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Mapping and identifying candidate genes involved in the novel fasciculate inflorescence in pepper (Capsicum annuum L.)

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Abstract

As a key determinant affecting yield and quality in pepper, inflorescence architecture is a significant feature of the ornamental plants. In our present study, a new mutant with fasciculate inflorescence named CL74 was derived from our germplasm resources. Genetic analysis of CL74 indicated that it was different from the fasciculate (fa) mutant, and its fasciculate inflorescence trait was controlled by a single recessive nuclear gene. A large F2 population was constructed and used for bulked segregant analysis (BSA) and linkage analysis. These findings revealed that the candidate gene was mapped to a segment with a physical distance of approximately 998 kb between Indel-197064077 and Indel-198110136. There were two agamous-like MADS-box protein genes Capanan11g001832 and Capanan11g001834 in the candidate region. Besides, two single nucleotide polymorphisms (SNPs) existed on the coding region of Capanan11g001832 in the CL74 mutant compared with the single-flower plants. In addition, the two SNPs were verified and fully co-segregated with fasciculate inflorescence phenotype in the F2 individuals. Collectively, Capanan11g001832 was a strong candidate gene for the fasciculate inflorescence. Furthermore, transcriptome analysis indicated that three WUSCHEL-like genes (Capana00g000667, Capana06g000476, and Capana11g000671) were downregulated and CLV1 (Capana04g000175) was upregulated in CL74. Moreover, we speculated that there was a complex relationship among the genes Capanan11g001832, Capanan11g001834, the three WUSCHEL-like genes, and CLV1, and these genes might co-regulate the formation of fasciculate inflorescence in pepper. Our study laid the foundation for the selection of high-yield, mechanized harvesting, or ornamental varieties of pepper.

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Funding

This work was financially supported by China Agriculture Research System (Grant No. CARS-24-A-05).

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Authors and Affiliations

  1. Longping Branch, Graduate School of Hunan University, Changsha, 410125, China

    Junheng Lv, Yuhua Liu, Zhoubin Liu, Jing Wang & Xuexiao Zou

  2. Vegetable Institution of Hunan Academy of Agricultural Science, Changsha, 410125, China

    Junheng Lv, Yanqing Ma, Zhuqing Zhang, Sha Yang & Wenchao Chen

  3. Horticulture and Landscape College, Hunan Agricultural University, Changsha, 410128, Hunan, China

    Lijun Ou & Xuexiao Zou

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  1. Junheng Lv
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Correspondence to Lijun Ou, Wenchao Chen or Xuexiao Zou.

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Junheng Lv, Yuhua Liu and Zhoubin Liu contributed equally to this work.

Electronic supplementary material

Fig. S1

Alignment of the gene fa gene coding sequences between the CL74 mutant and fa mutant (PNG 357 kb)

High Resolution Image (TIF 78 kb)

Fig. S2

qRT-PCR-based expression analysis of genes in the candidate region (PNG 333 kb)

High Resolution Image (TIF 311 kb)

Fig. S3

Alignment of the gene Capana11g001832 coding and amino acid sequences between the wild type and mutant type plants (PNG 2850 kb)

High Resolution Image (TIF 183 kb)

Fig. S4

(a) GO enrichment analysis for differentially expressed genes between CL74 and L816; (b) Scatter plot of KEGG pathway enrichment statistics for differentially expressed genes between CL74 and L816 (PNG 175 kb)

High Resolution Image (TIF 1.34 kb)

Fig. S5

qRT-PCR analysis of genes expression of significant related genes (PNG 228 kb)

High Resolution Image (TIF 21 kb)

Table S1

Primers used for map-based cloning (DOCX 16 kb)

Table S2

Primers for the detection of the expression level of selected genes (DOCX 16 kb)

Table S3

Phenotypic segregation identified by test for goodness-of-fit. (DOCX 15 kb)

Table S4

Gene function and expression level in the SAM of L816 and CL74 (DOCX 16 kb)

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Lv, J., Liu, Y., Liu, Z. et al. Mapping and identifying candidate genes involved in the novel fasciculate inflorescence in pepper (Capsicum annuum L.). Mol Breeding 39, 148 (2019). https://doi.org/10.1007/s11032-019-1050-z

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