Genotyping by sequencing reveals the interspecific C. maxima / C. reticulata admixture along the genomes of modern citrus varieties of mandarins, tangors, tangelos, orangelos and grapefruits.

Amel Oueslati,Hélène Vignes,Pierre Mournet,Patrick Ollitrault,Amel Salhi-Hannachi,François Luro,Randall P Niedz

doi:10.1371/journal.pone.0185618

Abstract

The mandarin horticultural group is an important component of world citrus production for the fresh fruit market. This group formerly classified as C. reticulata is highly polymorphic and recent molecular studies have suggested that numerous cultivated mandarins were introgressed by C. maxima (the pummelos). C. maxima and C. reticulata are also the ancestors of sweet and sour oranges, grapefruit, and therefore of all the “small citrus” modern varieties (mandarins, tangors, tangelos) derived from sexual hybridization between these horticultural groups. Recently, NGS technologies have greatly modified how plant evolution and genomic structure are analyzed, moving from phylogenetics to phylogenomics. The objective of this work was to develop a workflow for phylogenomic inference from Genotyping By Sequencing (GBS) data and to analyze the interspecific admixture along the nine citrus chromosomes for horticultural groups and recent varieties resulting from the combination of the C. reticulata and C. maxima gene pools. A GBS library was established from 55 citrus varieties, using the ApekI restriction enzyme and selective PCR to improve the read depth. Diagnostic polymorphisms (DPs) of C. reticulata/C. maxima differentiation were identified and used to decipher the phylogenomic structure of the 55 varieties. The GBS approach was powerful and revealed 30,289 SNPs and 8,794 Indels with 12.6% of missing data. 11,133 DPs were selected covering the nine chromosomes with a higher density in genic regions. GBS combined with the detection of DPs was powerful for deciphering the “phylogenomic karyotypes” of cultivars derived from admixture of the two ancestral species after a limited number of interspecific recombinations. All the mandarins, mandarin hybrids, tangelos and tangors analyzed displayed introgression of C. maxima in different parts of the genome. C. reticulata/C. maxima admixture should be a major component of the high phenotypic variability of this germplasm opening up the way for association studies based on phylogenomics.

Highlights

Citrus is the most important fruit crop in the world, with a production of over 156 million tons and a cultivated area of 9.8 million hectares
The objective of the present work was to develop an efficient Genotyping By Sequencing (GBS) approach in citrus, to analyze in depth the phylogenomic structures of modern varieties of the horticultural groups derived from the C. reticulata and C. maxima gene pools
GBS reveals the phylogenomic structures of modern citrus varieties calling

Summary

Introduction

Citrus is the most important fruit crop in the world, with a production of over 156 million tons and a cultivated area of 9.8 million hectares (http://www.fao.org/faostat/en/#data, 2014). The genetic and cytogenetic diversity of this group, revealed by molecular markers [5,6,7,8,9,10] and chromosomal banding patterns [11], is large. It displays a wide phenotypic diversity for fruit pomology, peel and leaf oils contents [12,13], and tolerance to biotic and abiotic stresses [14].This phenotypic and genetic variability reflects a long history of cultivation, in which many mutations and natural hybridizations, including introgression of C. maxima (Burm.) Merr. Mandarin x tangor, mandarin x tangelo and tangor x tangelo hybridizations were carried out [18]

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