Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum)

Authors: MENGIST, MOLLA - North Carolina State University; BOSTAN, HAMED - North Carolina State University; DE PAOLA, DOMENICO - Consiglio Nazionale Delle Ricerche; TERESI, SCOTT - Michigan State University; PLATTS, ADRIAN - Michigan State University; CREMONA, GAETANA - Consiglio Nazionale Delle Ricerche; QI, XINPENG - The Chinese University Of Hong Kong (CUHK); Mackey, Theodore - Ted; Bassil, Nahla; ASHRAFI, HAMID - North Carolina State University; GIONGO, LARA - Fondazione Edmund Mach; JIBRAN, RUBINA - Plant And Food Research; CHAGNE, DAVID - Plant And Food Research; BIANCO, LUCA - Fondazione Edmund Mach; LILA, MARY ANN - North Carolina State University; Rowland, Lisa; IOVENE, MARINA - Consiglio Nazionale Delle Ricerche; EDGER, PATRICK - Michigan State University; IORIZZO, MASSIMO - North Carolina State University

Submitted to: New Phytologist
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/1/2022
Publication Date: 8/13/2022
Citation: Mengist, M., Bostan, H., De Paola, D., Teresi, S., Platts, A., Cremona, G., Qi, X., Mackey, T.A., Bassil, N.V., Ashrafi, H., Giongo, L., Jibran, R., Chagne, D., Bianco, L., Lila, M., Rowland, L.J., Iovene, M., Edger, P.P., Iorizzo, M. 2022. Autopolyploid inheritance and a heterozygous reciprocal translocation shape chromosome genetic behavior in tetraploid blueberry (Vaccinium corymbosum). New Phytologist. 237(3):1024–1039. https://doi.org/10.1111/nph.18428.
DOI: https://doi.org/10.1111/nph.18428

Interpretive Summary: We present a high-quality genome assembly of a diploid highbush blueberry accession named W85. Comparing the genome of the new W85 genome sequence, against previously published blueberry genomes, revealed a high level of collinearity, high to moderate improvement in terms of sequence contiguity, ability to locate specialized regions of low-complexity repeats, in addition to a large sequence translocation on chromosomes 6 and 10. This translocation affects pairing and recombination of chromosomes 6 and 10, but it is not present in all tetraploid cultivars. This study provides new resources for genetic and comparative genomic studies in blueberry and related species.

Technical Abstract: A high-quality phased genome assembly of a diploid highbush blueberry (Vaccinium caesariense Mack., syn. diploid V. corymbosum L.) accession, W85, linkage maps and cytogenetic work were used to characterize centromeric repeats, chromosomal structural differences and investigate the recombination behavior of cultivated blueberry. Comparative genomic analysis of the new W85 genome assembly, against previously published blueberry genomes, revealed a high to moderate improvement in terms of sequence contiguity and enabling to locate the putative centromeres and other specialized regions enriched by low-complexity repeats. Furthermore, among the resolved haplotypes, more than 41% of the predicted genes harbored potential deleterious mutations and were biased towards genes functions involved in biotic and abiotic stress responses. This suggests that the high level of heterozygosity maintained in this species contributes to plant survival and adaptation while reducing inbreeding depression. Furthermore, comparative structural analysis with the tetraploid blueberry genome highlighted conserved centromeric repeats, a high level of collinearity, minor chimeric regions and a large translocation spanning one haplotype of chromosomes 6 and 10. Examination of multiple tetraploid genomes revealed that the translocation affects pairing and recombination of chromosomes 6 and 10, but that it is not present in all tetraploid cultivars. Finally, chromosome inheritance was examined, and findings demonstrated that tetraploid blueberry behaves as an autotetraploid during meiosis. This study provides novel resources for genetic and comparative genomic studies in Vaccinium species and new insights into blueberry genome structure and chromosome pairing behavior that are critical for advancing genomic-assisted breeding strategies in this crop.