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.
Highlights
Citrus and its relatives are native in Southern to Eastern Asia, Malaysia, New Caledonia, and Australia [1]
Citrus maxima originated in the Malay Archipelago and Indonesia, C. medica evolved in north-eastern India and the nearby region of Myanmar and China, C. reticulata diversification occurred over a region including Vietnam, southern China, and Japan [11,12] and C. micrantha seems to be originated from southern Philippian archipelago [1]
Tangelos, tangors, sweet oranges, sour oranges, grapefruits, and the orangelo provide a large range of phylogenomic constitutions between the C. reticulata and C. maxima clusters. This is favourable for genetic association studies based on phylogenomic structures of the germplasm
Summary
Citrus and its relatives are native in Southern to Eastern Asia, Malaysia, New Caledonia, and Australia [1]. Despite the difficulties involved in establishing a consensual classification of edible citrus, molecular analyses provided decisive information for the comprehension of domestication and the relations between various cultivated species of Citrus [4,5,6,7,8,9,10] These studies identified four ancestral taxa [C. medica L. Most of the genomes of cultivated Citrus are mosaics of large chromosome fragments from the basic taxa in frequent interspecific heterozygosity Another consequence of apomixis and horticultural vegetative propagation practices is that most citrus horticultural groups (sweet oranges, limes, lemons, grapefruits, clementines and satsumas) have minimal intragroup genetic diversity resulting from clonal variation/selection [17]. Diagnostic markers for ancestral taxa will aid the management of interspecific introgression in sexual breeding schemes and, more widely, will enable studies of sexual recombination at the diploid or polyploid levels and to analyse the mechanisms of 2n gamete formation for genotypes of interspecific origin
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