Abstract
Pigeonpea (Cajanus cajan L.) is a photoperiod-sensitive short-day plant. Understanding the flowering-related genes is critical to developing photoperiod insensitive cultivars. 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. 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. 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.
Highlights
Flowering is a critical event in a plant's life cycle [1]
The RNA-seq data generated from the reproductive leaf (RL) tissues of the genotypes ICP20338 and MAL3 grown under short day (SD) and long day (LD) conditions were analyzed to determine the level of expression of the CcCCT family genes
We identified a total of 33 CCT family genes in the genome of C. cajan (Table 1)
Summary
Flowering is a critical event in a plant's life cycle [1]. It is regulated by many intrinsic and extrinsic factors. The CO transcription factors sense the favorable photoperiod condition through their interactions with the products of several photo-inducible genes like GI, FKF1, CCA1, LHY, and PRR [12,13,14,15,16,17]. The CCT family genes include CONSTANS like (COL), PRR, CCT motif family (CMF), and GATA/tifi containing CCT (GTCC) genes [19] These genes regulate photoperiod-dependent flowering in various plant species [20,21]. They play vital roles in various physiological processes, including stomatal opening, photomorphogenesis, abiotic stress response, hormone metabolism, and help determine an array of morphological traits like shoot branching, sink size, plant height, and grain number [19]. We report an account of the orthologroups, intergeneric/interspecific sharing and phylogenetic relationships of CCT family genes of pigeonpea and other legumes
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