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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Plant Sci. | doi: 10.3389/fpls.2019.01128

Phylogenetic origin of primary and secondary metabolic pathway genes revealed by C. maxima and C. reticulata diagnostic SNPs

 Milena do Amaral Santos1,  Márcia Fabiana B. De Paula1, Frédérique Ollitrault2, Ronan Rivallan2,  Edson M. de Andrade Silva1,  Abelmon Gesteira3, François Luro4, Dominique Garcia2,  Patrick Ollitrault2* and  Fabienne Micheli2*
  • 1Universidade Estadual de Santa Cruz, Brazil
  • 2Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), France
  • 3Embrapa Mandioca e Fruticultura, Brazil
  • 4Institut National de la Recherche Agronomique (INRA), France

Modern cultivated Citrus species and varieties result from interspecific hybridization between four ancestral taxa. Among them, C. maxima and C. reticulata, closely associated with the pummelo and mandarin horticultural groups, respectively, were particularly important as the progenitors of sour and sweet oranges (C. aurantium and C. sinensis), grapefruits (C. paradisi) and hybrid types resulting from modern breeding programs (tangors, tangelos and orangelos). The differentiation between the four ancestral taxa and the phylogenomic structure of modern varieties widely drive the phenotypic diversity’s organization. In particular, strong phenotypic differences exist in the coloration and sweetness and represent important criteria for breeders. In this context, focusing on the genes of the sugar, carotenoid and chlorophyll biosynthesis pathways, the aim of this work was to develop a set of diagnostic single nucleotide polymorphism (DSNP) markers to distinguish the ancestral haplotypes of C. maxima and C. reticulata, and to provide information at the intraspecific diversity level (within C. reticulata or C. maxima). In silico analysis allowed the identification of 3,347 SNPs from selected genes. Among them, 1,024 were detected as potential differentiation markers between C. reticulata and C. maxima. A total of 115 SNPs were successfully developed using a competitive PCR technology. Their transferability among all Citrus species and the true citrus genera was very good, with only 0.87% of missing data. The ancestral alleles of the SNPs were identified, and we validated the usefulness of the developed markers for tracing the ancestral haplotype in large germplasm collections and sexually recombined progeny issued from the C. reticulata/C. maxima admixture gene pool. These markers will pave the way for targeted association studies based on ancestral haplotypes.

Keywords: mandarins, Pummelos, KASPar, Citrus quality, Carotenoids, Sugars

Received: 29 Apr 2019; Accepted: 15 Aug 2019.

Edited by:

Sergio LANTERI, University of Turin, Italy

Reviewed by:

Concetta Licciardello, Council for Agricultural and Economics Research, Italy
Umesh K. Reddy, West Virginia State University, United States
Mikeal L. Roose, University of California, Riverside, United States  

Copyright: © 2019 do Amaral Santos, De Paula, Ollitrault, Rivallan, de Andrade Silva, Gesteira, Luro, Garcia, Ollitrault and Micheli. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Patrick Ollitrault, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, 34000, Languedoc-Roussillon, France, patrick.ollitrault@cirad.fr
Mx. Fabienne Micheli, Centre de coopération internationale en recherche agronomique pour le développement (CIRAD), Montpellier, 34000, Languedoc-Roussillon, France, fabienne.micheli@cirad.fr