Genetic variations at BBX24 and MYB110a loci regulated anthocyanin accumulation in pear bud sports

Genetic variation contributes to the phenotypic diversity of plants. Most red pear cultivars that accumulate anthocyanins originated from somatic variation and are termed bud sports. ‘Hongzaosu’ is a bud sport derived from the green pear ‘Zaosu’. A new genetic map was constructed from a population derived from the cross of ‘Yuluxiang’ and ‘Hongzaosu’, from which PpBBX24 was identified as a crucial gene controlling anthocyanin accumulation. Genetic and phylogenetic evidence revealed that PpBBX24 is a repressor of anthocyanin biosynthesis in pear. A 14 bp deletion was detected in the third exon of PpBBX24 in ‘Hongzaosu’, resulting in premature termination of protein translation. The truncated PpBBX24 protein was a positive regulator of anthocyanin biosynthesis by activating the transcription of PpCHS and PpUFGT. Three independent variations in the BBX24 coding region that led to premature termination of translation were detected in other pear bud sports and the progeny of a bud sport that all accumulate anthocyanins. The genome of ‘Hongzaosu’ was assembled using both long-read and short-read sequences. By combining genomic and transcriptomic data, allele-specific expression of PpMYB110a was observed in the fruit skin of ‘Hongzaosu’, which was likely caused by large variation in the promoter. This work enhances understanding of coloration in red pears and provides a novel genomic resource for further studies on ‘Hongzaosu’ pear.