Nuclear Species-Diagnostic SNP Markers Mined from 454 Amplicon Sequencing Reveal Admixture Genomic Structure of Modern Citrus Varieties

Abstract

Most cultivated Citrus species originated from interspecific hybridisation between four ancestral taxa (C. reticulata, C. maxima, C. medica, and C. micrantha) with limited further interspecific recombination due to vegetative propagation. This evolution resulted in admixture genomes with frequent interspecific heterozygosity. Moreover, a major part of the phenotypic diversity of edible citrus results from the initial differentiation between these taxa. Deciphering the phylogenomic structure of citrus germplasm is therefore essential for an efficient utilization of citrus biodiversity in breeding schemes. The objective of this work was to develop a set of species-diagnostic single nucleotide polymorphism (SNP) markers for the four Citrus ancestral taxa covering the nine chromosomes, and to use these markers to infer the phylogenomic structure of secondary species and modern cultivars. Species-diagnostic SNPs were mined from 454 amplicon sequencing of 57 gene fragments from 26 genotypes of the four basic taxa. Of the 1,053 SNPs mined from 28,507 kb sequence, 273 were found to be highly diagnostic for a single basic taxon. Species-diagnostic SNP markers (105) were used to analyse the admixture structure of varieties and rootstocks. This revealed C. maxima introgressions in most of the old and in all recent selections of mandarins, and suggested that C. reticulata × C. maxima reticulation and introgression processes were important in edible mandarin domestication. The large range of phylogenomic constitutions between C. reticulata and C. maxima revealed in mandarins, tangelos, tangors, sweet oranges, sour oranges, grapefruits, and orangelos is favourable for genetic association studies based on phylogenomic structures of the germplasm. Inferred admixture structures were in agreement with previous hypotheses regarding the origin of several secondary species and also revealed the probable origin of several acid citrus varieties. The developed species-diagnostic SNP marker set will be useful for systematic estimation of admixture structure of citrus germplasm and for diverse genetic studies.

Changes in Anthocyanin Production during Domestication of Citrus

“…S5). Group A includes varieties of Japanese origin that show admixture from other species (Kitajima et al, 2007;Curk et al, 2015;GarciaLor et al, 2015). Our sequencing of genes other than Ruby in satsumas (C. unshiu) suggested introgression from pummelo that is different from that documented in Ponkan and Willowleaf (Wu et al, 2014).…”

Genetic Structure of Diploid Gametes for the Production of Triploid Citrus Hybrids

“…As for its genetic origin, Wu et al (2014) concluded that some mandarin types like `Ponkan´ and `Willowleaf´, result from interspecific introgressions of C. maxima (pummelo) into C. reticulata (wild mandarin). Later, García-Lor et al (2015) and Curk et al (2015) confirmed that the C. maxima genome was the main genome introgressed in the C. reticulata background of the mandarin germplasm.…”

“…A few cases of unreduced pollen gametes have been reported in citrus although that the the most important naturally cultivated triploid variety (`Tahiti´ lime) was probably originated through unreduced pollen from a diploid `Mexican´ lime (Curk et al, 2015). Luro et al (2004) identified a few triploid hybrids produced by 2n pollen from three different mandarins, `King´, `Hansen´ and `Ananas´, `Star Ruby´ grapefruit and `Tarroco Rosso´ and `Sanguinelli´ sweet oranges.…”

“…For `Mexican´ lime the allele inherited from C. medica and C. micrantha ancestors are respectively in first and second positions in table 3.1. Curk et al (2015) 1: Alleles. The numbers indicate the size of alleles in nucleotides for SSR markers and letters correspond to SNP markers alleles.…”

“…The lower diversity of diploid gametes produced by such meiotic mechanisms is also favorable to reconstruct phylogenomic structures similar to the two triploid limes ideotypes, optimizing the probability to select new variety phenotypically close to the ideotypes. The development and application of molecular markers diagnosis of the four ancestral taxa of cultivated citrus (Curk et al, 2015) will allow improving the efficiency of such reconstruction breeding strategies. On the other hand, the limitation of the effective interspecific recombination associated with predominant disomic inheritance, as illustrated by the decrease of the genetic length of the different genetic LGs for the tetraploid `Mexican´ lime, when compared with diploid and teraploid clementine maps, should impact breeding efficiency due to an increased linkage drag.…”