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Martins FB, Moraes ACL, Aono AH, Ferreira RCU, Chiari L, Simeão RM, Barrios SCL, Santos MF, Jank L, do Valle CB, Vigna BBZ, de Souza AP. A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:737919. [PMID: 34745171 PMCID: PMC8569613 DOI: 10.3389/fpls.2021.737919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.
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Affiliation(s)
- Felipe Bitencourt Martins
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Aline Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | | | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Liana Jank
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), São Paulo, Brazil
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Borin M, Palumbo F, Vannozzi A, Scariolo F, Sacilotto GB, Gazzola M, Barcaccia G. Developing and Testing Molecular Markers in Cannabis sativa (Hemp) for Their Use in Variety and Dioecy Assessments. PLANTS 2021; 10:plants10102174. [PMID: 34685983 PMCID: PMC8540786 DOI: 10.3390/plants10102174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 10/11/2021] [Accepted: 10/12/2021] [Indexed: 11/16/2022]
Abstract
Cannabis sativa (2n = 2x = 20) is a popular species belonging to the Cannabaceae family. Despite its use for medical, recreational, and industrial purposes as well as its long history, the genetic research on this species is in its infancy due to the legal implications and the prohibition campaigns. The recent legalization of Cannabis in many countries along with the use of genomics boosted the approaches aimed at marker-assisted selection, germplasm management, genetic discrimination, and authentication of cultivars. Nonetheless, the exploitation of molecular markers for the development of commercial varieties through marker-assisted breeding schemes is still rare. The present study aimed to develop an informative panel of simple sequence repeat markers to be used for the genotyping of high breeding value C. sativa lines. Starting from 41 nuclear SSR designated by in silico analyses, we selected 20 highly polymorphic and discriminant loci that were tested in 104 individuals belonging to 11 distinct hemp varieties. The selected markers were successful in accessing homozygosity, genetic uniformity, and genetic variation within and among varieties. Population structure analysis identified eight genetic groups, clustering individuals based on sexual behaviors (dioecious and monoecious) and geographical origins. Overall, this study provides important tools for the genetic characterization, authentication, conservation of biodiversity, genetic improvement and traceability of this increasingly important plant species.
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Affiliation(s)
- Marcello Borin
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37034 Verona, Italy;
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Fabio Palumbo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
| | - Francesco Scariolo
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
| | - Gio Batta Sacilotto
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Marco Gazzola
- Gruppo Padana Ortofloricoltura S.S., Via Olimpia 41, 31038 Treviso, Italy; (G.B.S.); (M.G.)
| | - Gianni Barcaccia
- Department of Agronomy, Food, Natural Resources, Animals and Environment (DAFNAE), University of Padova, Viale dell’Università 16, 35020 Padova, Italy; (F.P.); (A.V.); (F.S.)
- Correspondence:
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Ongom PO, Fatokun C, Togola A, Salvo S, Oyebode OG, Ahmad MS, Jockson ID, Bala G, Boukar O. Molecular Fingerprinting and Hybridity Authentication in Cowpea Using Single Nucleotide Polymorphism Based Kompetitive Allele-Specific PCR Assay. FRONTIERS IN PLANT SCIENCE 2021; 12:734117. [PMID: 34675950 PMCID: PMC8524091 DOI: 10.3389/fpls.2021.734117] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Optimization of a breeding program for increased genetic gain requires quality assurance (QA) and quality control (QC) at key phases of the breeding process. One vital phase in a breeding program that requires QC and QA is the choice of parents and successful hybridizations to combine parental attributes and create variations. The objective of this study was to determine parental diversity and confirm hybridity of cowpea F1 progenies using KASP (Kompetitive Allele-Specific PCR)-based single nucleotide polymorphism (SNP) markers. A total of 1,436 F1 plants were derived from crossing 220 cowpea breeding lines and landraces to 2 elite sister lines IT99K-573-1-1 and IT99K-573-2-1 as male parents, constituting 225 cross combinations. The progenies and the parents were genotyped with 17 QC SNP markers via high-throughput KASP genotyping assay. The QC markers differentiated the parents with mean efficiency of 37.90% and a range of 3.4-82.8%, revealing unique fingerprints of the parents. Neighbor-Joining cladogram divided the 222 parents into 3 clusters. Genetic distances between parents ranged from 0 to 3.74 with a mean of 2.41. Principal component analysis (PCA) depicted a considerable overlap between parents and F1 progenies with more scatters among parents than the F1s. The differentiation among parents and F1s was best contributed to by 82% of the markers. As expected, parents and F1s showed a significant contrast in proportion of heterozygous individuals, with mean values of 0.02 and 0.32, respectively. KASP markers detected true hybridity with 100% success rate in 72% of the populations. Overall, 79% of the putative F1 plants were true hybrids, 14% were selfed plants, and 7% were undetermined due to missing data and lack of marker polymorphism between parents. The study demonstrated an effective application of KASP-based SNP assay in fingerprinting, confirmation of hybridity, and early detection of false F1 plants. The results further uncovered the need to deploy markers as a QC step in a breeding program.
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Affiliation(s)
| | - Christian Fatokun
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Abou Togola
- International Institute of Tropical Agriculture (IITA), Kano, Nigeria
| | - Stella Salvo
- Bayer Research and Development Services LLC, Chesterfield, MO, United States
| | | | - Mansur Sani Ahmad
- International Institute of Tropical Agriculture (IITA), Kano, Nigeria
| | | | - Garba Bala
- International Institute of Tropical Agriculture (IITA), Kano, Nigeria
| | - Ousmane Boukar
- International Institute of Tropical Agriculture (IITA), Kano, Nigeria
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Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies. Int J Mol Sci 2021; 22:ijms22189713. [PMID: 34575872 PMCID: PMC8465131 DOI: 10.3390/ijms22189713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023] Open
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.
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NEGRÃO LD, SOUSA PVDL, BARRADAS AM, BRANDÃO ADCAS, ARAÚJO MADM, MOREIRA-ARAÚJO RSDR. Bioactive compounds and antioxidant activity of crisphead lettuce (Lactuca sativa L.) of three different cultivation systems. FOOD SCIENCE AND TECHNOLOGY 2021. [DOI: 10.1590/fst.04120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Mercati F, Sunseri F. Genetic Diversity Assessment and Marker-Assisted Selection in Crops. Genes (Basel) 2020; 11:genes11121481. [PMID: 33317175 PMCID: PMC7763926 DOI: 10.3390/genes11121481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/07/2020] [Indexed: 01/22/2023] Open
Affiliation(s)
- Francesco Mercati
- CNR—Consiglio Nazionale delle Ricerche, Istituto di Bioscienze e Biorisorse (IBBR), Corso Calatafimi 414, 90129 Palermo, Italy
- Correspondence: (F.M.); (F.S.)
| | - Francesco Sunseri
- Dipartimento di Agraria, Università Mediterranea degli Studi di Reggio Calabria, Loc. Feo di Vito, 89124 Reggio Calabria, Italy
- Correspondence: (F.M.); (F.S.)
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Genotyping by RAD Sequencing Analysis Assessed the Genetic Distinctiveness of Experimental Lines and Narrowed Down the Genomic Region Responsible for Leaf Shape in Endive ( Cichorium endivia L.). Genes (Basel) 2020; 11:genes11040462. [PMID: 32340299 PMCID: PMC7231076 DOI: 10.3390/genes11040462] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/21/2020] [Accepted: 04/21/2020] [Indexed: 11/18/2022] Open
Abstract
The characterization of genetic diversity in elite breeding stocks is crucial for the registration and protection of new varieties. Moreover, experimental population structure analysis and information about the genetic distinctiveness of commercial materials are essential for crop breeding programs. The purpose of our research was to assess the genetic relationships of 32 endive (Cichorium endivia L.) breeding lines, 18 from var. latifolium (escarole) and 14 from var. crispum (curly), using heterologous Cichorium intybus-derived simple sequence repeats (SSR) markers and single-nucleotide polymorphisms (SNP) markers. We found that 14 out of 29 SSR markers were successfully amplified, but only 8 of them were related to polymorphic loci. To overcome the limitation of the low number of informative SSR marker loci, an alternative SNP-based approach was employed. The 4621 SNPs produced by a restriction site-associated DNA marker sequencing approach were able to fully discriminate the 32 endive accessions; most importantly, as many as 50 marker loci were found to distinguish the curly group from the escarole group. Interestingly, 24 of the marker loci mapped within a peripheral segment of chromosome 8 of lettuce (Lactuca sativa L.), spanning a chromosomal region of 49.6 Mb. Following Sanger sequencing-based validation, three genes were determined to carry nonsynonymous SNPs, and one of them matched a putative ortholog of AtELP1, subunit 1 of the Elongator complex. Considering that several previously characterized Elongator complex subunit mutants exhibited elongated and/or curly leaf phenotypes, this gene should be taken into consideration for a better understanding of the underlying mechanism controlling leaf shape in endive.
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Barcaccia G, Palumbo F, Scariolo F, Vannozzi A, Borin M, Bona S. Potentials and Challenges of Genomics for Breeding Cannabis Cultivars. FRONTIERS IN PLANT SCIENCE 2020; 11:573299. [PMID: 33101342 PMCID: PMC7546024 DOI: 10.3389/fpls.2020.573299] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 09/07/2020] [Indexed: 05/12/2023]
Abstract
Cannabis (Cannabis sativa L.) is an influential yet controversial agricultural plant with a very long and prominent history of recreational, medicinal, and industrial usages. Given the importance of this species, we deepened some of the main challenges-along with potential solutions-behind the breeding of new cannabis cultivars. One of the main issues that should be fixed before starting new breeding programs is the uncertain taxonomic classification of the two main taxa (e.g., indica and sativa) of the Cannabis genus. We tried therefore to examine this topic from a molecular perspective through the use of DNA barcoding. Our findings seem to support a unique species system (C. sativa) based on two subspecies: C. sativa subsp. sativa and C. sativa subsp. indica. The second key issue in a breeding program is related to the dioecy behavior of this species and to the comprehension of those molecular mechanisms underlying flower development, the main cannabis product. Given the role of MADS box genes in flower identity, we analyzed and reorganized all the genomic and transcriptomic data available for homeotic genes, trying to decipher the applicability of the ABCDE model in Cannabis. Finally, reviewing the limits of the conventional breeding methods traditionally applied for developing new varieties, we proposed a new breeding scheme for the constitution of F1 hybrids, without ignoring the indisputable contribution offered by genomics. In this sense, in parallel, we resumed the main advances in the genomic field of this species and, ascertained the lack of a robust set of SNP markers, provided a discriminant and polymorphic panel of SSR markers as a valuable tool for future marker assisted breeding programs.
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