Identification and functional characterization of conserved cis-regulatory elements responsible for early fruit development in cucurbit crops

Hongjia Xin; Xin Liu; Sen Chai; Xueyong Yang; Hongbo Li; Bowen Wang; Yuanchao Xu; Shengnan Lin; Xiaoyun Zhong; Bin Liu; Zefu Lu; Zhonghua Zhang

doi:10.1093/plcell/koae064

Identification and functional characterization of conserved cis-regulatory elements responsible for early fruit development in cucurbit crops

Plant Cell. 2024 Feb 29:koae064. doi: 10.1093/plcell/koae064. Online ahead of print.

Authors

Hongjia Xin^{1

2}, Xin Liu^{1

3}, Sen Chai², Xueyong Yang¹, Hongbo Li³, Bowen Wang^{1

3}, Yuanchao Xu^{1

3}, Shengnan Lin⁴, Xiaoyun Zhong¹, Bin Liu⁵, Zefu Lu⁶, Zhonghua Zhang²

Affiliations

¹ State Key Laboratory of Vegetable Biobreeding, Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
² Engineering Laboratory of Genetic Improvement of Horticultural Crops of Shandong Province, College of Horticulture, Qingdao Agricultural University, Qingdao 266109, China.
³ Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
⁴ Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan 430070, China.
⁵ Hami-melon Research Center, Xinjiang Academy of Agricultural Sciences, Urumqi, 830091 China.
⁶ National Key Facility of Crop Gene Resource and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

PMID: 38421027
DOI: 10.1093/plcell/koae064

Abstract

A number of cis-regulatory elements (CREs) conserved during evolution have been found to be responsible for phenotypic novelty and variation. Cucurbit crops such as cucumber (Cucumis sativus), watermelon (Citrullus lanatus), melon (Cucumis melo) and squash (Cucurbita maxima) develop fruits from an inferior ovary and share some similar biological processes during fruit development. Whether conserved regulatory sequences play critical roles in fruit development of cucurbit crops remains to be explored. In six well-studied cucurbit species, we identified 392,438 conserved non-coding sequences (CNSs), including 82,756 that are specific to cucurbits, by comparative genomics. Genome-wide profiling of accessible chromatin regions (ACRs) and gene expression patterns mapped 20,865-43,204 ACRs and their potential target genes for two fruit tissues at two key developmental stages in six cucurbits. Integrated analysis of CNSs and ACRs revealed 4,431 syntenic orthologous CNSs, including 1,687 cucurbit-specific CNSs that overlap with ACRs that are present in all six cucurbit crops and that may regulate the expression of 757 adjacent orthologous genes. CRISPR mutations targeting two CNSs present in the 1,687 cucurbit-specific sequences resulted in substantially altered fruit shape and gene expression patterns of adjacent NAC1 (NAM, ATAF1/2 and CUC2) and EXT-like (EXTENSIN-like) genes, validating the regulatory roles of these CNSs in fruit development. These results not only provide a number of target CREs for cucurbit crop improvement, but also provide insight into the roles of CREs in plant biology and during evolution.