Dataset Information

Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs.

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.

SUBMITTER: Sion S

PROVIDER: S-EPMC6724140 | biostudies-literature | 2019 Aug

REPOSITORIES: biostudies-literature

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Publications

Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs.

Sion S S Taranto F F Montemurro C C Mangini G G Camposeo S S Falco V V Gallo A A Mita G G Debbabi O Saddoud OS Amar F Ben FB Pavan S S Roseti V V Miazzi M M MM

Plants (Basel, Switzerland) 20190805 8

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 A ...[more]

PMID: 31387331

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Project description:Olive (Olea europaea L.) is a major fruit crop in the Mediterranean Basin. Ex-situ olive management is essential to ensure optimal use of genetic resources in breeding programs. The Worldwide Olive Germplasm Bank of Córdoba (WOGBC), Spain, and Marrakech (WOGBM), Morocco, are currently the largest existing olive germplasm collections. Characterization, identification, comparison and authentication of all accessions in both collections could thus provide useful information for managing olive germplasm for its preservation, exchange within the scientific community and use in breeding programs. Here we applied 20 microsatellite markers (SSR) and 11 endocarp morphological traits to discriminate and authenticate 1091 olive accessions belonging to WOGBM and WOGBC (554 and 537, respectively). Of all the analyzed accessions, 672 distinct SSR profiles considered as unique genotypes were identified, but only 130 were present in both collections. Combining SSR markers and endocarp traits led to the identification of 535 cultivars (126 in common) and 120 authenticated cultivars. No significant differences were observed between collections regarding the allelic richness and diversity index. We concluded that the genetic diversity level was stable despite marked contrasts in varietal composition between collections, which could be explained by their different collection establishment conditions. This highlights the extent of cultivar variability within WOGBs. Moreover, we detected 192 mislabeling errors, 72 of which were found in WOGBM. A total of 228 genotypes as molecular variants of 74 cultivars, 79 synonyms and 39 homonyms as new cases were identified. Both collections were combined to define the nested core collections of 55, 121 and 150 sample sizes proposed for further studies. This study was a preliminary step towards managing and mining the genetic diversity in both collections while developing collaborations between olive research teams to conduct association mapping studies by exchanging and phenotyping accessions in contrasted environmental sites.

Project description:BackgroundBreeders and geneticists use statistical models to separate genetic and environmental effects on phenotype. A common way to separate these effects is to model a descriptor of an environment, a contemporary group or herd, and account for genetic relationship between animals across environments. However, separating the genetic and environmental effects in smallholder systems is challenging due to small herd sizes and weak genetic connectedness across herds. We hypothesised that accounting for spatial relationships between nearby herds can improve genetic evaluation in smallholder systems. Furthermore, geographically referenced environmental covariates are increasingly available and could model underlying sources of spatial relationships. The objective of this study was therefore, to evaluate the potential of spatial modelling to improve genetic evaluation in dairy cattle smallholder systems.MethodsWe performed simulations and real dairy cattle data analysis to test our hypothesis. We modelled environmental variation by estimating herd and spatial effects. Herd effects were considered independent, whereas spatial effects had distance-based covariance between herds. We compared these models using pedigree or genomic data.ResultsThe results show that in smallholder systems (i) standard models do not separate genetic and environmental effects accurately, (ii) spatial modelling increases the accuracy of genetic evaluation for phenotyped and non-phenotyped animals, (iii) environmental covariates do not substantially improve the accuracy of genetic evaluation beyond simple distance-based relationships between herds, (iv) the benefit of spatial modelling was largest when separating the genetic and environmental effects was challenging, and (v) spatial modelling was beneficial when using either pedigree or genomic data.ConclusionsWe have demonstrated the potential of spatial modelling to improve genetic evaluation in smallholder systems. This improvement is driven by establishing environmental connectedness between herds, which enhances separation of genetic and environmental effects. We suggest routine spatial modelling in genetic evaluations, particularly for smallholder systems. Spatial modelling could also have a major impact in studies of human and wild populations.

Dataset Information

Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs.

Publications

Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs.

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