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Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense)


Key message

The sy - 2 temperature-sensitive gene from Capsicum chinense was fine mapped to a 138.8-kb region at the distal portion of pepper chromosome 1. Based on expression analyses, two putative F-box genes were identified as sy - 2 candidate genes.


Seychelles-2 (‘sy-2’) is a temperature-sensitive natural mutant of Capsicum chinense, which exhibits an abnormal leaf phenotype when grown at temperatures below 24 °C. We previously showed that the sy-2 phenotype is controlled by a single recessive gene, sy-2, located on pepper chromosome 1. In this study, a high-resolution genetic and physical map for the sy-2 locus was constructed using two individual F2 mapping populations derived from a cross between C. chinense mutant ‘sy-2’ and wild-type ‘No. 3341’. The sy-2 gene was fine mapped to a 138.8-kb region between markers SNP 5-5 and SNP 3-8 at the distal portion of chromosome 1, based on comparative genomic analysis and genomic information from pepper. The sy-2 target region was predicted to contain 27 genes. Expression analysis of these predicted genes showed a differential expression pattern for ORF10 and ORF20 between mutant and wild-type plants; with both having significantly lower expression in ‘sy-2’ than in wild-type plants. In addition, the coding sequences of both ORF10 and ORF20 contained single nucleotide polymorphisms (SNPs) causing amino acid changes, which may have important functional consequences. ORF10 and ORF20 are predicted to encode F-box proteins, which are components of the SCF complex. Based on the differential expression pattern and the presence of nonsynonymous SNPs, we suggest that these two putative F-box genes are most likely responsible for the temperature-sensitive phenotypes in pepper. Further investigation of these genes may enable a better understanding of the molecular mechanisms of low temperature sensitivity in plants.

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This research was supported by the Golden Seed Project (213002-04-3-CG900), the Ministry of Agriculture, Food and Rural Affairs (MAFRA), the Ministry of Oceans and Fisheries (MOF), the Rural Development Administration (RDA), and the Korea Forest Service (KFS), Republic of Korea, and a Grant (710001-07) from the Vegetable Breeding Research Center through the Agriculture, Food and Rural Affairs Research Center Support Program, Ministry of Agriculture, Food and Rural Affairs.

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Correspondence to Byoung-Cheorl Kang.

Additional information

Communicated by R. G.F. Visser.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Fig. S1 BAC library screening and BAC clone sequence analysis. Seven BAC end markers (gap 2-1, gap 3-6, gap 3-1, gap 3-3-2, gap 4-3, gap 4-5, and gap 4-1) derived from scaffold sequencing were developed for screening a C. annuum cv. ‘CM334’ BAC library (Yoo et al. 2003). Fourteen positive BAC clones were obtained and placed on the sy-2 locus according to their end sequences. Four BAC clones (422K18, 547H22, 534N9, and 343L4) were completely sequenced to eliminate a gap between scaffolds 3515 and 2510, and two additional SNP markers (SNP 5-3 and SNP 3-13) were identified based on the BAC sequences (TIFF 326 kb)

Fig. S2 Multiple sequence alignment of the predicted pepper F-box proteins with the Arabidopsis F-box/kelch-like protein sequences. The predicted F-box domain and kelch repeats containing domains are boxed with black and red, respectively. ‘sy-2’ mutated amino acid positions in ORF10 and ORF20 are indicated with yellow circles (TIFF 12317 kb)

Fig. S3 Gene ontology (GO) term analysis of differentially expressed genes of Capsicum under low temperature (20 °C). GO analysis was carried out using the Blast2go program. The GO terms were grouped into different categories at level 2 (TIFF 35930 kb)

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Liu, L., Venkatesh, J., Jo, Y.D. et al. Fine mapping and identification of candidate genes for the sy-2 locus in a temperature-sensitive chili pepper (Capsicum chinense). Theor Appl Genet 129, 1541–1556 (2016). https://doi.org/10.1007/s00122-016-2723-1

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  • Amino Acid Change
  • COSII Marker
  • Putative Uncharacterized Protein
  • Pepper Chromosome