Ploidy variation on gene differential expression in cowpea

Qiu, Xuewen; Kuang, Huiyun; Zeng, Chuntao; Li, Dan; Yang, Youxin; Gan, Yudi; Fan, Shuying; Wu, Caijun

doi:10.1590/0103-8478cr20230108

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BIOLOGY • Cienc. Rural 54 (8) • 2024 • https://doi.org/10.1590/0103-8478cr20230108 copy

Ploidy variation on gene differential expression in cowpea

Efeitos da variação da ploidia na expressão diferencial de genes em feijão-caupi

Authorship SCIMAGO INSTITUTIONS RANKINGS

ABSTRACT:

This study investigated the differences in gene expression profiles of diploid and autotetraploid in cowpea, and provided theoretical basis for screening key genes of differential expression and ploidy breeding. The phenotypes and contents of chlorophyll, soluble sugar and soluble protein of diploid and autotetraploid of cowpea were compared and transcriptome sequencing was performed. The autotetraploid leaves of cowpea were thicker and darker green than diploid leaves, and the contents of chlorophyll, soluble sugar and soluble protein in leaves were higher. A total of 2678 differentially expressed genes (DEGs) were analyzed in the diploid and autotetraploid of cowpea. Among them, there were 421 genes with higher expression of tetraploid than diploid, and 2257 genes with lower expression of tetraploid than diploid. All 2678 DEGs were annotated into the Gene Ontology (GO) functional library. The DEGs were mainly concentrated in metabolism and cell composition. Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway analysis showed that cowpea diploid and autotetraploid have significant differences in flavonoid biosynthesis, degradation of other glycan, phenylpropane biosynthesis, starch sucrose metabolism, keratin, amber and wax biosynthesis, circadian rhythm and plant pathways.

Key words:
Vignaunguiculata,polyploidy; phenotype and physiological characteristics,transcriptome sequencing,differentially expressed gene (DEG)

Group	Thick stem/mm	---------------Leaf---------------		Thickness of leaf/mm	------------------------------Pod------------------------------
		Length/cm	Width/cm		Diameter/mm	Pod length/cm	Fresh weight/g
Diploids	3.45±0.32b	9.53±0.21b	6.05±0.44b	0.33±0.01b	7.65±0.34b	43.40±1.40b	19.54±1.02b
Tetraploids	4.44±0.19a	10.2±0.28a	7.38±0.06a	0.43±0.02a	9.33±0.36a	50.00±1.70a	26.75±1.15a

Classify 1	-----------------------Classify 2-----------------------	All gene number	--DEG number--	-----Ratio/%-----
Biological process	Cellular process	84978	635	23.72
	Metabolic process	52825	571	21.32
	Biological regulation	43322	252	9.41
	Response to stimulus	9552	239	8.92
	Cellular component organization or Biogenesis	12916	143	5.34
	Localization	18920	139	5.19
	Signaling	695	65	2.43
	Developmental process	1464	57	2.13
	Multicellular organismal process	3346	46	1.72
	Multi-organism process	1483	42	1.57
	Reproduction	347	38	1.42
	Reproductive process	531	38	1.42
	Immune system process	57	8	0.30
Cellular component	Membrane	7750	882	32.94
	Membrane part	20116	825	30.81
	Cell	46828	780	29.13
	Organelle	12844	526	19.64
	Organelle part	21332	157	5.86
	Extracellular region	556	131	4.89
	Protein-containing complex	5376	82	3.06
	Cell junction	316	26	0.97
	Symplast	316	26	0.97
	Supramolecular complex	340	22	0.82
	Membrane-enclosed lumen	484	20	0.75
Molecular function	Catalytic activity	57516	1186	44.29
	Binding	98052	1095	40.89
	Transporter activity	10249	151	5.64
	Transcription regulator activity	1491	117	4.37
	Molecular function regulator	1713	53	1.98
	Antioxidant activity	296	29	1.08
	Molecular transducer activity	641	29	1.08
	Structural molecule activity	909	17	0.63
	Nutrient reservoir activity	35	9	0.34

Classify 1	---------------------Classify 2---------------------	All gene number	DEG number	--Ratio/%--
Cellular Processes	Transport and catabolism	801	67	2.50
Environmental Information Processing	Signal transduction	1529	187	6.99
	Membrane transport	245	33	1.23
Genetic Information Processing	Folding，sorting and degradation	1308	106	3.96
	Translation	1829	106	3.96
	Transcription	884	90	3.36
	Replication and repair	833	27	1.01
Metabolism	Global and overview maps	1182	540	20.16
	Carbohydrate metabolism	2724	235	8.78
	Biosynthesis of other secondary metabolites	1096	175	6.53
	Lipid metabolism	1204	138	5.15
	Amino acid metabolism	1260	82	3.06
	Metabolism of other amino acids	536	77	2.88
	Metabolism of terpenoids and polyketides	468	61	2.28
	Glycan biosynthesis and metabolism	504	46	1.72
	Metabolism of cofactors and vitamins	440	34	1.27
	Energy metabolism	629	29	1.08
	Nucleotide metabolism	287	19	0.71
Organismal Systems	Environmental adaptation	1026	144	5.38

ID	----------------------Pathway name----------------------	-------------Number-------------	-------------P value-------------
ko00940	Phenylpropanoid biosynthesis	112	0.0195
ko00500	Starch and sucrose metabolism	89	0.0286
ko04712	Circadian rhythm-plant	39	0.049
ko00941	Flavonoid biosynthesis	33	0.0142
ko00511	Other glycan degradation	33	0.0195
ko00073	Cutin, suberine and wax biosynthesis	20	0.0377

Universidade Federal de Santa Maria Universidade Federal de Santa Maria, Centro de Ciências Rurais , 97105-900 Santa Maria RS Brazil , Tel.: +55 55 3220-8698 , Fax: +55 55 3220-8695 - Santa Maria - RS - Brazil
E-mail: cienciarural@mail.ufsm.br

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[1] E-mail:wucj12@126.com. ^*Corresponding author.

Group	Chlorophyll a content/mg·g^-1	Chlorophyll b content/mg·g^-1	Chlorophyll content/mg·g^-1	Soluble sugar content/mg·g^-1	Soluble protein content/mg·g^-1
Diploids	1.959±0.003b	0.624±0.003b	2.584±0.001b	0.89±0.02b	0.78±0.01b
Tetraploids	2.642±0.145a	0.851±0.048a	3.493±0.192a	1.14±0.03a	1.04±0.01a

Sample	Raw Reads (M)	Clean Reads (M)	Clean Bases (Gb)	Clean Reads Q20 (%)	Clean Reads Q30 (%)	Clean Reads Ratio (%)
Diploid 1	45.57	43.35	6.5	97.3	89.72	95.11
Diploid 2	45.57	43.15	6.47	97.28	89.65	94.68
Diploid 3	45.57	42.59	6.39	97.38	89.97	93.45
Tetraploid 1	45.57	43.12	6.47	97.31	89.75	94.61
Tetraploid 2	45.57	43.26	6.49	97.43	90.12	94.92
Tetraploid 3	49.08	46.38	6.96	97.18	89.5	94.5