Analysis of Differentially Expressed Genes in Lettuce Leaves Under Different Optical Spectrophotometric Films Based on Transcriptome Sequencing

doi:10.3969/j.issn.1000-2561.2020.02.016

Abstract

Abstract:

New photovoltaic agriculture can generate photovoltaic power under the light demand of crop growth. To study the differential gene expression in lettuce leaves under different spectrophotometric films, the ‘Adina’ lettuce variety was used as the experimental material, and the gene expression level of lettuce leaves under the conditions of red and blue filter film (RBFF) and far infrared cut-off film (RICF) was analyzed by the transcriptome sequencing (RNA-seq) technique. The results showed that 2685 genes were differentially expressed in RBFF, including 1380 up-regulated genes and 1305 down-regulated genes; 3264 genes were differentially expressed in RICF, of which 881 were up-regulation and 2383 down-regulation. Further analysis revealed that 1498 differentially expressed genes were expressed in both RBFF and RICF, 1187 genes were differentially expressed in the RBFF, while 1766 were differentially expressed in RICF. Ten genes related to light stress were screened from the differentially expressed genes, and the reliability of transcriptome data was verified by qRT-PCR. The results of expression analysis of light response related genes showed that most of the genes under red-blue filter film were expressed in large quantities, and the expression reached peak at 15 d; under far infrared cut-off film, the expression of three genes was higher, while the expression of others was lower. The expression of most genes reached peak at 15-21 d. This study would provide a theoretical basis and data support for further exploring photoresponsive genes in the lettuce genome and revealing the molecular mechanism of the lettuce response to light.

Key words: lettuce, optical spectrophotometric film, transcriptome analysis, quantitative real-time PCR (qRT-PCR)

CLC Number:

ZHOU Niannian,GAO Jie,DING Mingzhu,AN Yulan,ZHAI Keqing,SHI Jiayin,GAN Defang,LIU Wen. Analysis of Differentially Expressed Genes in Lettuce Leaves Under Different Optical Spectrophotometric Films Based on Transcriptome Sequencing[J]. Chinese Journal of Tropical Crops, 2020, 41(2): 323-332.

Figures/Tables 12

Tab. 1 Basic information of lettuce homologous genes of photoresponse related and qRT-PCR primer sequences

基因编号 Gene No.	基因号 Gene ID	特性Characterization	实时荧光定量引物Primers for Quantitative RT-PCR
基因编号 Gene No.	基因号 Gene ID	特性Characterization	正向引物Former Primer（5°-3°）		反向引物Reverse Primer（5°-3°）
Ls1	LSAT_3X58041	PIF4		GAACAAAGTCCAGTCCCTACAG	CGATCGGTCGTCACAGCATA
Ls2	LSAT_6X401	PHYB		TCGAAGAGGGCTACAGTCAT	CCATAACCACCTCCTCCATA
Ls3	LSAT_9X83701	PHYA		GCCCTCCAATCCTACAAACA	AGCCATCACCCGATCATAAC
Ls4	LSAT_3X81620	MYB75,PAP1		GGGAACAGGTGGTCATTGATAG	GGGAGCGAAGATGAGTATTCCAGT
Ls5	LSAT_2X122581	LHY		GGGGGACAAGAGAACAGAACAAATGG	CCTCGTACTGTTGTCTCACTTCG
Ls6	LSAT_8X31220	PIF3		GGGAAATGCTACTCAAGGAGTG	GGGTTGTGTGGTATGGCAATGAAG
Ls7	LSAT_3X127881	Pme2		GCAACGCTGCTGTGGTATT	CCTTCCACGGTCTACCAAGAT
Ls8	LSAT_3X101980	PMA		AGTCCCTCCCTGTAACAAAGC	GTAGAGTCTACAAGATGTGCAGCC
Ls9	LSAT_2X76880	CHS		GACCTCGCTGAGAACAACAA	ATCAAGGTGGGTGTCGTTAG
Ls10	LSAT_2X79501	RbcL		CCAATGGTGGAAGAGTGCAATG	CTTGTTGCGGAGAAGGTAGTC
Lsactin	LSAT_8X116260	LSACT		GGCAACTGGGATGACATGGAAA	GCACAGCCTGGATAGCAACATA

Tab. 2 Quality statistics of filtered reads

样品名Sample	CG	RBFF	RICF
过滤前的reads数	69.73	69.73	69.73
过滤后的reads数	65.70	66.18	65.50
过滤后的碱基总数	6.57	6.62	6.55
过滤后质量值>20的碱基数比例	97.72	97.99	97.84
过滤后质量值>30的碱基数比例	91.09	91.55	91.40
过滤后的reads比例	94.22	94.91	93.94

Tab. 3 Statistics of reference genome comparison results

样品名Sample	CG	RBFF	RICF
过滤后的reads总数	65 699 706	66 180 828	65 498 632
比对上参考基因组的clean reads比例	92.03	92.20	91.75
唯一比对上参考基因组某一位置的clean reads比例	76.04	76.89	75.03

Fig. 1 Correlation analysis of inter-samples

Fig. 2 Statistical map of differentially expressed genes

Fig. 3 Venn diagram of differentially expressed gene

Fig. 4 GO functional classification of the differentially expressed genes

Fig. 5 Pathway classification chart of differentially expressed genes A: CG-VS-RBFF; B: CG-VS-RICF; The X-axis represents the proportion of the gene, the Y-axis represents the KEGG functional classification.

Fig. 6 Pathway enrichment results of differentially expressed genes A: CG-VS-RBFF; B: CG-VS-RICF. The X-axis represents the enrichment factor value (Rich Factor), which is the quotient of the foreground value (number of differential genes) of a pathway on the annotation and the background value (number of all genes) of a pathway on the annotation, and the larger the data, the more obvious the enrichment results. The Y-axis represents the path name. The color of the dots in the figure represents the Q-value, and the lighter the color, the greater the value, the deeper the smaller, the latter represents the more significant the enrichment results; the size of the dots represents the number of DEGs, and the larger the number represents, the smaller the number represents.

Fig. 7 Expression analysis of qRT-PCR

Fig. 8 Expression analysis of light response genes under red-blue filter film (RBFF)

Fig. 9 Expression analysis of light response genes under far infrared cut-off film(RICF)

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