Construction of the super pan-genome for the genus Actinidia reveals structural variations linked to phenotypic diversity

Horticulture Research, Journal Year: 2025, Volume and Issue: 12(6)

Published: March 3, 2025

Kiwifruits, belonging to the genus Actinidia, are acknowledged as one of most successfully domesticated fruits in twentieth century. Despite rich wild resources and diverse phenotypes within this genus, insights into genomic changes still limited. Here, we conducted whole-genome sequencing on seven representative materials from highly diversified sections leading assembly annotation 14 haplotype genomes with sizes spanning 602.0 699.6 Mb. By compiling these genomes, constructed a super pan-genome for genus. We identified numerous structural variations (SVs, including gene copy number) diverged regions genomes. Notably, significant SV variability was observed intronic MED25 TTG1 genes across different materials, suggesting their potential roles influencing fruit size trichome formation. Intriguingly, our findings indicated high genetic divergence between two individual, tentatively named Actinidia × leiocacarpae, sect. Leiocacarpae. This likely hybrid heterozygous genome exhibited notable adaptations related resistance against bacterial canker, particularly through upregulation RPM1 gene, which contains specific SV, after infection by Pseudomonas syringae pv. actinidiae. In addition, also discussed interlineage hybridizations taxonomic treatments Actinidia. Overall, comprehensive here, along findings, lays foundation examining compositions markers, those SVs, facilitate breeding aimed at developing desired kiwifruits.

Language: Английский

Haplotype‐resolved genome of a heterozygous wild peach reveals the PdaWRKY4‐PdaCYP716A1 module mediates resistance to aphids by regulating betulin biosynthesis

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: unknown

Published: Oct. 25, 2024

ABSTRACT Wild species of domesticated crops provide valuable genetic resources for resistance breeding. Prunus davidiana , a wild relative peach with high heterozygosity and diverse stress tolerance, exhibits against aphids. However, the highly heterozygous genome P. makes determining underlying factors influencing traits challenging. Here, we present 501.7 Mb haplotype‐resolved assembly . Genomic comparisons two haplotypes revealed 18,152 structural variations, 2,699 Pda_hap1‐specific 2,702 Pda_hap2‐specific genes, 1,118 allele‐specific expressed genes. Genome composition indicated 4.1% was non‐peach origin, out which 94.5% derived from almond. Based on haplotype genome, aphid quantitative trait locus (QTL) mapped at end Pda03. From QTL, PdaWRKY4 identified as major dominant gene, 9‐bp deletion in its promoter resistant phenotype. Specifically, regulates by promoting PdaCYP716A1 ‐mediated anti‐aphid metabolite betulin biosynthesis. Moreover, employed design to develop breeding workflow rapidly precisely producing aphid‐resistant peaches. In conclusion, this study identifies novel gene provides insights into development fruit cultivars.

Language: Английский

Unlocking diversity from wild relatives of perennial fruit crops in the pan-genomics era

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102652 - 102652

Published: Oct. 31, 2024

Language: Английский