Next generation haplotyping to decipher nuclear genomic interspecific admixture in Citrusspecies: analysis of chromosome 2

Abstract

BackgroundThe most economically important Citrus species originated by natural interspecific hybridization between four ancestral taxa (Citrus reticulata, Citrus maxima, Citrus medica, and Citrus micrantha) and from limited subsequent interspecific recombination as a result of apomixis and vegetative propagation. Such reticulate evolution coupled with vegetative propagation results in mosaic genomes with large chromosome fragments from the basic taxa in frequent interspecific heterozygosity. Modern breeding of these species is hampered by their complex heterozygous genomic structures that determine species phenotype and are broken by sexual hybridisation. Nevertheless, a large amount of diversity is present in the citrus gene pool, and breeding to allow inclusion of desirable traits is of paramount importance. However, the efficient mobilization of citrus biodiversity in innovative breeding schemes requires previous understanding of Citrus origins and genomic structures. Haplotyping of multiple gene fragments along the whole genome is a powerful approach to reveal the admixture genomic structure of current species and to resolve the evolutionary history of the gene pools. In this study, the efficiency of parallel sequencing with 454 methodology to decipher the hybrid structure of modern citrus species was assessed by analysis of 16 gene fragments on chromosome 2.Results454 amplicon libraries were established using the Fluidigm array system for 48 genotypes and 16 gene fragments from chromosome 2. Haplotypes were established from the reads of each accession and phylogenetic analyses were performed using the haplotypic data for each gene fragment. The length of 454 reads and the level of differentiation between the ancestral taxa of modern citrus allowed efficient haplotype phylogenetic assignations for 12 of the 16 gene fragments. The analysis of the mixed genomic structure of modern species and cultivars (i) revealed C. maxima introgressions in modern mandarins, (ii) was consistent with previous hypotheses regarding the origin of secondary species, and (iii) provided a new picture of the evolution of chromosome 2.Conclusions454 sequencing was an efficient strategy to establish haplotypes with significant phylogenetic assignations in Citrus, providing a new picture of the mixed structure on chromosome 2 in 48 citrus genotypes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-014-0152-1) contains supplementary material, which is available to authorized users.

Changes in Anthocyanin Production during Domestication of Citrus

“…This hybrid, yet to be identified, also might have been involved in the derivation of Meyer lemon, which also contains the r DEL0.8 allele. The composition of Ruby alleles (r DEL2 and R C ) in limetta (C. limetta) was consistent with the involvement of sour orange and citron as parents (Curk et al, 2014(Curk et al, , 2016. For Rangpur lime (C. limonia), the composition of Ruby alleles (r DEL2 and R C ) suggested a mandarin (group B) 3 citron origin.…”

“…form Soh Synteng; Table I), which argues against the contribution of either sweet or sour orange, as suggested by Nicolosi et al (2000), and, rather, suggests the presence of a pummelo 3 mandarin hybrid in its parentage, as proposed by Curk et al (2014Curk et al ( , 2016, based on haplotyping and nuclear and cytoplasmic DNA marker analyses. This hybrid, yet to be identified, also might have been involved in the derivation of Meyer lemon, which also contains the r DEL0.8 allele.…”

Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

“…limon (L.) Burm.f.) arose from hybridization between sour orange and mandarin [33,34,45,47,126]. The allele-sharing test inferred that bergamot arose from hybridization of lemon and sour orange as previously demonstrated [48].…”

Creating new interspecific hybrid and polyploid crops

“…The genomes of species that have originated via natural interspecific hybridisation, such as many citrus crops, can also be characterised to identify the chromosomal fragments that are contributed by the different ancestral genomes. This allows the identification of desirable (and undesirable) traits, and can be used for optimising breeding, as shown using 454 sequencing [54].…”