Chromosome length haplotype analysis of 50 Citrus cultivars reveals shared ancestry and selection

Understanding the genome composition of citrus cultivars and germplasm illuminates their ancestry and facilitates the prediction of the genome composition and characteristics of hybrids.
Haplotypes are the actual physical organization of maternal and paternal DNA into each pair of homologous chromosomes.
High-throughput sequencing approaches reveal the genotype of an individual at each base but provide haplotype information on only short regions.
Long-read sequencing can allow assembly of citrus genomes into their component haplotypes, but it is relatively expensive per genome.
We developed methods to amplify DNA from single, haploid pollen grains and determine chromosome-length haplotypes by genotyping or sequencing a few pollen grains per individual.
Here we describe highlights from an analysis of the haplotypes of 50 citrus accessions based on ~52,000 SNPs genotyped with a SNP array.
Regions identical-by-descent in various accessions were identified and interpreted in the context of parentage information.
Haplotypes identical to those of sweet orange are observed in many mandarin types, some not previously suspected to be derived from sweet orange.
Selection is reflected in differences in the frequency of the two sweet orange haplotypes in F₁ hybrids and later generations.
Clustering haplotypes into groups identifies probable relatives and can help breeders avoid crossing close relatives that may lead to inbreeding depression.

XV International Citrus Congress

M.L. Roose, S.P. Ferrante

SNP array, haplotype sharing

https://doi.org/10.17660/ActaHortic.2026.1448.28