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Article|19 Dec 2023|OPEN
Genome variation and LTR-RT analyses of an ancient peach landrace reveal mechanism of blood-flesh fruit color formation and fruit maturity date advancement
Jiao Wang1 , Ke Cao1 , Yong Li1 , Jinlong Wu1 , Wenqing Li1 , Qi Wang1 , Gengrui Zhu1 , Weichao Fang1 , Changwen Chen1 , Xinwei Wang1 , Wenxuan Dong2 , , Weisheng Liu3 , and Lirong Wang,1 ,
1The Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Fruit TreeBreeding Technology), Ministry of Agriculture, Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
2College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
3Liaoning Institute of Pomology, Yingkou 115009, Liaoning, China
*Corresponding author. E-mail: dongwx63@syau.edu.cn,wsliulaas@163.com,wanglirong@caas.cn

Horticulture Research 11,
Article number: uhad265 (2024)
doi: https://doi.org/10.1093/hr/uhad265
Views: 80

Received: 09 Feb 2023
Accepted: 01 Dec 2023
Published online: 19 Dec 2023

Abstract

Peach (Prunus persica) landrace has typical regional characteristics, strong environmental adaptability, and contains many valuable genes that provide the foundation for breeding excellent varieties. Therefore, it is necessary to assemble the genomes of specific landraces to facilitate the localization and utilization of these genes. Here, we de novo assembled a high-quality genome from an ancient blood-fleshed Chinese landrace Tianjin ShuiMi (TJSM) that originated from the China North Plain. The assembled genome size was 243.5 Mb with a contig N50 of 23.7 Mb and a scaffold N50 of 28.6 Mb. Compared with the reported peach genomes, our assembled TJSM genome had the largest number of specific structural variants (SVs) and long terminal repeat-retrotransposons (LTR-RTs). Among the LTR-RTs with the potential to regulate their host genes, we identified a 6688 bp LTR-RT (named it blood TE) in the promoter of NAC transcription factor-encoding PpBL, a gene regulating peach blood-flesh formation. The blood TE was not only co-separated with the blood-flesh phenotype but also associated with fruit maturity date advancement and different intensities of blood-flesh color formation. Our findings provide new insights into the mechanism underlying the development of the blood-flesh color and determination of fruit maturity date and highlight the potential of the TJSM genome to mine more variations related to agronomic traits in peach fruit.