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Bourguiba H, Batnini MA, Naccache C, Zitouna N, Trifi-Farah N, Audergon JM, Krichen L. Chloroplastic and nuclear diversity of endemic Prunus armeniaca L. species in the oasis agroecosystems. Genetica 2021; 149:239-251. [PMID: 34231081 DOI: 10.1007/s10709-021-00127-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/28/2021] [Indexed: 11/26/2022]
Abstract
Tunisia is characterized by the presence of specific seed-propagated apricot (Prunus armeniaca L.) material which is found in the oasis agroecosystems. In order to highlight the genetic diversity, population structure, and demographic history of this germplasm, 33 apricot accessions collected from six different oasis regions in southwestern Tunisia were genotyped using 24 microsatellite markers. A total number of 111 alleles was detected with an average of 4.62 alleles per locus. Bayesian model-based clustering analysis indicated four subdivisions within the collection sampled that corresponded mainly to the geographic origin of the material. The analysis of the 33 accessions using chloroplast markers allowed the identification of 32 haplotypes. Overall, the present study highlighted the high Tunisian apricot's diversity in the traditional oasis agroecosystems with low genetic differentiation. Understanding the structure of seed-propagated apricot collection is crucial for managing collections in regard to adaptive traits for Arid and Saharan climates as well as for identifying interesting genotypes that can be integrated into international coordinated actions of breeding programs.
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Affiliation(s)
- Hedia Bourguiba
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia.
| | - Mohamed-Amine Batnini
- Department of Plant Pathology, OARDC/OSU, 120 Selby, 1680 Madison Ave, Wooster, OH, 44691, USA
| | - Chahnez Naccache
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Biochimie et Biotechnology (LR01ES05), Tunis, Tunisia
| | - Nadia Zitouna
- LR16IPT05, Laboratoire de Génomique Biomédicale et Oncogénétique, Institut Pasteur de Tunis, Université de Tunis El Manar, Tunis, Tunisia
| | - Neila Trifi-Farah
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia
| | - Jean-Marc Audergon
- INRAe Centre PACA, UR 1052 GAFL, Domaine St Maurice, 67, allée des chênes, CS60094, 84143, Montfavet Cedex, France
| | - Lamia Krichen
- Université Tunis El Manar (UTM) - Faculté Des Sciences De Tunis (FST), Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie (LGMIB) (LR99ES12), Campus universitaire Farhat Hached, Tunis, Tunisia
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Production, pomological and nutraceutical properties of apricot. Journal of Food Science and Technology 2019; 56:12-23. [PMID: 30728542 DOI: 10.1007/s13197-018-3481-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Revised: 10/10/2018] [Accepted: 10/29/2018] [Indexed: 10/27/2022]
Abstract
Apricot (Prunus sp.) is an important fruit crop worldwide. Despite recent advances in apricot research, much is still to be done to improve its productivity and environmental adaptability. The availability of wild apricot germplasms with economically interesting traits is a strong incentive to increase research panels toward improving its economic, environmental and nutritional characteristics. New technologies and genomic studies have generated a large amount of raw data that the mining and exploitation can help decrypt the biology of apricot and enhance its agronomic values. Here, we outline recent findings in relation to apricot production, pomological and nutraceutical properties. In particular, we retrace its origin from central Asia and the path it took to attain Europe and other production areas around the Mediterranean basin while locating it in the rosaceae family and referring to its genetic diversities and new attempts of classification. The production, nutritional, and nutraceutical importance of apricot are recapped in an easy readable and comparable way. We also highlight and discuss the effects of late frost damages on apricot production over different growth stages, from swollen buds to green fruits formation. Issues related to the length of production season and biotic and abiotic environmental challenges are also discussed with future perspective on how to lengthen the production season without compromising the fruit quality and productivity.
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Hamadeh B, Chalak L, Coppens d’Eeckenbrugge G, Benoit L, Joly HI. Evolution of almond genetic diversity and farmer practices in Lebanon: impacts of the diffusion of a graft-propagated cultivar in a traditional system based on seed-propagation. BMC PLANT BIOLOGY 2018; 18:155. [PMID: 30081821 PMCID: PMC6080396 DOI: 10.1186/s12870-018-1372-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 07/26/2018] [Indexed: 05/20/2023]
Abstract
BACKGROUND Under cultivation, many outcrossing fruit tree species have switched from sexual reproduction to vegetative propagation. Traditional production systems have persisted, where cultivar propagation is based on a mixed reproductive system. For millenia, almond, Prunus dulcis, has been propagated by seeds. Almond grafting remained of little importance until recently. In Lebanon, both sexual and clonal reproductions are used for almond propagation. We used 15 microsatellite markers to investigate the effect of introducing graft-propagated cultivars and associated practices, on the structure of the genetic diversity among and within the two main Lebanese cultivars. RESULTS As expected, the sexually propagated cultivar Khachabi exhibited more genotypic and genetic diversity than the vegetatively propagated cultivar Halwani. It also exhibited lower differentiation among populations. The distribution of clones showed that propagation modes were not exclusive: farmers have introduced clonal propagation in the seed-propagated cultivar while they have maintained a diversity of genotypes within populations that were mostly graft-propagated. These practices are also important to avoid mate limitations that hamper fruit production in a self-incompatible species. 'Khachabi' is structured into two gene pools separated by the Lebanese mountains. As to 'Halwani', two different gene pools were introduced. The most ancient one shares the same geographic range as 'Khachabi'; longtime coexistence and sexual reproduction have resulted in admixture with 'Khachabi'. In contrast, the more recent introduction of the second gene pool in the Bekaa region followed an evolution towards more extensive clonal propagation of 'Halwani' limiting hybridizations. Furthermore, some pairs of geographically distant 'Halwani' orchards, exhibited low genetic distances, suggesting that a network of exchanges between farmers was effective on a large scale and/or that farmers brought clonal plant material from a common source. CONCLUSIONS Almond diversification in Lebanon is clearly related to the evolution of propagation practices adapted to self-incompatible cultivars. The comparison between both cultivars demonstrated the genetic effects of the introduction of a new cultivar and the associated grafting propagation practices. Our study provided information to develop a strategy for in situ conservation of cultivars and to limit gene flow from introduced material to ancient orchards.
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Affiliation(s)
- Bariaa Hamadeh
- Lebanese Agricultural Research Institute, Fanar, Lebanon
- Université Montpellier 2, UMR CEFE, 34293 Montpellier Cedex, France
- Doctoral School of Sciences and Technologies, Lebanese University, Hadath, Lebanon
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Lamis Chalak
- Faculty of Agriculture, Lebanese University, Dekwaneh, Lebanon
| | - Geo Coppens d’Eeckenbrugge
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
| | - Laure Benoit
- CIRAD, UMR CBGP, F-34398 Montpellier, France
- CBGP, Univ Montpellier, CIRAD, INRA, IRD, Montpellier SupAgro, Montpellier, France
| | - Hélène I. Joly
- CIRAD, UMR AGAP, Dynamiques de la Diversité, Sociétés et Environnements (DDSE), TA A-61/03 Avenue Agropolis, F-34398 Montpellier Cedex 5, France
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Jiao Y, Jia HM, Li XW, Chai ML, Jia HJ, Chen Z, Wang GY, Chai CY, van de Weg E, Gao ZS. Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra). BMC Genomics 2012; 13:201. [PMID: 22621340 PMCID: PMC3505174 DOI: 10.1186/1471-2164-13-201] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 04/03/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in recent years has stimulated its extension in China and introduction to Australia. A limited number of co-dominant markers have been developed and applied in genetic diversity and identity studies. Here we report, for the first time, a survey of whole genome shotgun data to develop a large number of simple sequence repeat (SSR) markers to analyse the genetic diversity of the common cultivated Chinese bayberry and the relationship with three other Myrica species. RESULTS The whole genome shotgun survey of Chinese bayberry produced 9.01Gb of sequence data, about 26x coverage of the estimated genome size of 323 Mb. The genome sequences were highly heterozygous, but with little duplication. From the initial assembled scaffold covering 255 Mb sequence data, 28,602 SSRs (≥5 repeats) were identified. Dinucleotide was the most common repeat motif with a frequency of 84.73%, followed by 13.78% trinucleotide, 1.34% tetranucleotide, 0.12% pentanucleotide and 0.04% hexanucleotide. From 600 primer pairs, 186 polymorphic SSRs were developed. Of these, 158 were used to screen 29 Chinese bayberry accessions and three other Myrica species: 91.14%, 89.87% and 46.84% SSRs could be used in Myrica adenophora, Myrica nana and Myrica cerifera, respectively. The UPGMA dendrogram tree showed that cultivated Myrica rubra is closely related to Myrica adenophora and Myrica nana, originating in southwest China, and very distantly related to Myrica cerifera, originating in America. These markers can be used in the construction of a linkage map and for genetic diversity studies in Myrica species. CONCLUSION Myrica rubra has a small genome of about 323 Mb with a high level of heterozygosity. A large number of SSRs were identified, and 158 polymorphic SSR markers developed, 91% of which can be transferred to other Myrica species.
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Affiliation(s)
- Yun Jiao
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Hui-min Jia
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Xiong-wei Li
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Ming-liang Chai
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Hui-juan Jia
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
| | - Zhe Chen
- BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China
| | - Guo-yun Wang
- Fruit Research Institute, Yuyao, Ningbo, 315400, China
| | - Chun-yan Chai
- Forestry Technology Extension Center, Cixi Ningbo, 315300, China
| | - Eric van de Weg
- Plant Breeding-Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Zhong-shan Gao
- Department of Horticulture, The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Hangzhou 310058, China
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Bourguiba H, Audergon JM, Krichen L, Trifi-Farah N, Mamouni A, Trabelsi S, D’Onofrio C, Asma BM, Santoni S, Khadari B. Loss of genetic diversity as a signature of apricot domestication and diffusion into the Mediterranean Basin. BMC PLANT BIOLOGY 2012; 12:49. [PMID: 22510209 PMCID: PMC3511222 DOI: 10.1186/1471-2229-12-49] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2011] [Accepted: 02/23/2012] [Indexed: 05/06/2023]
Abstract
BACKGROUND Domestication generally implies a loss of diversity in crop species relative to their wild ancestors because of genetic drift through bottleneck effects. Compared to native Mediterranean fruit species like olive and grape, the loss of genetic diversity is expected to be more substantial for fruit species introduced into Mediterranean areas such as apricot (Prunus armeniaca L.), which was probably primarily domesticated in China. By comparing genetic diversity among regional apricot gene pools in several Mediterranean areas, we investigated the loss of genetic diversity associated with apricot selection and diffusion into the Mediterranean Basin. RESULTS According to the geographic origin of apricots and using Bayesian clustering of genotypes, Mediterranean apricot (207 genotypes) was structured into three main gene pools: 'Irano-Caucasian', 'North Mediterranean Basin' and 'South Mediterranean Basin'. Among the 25 microsatellite markers used, only one displayed deviations from the frequencies expected under neutrality. Similar genetic diversity parameters were obtained within each of the three main clusters using both all SSR loci and only 24 SSR loci based on the assumption of neutrality. A significant loss of genetic diversity, as assessed by the allelic richness and private allelic richness, was revealed from the 'Irano-Caucasian' gene pool, considered as a secondary centre of diversification, to the northern and southwestern Mediterranean Basin. A substantial proportion of shared alleles was specifically detected when comparing gene pools from the 'North Mediterranean Basin' and 'South Mediterranean Basin' to the secondary centre of diversification. CONCLUSIONS A marked domestication bottleneck was detected with microsatellite markers in the Mediterranean apricot material, depicting a global image of two diffusion routes from the 'Irano-Caucasian' gene pool: North Mediterranean and Southwest Mediterranean. This study generated genetic insight that will be useful for management of Mediterranean apricot germplasm as well as genetic selection programs related to adaptive traits.
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Affiliation(s)
- Hedia Bourguiba
- INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), F-34398, Montpellier, France
- INRA Centre PACA – UR1052 GAFL, Domaine St Maurice, BP94, 84143, Montfavet Cedex, France
- Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus Universitaire, 2092, El Manar, Tunisia
| | - Jean-Marc Audergon
- INRA Centre PACA – UR1052 GAFL, Domaine St Maurice, BP94, 84143, Montfavet Cedex, France
| | - Lamia Krichen
- Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus Universitaire, 2092, El Manar, Tunisia
| | - Neila Trifi-Farah
- Faculté des Sciences de Tunis, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Campus Universitaire, 2092, El Manar, Tunisia
| | - Ali Mamouni
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknès, Morocco
| | - Samia Trabelsi
- Université de Blida, Chaire d’arboriculture, Blida, Algeria
| | - Claudio D’Onofrio
- Department of Fruit Science and Plant Protection of Woody Species “G. Scaramuzzi”, section of Fruit Science, University of Pisa, Via del Borghetto, 80, 56124, Pisa, Italy
| | - Bayram M Asma
- Department of Biology, Inonu University, Malatya, 44280, Turkey
| | - Sylvain Santoni
- INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), F-34398, Montpellier, France
| | - Bouchaib Khadari
- INRA, UMR 1334 Amélioration Génétique et Adaptation des Plantes (AGAP), F-34398, Montpellier, France
- CBNMED, UMR 1334 AGAP, F-34398, Montpellier, France
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