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Article|08 Apr 2024|OPEN
Haplotype-resolved genome of Prunus zhengheensis provides insight into its evolution and low temperature adaptation in apricot
Wei Tan1 , Pengyu Zhou1 , Xiao Huang1 , Ruyu Liao2 , Xiaoan Wang2 , Yaoyao Wu1 , Zhaojun Ni1 , Ting Shi1 , Xiaqing Yu1 , Huiqin Zhang3 , Chengdong Ma1 , Feng Gao1 , Yufan Ma1 , Yang Bai1 , Faisal Hayat4 , Ouma Kenneth Omondi1,5 and Daouda Coulibaly1,6 , Zhihong Gao,1 ,
1College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
2Institute of Fruit, Fujian Academy of Agricultural Sciences, Fuzhou 350013, China
3Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
4Department of Pomology, College of Horticulture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
5Department of Crops, Horticulture and Soils, Faculty of Agriculture, Egerton University, P.O. Box 536, Egerton 20115, Kenya
6Department of Agricultural Sciences and Techniques-Horticulture, Rural Polytechnic Institute for Training and Applied Research (IPR/IFRA) of Katibougou, Koulikoro B.P.224, Mali
*Corresponding author. E-mail: gaozhihong@njau.edu.cn

Horticulture Research 11,
Article number: uhae103 (2024)
doi: https://doi.org/10.1093/hr/uhae103
Views: 279

Received: 19 Nov 2023
Accepted: 31 Mar 2024
Published online: 08 Apr 2024

Abstract

Prunus zhengheensis, an extremely rare population of apricots, originated in warm South-East China and is an excellent material for genetic breeding. However, most apricots and two related species (P. sibiricaPmandshurica) are found in the cold northern regions in China and the mechanism of their distribution is still unclear. In addition, the classification status of P. zhengheensis is controversial. Thus, we generated a high-quality haplotype-resolved genome for Pzhengheensis, exploring key genetic variations in its adaptation and the causes of phylogenetic incongruence. We found extensive phylogenetic discordances between the nuclear and organelle phylogenies of Pzhengheensis, which could be explained by incomplete lineage sorting. A 242.22-Mb pan-genome of the Armeniaca section was developed with 13 chromosomal genomes. Importantly, we identified a 566-bp insertion in the promoter of the HSFA1d gene in apricot and showed that the activity of the HSFA1d promoter increased under low temperatures. In addition, HSFA1d overexpression in Arabidopsis thaliana indicated that HSFA1d positively regulated plant growth under chilling. Therefore, we hypothesized that the insertion in the promoter of HSFA1d in apricot improved its low-temperature adaptation, allowing it to thrive in relatively cold locations. The findings help explain the weather adaptability of Armeniaca plants.