Cotton Science

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Comparison of the transcriptomes between pink flower buds and yellow flower buds in upland cotton

Liu Linqiang, Han Xiao, Yang Lan, Yan Qingdi, Hu Wei, Jin Yuying, Yu Jie, Yang Zhaoen, Li Fuguang

Cotton Science, 2023, 35(4): 259-273. DOI: 10.11963/cs20200102

基因编号 Gene ID	上游引物 Forward primer	下游引物 Reverse primer
Gh_D07G080000	GTGCTCAGCTGCCAACAAAA	TGGTCTCCCACCATGCATTC
Gh_D13G166600	AGGACAGTCGGGATGTGAGA	TTGGTGGACTGGGTTCACTG
Gh_A06G151100	AACGGTTTTCCGCATGAAGC	GCGGTAAGGGCATCCGTAAT
Gh_D09G224800	TGCAATTCGCATCAGGTTTTCC	TGGTTACGATGGCACTGGTC
Gh_D09G172600	TACCATAGTCCCAAAGCCGC	TGGAGAAGCTCTTTGGCCTG
Gh_D07G106300	AACCATTCACCATTGCGCTG	CCCACAACTTGCCACCTGTA
Gh_A07G079800	GTGCTCAGCTGCCAACAAAA	CCACCATGCATTCACATGCT
Gh_A07G083500	TCAAGCCTCGGCCTCATATC	CTCATCGTGGTCATTCGGGA
Gh_D03G042200	CTTCAAGACTGATTTGCGTTTC	GCGCAAAGGTTGGTGTCTTC

Table 1 Primers used in this study

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Fig. 1 Flowers and buds at different development stages of CCRI 24 and Zhongyihong A: Flowers and buds at different development stages of CCRI 24 (upper panel) and Zhongyihong (bottorn panel); B: Flowers of CCRI 24 (right) and Zhongyihong (left), photos were taken at the flowering day; C: The color of petals at different development stages of CCRI 24 (upper panel) and Zhongyihong (bottorn panel).
Table 2 Anthocyanin content in buds at B1 and A9 stages of CCRI 24 and Zhongyihong
Table 3 Basic information for transcriptome sequencing data
Fig. 2 Correlation analysis between different samples based on gene expression levels 1, 2, and 3 followed W-B1, W-A9, P-B1 and P-A9 indicate three replicates. r is the correlation coefficient.
Fig. 3 Comparison of gene expression profiles between qRT-PCR and RNA-Seq Black bars represent gene expression level detected by qRT-PCR, and gray bars represent TPM of genes by RNA-seq.
Table 4 Numbers of DEG between different sample group
Fig. 4 Venn analysis of DEG in buds of CCRI 24 and Zhongyihong at different developmental stages
Fig. 5 The expression profiles of Gh_A07G083500 and Gh_A07G079800 Statistical analyses have been the Student’s test. ** and **** indicate significance at the 0.01 and 0.000 1 probability level, respectively.
Fig. 6 GO enrichment analysis of DEG A: GO enrichment analysis of up-regulated DEG, B: GO enrichment analysis of down-regulated DEG.
Table 5 Metabolic pathways of up-regulated PEG
Table 6 Metabolic pathways of down-regulated DEG
Fig. 7 Gene expression level involved in the biosynthesis, modification and transport pathway of anthocyanin
Fig. 8 The regulation and transport model of anthocyanin in pink flower The dotted line indicates the genes not enriched in this pathway in this study.

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