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Structural and functional analysis of CCT family genes in pigeonpea

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Abstract

Background

Pigeonpea (Cajanus cajan L.) is a photoperiod-sensitive short-day plant. Understanding the flowering-related genes is critical to developing photoperiod insensitive cultivars.

Methods

The CCT family genes were identified using ‘CCT DOMAIN PROTEIN’ as a keyword and localized on the chromosomes using the BLAST search option available at the LIS database. The centromeric positions were identified through BLAST search using the centromeric repeat sequence of C. cajan as a query against the chromosome-wise FASTA files downloaded from the NCBI database. The CCT family genes were classified based on additional domains and/or CCT domains. The orthologous and phylogenetic relationships were inferred using the OrthoFinder and MEGA 10.1 software, respectively. The CCT family genes′ expression level in photoperiod-sensitive and insensitive genotypes was compared using RNA-seq data and qRT-PCR analysis.

Results

We identified 33 CCT family genes in C. cajan distributed on ten chromosomes and nine genomic scaffolds. They were classified into CMF-type, COL-type, PRR-type, and GTCC- type. The CCT family genes of legumes exhibited an extensive orthologous relationship. Glycine max showed the maximum similarity of CCT family genes with C. cajan. The expression analysis of CCT family genes using photoperiod insensitive (ICP20338) and photoperiod sensitive (MAL3) genotypes of C. cajan demonstrated that CcCCT4 and CcCCT23 are the active CONSTANS in ICP20338. In contrast, only CcCCT23 is active in MAL3.

Conclusion

The CCT family genes in C. cajan vary considerably in structure and domain types. They are maximally similar to soybean’s CCT family genes. The differential photoperiod response of pigeonpea genotypes, ICP20338 and MAL3, is possibly due to the difference in the number and types of active CONSTANS in them.

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Acknowledgements

We sincerely acknowledge the Director, ICAR-NIPB, New Delhi; Director, ICAR-IARI, New Delhi; Director, ICAR-IIAB, Ranchi; and the Incharge, National Phytotron Facility, ICAR- IARI, New Delhi for providing the necessary facilities to carry out the research work.

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Authors and Affiliations

  1. ICAR—National Institute for Plant Biotechnology (NIPB), New Delhi, Delhi, 110012, India

    Kishor U. Tribhuvan, Tanvi Kaila, Harsha Srivastava, Kuldeep Kumar, Nagendra K. Singh & Kishor Gaikwad

  2. ICAR—Indian Institute of Agricultural Biotechnology (IIAB), Ranchi, Jharkhand, 834010, India

    Kishor U. Tribhuvan & Binay K. Singh

  3. ICAR—Indian Agricultural Research Institute (IARI), New Delhi, Delhi, 110012, India

    Kumar Durgesh & Rekha Joshi

  4. ICAR—Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, 208024, India

    Kuldeep Kumar

  5. ICAR—Central Institute for Subtropical Horticulture (CISH), Lucknow, Uttar Pradesh, 226101, India

    Antara Das

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  1. Kishor U. Tribhuvan
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Contributions

KG and NKS designed the work. KUT, HS, and TK conducted the experiments. BKS, AD, KK, KD and RJ analyzed and interpreted the data and wrote and revised the manuscript critically. All the authors read the manuscript and approved the final version for publication.

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Correspondence to Kishor Gaikwad.

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Tribhuvan, K.U., Kaila, T., Srivastava, H. et al. Structural and functional analysis of CCT family genes in pigeonpea. Mol Biol Rep 49, 217–226 (2022). https://doi.org/10.1007/s11033-021-06860-6

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