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Rajendran S, Kang YM, Yang IB, Eo HB, Baek KL, Jang S, Eybishitz A, Kim HC, Je BI, Park SJ, Kim CM. Functional characterization of plant specific Indeterminate Domain (IDD) transcription factors in tomato (Solanum lycopersicum L.). Sci Rep 2024; 14:8015. [PMID: 38580719 PMCID: PMC10997639 DOI: 10.1038/s41598-024-58903-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 04/04/2024] [Indexed: 04/07/2024] Open
Abstract
Plant-specific transcription factors (TFs) are responsible for regulating the genes involved in the development of plant-specific organs and response systems for adaptation to terrestrial environments. This includes the development of efficient water transport systems, efficient reproductive organs, and the ability to withstand the effects of terrestrial factors, such as UV radiation, temperature fluctuations, and soil-related stress factors, and evolutionary advantages over land predators. In rice and Arabidopsis, INDETERMINATE DOMAIN (IDD) TFs are plant-specific TFs with crucial functions, such as development, reproduction, and stress response. However, in tomatoes, IDD TFs remain uncharacterized. Here, we examined the presence, distribution, structure, characteristics, and expression patterns of SlIDDs. Database searches, multiple alignments, and motif alignments suggested that 24 TFs were related to Arabidopsis IDDs. 18 IDDs had two characteristic C2H2 domains and two C2HC domains in their coding regions. Expression analyses suggest that some IDDs exhibit multi-stress responsive properties and can respond to specific stress conditions, while others can respond to multiple stress conditions in shoots and roots, either in a tissue-specific or universal manner. Moreover, co-expression database analyses suggested potential interaction partners within IDD family and other proteins. This study functionally characterized SlIDDs, which can be studied using molecular and bioinformatics methods for crop improvement.
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Affiliation(s)
- Sujeevan Rajendran
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Yu Mi Kang
- Department of Horticultural and Life Science, Pusan National University, Milyang, 50463, Korea
| | - In Been Yang
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Hye Bhin Eo
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Kyung Lyung Baek
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jeollabuk-do, 55365, Republic of Korea
| | - Assaf Eybishitz
- World Vegetable Center, P.O. Box 42, Tainan, 74199, Shanhua, Taiwan
| | - Ho Cheol Kim
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea
| | - Byeong Il Je
- Department of Horticultural and Life Science, Pusan National University, Milyang, 50463, Korea
| | - Soon Ju Park
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, Korea
| | - Chul Min Kim
- Department of Horticulture Industry, Wonkwang University, Iksan, 54538, Republic of Korea.
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Lazaridi E, Kapazoglou A, Gerakari M, Kleftogianni K, Passa K, Sarri E, Papasotiropoulos V, Tani E, Bebeli PJ. Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding. PLANTS (BASEL, SWITZERLAND) 2024; 13:758. [PMID: 38592762 PMCID: PMC10975389 DOI: 10.3390/plants13060758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/23/2024] [Accepted: 03/02/2024] [Indexed: 04/10/2024]
Abstract
Landraces and indigenous varieties comprise valuable sources of crop species diversity. Their utilization in plant breeding may lead to increased yield and enhanced quality traits, as well as resilience to various abiotic and biotic stresses. Recently, new approaches based on the rapid advancement of genomic technologies such as deciphering of pangenomes, multi-omics tools, marker-assisted selection (MAS), genome-wide association studies (GWAS), and CRISPR/Cas9 gene editing greatly facilitated the exploitation of landraces in modern plant breeding. In this paper, we present a comprehensive overview of the implementation of new genomic technologies and highlight their importance in pinpointing the genetic basis of desirable traits in landraces and indigenous varieties of annual, perennial herbaceous, and woody crop species cultivated in the Mediterranean region. The need for further employment of advanced -omic technologies to unravel the full potential of landraces and indigenous varieties underutilized genetic diversity is also indicated. Ultimately, the large amount of genomic data emerging from the investigation of landraces and indigenous varieties reveals their potential as a source of valuable genes and traits for breeding. The role of landraces and indigenous varieties in mitigating the ongoing risks posed by climate change in agriculture and food security is also highlighted.
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Affiliation(s)
- Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece;
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Kondylia Passa
- Department of Agriculture, University of Patras, Nea Ktiria, 30200 Messolonghi, Greece;
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Vasileios Papasotiropoulos
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece; (E.L.); (M.G.); (K.K.); (E.S.); (V.P.); (E.T.)
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Shah LR, Ahmed N, Hussain K, Mansoor S, Khan T, Khan I, Narayan S, Afroza B, Murtaza I, Shikari AB, Bhat B, Masoodi KZ. Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics. BMC Genom Data 2024; 25:9. [PMID: 38281048 PMCID: PMC10822167 DOI: 10.1186/s12863-024-01190-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 01/01/2024] [Indexed: 01/29/2024] Open
Abstract
The cold stress susceptibility of tomato (Solanum lycopersicum) curtails its cultivation, with significant impact in temperate regions and on cropping seasons. To unravel genomic regions responsible for cold stress resilience, a diverse set of fifty genotypes encompassing cultivated, wild species, and landraces were genotyped using genotyping-by-sequencing. Over two years and six trials employing both early and late sowing, these lines were evaluated. Illumina-based next-generation sequencing produced up to 3 million reads per sample from individually sequenced library pools. The Tassel pipeline yielded 10,802 variants, subsequently filtered to 3,854 SNPs for genome-wide association analysis (GWAS). Employing clustering methods (population structure) via TASSEL, SNPhylo, and Kinship matrix, the fifty genotypes clustered into four distinct gene pools. The GWAS for cold tolerance in tomato integrated key traits including yield. Using six independent phenotypic datasets representing various environments, the study identified 4,517 significant marker-trait associations for cold tolerance traits. Notably, pivotal variations (> 10%) in cold stress tolerance, particularly proline content, were linked to marker-trait associations. Additionally, 5,727 significant marker-trait associations for yield and yield-related traits were unveiled, shedding light on fruit yield and directly associated attributes. The investigation pinpointed 685 candidate genes across all examined traits, including 60 genes associated with biological processes within these genomic regions. Remarkably, 7 out of the 60 genes were directly linked to abiotic stress tolerance, functioning as stress-responsive genes either directly or indirectly. The identified genes, particularly those associated with stress response, could hold the key to enhancing cold tolerance and overall crop productivity in tomato cultivation.
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Affiliation(s)
- Labiba Riyaz Shah
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Nazeer Ahmed
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Khursheed Hussain
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Sheikh Mansoor
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Republic of Korea.
| | - Tamana Khan
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Imran Khan
- Division of Statistics, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Sumati Narayan
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Baseerat Afroza
- Division of Vegetable Science, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Imtiyaz Murtaza
- Division of Basic Sciences and Humanities, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India
| | - Asif Bashir Shikari
- Division of Genetics and Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Jammu and Kashmir, Wadoora, Sopore, 193201, India
| | - Basharat Bhat
- NAHEP, IDP, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, J&K, 190025, India
| | - Khalid Z Masoodi
- Transcriptomics Lab (K-Lab), Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, 190025, India.
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Posadinu CM, Rodriguez M, Conte P, Piga A, Attene G. Fruit quality and shelf-life of Sardinian tomato (Solanum lycopersicum L.) landraces. PLoS One 2023; 18:e0290166. [PMID: 38064465 PMCID: PMC10707699 DOI: 10.1371/journal.pone.0290166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/02/2023] [Indexed: 12/18/2023] Open
Abstract
The conservation and characterization of landraces have key roles in the safeguarding and valorization of agrobiodiversity. Indeed, these plant genetic resources represent an important crop heritage with quality and sensory characteristics that can be of great use to consumers and industry. In addition, the preservation of genetic resources from the risk of progressive genetic erosion, and the enhancement of their potential can contribute to food security and improve the nutritional value of food. Accordingly, this study aimed to investigate a collection of Sardinian tomato landraces for parameters that have determinant roles in evaluating their responses to conservation, and therefore to consumer acceptance. Six Sardinian landraces and two commercial varieties were cultivated in a two-years off-season trial, harvested at two different maturity stages (turning, red-ripe) and characterized using 14 fruit-related quality parameters that define the marketability, nutritional value, and flavor of the fruit. Data were collected at intervals of 10 days, starting from the harvest date and over 30 days of storage under refrigeration. The simultaneous analysis of all the qualitative characteristics for the different genotypes allowed to clearly differentiate the local varieties from the commercial varieties and a few landraces emerged for their satisfactory performances, e.g. "Tamatta kaki" ad "Tamatta groga de appiccai". In particular, the "Tamatta groga de appiccai" showed satisfactory lycopene content at marketable stages (average 5.65 mg 100g-1 FF), a peculiar orange-pink color with the highest hue angle values (range: H°T0 = 72.55-H°T30 = 48.26), and the highest firmness among the landraces of the red-ripe group (range: EpT0 = 1.64-EpT30 = 0.54 N mm-1). These results highlight the potential of some of the Sardinian tomato landraces for developing new varieties or promoting their direct valorization in local markets and could considerably increase the effectiveness and efficiency of agrobiodiversity conservation strategies.
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Affiliation(s)
| | - Monica Rodriguez
- Department of Agriculture, University of Sassari, Sassari, Italy
- Centro Interdipartimentale per la Conservazione e Valorizzazione della Biodiversità Vegetale, University of Sassari, Alghero, Italy
| | - Paola Conte
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Antonio Piga
- Department of Agriculture, University of Sassari, Sassari, Italy
| | - Giovanna Attene
- Department of Agriculture, University of Sassari, Sassari, Italy
- Centro Interdipartimentale per la Conservazione e Valorizzazione della Biodiversità Vegetale, University of Sassari, Alghero, Italy
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Pushkova EN, Borkhert EV, Novakovskiy RO, Dvorianinova EM, Rozhmina TA, Zhuchenko AA, Zhernova DA, Turba AA, Yablokov AG, Sigova EA, Krasnov GS, Bolsheva NL, Melnikova NV, Dmitriev AA. Selection of Flax Genotypes for Pan-Genomic Studies by Sequencing Tagmentation-Based Transcriptome Libraries. PLANTS (BASEL, SWITZERLAND) 2023; 12:3725. [PMID: 37960081 PMCID: PMC10650069 DOI: 10.3390/plants12213725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023]
Abstract
Flax (Linum usitatissimum L.) products are used in the food, pharmaceutical, textile, polymer, medical, and other industries. The creation of a pan-genome will be an important advance in flax research and breeding. The selection of flax genotypes that sufficiently cover the species diversity is a crucial step for the pan-genomic study. For this purpose, we have adapted a method based on Illumina sequencing of transcriptome libraries prepared using the Tn5 transposase (tagmentase). This approach reduces the cost of sample preparation compared to commercial kits and allows the generation of a large number of cDNA libraries in a short time. RNA-seq data were obtained for 192 flax plants (3-6 individual plants from 44 flax accessions of different morphology and geographical origin). Evaluation of the genetic relationship between flax plants based on the sequencing data revealed incorrect species identification for five accessions. Therefore, these accessions were excluded from the sample set for the pan-genomic study. For the remaining samples, typical genotypes were selected to provide the most comprehensive genetic diversity of flax for pan-genome construction. Thus, high-throughput sequencing of tagmentation-based transcriptome libraries showed high efficiency in assessing the genetic relationship of flax samples and allowed us to select genotypes for the flax pan-genomic analysis.
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Affiliation(s)
- Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Tatiana A. Rozhmina
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia; (T.A.R.); (A.A.Z.)
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Daiana A. Zhernova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Anastasia A. Turba
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Arthur G. Yablokov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (E.N.P.); (E.V.B.); (R.O.N.); (E.M.D.); (D.A.Z.); (A.A.T.); (A.G.Y.); (E.A.S.); (G.S.K.); (N.L.B.)
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Gómez-Espejo AL, Sansaloni CP, Burgueño J, Toledo FH, Benavides-Mendoza A, Reyes-Valdés MH. Worldwide Selection Footprints for Drought and Heat in Bread Wheat (Triticum aestivum L.). PLANTS 2022; 11:plants11172289. [PMID: 36079671 PMCID: PMC9460392 DOI: 10.3390/plants11172289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/18/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022]
Abstract
Genome–environment Associations (GEA) or Environmental Genome-Wide Association scans (EnvGWAS) have been poorly applied for studying the genomics of adaptive traits in bread wheat landraces (Triticum aestivum L.). We analyzed 990 landraces and seven climatic variables (mean temperature, maximum temperature, precipitation, precipitation seasonality, heat index of mean temperature, heat index of maximum temperature, and drought index) in GEA using the FarmCPU approach with GAPIT. Historical temperature and precipitation values were obtained as monthly averages from 1970 to 2000. Based on 26,064 high-quality SNP loci, landraces were classified into ten subpopulations exhibiting high genetic differentiation. The GEA identified 59 SNPs and nearly 89 protein-encoding genes involved in the response processes to abiotic stress. Genes related to biosynthesis and signaling are mainly mediated by auxins, abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonates (JA), which are known to operate together in modulation responses to heat stress and drought in plants. In addition, we identified some proteins associated with the response and tolerance to stress by high temperatures, water deficit, and cell wall functions. The results provide candidate regions for selection aimed to improve drought and heat tolerance in bread wheat and provide insights into the genetic mechanisms involved in adaptation to extreme environments.
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Affiliation(s)
- Ana L. Gómez-Espejo
- Programa de Doctorado en Recursos Fitogenéticos para Zonas Áridas, Universidad Autónoma Agraria Antonio Narro (UAAAN), Saltillo 25315, Mexico or
| | | | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico
| | - Fernando H. Toledo
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico
| | - Adalberto Benavides-Mendoza
- Programa de Doctorado en Recursos Fitogenéticos para Zonas Áridas, Universidad Autónoma Agraria Antonio Narro (UAAAN), Saltillo 25315, Mexico or
| | - M. Humberto Reyes-Valdés
- Programa de Doctorado en Recursos Fitogenéticos para Zonas Áridas, Universidad Autónoma Agraria Antonio Narro (UAAAN), Saltillo 25315, Mexico or
- Correspondence:
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Farinon B, Picarella ME, Siligato F, Rea R, Taviani P, Mazzucato A. Phenotypic and Genotypic Diversity of the Tomato Germplasm From the Lazio Region in Central Italy, With a Focus on Landrace Distinctiveness. FRONTIERS IN PLANT SCIENCE 2022; 13:931233. [PMID: 35937347 PMCID: PMC9355589 DOI: 10.3389/fpls.2022.931233] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Italy is a recognized secondary center of diversification for cultivated tomato (Solanum lycopersicum L.). The study of phenotypic and genetic diversity in landrace collections is important for germplasm conservation and valorization. Here, we set up to study the tomato germplasm collected in the region of Lazio in Central Italy, with a focus on the distinctiveness among landraces and the attribution of membership to unnamed accessions. Our regional collection included 32 accessions belonging to eight different locally recognized landraces and 19 unnamed accessions. All accessions were gathered from local farmers and are preserved in the collection held at the Regional Agency for the Development and the Innovation of Lazio Agriculture (ARSIAL) and at the University of Tuscia. We included 13 control genotypes comprising nine landraces from neighbor regions and four reference cultivars. The collection showed wide phenotypic variability for several qualitative and quantitative traits, such as leaf border and shape, inflorescence type, fruit shape, green shoulder, fruit weight (range 14-277 g), locule number (2-12), shape index (0.54-2.65), yield (0.24-3.08 kg/plant), and soluble solids (3.4-7.5°B). A few landraces showed uncommon phenotypes, such as potato leaf, colorless fruit epidermis, or delayed ripening. Multivariate analysis of 25 cardinal phenotypic variables separated the accessions into two distinct groups; accessions showing a flattened-ribbed fruit were distinguished from those with round to elongate fruits with smooth structure. Genotyping analysis of 7,720 SNPs was performed using the tomato array platform SolCAP, to point out the genetic relationship among the studied accessions. A neighbor-joining tree analysis allowed to confirm or deny phenotypic data and to assign some of the unnamed accessions to recognized groups. Allelic status at marker loci linked to resistance genes commonly used in breeding identified accessions putatively derived from modern material or commercial hybrids, thus not classifiable as landraces. Overall, this study provided the information useful to preserve, valorize, and juridically protect tomato local landraces from the Lazio region and will in addition be helpful to their improvement by breeding.
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Affiliation(s)
- Barbara Farinon
- Laboratory of Biotechnologies of Vegetable Crops, Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Maurizio E. Picarella
- Laboratory of Biotechnologies of Vegetable Crops, Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Francesca Siligato
- Laboratory of Biotechnologies of Vegetable Crops, Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | - Roberto Rea
- ARSIAL, Regional Agency for the Development and the Innovation of Lazio Agriculture, Rome, Italy
| | - Paola Taviani
- ARSIAL, Regional Agency for the Development and the Innovation of Lazio Agriculture, Rome, Italy
| | - Andrea Mazzucato
- Laboratory of Biotechnologies of Vegetable Crops, Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
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Rau D, Attene G, Rodriguez M, Baghino L, Pisanu AB, Sanna D, Acquadro A, Portis E, Comino C. The Population Structure of a Globe Artichoke Worldwide Collection, as Revealed by Molecular and Phenotypic Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:898740. [PMID: 35865281 PMCID: PMC9294547 DOI: 10.3389/fpls.2022.898740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/13/2022] [Indexed: 05/27/2023]
Abstract
The knowledge of the organization of the domesticated gene pool of crop species is an essential requirement to understand crop evolution, to rationalize conservation programs, and to support practical decisions in plant breeding. Here, we integrate simple sequence repeat (SSR) analysis and phenotypic characterization to investigate a globe artichoke collection that comprises most of the varieties cultivated worldwide. We show that the cultivated gene pool of globe artichoke includes five distinct genetic groups associated with the major phenotypic typologies: Catanesi (which based on our analysis corresponds to Violetti di Provenza), Spinosi, Violetti di Toscana, Romaneschi, and Macau. We observed that 17 and 11% of the molecular and phenotypic variance, respectively, is between these groups, while within groups, strong linkage disequilibrium and heterozygote excess are evident. The divergence between groups for quantitative traits correlates with the average broad-sense heritability within the groups. The phenotypic divergence between groups for both qualitative and quantitative traits is strongly and positively correlated with SSR divergence (FST) between groups. All this implies a low population size and strong bottleneck effects, and indicates a long history of clonal propagation and selection during the evolution of the domesticated gene pool of globe artichoke. Moreover, the comparison between molecular and phenotypic population structures suggests that harvest time, plant architecture (i.e., plant height, stem length), leaf spininess, head morphology (i.e., head shape, bract shape, spininess) together with the number of heads per plant were the main targets of selection during the evolution of the cultivated germplasm. We emphasize our findings in light of the potential exploitation of this collection for association mapping studies.
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Affiliation(s)
- Domenico Rau
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Giovanna Attene
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Monica Rodriguez
- Dipartimento di Agraria, Sezione di Agronomia, Coltivazioni Erbacee e Genetica (SACEG), Università degli Studi di Sassari, Sassari, Italy
| | - Limbo Baghino
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Anna Barbara Pisanu
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Davide Sanna
- Agenzia AGRIS Sardegna (Servizio Ricerca sui Sistemi Colturali Erbacei, Settore Innovazione dei Modelli Gestionali e Studio Della Biodiversità Nelle Colture Intensive), Oristano, Italy
| | - Alberto Acquadro
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Ezio Portis
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
| | - Cinzia Comino
- Dipartimento di Scienze Agrarie, Forestali ed Alimentari (DISAFA), Genetica Vegetale (Plant Genetics), Università degli Studi di Torino, Turin, Italy
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Zhu F, Fernie AR, Scossa F. Preparation and Curation of Omics Data for Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:127-150. [PMID: 35641762 DOI: 10.1007/978-1-0716-2237-7_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
With the development of large-scale molecular phenotyping platforms, genome-wide association studies have greatly developed, being no longer limited to the analysis of classical agronomic traits, such as yield or flowering time, but also embracing the dissection of the genetic basis of molecular traits. Data generated by omics platforms, however, pose some technical and statistical challenges to the classical methodology and assumptions of an association study. Although genotyping data are subject to strict filtering procedures, and several advanced statistical approaches are now available to adjust for population structure, less attention has been instead devoted to the preparation of omics data prior to GWAS. In the present chapter, we briefly present the methods to acquire profiling data from transcripts, proteins, and small molecules, and discuss the tools and possibilities to clean, normalize, and remove the unwanted variation from large datasets of molecular phenotypic traits prior to their use in GWAS.
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, China
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Federico Scossa
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.
- Council for Agricultural Research and Economics (CREA), Research Centre for Genomics and Bioinformatics (CREA-GB), Rome, Italy.
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Tripodi P, Soler S, Campanelli G, Díez MJ, Esposito S, Sestili S, Figàs MR, Leteo F, Casanova C, Platani C, Soler E, Bertone A, Pereira-Dias L, Palma D, Burguet R, Pepe A, Rosa-Martínez E, Prohens J, Cardi T. Genome wide association mapping for agronomic, fruit quality, and root architectural traits in tomato under organic farming conditions. BMC PLANT BIOLOGY 2021; 21:481. [PMID: 34686145 PMCID: PMC8532347 DOI: 10.1186/s12870-021-03271-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 10/11/2021] [Indexed: 05/12/2023]
Abstract
BACKGROUND Opportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Large panels of tomato varieties represent a valuable resource of traits of interest under sustainable cultivation systems and for genome-wide association studies (GWAS). For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we used a heterogeneous set of 244 traditional and improved tomato accessions grown under organic field trials. Here we report comprehensive phenotyping and GWAS using over 37,300 SNPs obtained through double digest restriction-site associated DNA (dd-RADseq). RESULTS A wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most traits. A variable level of heritability was observed with values up to 69% for morphological traits while, among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has been a minor objective for breeding activities. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families. Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits. CONCLUSIONS Results of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.
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Affiliation(s)
- Pasquale Tripodi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy.
| | - Salvador Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Gabriele Campanelli
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP, Italy
| | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Salvatore Esposito
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
| | - Sara Sestili
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP, Italy
| | - Maria R Figàs
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Fabrizio Leteo
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP, Italy
| | - Cristina Casanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Cristiano Platani
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP, Italy
| | - Elena Soler
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Aldo Bertone
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP, Italy
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Daniela Palma
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP, Italy
| | - Resurrección Burguet
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Andrea Pepe
- CREA Research Centre for Vegetable and Ornamental Crops, Monsampolo del Tronto, AP, Italy
| | - Elena Rosa-Martínez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, 46022, Valencia, Spain.
| | - Teodoro Cardi
- CREA Research Centre for Vegetable and Ornamental Crops, Via dei Cavalleggeri 25, 84098, Pontecagnano Faiano, SA, Italy
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