Targeting a cysteine proteinase inhibitor and a defensin-like protein in Litchi chinensis seed development leveraging endosperm single-nucleus transcriptome

Zhi-Chan Liao; Ming-Chao Yang; Dan-Rong Xie; Farhat Abbas; Ren-Fang Zeng; Xu-Ming Huang; Hui-Cong Wang

doi:10.1016/j.ijbiomac.2025.139708

Targeting a cysteine proteinase inhibitor and a defensin-like protein in Litchi chinensis seed development leveraging endosperm single-nucleus transcriptome

Int J Biol Macromol. 2025 Jan 9:139708. doi: 10.1016/j.ijbiomac.2025.139708. Online ahead of print.

Authors

Zhi-Chan Liao¹, Ming-Chao Yang², Dan-Rong Xie³, Farhat Abbas⁴, Ren-Fang Zeng⁵, Xu-Ming Huang⁶, Hui-Cong Wang⁷

Affiliations

¹ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China. Electronic address: liaozhichan@stu.scau.edu.cn.
² Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences/Key Laboratory of Genetic Resources and Utilization of Tropical Fruits and Vegetables, Haikou 571100, Hainan, China.
³ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China.
⁴ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China; Institute of Tropical Fruit Trees, Hainan Academy of Agricultural Sciences/Key Laboratory of Genetic Resources and Utilization of Tropical Fruits and Vegetables, Haikou 571100, Hainan, China.
⁵ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China. Electronic address: renfzeng@scau.edu.cn.
⁶ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China. Electronic address: huangxm@scau.edu.cn.
⁷ Key Laboratory of Biology and Genetic Improvement of Horticultural Crops-South China/Guangdong Litchi Engineering Research Center, College of Horticulture, South China Agricultural University, Guangzhou, China. Electronic address: wanghc1972@263.net.

PMID: 39798746
DOI: 10.1016/j.ijbiomac.2025.139708

Abstract

Seed development is one of the most important agricultural traits, determining both the crop yield and quality of fleshy fruits. A typically abortive litchi cultivar, Guiwei, exhibits heterogeneity in seed size across production areas, years, and individual trees. Previous studies have shown that 'Guiwei' seed development failure is associated with endosperm arrest and chilling conditions. Herein, we identified a cysteine proteinase inhibitor (LcCPI5) and defensin-like protein (LcDEFL) as key genes in determining 'Guiwei' seed development through combined analysis of 'Guiwei' and 'Huaizhi' endosperm single-nucleus RNA-sequence and transcriptome data of 'Guiwei' seed subjected to different temperature treatments. LcCPI5 was exclusively expressed in the endosperm sample of 'Guiwei' at 25 days post-anthesis, and its expression decreased in response to chilling. The silencing of LcCPI5 led to significantly larger seeds, whereas employing the cysteine proteinase inhibitor E-64 resulted in smaller seeds in the cultivar 'Guiwei'. Unlike LcCPI5, LcDEFL promotes litchi seed development. The large seed cultivar 'Huaizhi' had substantially higher expression of LcDEFL than the partly abortive cultivar 'Guiwei'. LcDEFL silencing led to a notable reduction in the size of litchi seeds. These findings point to the post-translational modulation of cysteine proteinase and the critical role of cysteine-rich proteins in litchi seed development.

Keywords: Cysteine proteinase inhibitor; Defensin-like protein; Endosperm development; Litchi chinensis; Single-nucleus transcriptome.