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Article|02 Dec 2022|OPEN
Genome assembly of wild loquat (Eriobotrya japonica) and resequencing provide new insights into the genomic evolution and fruit domestication in loquat
Danlong Jing1,2 ,† , Xinya Liu1,2 ,† , Qiao He1,2 ,† , Jiangbo Dang1,2 , Ruoqian Hu1,2 , Yan Xia1,2 , Di Wu1,2 , Shuming Wang1,2 , Yin Zhang1,2 , Qingqing Xia1,2 , Chi Zhang1,2 , Yuanhui Yu1,2 , Qigao Guo1,2 , , Guolu Liang,1,2 ,
1Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
2Academy of Agricultural Sciences of Southwest University, State Cultivation Base of Crop Stress Biology for Southern Mountainous Land, Chongqing 400715, China
*Corresponding author. E-mail:,
Danlong Jing and Xinya Liu,Qiao He contributed equally to the study.

Horticulture Research 10,
Article number: uhac265 (2023)
Views: 82

Received: 07 Sep 2022
Accepted: 21 Nov 2022
Published online: 02 Dec 2022


Wild loquats (Eriobotrya japonica Lindl.) provide remarkable genetic resources for studying domestication and breeding improved varieties. Herein, we generate the first high-quality chromosome-level genome assembly of wild loquat, with 45 791 predicted protein-coding genes. Analysis of comparative genomics indicated that loquat shares a common ancestor with apple and pear, and a recent whole-genome duplication event occurred in loquat prior to its divergence. Genome resequencing showed that the loquat germplasms can be distinctly classified into wild and cultivated groups, and the commercial cultivars have experienced allelic admixture. Compared with cultivated loquats, the wild loquat genome showed very few selected genomic regions and had higher levels of genetic diversity. However, whole-genome scans of selective sweeps were mainly related to fruit quality, size, and flesh color during the domestication process. Large-scale transcriptome and metabolome analyses were further performed to identify differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) in wild and cultivated loquats at various fruit development stages. Unlike those in wild loquat, the key DEGs and DAMs involved in carbohydrate metabolism, plant hormone signal transduction, flavonoid biosynthesis, and carotenoid biosynthesis were significantly regulated in cultivated loquats during fruit development. These high-quality reference genome, resequencing, and large-scale transcriptome/metabolome data provide valuable resources for elucidating fruit domestication and molecular breeding in loquat.