Genome-Wide Association Studies Reveal Candidate Genes Related to Stem Diameter in Cucumber (Cucumis sativus L.)

Yingying Yang; Shaoyun Dong; Han Miao; Xiaoping Liu; Zhuonan Dai; Xiangsheng Li; Xingfang Gu; Shengping Zhang

doi:10.3390/genes13061095

Genome-Wide Association Studies Reveal Candidate Genes Related to Stem Diameter in Cucumber (Cucumis sativus L.)

Genes (Basel). 2022 Jun 19;13(6):1095. doi: 10.3390/genes13061095.

Authors

Yingying Yang¹, Shaoyun Dong¹, Han Miao¹, Xiaoping Liu¹, Zhuonan Dai¹, Xiangsheng Li¹, Xingfang Gu¹, Shengping Zhang¹

Affiliation

¹ Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, China.

Abstract

The stem diameter, an important agronomic trait, affects cucumber growth and yield. However, no genes responsible for cucumber stem diameter have been identified yet. In this study, the stem diameter of 88 cucumber core germplasms were measured in spring 2020, autumn 2020 and autumn 2021, and a genome-wide association study (GWAS) was carried out based on the gene sequence and stem diameter of core germplasms. A total of eight loci (gSD1.1, gSD2.1, gSD3.1, gSD3.2, gSD4.1, gSD5.1, gSD5.2, and gSD6.1) significantly associated with cucumber stem diameter were detected. Of these, five loci (gSD1.1, gSD2.1, gSD3.1, gSD5.2, and gSD6.1) were repeatedly detected in two or more seasons and were considered as robust and reliable loci. Based on the linkage disequilibrium sequences of the associated SNP loci, 37 genes were selected. By further investigating the five loci via analyzing Arabidopsis homologous genes and gene haplotypes, five genes (CsaV3_1G028310, CsaV3_2G006960, CsaV3_3G009560, CsaV3_5G031320, and CsaV3_6G031260) showed variations in amino acid sequence between thick stem lines and thin stem lines. Expression pattern analyses of these genes also showed a significant difference between thick stem and thin stem lines. This study laid the foundation for gene cloning and molecular mechanism study of cucumber stem development.

Keywords: candidate gene; cucumber core germplasm; genome-wide association study; stem diameter.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Cucumis sativus* / genetics
Genome-Wide Association Study
Glycogen Storage Disease Type II*
Linkage Disequilibrium
Phenotype

Grants and funding

This research was funded by Key-Area Research and Development Program of Guangdong Province (2020B020220001); Key-Area Research and Development Program of Shandong Province (2021LZGC016); the Earmarked Fund for Modern Agro-industry Technology Research System (CARS-23), Science and Technology Innovation Program of the Chinese Academy of Agricultural Science (CAAS-ASTIP-IVFCAAS), and Central Public-Interest Scientific Institution Basal Research Fund (No.Y2017PT52); the key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture and Rural Affairs, P.R.China.