationships. A dramatic reduction in genetic diversity was detected in cultivated tomatoes, nonetheless, a few de novo mutations, which still differentiated the cultivated tomatoes from the closest wild relative S. pimpinellifolium, were detected and are potentially utilizable as diagnostic markers. Phylogenetic analyses confirmed that S. pimpinellifolium is the closest ancestor of all cultivated tomatoes. Local accessions all clustered together and were strictly related with other cultivated tomatoes (S. lycopersicum group). Noteworthy, S. lycopersicum var. cerasiforme resulted in a mixture of both cultivated and wild tomato genotypes since one of the two analyzed accessions clustered with cultivated tomato, whereas the other with S. pimpinellifolium. Overall, our results revealed a very reduced cytoplasmic variability in cultivated tomatoes and suggest the occurrence of a cytoplasmic bottleneck during their domestication.
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Affiliation(s)
- Rachele Tamburino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Lorenza Sannino
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
| | - Donata Cafasso
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Concita Cantarella
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Luigi Orrù
- CREA Research Centre for Genomics and Bioinformatics, via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy;
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
| | - Salvatore Cozzolino
- Department of Biology, University of Naples Federico II, Via Cinthia, 80126 Naples, Italy; (D.C.); (S.C.)
| | - Nunzio D’Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098 Pontecagnano Faiano (SA), Italy; (C.C.); (T.C.); (N.D.)
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 133, 80055 Portici (NA), Italy
| | - Nunzia Scotti
- CNR-IBBR, National Research Council of Italy, Institute of Biosciences and BioResources, Via Università 133, 80055 Portici (NA), Italy; (R.T.); (L.S.)
- Correspondence: ; Tel.: +39-0812-53-9482
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