Structural and functional analysis of CCT family genes in pigeonpea

Abstract

Pigeonpea (Cajanus cajan (L) Millsp) is a short-day plant in which the owering is highly sensitive to photoperiod. A better understanding of the genes modulating photoresponse and owering time is critical to developing photoperiod insensitive pigeonpea cultivars for cultivation across the seasons. We identi ed 33 CCT family genes (CcCCT1-CcCCT33) in C. cajan and localized them on 10 chromosomes and nine genomic scaffolds. The structural analysis of CCT family genes revealed a considerable variation in length and distribution of exons and introns. Based on the type of domain(s), we classi ed the CCT family genes into CCT motif family (CMF) type, CONSTANS like (COL) type, Pseudo-response Regulator (PRR) type, and GATA and ti containing CCT (GTCC) type. The CCT family genes of C. cajan exhibited an extensive orthologous relationship with the CCT family genes of other legume species. We also observed signi cant sharing of CCT family genes among the legume species. Glycine max exhibited the maximum sharing of CCT family genes with C. cajan. The analysis of CCT family proteins-based phylogenic relationships revealed a general congruence with the legumes' taxonomic relationships. The expression analysis of CCT family genes of pigeonpea demonstrated that CcCCT4 and CcCCT23 are the active CONSTANS (CO) in ICP20338. In contrast, only CcCCT23 is active in MAL3, explaining the differential response of ICP20338 and MAL3 to photoperiod. The chromosomes of C. cajan contain a variable number of CCT family genes. A majority of these genes are localized in the centromeric regions. The COL type CCT genes are structurally highly diverse and contain a variable number of B-box domains. The CCT family genes of different legume species exhibit all three kinds of relationships: one-to-one, many-to-one, and many-tomany types. The photoperiod insensitive cultivar ICP20338 contains CcCCT4 and CcCCT23, while the photoperiod sensitive cultivar MAL3 contains only CcCCT23 as active CONSTANS (CO), which may be the plausible reason for their differential photoperiod response.

Genome-Wide Identification of BrCMF Genes in Brassica rapa and Their Expression Analysis under Abiotic Stresses

“…A total of 26 BrCMF genes were identified based on comparison of homologous genes of the known AtCMF family with those in the B. rapa genome database. A gene member without the CCT domain was identified and omitted, which yielded a total of 25 predicted CMF genes, exceeding the number of CMF genes reported in Oryza sativa (19) [ 7 ], Oryza rufipogon (19) [ 9 ], Zea mays (14) [ 13 ], Setaria italica (19) [ 11 ], Aegilops tauschii (12) [ 14 ], Medicago truncatula (18) [ 10 ], Glycine max (19) [ 12 ], Cajanus cajan L. (12) [ 15 ], and Populus trichocarpa (14) [ 16 ]. These genes were named according to their chromosomal distribution.…”

“…Medicago truncatula (18) [10], Glycine max (19) [12], Cajanus cajan L. (12) [15], and Populus trichocarpa (14) [16]. These genes were named according to their chromosomal distribution.…”

“…CMF genes have been identified in various plants, including Arabidopsis thaliana [ 4 ], Triticum aestivum L. [ 8 ], Oryza sativa [ 7 ], Oryza rufipogon [ 9 ], Medicago truncatula [ 10 ], Setaria italica [ 11 ], Glycine max [ 12 ], Zea mays [ 13 ], Aegilops tauschii [ 14 ], Cajanus cajan L. [ 15 ], and Populus trichocarpa [ 16 ]. Several CMF genes in gramineous plants have been shown to play a role in circadian rhythm regulation, as well as heading and flowering time regulation.…”

Registration of indeterminate and photoperiod‐insensitive IIPG‐7 and IIPG‐11 pigeonpea germplasm

“…With this, homozygous genotypes to this trait could be achieved rapidly. Also, because a low frequency of plants that flower is expected (Tribhuvan et al, 2022; this study), the space and labor should not be a problem to carry out progeny tests. The bulk method should be used in later generations (F 5 -F 7 ) to select photoperiod-insensitive genotypes that have a higher agronomic performance and commercial seed size and color, especially if labor and space conditions are limited.…”

“…The genetics for the indeterminate flowering habit and photoperiod sensitivity have been reported to be inherited by one or multiple dominant genes (Kapoor & Gupta, 1991;Mir et al, 2014;Saxena et al, 2021a). The CcTFL1 locus, located on chromosome 3, was reported as the candidate gene for flowering habit (Mendapara et al, 2023;Mir et al, 2014;Saxena et al, 2017), while the CCT family of genes mostly observed on chromosomes 3, 7, and 11 was reported to be responsible for photoperiod sensitivity in pigeonpea (Tribhuvan et al, 2022). Readers interested in a detailed explanation of the position and expression of these genes can refer to Bhattacharjee et al (2023), Mendapara et al (2023), Saxena et al (2017), and Tribhuvan et al (2020.…”