Discovery of multi-megabase polymorphic inversions by chromosome conformation capture sequencing in large-genome plant species

Himmelbach, A., Ruban, A., Walde, I., Šimková, H., Doležel, J., Hastie, A., Stein, N., Mascher, M.
PLANT JOURNAL 96: 1309-1316, 2018

Keywords: Hordeum vulgare ; barley; chromosomal inversions; chromosome conformation capture sequencing; genomics; optical mapping; technical advance
Abstract: Chromosomal inversions occur in natural populations of many species, and may underlie reproductive isolation and local adaptation. Traditional methods of inversion discovery are labor-intensive and lack sensitivity. Here, we report the use of three-dimensional contact probabilities between genomic loci as assayed by chromosome-conformation capture sequencing (Hi-C) to detect multi-megabase polymorphic inversions in four barley genotypes. Inversions are validated by fluorescence in situ hybridization and Bionano optical mapping. We propose Hi-C as a generally applicable method for inversion discovery in natural populations.
DOI: 10.1111/tpj.14109
IEB authors: Jaroslav Doležel, Hana Šimková