Two nearly complete genomes reveal the molecular mechanism underlying the significant fruit quality differences caused by bud sport between yellow and white‐fleshed loquat ( Eriobotrya japonica L.)

SUMMARY

Bud sport is a common and stable somatic variation in perennial fruit trees. Loquat ( Eriobotrya japonica L.) is an evergreen fruit tree that can be categorized into yellow‐fleshed and white‐fleshed types based on the flesh color. To uncover the genetic basis, we herein assembled two nearly complete genomes for a yellow‐fleshed ‘Dongting’ loquat (TBY) and its white‐fleshed bud sport (TBW). The final sizes of assemblies were 773.29 Mb and 728.86 Mb with contig N50 of 31.87 Mb and 28.63 Mb for TBY and TBW, respectively. Comparative genomics analysis indicated that the heterozygosity ratio of TBY was nearly two‐fold higher than that of TBW (0.53% vs. 0.27%). Integrated multi‐omics and molecular marker detection results revealed that homozygosity of the EjPSY2A ^d / EjPSY2A ^d allele is the cause of the change in flesh color from yellow to white in TBY. Additionally, EjSUSs ( −1 , −2 , −3 , −12 ) and EjSPS3 might be the key genes responsible for the significant accumulation of hexoses and sucrose, respectively, in the flesh of TBY and TBW. Furthermore, high expression of EjC4H8 and Ej4CLs ( −7 , −10 , −20 ) in TBY might lead to the accumulation of more lignin in its flesh. Taken together, these findings provide valuable insights into the molecular mechanism differences between yellow‐ and white‐fleshed loquat and highlight the significance of bud sport as a valuable approach for generating novel germplasm resources in fruit trees.