GWAS reveals novel loci and identifies a pentatricopeptide repeat-containing protein (CsPPR) that improves low temperature germination in cucumber

• DOI: 10.3389/fpls.2023.1116214
• Publication Date: 2023-04-26T05:37:16Z
• Authors: Caixia Li; Shaoyun Dong; Diane M. Beckles; Xiaoping Liu; Jiantao Guan; Xingfang Gu; Han Miao; Shengping Zhang
• Keywords: Pentatricopeptide repeat; Cucumis; Genome-wide Association Study; Ecotype; Candidate gene; SNP

Low temperatures (LTs) negatively affect the percentage and rate of cucumber ( Cucumis sativus L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify genetic loci underlying low temperature germination (LTG) in 151 accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative (RGR), energy (RGE), index (RGI) radical length (RRL), were collected environments, 17 found be highly cold tolerant using cluster analysis. A total 1,522,847 significantly associated single-nucleotide polymorphism (SNP) identified, with LTG, four chromosomes, detected: gLTG1.1 , gLTG1.2 gLTG1.3 gLTG4.1 gLTG5.1 gLTG5.2 gLTG6.1 after resequencing accessions. Of loci, three, showed strong signals consistent over years indices, are thus stable LTG. Eight candidate genes abiotic stress three them potentially causal LTG: CsaV3_1G044080 (a pentatricopeptide repeat-containing protein) CsaV3_4G013480 RING-type E3 ubiquitin transferase) CsaV3_5G029350 serine/threonine-protein kinase) gLTG5.2. The function CsPPR ) regulating confirmed, as Arabidopsis lines ectopically expressing higher survival rates at 4°C compared wild-type, preliminarily illustrates positively regulates tolerance stage. This will provide insights into LT-tolerance mechanisms further promote breeding development.