Comparative genomics and evolution of citrus

Recent advances in citrus genomics are now rapidly advancing knowledge of citrus evolution and enabling more rapid progress in citrus breeding. High quality genome sequences for a range of cultivars and species are increasingly available, and these high quality genomes facilitate analysis of SNP data from high-density arrays and short-read sequencing of large collections and populations. Analysis of this deluge of information has clarified the detailed structure of citrus genomes. Most modern cultivars have genomes that reflect admixture, that is, past interspecific hybridization, often followed by further sexual reproduction resulting in genomes that are a patchwork of fragments derived from two or more species. These patterns can now be inferred with great precision, including the species and sometimes the cultivar from which each chromosome segment is derived. Analyses also show that clonally propagated cultivars sometimes diverge by accumulation of structural rearrangements such as relatively large, heterozygous deletions. Genotyping single pollen grains allow inference of chromosome level haplotypes that are useful to predict inheritance patterns of gene combinations in various crosses. We can look forward to development of large sequence databases that provide a foundation for comparison of accessions in collections around the world. Identification of genes and interactions responsible for variation in citrus is likely to progress rapidly over the next 10 years and facilitate accelerated progress in breeding by hybridization and gene manipulation.