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Genetic structure analysis and selection of a core collection for carob tree germplasm conservation and management

  • M. Di Guardo
  • F. Scollo
  • A. Ninot
  • M. Rovira
  • J. F. Hermoso
  • G. Distefano
  • S. La MalfaEmail author
  • I. Batlle
Original Article
Part of the following topical collections:
  1. Population structure

Abstract

Carob (Ceratonia siliqua L.) is an important evergreen tree of the Mediterranean landscape. Its economic interest is increasing thanks also to the presence, in the seeds, of the locust bean gum (LBG), a galactomannan largely used by the food industry as a stabilizer and thickening agent. Its economic and ecological values make the understanding of carob genetic diversity of great interest both for breeding and conservation purposes. The world’s largest carob germplasm collection was genotyped using both eight carob-specific nuclear short sequence repeat (nSSR) and the sequencing of a chloroplast locus. The collection is composed of 215 accessions introduced from 12 countries of origin spanning from traditional to novel areas of cultivation. To assess the genetic diversity of the collection, several approaches were coupled: structure analysis, principal component analysis (PCA), and graphic clustering either from dissimilarity data and coancestry data. Structure analysis suggested the presence of two distinct genetic pools: one characterizing northeastern Spain and the second spread in other countries and southern Spain. The PCA and discriminant analysis of principal component (DAPC) complemented the structure results allowing a better understanding of the genetic differences between countries while the network-joining analysis provided additional insights on the similarity between individuals. Short sequence repeat (SSR) data coupled with phenotypic data (floral sex and status) were also used to define the first core collection of carobs. Multi-approach analysis of genetic diversity together with the definition of a core collection represent useful tools for the setup of genetic-guided intervention both for conservation and breeding purposes.

Keywords

Ceratonia siliqua L. Simple sequence repeats Chloroplast Genetic structure Principal component analysis 

Notes

Acknowledgments

The authors gratefully acknowledge Alex Baumel, Aix Marseille Universite, Marseille, France, for providing matK4LF sequence. A.N., M.R., J.F.H., and I.B. are grateful to CERCA Institution from the Generalitat of Catalonia for its support.

This study has been partially supported by the international project DYNAMIC “Deciphering sYmbiotic Networks in cArob-based MedIterranean agro-eCosystems” (https://dynamic.cirad.fr/en) supported by the French national research agency (ANR-14-CE02-0016).

Data archiving statement

Raw genotypic data were presented in Supplementary Table 2.

Supplementary material

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Supplementary Table 1 (DOCX 82 kb)
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Supplementary Table 2 (DOCX 48 kb)
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Supplementary Table 3 (DOCX 13 kb)
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Supplementary Table 4 (DOCX 12 kb)
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Supplementary Figure 1

Electropherograms of the sequencing of the matK4LF chloroplast locus. The alignment of the sequencing data allowed the detection of a T/G polymorphism at approximately 622 bp position (PNG 144 kb)

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High resolution image (TIFF 1054 kb)
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Supplementary Figure 2

Log likelihood curve (ΔK) calculated according to Evanno et al. (2005) plotted against increasing K value. A: plot of the whole carob collection, B: plot of the subset of individuals deemed as Subpop 1, C: plot of the subset of individuals deemed as Subpop 2 (PNG 741 kb)

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High resolution image (TIF 400 kb)
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Supplementary Figure 3

Absolute frequency of the sex of the accessions according to the country/region of origin (PNG 164 kb)

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High resolution image (TIF 523 kb)
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Supplementary Figure 4

Relative frequency of the distribution of the two haplotypes detected through the sequencing of the matK4LF chloroplast locus (PNG 76 kb)

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High resolution image (TIFF 29297 kb)
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Supplementary Figure 5

Discriminant Analysis of Principal Components (DAPC) based on the genetic data. Countries or regions of collection were used as grouping factor (PNG 753 kb)

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High resolution image (TIFF 73242 kb)

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Copyright information

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Authors and Affiliations

  1. 1.Dipartimento di Agricoltura, Alimentazione ed AmbienteUniversità di CataniaCataniaItaly
  2. 2.Institut de Recerca i Tecnologia Agroalimentàries, IRTA Fruit ProductionMas BovéTarragonaSpain

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