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Şahin ES, Talapov T, Ateş D, Can C, Tanyolaç MB. Genome wide association study of genes controlling resistance to Didymella rabiei Pathotype IV through genotyping by sequencing in chickpeas (Cicer arietinum). Genomics 2023; 115:110699. [PMID: 37597791 DOI: 10.1016/j.ygeno.2023.110699] [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] [Received: 02/28/2023] [Revised: 08/08/2023] [Accepted: 08/15/2023] [Indexed: 08/21/2023]
Abstract
Ascochyta blight (AB) is a major disease in chickpeas (Cicer arietinum L.) that can cause a yield loss of up to 100%. Chickpea germplasm collections at the center of origin offer great potential to discover novel sources of resistance to pests and diseases. Herein, 189 Cicer arietinum samples were genotyped via genotyping by sequencing. This chickpea collection was phenotyped for resistance to an aggressive Turkish Didymella rabiei Pathotype IV isolate. Genome-wide association studies based on different models revealed 19 single nucleotide polymorphism (SNP) associations on chromosomes 1, 2, 3, 4, 7, and 8. Although eight of these SNPs have been previously reported, to the best of our knowledge, the remaining ten were associated with AB resistance for the first time. The regions identified in this study can be addressed in future studies to reveal the genetic mechanism underlying AB resistance and can also be utilized in chickpea breeding programs to improve AB resistance in new chickpea varieties.
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Affiliation(s)
- Erdem Sefa Şahin
- Republic of Turkey, Ministry of Agriculture and Forestry, Aegean Agricultural Research Institute, Izmir, Turkey; Department of Bioengineering, Molecular Genetic Laboratory, Ege University, Izmir, Turkey
| | - Talap Talapov
- Department of Biology, Gaziantep University, Gaziantep, Turkey
| | - Duygu Ateş
- Department of Bioengineering, Molecular Genetic Laboratory, Ege University, Izmir, Turkey
| | - Canan Can
- Department of Biology, Gaziantep University, Gaziantep, Turkey
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Srungarapu R, Mahendrakar MD, Mohammad LA, Chand U, Jagarlamudi VR, Kondamudi KP, Kudapa H, Samineni S. Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm. Cells 2022; 11:cells11152457. [PMID: 35954301 PMCID: PMC9367858 DOI: 10.3390/cells11152457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.
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Affiliation(s)
- Rajasekhar Srungarapu
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Department of Molecular Biology and Biotechnology, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Mahesh Damodhar Mahendrakar
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Lal Ahamed Mohammad
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Uttam Chand
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Venkata Ramana Jagarlamudi
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Kiran Prakash Kondamudi
- Department of Statistics and Computer Applications, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Himabindu Kudapa
- Genomics, Pre-Breeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Srinivasan Samineni
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Correspondence:
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Rocchetti L, Gioia T, Logozzo G, Brezeanu C, Pereira LG, la Rosa LD, Marzario S, Pieri A, Fernie AR, Alseekh S, Susek K, Cook DR, Varshney RK, Agrawal SK, Hamwieh A, Bitocchi E, Papa R. Towards the Development, Maintenance and Standardized Phenotypic Characterization of Single-Seed-Descent Genetic Resources for Chickpea. Curr Protoc 2022; 2:e371. [PMID: 35179832 DOI: 10.1002/cpz1.371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Here we present the approach used to develop the INCREASE "Intelligent Chickpea" Collections, from analysis of the information on the life history and population structure of chickpea germplasm, the availability of genomic and genetic resources, the identification of key phenotypic traits and methodologies to characterize chickpea. We present two phenotypic protocols within H2O20 Project INCREASE to characterize, develop, and maintain chickpea single-seed-descent (SSD) line collections. Such protocols and related genetic resource data from the project will be available for the legume community to apply the standardized approaches to develop Chickpea Intelligent Collections further or for multiplication/seed-increase purposes. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Characterization of chickpea seeds for seed-trait descriptors Basic Protocol 2: Characterization of chickpea lines for plant-trait descriptors specific for primary seed increase.
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Affiliation(s)
- Lorenzo Rocchetti
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Tania Gioia
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Giuseppina Logozzo
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Creola Brezeanu
- Staţiunea de Cercetare Dezvoltare Pentru Legumicultură, Bacău, Romania
| | - Luis Guasch Pereira
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), Alcalá de Henares, Madrid, Spain
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology (CRF-INIA-CSIC), Alcalá de Henares, Madrid, Spain
| | - Stefania Marzario
- School of Agriculture, Forestry, Food, and Environmental Sciences, University of Basilicata, Potenza, Italy
| | - Alice Pieri
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology, Plovdiv, Bulgaria
| | - Karolina Susek
- Legume Genomics Team, Institute of Plant Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Douglas R Cook
- Department of Plant Pathology, University of California Davis, Davis, California
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India
| | - Shiv Kumar Agrawal
- Genetic Resources Section, International Center for Agricultural Research in Dry Areas (ICARDA), Agdal Rabat, Morocco
| | - Aladdin Hamwieh
- Genetic Resources Section, International Center for Agricultural Research in Dry Areas (ICARDA), Agdal Rabat, Morocco
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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Pasqualone A, Summo C, De Angelis D, Cucci G, Caranfa D, Lacolla G. Effect of Mineral and Organic Fertilization on desi and kabuli Chickpea ( Cicer arietinum L.): Plant Growth and Production, Hydration Properties, Bioactive Compounds, and Antioxidant Activity. PLANTS 2021; 10:plants10071441. [PMID: 34371640 PMCID: PMC8309255 DOI: 10.3390/plants10071441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/09/2021] [Accepted: 07/12/2021] [Indexed: 01/24/2023]
Abstract
Composting is a strategic technology to convert organic waste into environmentally friendly soil improvers, mitigating the pressure on landfills and contributing to sustainability. This research evaluates the effects of different doses of mineral/organic fertilizers on two chickpea types: desi and kabuli. A randomized block design with three replications and six conditions was adopted: non-fertilized control, two mineral fertilizations (M1, M2), and three organic fertilizations (B1, B2, B3). M1 and B1 provided for comparable NPK amounts. Fertilization and variety significantly influenced plant growth and production, and seed hydration. Fertilization had a lower influence on bioactive compounds. The highest seed yields were obtained with M2 (30–40–100 kg ha−1 of N, P2O5, and K2O, respectively. An addition of 40 kg ha−1 of P2O5 (M1) had no effect on seed yield. B1 (10 Mg ha−1 of Bio Vegetal) and M1 led to the same yield, which did not increase using higher doses of green compost. Mineral and organic fertilizations favored hydration and swelling of chickpeas. Desi chickpea showed a significantly higher seed yield but a lower seed weight than kabuli. Organic fertilization, combined with the recovery of peculiar chickpeas, which are more productive and richer in bioactive compounds, promotes a more sustainable food system.
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Affiliation(s)
- Antonella Pasqualone
- Department of Soil, Plant, and Food Science (Di.S.S.P.A.), University of Bari ‘Aldo Moro’, Via Amendola, 165/A, I-70126 Bari, Italy; (A.P.); (C.S.); (D.D.A.)
| | - Carmine Summo
- Department of Soil, Plant, and Food Science (Di.S.S.P.A.), University of Bari ‘Aldo Moro’, Via Amendola, 165/A, I-70126 Bari, Italy; (A.P.); (C.S.); (D.D.A.)
| | - Davide De Angelis
- Department of Soil, Plant, and Food Science (Di.S.S.P.A.), University of Bari ‘Aldo Moro’, Via Amendola, 165/A, I-70126 Bari, Italy; (A.P.); (C.S.); (D.D.A.)
| | - Giovanna Cucci
- Department of Agricultural and Environmental Science (Di.S.A.A.T.), University of Bari ‘Aldo Moro’, Via Amendola, 165/A, I-70126 Bari, Italy; (D.C.); (G.L.)
- Correspondence:
| | - Davide Caranfa
- Department of Agricultural and Environmental Science (Di.S.A.A.T.), University of Bari ‘Aldo Moro’, Via Amendola, 165/A, I-70126 Bari, Italy; (D.C.); (G.L.)
| | - Giovanni Lacolla
- Department of Agricultural and Environmental Science (Di.S.A.A.T.), University of Bari ‘Aldo Moro’, Via Amendola, 165/A, I-70126 Bari, Italy; (D.C.); (G.L.)
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Molecular Genetic Diversity and Population Structure in Ethiopian Chickpea Germplasm Accessions. DIVERSITY 2021. [DOI: 10.3390/d13060247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Chickpea (Cicer arietinum L.) is a cheap source of protein and rich in minerals for people living in developing countries. In order to assess the existing molecular genetic diversity and determine population structures in selected Ethiopian chickpea germplasm accessions (118), a set of 46 simple sequence repeat (SSR) markers equally distributed on the chickpea genome were genotyped. A total of 572 alleles were detected from 46 SSR markers, and the number of alleles per locus varied from 2 (ICCM0289) to 28 (TA22). The average number of alleles per locus, polymorphism information content, and expected heterozygosity were 12, 0.684, and 0.699, respectively. Phylogenetic analysis grouped the 118 chickpea genotypes from diverse sources into three evolutionary and/or biological groups (improved desi, improved kabuli, and landraces). The population structure analysis revealed six sub-populations from 118 chickpea genotypes studied. AMOVA revealed that 57%, 29%, and 14% of the total genetic variations were observed among individuals, within populations, and among populations. The insights into the genetic diversity at molecular levels in the Ethiopian germplasm lines can be used for designing conservation strategies as well as the diverse germplasm lines identified in this study can be used for trait dissection and trait improvement.
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Costantini M, Summo C, Centrone M, Rybicka I, D’Agostino M, Annicchiarico P, Caponio F, Pavan S, Tamma G, Pasqualone A. Macro- and Micro-Nutrient Composition and Antioxidant Activity of Chickpea and Pea Accessions. POL J FOOD NUTR SCI 2021. [DOI: 10.31883/pjfns/135813] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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Gunnabo AH, van Heerwaarden J, Geurts R, Wolde-Meskel E, Degefu T, Giller KE. Phylogeography and Symbiotic Effectiveness of Rhizobia Nodulating Chickpea (Cicer arietinum L.) in Ethiopia. MICROBIAL ECOLOGY 2021; 81:703-716. [PMID: 33098438 PMCID: PMC7982387 DOI: 10.1007/s00248-020-01620-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/12/2020] [Indexed: 06/11/2023]
Abstract
Chickpea (Cicer arietinum L.) used to be considered a restrictive host that nodulated and fixed nitrogen only with Mesorhizobium ciceri and M. mediterraneum. Recent analysis revealed that chickpea can also establish effective symbioses with strains of several other Mesorhizobium species such as M. loti, M. haukuii, M. amorphae, M. muleiense, etc. These strains vary in their nitrogen fixation potential inviting further exploration. We characterized newly collected mesorhizobial strains isolated from various locations in Ethiopia to evaluate genetic diversity, biogeographic structure and symbiotic effectiveness. Symbiotic effectiveness was evaluated in Leonard Jars using a locally released chickpea cultivar "Nattoli". Most of the new isolates belonged to a clade related to M. plurifarium, with very few sequence differences, while the total collection of strains contained three additional mesorhizobial genospecies associated with M. ciceri, M. abyssinicae and an unidentified Mesorhizobium species isolated from a wild host in Eritrea. The four genospecies identified represented a subset of the eight major Mesorhizobium clades recently reported for Ethiopia based on metagenomic data. All Ethiopian strains had nearly identical symbiotic genes that grouped them in a single cluster with M. ciceri, M. mediterraneum and M. muleiense, but not with M. plurifarium. Some phylogeographic structure was observed, with elevation and geography explaining some of the genetic differences among strains, but the relation between genetic identity and symbiotic effectiveness was observed to be weak.
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Affiliation(s)
- A H Gunnabo
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands.
| | - J van Heerwaarden
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands.
| | - R Geurts
- Laboratory of Molecular Biology, Department of Plant Science, Wageningen University, Wageningen, The Netherlands
| | - E Wolde-Meskel
- World Agroforestry Centre (ICRAF), Addis Ababa, Ethiopia
| | - T Degefu
- International Crops Research Institute for the Semi-Arid Tropics, Addis Ababa, Ethiopia
| | - K E Giller
- Plant Production Systems Group, Wageningen University and Research, Wageningen, The Netherlands
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In Vitro and In Vivo Nutraceutical Characterization of Two Chickpea Accessions: Differential Effects on Hepatic Lipid Over-Accumulation. Antioxidants (Basel) 2020; 9:antiox9030268. [PMID: 32214012 PMCID: PMC7139887 DOI: 10.3390/antiox9030268] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/20/2020] [Accepted: 03/22/2020] [Indexed: 12/23/2022] Open
Abstract
Dietary habits are crucially important to prevent the development of lifestyle-associated diseases. Diets supplemented with chickpeas have numerous benefits and are known to improve body fat composition. The present study was undertaken to characterize two genetically and phenotypically distinct accessions, MG_13 and PI358934, selected from a global chickpea collection. Rat hepatoma FaO cells treated with a mixture of free fatty acids (FFAs) (O/P) were used as an in vitro model of hepatic steatosis. In parallel, a high-fat diet (HFD) animal model was also established. In vitro and in vivo studies revealed that both chickpea accessions showed a significant antioxidant ability. However, only MG_13 reduced the lipid over-accumulation in steatotic FaO cells and in the liver of HFD fed mice. Moreover, mice fed with HFD + MG_13 displayed a lower level of glycemia and aspartate aminotransferase (AST) than HFD mice. Interestingly, exposure to MG_13 prevented the phosphorylation of the inflammatory nuclear factor kappa beta (NF-kB) which is upregulated during HFD and known to be linked to obesity. To conclude, the comparison of the two distinct chickpea accessions revealed a beneficial effect only for the MG_13. These findings highlight the importance of studies addressing the functional characterization of chickpea biodiversity and nutraceutical properties.
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Recovery, Assessment, and Molecular Characterization of Minor Olive Genotypes in Tunisia. PLANTS 2020; 9:plants9030382. [PMID: 32244853 PMCID: PMC7154912 DOI: 10.3390/plants9030382] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/26/2022]
Abstract
Olive is one of the oldest cultivated species in the Mediterranean Basin, including Tunisia, where it has a wide diversity, with more than 200 cultivars, of both wild and feral forms. Many minor cultivars are still present in marginal areas of Tunisia, where they are maintained by farmers in small local groves, but they are poorly characterized and evaluated. In order to recover this neglected germplasm, surveys were conducted in different areas, and 31 genotypes were collected, molecularly characterized with 12 nuclear microsatellite (simple sequence repeat (SSR)) markers, and compared with 26 reference cultivars present in the Tunisian National Olive collection. The analysis revealed an overall high genetic diversity of this olive's germplasm, but also discovered the presence of synonymies and homonymies among the commercialized varieties. The structure analysis showed the presence of different gene pools in the analyzed germplasm. In particular, the marginal germplasm from Ras Jbal and Azmour is characterized by gene pools not present in commercial (Nurseries) varieties, pointing out the very narrow genetic base of the commercialized olive material in Tunisia, and the need to broaden it to avoid the risk of genetic erosion of this species in this country.
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Serendipitous In Situ Conservation of Faba Bean Landraces in Tunisia: A Case Study. Genes (Basel) 2020; 11:genes11020236. [PMID: 32102450 PMCID: PMC7074078 DOI: 10.3390/genes11020236] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Revised: 02/13/2020] [Accepted: 02/16/2020] [Indexed: 12/19/2022] Open
Abstract
Cultivation of faba bean (Vicia faba L.) in Tunisia is largely based on improved varieties of the crop. However, a few farmers continue to produce local cultivars or landraces. The National Gene Bank of Tunisia (NGBT) recently launched a collection project for faba bean landraces, with special focus on the regions of the North West, traditionally devoted to cultivating grain legumes, and where around 80% of the total national faba bean cultivation area is located. The seed phenotypic features of the collected samples were studied, and the genetic diversity and population structure analyzed using simple sequence repeat markers. The genetic constitution of the present samples was compared to that of faba bean samples collected by teams of the International Center for Agricultural Research in the Dry Areas (ICARDA) in the 1970s in the same region, and stored at the ICARDA gene bank. The results of the diversity analysis demonstrate that the recently collected samples and those stored at ICARDA largely overlap, thus demonstrating that over the past 50 years, little genetic change has occurred to the local faba bean populations examined. These findings suggest that farmers serendipitously applied international best practices for in situ conservation of agricultural crops.
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Ricciardi L, Mazzeo R, Marcotrigiano AR, Rainaldi G, Iovieno P, Zonno V, Pavan S, Lotti C. Assessment of Genetic Diversity of the "Acquaviva Red Onion" ( Allium cepa L.) Apulian Landrace. PLANTS 2020; 9:plants9020260. [PMID: 32085407 PMCID: PMC7076509 DOI: 10.3390/plants9020260] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/13/2020] [Accepted: 02/14/2020] [Indexed: 11/18/2022]
Abstract
Onion (Allium cepa L.) is the second most important vegetable crop worldwide and is widely appreciated for its health benefits. Despite its significant economic importance and its value as functional food, onion has been poorly investigated with respect to its genetic diversity. Herein, we surveyed the genetic variation in the “Acquaviva red onion” (ARO), a landrace with a century-old history of cultivation in a small town in the province of Bari (Apulia, Southern of Italy). A set of 11 microsatellite markers were used to explore the genetic variation in a germplasm collection consisting of 13 ARO populations and three common commercial types. Analyses of genetic structure with parametric and non-parametric methods highlighted that the ARO represents a well-defined gene pool, clearly distinct from the Tropea and Montoro landraces with which it is often mistaken. In order to provide a description of bulbs, usually used for fresh consumption, soluble solid content and pungency were evaluated, showing higher sweetness in the ARO with respect to the two above mentioned landraces. Overall, the present study is useful for the future valorization of the ARO, which could be promoted through quality labels which could contribute to limit commercial frauds and improve the income of smallholders.
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Affiliation(s)
- Luigi Ricciardi
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Rosa Mazzeo
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- Correspondence: (R.M.); (C.L.)
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Guglielmo Rainaldi
- Department of Biosciences, Biotechnologies and Biopharmaceuticals, University of Bari, Via Orabona 4, 70125 Bari, Italy;
| | - Paolo Iovieno
- Department of Energy Technologies, Bioenergy, Biorefinery and Green Chemistry Division, ENEA Trisaia Research Center, S.S. 106 Ionica, km 419+500, 75026 Rotondella (MT), Italy;
| | - Vito Zonno
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, Plant Genetics and Breeding Unit University of Bari, Via Amendola 165/A, 70125 Bari, Italy; (L.R.); (A.R.M.); (V.Z.); (S.P.)
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Via Napoli 25, 71122 Foggia, Italy
- Correspondence: (R.M.); (C.L.)
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Summo C, De Angelis D, Ricciardi L, Caponio F, Lotti C, Pavan S, Pasqualone A. Nutritional, physico-chemical and functional characterization of a global chickpea collection. J Food Compost Anal 2019. [DOI: 10.1016/j.jfca.2019.103306] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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13
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Pavan S, Bardaro N, Fanelli V, Marcotrigiano AR, Mangini G, Taranto F, Catalano D, Montemurro C, De Giovanni C, Lotti C, Ricciardi L. Genotyping by Sequencing of Cultivated Lentil ( Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables. Front Genet 2019; 10:872. [PMID: 31620173 PMCID: PMC6759463 DOI: 10.3389/fgene.2019.00872] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 08/20/2019] [Indexed: 11/13/2022] Open
Abstract
Cultivated lentil (Lens culinaris Medik.) is one of the oldest domesticated crops and one of the most important grain legumes worldwide. The Mediterranean Basin holds large part of lentil biodiversity; however, no genetic structure was defined within the Mediterranean gene pool. In this study, we used high-throughput genotyping by sequencing to resolve the genetic structure of the Mediterranean ex situ lentil collection held at the Italian National Research Council. Sequencing of a 188-plex genotyping-by-sequencing library and bioinformatics treatment of data yielded 6,693 single nucleotide polymorphisms. Analysis of nonredundant genotypes with nonparametric and parametric methods highlighted the occurrence of five highly differentiated genetic clusters. Clustering could be related to geographic patterns and phenotypic traits, indicating that post-domestication routes introducing cultivation in Mediterranean countries and selection were major forces shaping lentil population structure. The estimation of the fixation index FST at individual single nucleotide polymorphism loci allowed the identification of distinctive alleles across clusters, suggesting the possibility to set up molecular keys for the assignment of lentil germplasm to specific genetic groups. Finally, significant associations between markers and phenotypic data were identified. Overall, the results of this study are of major importance for lentil conservation genetics and breeding and provide insights on the lentil evolutionary history.
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Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy.,Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Nicoletta Bardaro
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Angelo Raffaele Marcotrigiano
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Giacomo Mangini
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Francesca Taranto
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy.,CREA Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Domenico Catalano
- Institute of Biomedical Technologies, National Research Council (CNR), Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Claudio De Giovanni
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Concetta Lotti
- Department of Agricultural, Food and Environmental Sciences, University of Foggia, Foggia, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, Section of Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
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14
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Farahani S, Maleki M, Mehrabi R, Kanouni H, Scheben A, Batley J, Talebi R. Whole Genome Diversity, Population Structure, and Linkage Disequilibrium Analysis of Chickpea ( Cicer arietinum L.) Genotypes Using Genome-Wide DArTseq-Based SNP Markers. Genes (Basel) 2019; 10:E676. [PMID: 31487948 PMCID: PMC6770975 DOI: 10.3390/genes10090676] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/26/2019] [Accepted: 08/20/2019] [Indexed: 01/09/2023] Open
Abstract
Characterization of genetic diversity, population structure, and linkage disequilibrium is a prerequisite for proper management of breeding programs and conservation of genetic resources. In this study, 186 chickpea genotypes, including advanced "Kabuli" breeding lines and Iranian landrace "Desi" chickpea genotypes, were genotyped using DArTseq-Based single nucleotide polymorphism (SNP) markers. Out of 3339 SNPs, 1152 markers with known chromosomal position were selected for genome diversity analysis. The number of mapped SNP markers varied from 52 (LG8) to 378 (LG4), with an average of 144 SNPs per linkage group. The chromosome size that was covered by SNPs varied from 16,236.36 kbp (LG8) to 67,923.99 kbp (LG5), while LG4 showed a higher number of SNPs, with an average of 6.56 SNPs per Mbp. Polymorphism information content (PIC) value of SNP markers ranged from 0.05 to 0.50, with an average of 0.32, while the markers on LG4, LG6, and LG8 showed higher mean PIC value than average. Unweighted neighbor joining cluster analysis and Bayesian-based model population structure grouped chickpea genotypes into four distinct clusters. Principal component analysis (PCoA) and discriminant analysis of principal component (DAPC) results were consistent with that of the cluster and population structure analysis. Linkage disequilibrium (LD) was extensive and LD decay in chickpea germplasm was relatively low. A few markers showed r2 ≥ 0.8, while 2961 pairs of markers showed complete LD (r2 = 1), and a huge LD block was observed on LG4. High genetic diversity and low kinship value between pairs of genotypes suggest the presence of a high genetic diversity among the studied chickpea genotypes. This study also demonstrates the efficiency of DArTseq-based SNP genotyping for large-scale genome analysis in chickpea. The genotypic markers provided in this study are useful for various association mapping studies when combined with phenotypic data of different traits, such as seed yield, abiotic, and biotic stresses, and therefore can be efficiently used in breeding programs to improve chickpea.
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Affiliation(s)
- Somayeh Farahani
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Mojdeh Maleki
- Department of Plant Protection, Varamin-Pishva Branch, Islamic Azad University, Varamin, P.O.Box: 33817-74895, Iran
| | - Rahim Mehrabi
- Department of Biotechnology, College of Agriculture, Isfahan University of Technology, Isfahan P.O. Box: 8415683111, Iran
| | - Homayoun Kanouni
- Kordestan Agricultural and Natural Resources and Education Center, Agricultural Research, Education and Extension Organization (AREEO), Sanandaj, P.O.Box:714, Iran
| | - Armin Scheben
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
| | - Reza Talebi
- Department of Agronomy & Plant Breeding, College of Agriculture, Sanandaj Branch, Islamic Azad University, Sanandaj, P.O. Box:618, Iran.
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15
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Sion S, Taranto F, Montemurro C, Mangini G, Camposeo S, Falco V, Gallo A, Mita G, Debbabi OS, Amar FB, Pavan S, Roseti V, Miazzi MM. Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs. PLANTS (BASEL, SWITZERLAND) 2019; 8:E268. [PMID: 31387331 PMCID: PMC6724140 DOI: 10.3390/plants8080268] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 11/17/2022]
Abstract
The olive is a fruit tree species with a century-old history of cultivation in theMediterranean basin. In Apulia (Southern Italy), the olive is of main social, cultural and economicimportance, and represents a hallmark of the rural landscape. However, olive cultivation in thisregion is threatened by the recent spread of the olive quick decline syndrome (OQDS) disease, thusthere is an urgent need to explore biodiversity and search for genetic sources of resistance. Herein,a genetic variation in Apulian olive germplasm was explored, as a first step to identify genotypeswith enhanced bio-agronomic traits, including resistance to OQDS. A preselected set of nuclearmicrosatellite markers allowed the acquisition of genotypic profiles, and to define geneticrelationships between Apulian germplasm and widespread cultivars. The analysis highlighted thebroad genetic variation in Apulian accessions and the presence of different unique genetic profiles.The results of this study lay a foundation for the organization of new breeding programs for olivegenetic improvement.
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Affiliation(s)
- S Sion
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - F Taranto
- Research Centre for Cereal and Industrial Crops, (CREA-CI), S.S. 71122 Foggia, Italy.
| | - C Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy.
| | - G Mangini
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - S Camposeo
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - V Falco
- CNR Institute of Sciences of Food Production, Unit of Lecce, 73100 Lecce, Italy
| | - A Gallo
- CNR Institute of Sciences of Food Production, Unit of Lecce, 73100 Lecce, Italy
| | - G Mita
- CNR Institute of Sciences of Food Production, Unit of Lecce, 73100 Lecce, Italy
| | | | - F Ben Amar
- Institut de l'Olivier, Route de l'aéroport, BP 1087, Sfax 3000, Tunisia
| | - S Pavan
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - V Roseti
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - M M Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
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16
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018; 8:43. [PMID: 29354354 PMCID: PMC5750240 DOI: 10.1007/s13205-017-1057-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/19/2017] [Indexed: 12/27/2022] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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17
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018. [PMID: 29354354 DOI: 10.1007/s1320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- 3Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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