Evolution and domestication-trait associations of ultra-long centromere haplotypes in pepper plants

Centromeric and pericentromeric regions of most eukaryotic genomes are highly repetitive and strongly recombination-suppressed, confounding efforts to resolve genetic variation, population structure, and phenotypic associations within these regions. In pepper (Capsicum annuum), centromeres are nearly devoid of satellite repeats, making it a tractable system for centromere biology. Here, we integrate nine near-complete genome assemblies, CENH3 ChIP–seq profiles from 26 diverse accessions, and resequencing and phenotypic data from ~400 cultivated and wild accessions to investigate population-level diversity and phenotypic relevance of pepper peri/centromeric regions. Functional centromere positions are largely fixed on eight of the twelve chromosomes, whereas the remaining four carry distinct centromeric epialleles shaped mainly by centromere repositioning and pericentromeric inversions. Pepper centromeres are embedded within ultra-long centromere-spanning haplotype (cenhap) blocks ranging from 29.8 to 112.9 Mb and collectively covering 23.96% of the genome; each block contains only one to four major haplotypes. Some cenhaps show supergene-like properties and are strongly associated with fruit traits, likely because recombination-suppressed intervals harbor multiple fruit-related genes, including OFP and F-box genes. F₂ segregation assays further reveal transmission distortion of chromosomes carrying alternative cenhaps. Together, these findings highlight peri/centromeric regions as underrecognized reservoirs of agronomically important variation.