Transcriptome Analysis to Identify Putative Genes Involved in Flowering Time Under Different Photoperiods in ‘Hong jin gou’ Common Bean

in Journal of the American Society for Horticultural Science

Flowering time influences pod yield and quality of common bean (Phaseolus vulgaris); however, our knowledge of flowering time genes and flowering mechanisms in common bean remain limited. We performed RNA-sequencing (RNA-seq) analyses [long-day (LD) condition and short-day (SD) condition] to identify the flowering time genes and analyzed differentially expressed genes to examine their expression levels in relation to flowering time in ‘Hong Jin Gou’ common bean, a cultivar highly sensitive to photoperiod. The circadian patterns of related genes were identified using quantitative real-time polymerase chain reaction (qRT-PCR). Flowering time in ‘Hong Jin Gou’ was influenced by day length: SD conditions promoted flowering. A total of eight flowering time–related genes were identified, which were classified into photoperiod pathways. Homologs of pseudo-response regulator 5, pseudo-response regulator 7, and gigantea were more highly expressed under SD conditions than under LD conditions. Homologs of late elongated hypocotyl and timing of cab expression 1 were differentially expressed under light and dark conditions. Early flowering 3 is a key regulator of the pathway, which coordinates light and circadian clock inputs in leaves to trigger the expression of downstream genes. The present study provides critical information that could facilitate further investigations on the genetic mechanism of flowering time in common bean.

Contributor Notes

Financial support was provided by the China Postdoctoral Science Foundation (grant number 2018M631973); the basic scientific research operating expenses of provincial College in Heilongjiang province (grant numbers KJCXYB201707 and KJCXYB201705); the National Natural Science Funds of China (grant number 31771869); and the applied technology research and development plan of Heilongjiang province (grant number GY2019YF0059).

These authors contributed equally to this work and share first authorship.

Corresponding authors.

E-mail: jianlongedu@163.com or feng998@126.com.

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    ‘Hong jin gou’ common bean [indeterminate climbing, yellow pod with red streak (developed at Heilongjiang University, Harbin, China)] cultivated in climate chambers at 25 °C under long-day (LD) conditions (16/8 h light/dark) with 300 µmol·m−2·s−1 of white light. All plants were cultivated in this climate chamber at first. Half of the plants were transferred to short-day (SD) conditions (8/16 h light/dark) under a similar temperature regimen after the trifoliate leaves emerged. SD condition promoted flowering in ‘Hong jin gou’. The date of flowering initiation was 33 d after sowing under the SD condition. (The arrows marks the position of flower.) In contrast, under the LD condition, the date of flowering initiation was delayed by ≈37 d.

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    Gene expression reprogramming under different photoperiod conditions in common bean. (A) Venn diagrams displaying the overlaps among differentially expressed genes identified in common bean plants exposed to light and dark conditions. Numbers in parentheses denote percentages with respect to the total upregulated (a) or downregulated (b) genes; long-day [LD (16/8 h light/dark)] and short-day [SD (8/16 h light/dark)] photoperiod × sampling time-point combination [LD-L (0600 hr), LD-D (1400 hr), SD-L (0600 hr), and SD-D (1400 hr)]. (B) Selected gene ontology (GO) terms enriched among differentially expressed genes identified in common bean. Color panels display the probability values of GO term enrichments.

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    Quantitative reverse transcription polymerase chain reaction (qRT-PCR) validation of the relative expression levels of genes selected from the RNA-sequencing (RNA-seq) analysis of common bean–photoperiod {long-day [LD (16/8 h light/dark)] and short-day [SD (8/16 h light/dark)]} interaction. Expression profiles of eight genes (color coded) as determined by qRT-PCR and RNA-seq. The x-axis indicates two groups of comparisons: LD-D vs. SD-D. and LD-L vs. SD-L [LD-L (0600 hr), LD-D (1400 hr), SD-L (0600 hr), and SD-D (1400 hr)]. The y-axis shows the fold change increases/decreases in expression levels of genes; LRZFP1 = LR zinc finger protein, GI = gigantea, HST = homogentisate solanesyl transferase.

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    Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway. Regulation of circadian rhythm genes in response to photoperiod in common bean. Schematic representation of key circadian clock components identified in common bean and their transcriptional interactions (red: upregulation, blue: downregulation). LHY = late elongated hypocotyl, PIF3 = phytochrome-interacting factor 3, PRR9 = pseudo-response regulator 9, PRR7 = pseudo-response regulator 7, PRR5 = pseudo-response regulator 5, PHYB = phytochrome, CRY = cryptochrome, TOC1 = timing of cab expression 1, HY5 = long hypocotyl 5, FT = flowering locus T, GI = gigantea, ELF3 = early flowering 3, CO = constans, PHYA = phytochrome A, COP1 = E3 ubiquitin-protein ligase RFWD2, FKF1 = flavin-binding kelch repeat F-box protein 1, ZTL = clock-associated PAS protein, CHE = transcription factor TCP21, CCA1 = circadian clock associated 1, CK2 = casein kinase II, CHS = chalcone synthase, PAP1 = transcription factor MYB75, CDF1 = Dof zinc finger protein DOF5.5.

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