Environmental factors (daylength and temperature) and internal signals (gibberellins and autonomous pathways) simultaneously regulate flowering time in plants (Bhakta et al., 2017; Putterill et al., 2004). Higher plants detect fluctuations in daylength, which influence flowering time with changes in seasons. Common bean is a tropical facultative SD legume that is currently grown in tropical and temperate zones. The observation underscores how domestication and modern breeding practices can alter the adaptive phenology of a species (Moyses et al., 2018). During common bean domestication and dissemination from its centers of domestication, selection for photoperiod insensitivity allowed common bean to spread to higher latitudes (Gepts and Debouck, 1991). In addition, the determinate growth habit has been exploited in crop breeding activities to accelerate flowering and shorten the flowering period (Cober and Tanner, 1995).
In comparison with LD plants like Arabidopsis thaliana, much less is known about the genetic mechanisms that regulate flowering in SD plants, such as soybean (Glycine max), rice (Oryza sativa), and maize (Zea mays), among others; however, some progress has been made in such species through genetic analyses that have facilitated the identification of numerous genes. As a first step toward isolating the genes in common bean, we sought to use information obtained in model species such as A. thaliana using a candidate gene approach. Photoreceptors, circadian clock components, bio-clock, and light-regulated genes are key components for daylength detection using the external coincidence model. Among the clock and light-regulated genes, constans (CO) has been identified as a key gene participating in the integration of light and clock signals. The overexpression of the CO gene leads to early flowering in A. thaliana through the regulation of the expression of downstream genes, such as flowering locust (FT), apetala1 (AP1), and leafy (LFY), regardless of the length of daylight (Aidyn et al., 2002; Suárez-López et al., 2001; Yanovsky and Kay, 2002).
Intriguingly, more detailed molecular genetics analyses have revealed that several quantitative trait locus (QTL) associated with time-to-flower in SD species are orthologs of genes that regulate flowering in A. thaliana (Lee and An, 2007; Simpson and Dean, 2002; Salome et al., 2011). For example, rice QTL, HD1, and HD3a were found to be orthologs of A. thaliana CO and FT, respectively (Kojima et al., 2002; Tamaki et al., 2007). Such analyses have also discovered some flowering QTL that do not have orthologs in A. thaliana, like the early heading date 1 QTL in rice, a gene that regulates the expression of FT (Itoh et al., 2010). The observation suggests that additional mechanisms that control time-to-flower are likely to be discovered in SD plants. Buttressing this point is the discovery that setaria (Setaria viridis), a SD grass, has a secondary mechanism that operates under long days (Doust et al., 2017). RNA-seq technology facilitates the discernment of novel perspectives in transcriptome sequence analysis by providing comprehensive coverage of transcripts. In addition, RNA-seq could be used as an alternative to other transcript quantification approaches with the benefit of higher sensitivity and the potential to distinguish between very similar paralogs of a gene that differ based only on a few nucleotides. RNA-seq has been used to characterize transcriptional changes resulting from different flowering times (Kitae et al., 2017), and the differentially expressed genes (DEGs) identified were found to be useful for predicting differences in tolerance between common bean cultivars. Previous investigations have identified a dominant photoperiod-sensitive gene regulating flowering time in beans (Gu et al., 1998; Kornegay et al., 1993; Kwak et al., 2008; Wallace et al., 1991; White and Laing, 1989; White et al., 1996), but a comprehensive genetic analysis of the trait has not been carried out. In the present study, we used RNA-seq and quantitative reverse transcription PCR (qRT-PCR) to investigate potential changes in the common bean transcriptome in response to the changes in daylength. Known genes and novel predicted genes were identified and the functions of the molecules associated with the regulation of flowering time were evaluated. The findings could provide a theoretical basis for the enhancement of the adaptation of common bean cultivars to different photoperiods.
Bhakta, M.S., Gezan, S.A., Clavijo Michelangeli, J.A., Carvalho, M., Zhang, L. & Jones, J.W. 2017 A predictive model for time-to-flowering in the common bean based on QTL and environmental variables Genes Genomes Genet. 7 3901 3912
Cober, E.R. & Tanner, J.W. 1995 Performance of related indeterminate and tall determinate soybean lines in short-season areas Crop Sci. 35 361 364
Covington, M.F., Panda, S., Liu, X.L., Strayer, C.A., Wagner, D.R. & Kay, S.A. 2001 ELF3 modulates resetting of the circadian clock in Arabidopsis Plant Cell 13 1305 1315
Doust, A.N., Mauro-Herrera, M., Hodge, J.G. & Stromski, J. 2017 The C4 model grass Setaria is a short day plant with secondary long day genetic regulation Front. Plant Sci. 8 1062
Fujiwara, S., Oda, A. & Yoshida, R. 2008 Circadian clock proteins LHY and CCA1 regulate SVP protein accumulation to control flowering in Arabidopsis Plant Cell 20 2960 2971
Gepts, P. & Debouck, D.G. 1991 Origin, domestication, and evolution of the common bean (Phaseolus vulgaris L.), p. 7–53. In: A. van Schoonhoven and O. Voysest (eds.). Common beans: Research for crop improvement. Commonwealth Agricultural Bureaux Intl., Wallingford, UK
Gu, W., Zhu, J., Wallace, D., Singh, S. & Weeden, N. 1998 Analysis of genes controlling photoperiod sensitivity in common bean using DNA markers Euphytica 102 125 132
Itoh, H., Nonoue, Y., Yano, M. & Izawa, T. 2010 A pair of floral regulators sets critical day length for Hd3a florigen expression in rice Nat. Genet. 42 635 638
Kojima, S., Takahashi, Y., Kobayashi, Y., Monna, L. & Sasaki, T. 2002 Hd3a, a rice ortholog of the Arabidopsis FT gene, promotes transition to flowering downstream of Hd1 under short-day conditions Plant Cell Physiol. 43 1096 1105
Kornegay, J., White, J.W., Dominguez, J.R., Tejada, G. & Cajiao, C. 1993 Inheritance of photoperiod response in Andean and Mesoamerican common bean Crop Sci. 33 977 984
Kwak, M., Velasco, D. & Gepts, P. 2008 Mapping homologous sequences for determinacy and photoperiod sensitivity in common bean (Phaseolus vulgaris) J. Hered. 99 283 291
Kitae, S., Chul, K.H., Seungho, S., Kyung-Hee, K., Jun-Cheol, M. & Yoo, K.J. 2017 Transcriptome analysis of flowering time genes under drought stress in maize leaves Front. Plant Sci. 8 267
Liu, X.L., Covington, M.F., Fankhauser, C., Chory, J. & Wagner, D.R. 2001 ELF3 encodes a circadian clock-regulated nuclear protein that functions in an Arabidopsis PHYB signal transduction pathway Plant Cell 13 1293 1304
Li, R., Yu, C., Li, Y., Lam, T.W., Yiu, S.M., Kristiansen, K. & Wang, J. 2009 SOAP2: An improved ultrafast tool for short read alignment Bioinformatics 25 1966 1967
Lu, S.X., Knowles, S.M., Andronis, C., Ong, M.S. & Tobin, E.M. 2009 Circadian clock associated1 and late elongated hypocotyl function synergistically in the circadian clock of Arabidopsis Plant Physiol. 150 834 843
McWatters, H.G., Bastow, R.M., Hall, A. & Millar, A.J. 2000 The ELF3 zeitnehmer regulates light signalling to the circadian clock Nature 408 716 720
Moyses, N., Nascimento, A.C.C. & Silva, F.F.E. 2018 Quantile regression for genome-wide association study of flowering time-related traits in common bean PLoS One 13 0190303
Rajkumar, A.P., Qvist, P., Lazarus, R., Lescai, F., Ju, J., Nyegaard, M., Mors, O., Børglum, A.D., Li, Q. & Christensen, J.H. 2015 Experimental validation of methods for differential gene expression analysis and sample pooling in RNA-seq BMC Genomics 16 548
Salome, P.A., Bomblies, K., Laitinen, R.A.E., Yant, L. & Mott, R. 2011 Genetic architecture of flowering-time variation in Arabidopsis thaliana Genetics 188 421 433
Suárez-López, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F. & Coupland, G. 2001 CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis Nature 410 1116 1120
Wallace, D.H., Gniffke, P.A., Masaya, P.N. & Zobel, R.W. 1991 Photoperiod, temperature, and interaction effects on days and nodes required for flowering of bean J. Amer. Soc. Hort. Sci. 116 534 543
White, J. & Laing, D. 1989 Photoperiod response of flowering in diverse genotypes of common bean (Phaseolus vulgaris) Field Crops Res. 22 113 128
White, J., Kornegay, J. & Cajiao, C. 1996 Inheritance of temperature sensitivity of the photoperiod response in common bean (Phaseolus vulgaris L.) Euphytica 91 5 8
List of common bean cultivars, growth habits, and phenotypes used in this study. A total of 215 common bean cultivars were sown in Harbin [northeast China (lat. 44°30′24″N, long. 125°42′41″E)] and Sanya [south China (lat. 18°09′34″N, long. 108°56′30″E)] on 21 May and 1 Nov. 2017, respectively.
List of primers used to amplify the selected genes for quantitative reverse transcription polymerase chain reaction (qRT-PCR) analyses. Eight genes with varying expression patterns revealed through RNA-sequencing were randomly selected for validation by qRT-PCR. RNA extracted from the leaves of the three independent biological replicates of the different sampling times were used for qRT-PCR validation. Gene copy specific primers for qRT-PCR were designed based on the corresponding sequences using Primer6; LRZFP1 = LR zinc finger protein, GI = gigantea, HST = homogentisate solanesyl transferase.