Genome-wide identification of the Beta vulgaris ABF （BvABF） gene family and analysis of the expression pattern in sugar beet under ABA treatment

doi:10.11686/cyxb2023379

Abstract

Abstract:

Abscisic acid （ABA）-responsive （ABRE） binding factor proteins （ABF） are a unique subfamily of bZIP transcription factor proteins in plants， and play important roles in ABA-dependent and ABA-independent signaling pathways. To explore and identify the biological functions and expression patterns of the BvABF gene family in sugar beet （Beta vulgaris）， in the present study， the physicochemical properties， phylogeny， chromosomal localization， gene structure， conserved motifs， cis-acting elements， secondary structure and protein interaction network of BvABFs were predicted by bioinformatics methods， and their expression patterns in roots and leaves of sugar beet under 100 μmol·L^-1 ABA treatments were analyzed by qRT-PCR. A total of six BvABF genes were identified in sugar beet， and divided into groups A， B， and C， all of which contained a bZIP region. The BvABF genes are located on chromosomes 1， 3， 6， 7， and 9， and they contain 3-4 exons. The identified BvABF proteins possess 4 conserved regions， C1， C2， C3， and C4， each containing potential phosphorylation sites （R-X-X-S/T）. The C-terminal region contains a basic region and four repeating heptapeptide repeats consisting of leucine residues. The promoter region of BvABFs contained multiple hormone and light responsive elements， with 4 genes containing an ABRE element. In addition， a myeloblastosis （MYB） binding site involved in drought-inducibility （MBS）， a low-temperature-responsive element and an anaerobic responsive element were also found among the BvABF genes. Furthermore， BvABF may interact with phosphorylation-related proteins （PP2CCNBD-X2， SRK2I， SRK2E-X1， and PP2C50） and ABA receptors （PYL2， PYL4， and PYR1）. The expression patterns of BvABF were further analyzed in different tissues of sugar beet under ABA treatment， and it was found that all the BvABF genes were induced and regulated by ABA both in the roots and leaves， while different gene members exhibited different expression patterns under ABA treatment. These results suggest that BvABFs play important roles in the response of the sugar beet crop to ABA.

Key words: sugar beet, BvABF family, genome-wide identification, abscisic acid, cis-acting elements

Ya-jing MENG, Guo-qiang WU, Ming WEI. Genome-wide identification of the Beta vulgaris ABF （BvABF） gene family and analysis of the expression pattern in sugar beet under ABA treatment[J]. Acta Prataculturae Sinica, 2024, 33(9): 94-110.

Figures/Tables 12

References 92

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基因名称 Gene name	正向引物 Forward primer sequence （5′-3′）	溶解温度 Melting temperature （℃）	反向引物 Reverse primer sequence （5′-3′）	溶解温度 Melting temperature （℃）
BvABF1	GCCGAATACCTTGCTTGATGCT	58.2	GAATTTCCGCATCCTCGCCAT	58.4
BvABF2	CTCAATTGGCAGTTTCAACCAC	54.7	CTCAACAGTCTTCTCGACCAC	55.4
BvABF3	CTGGAGTTGGAAGTTGTCCAATA	54.3	AGCATGGCGTTTTCTTTCGTT	49.3
BvABF4	AATGCACAATTAAAGCAAGCC	51.6	GCCCTGCTTAGTATTACCTGT	54.0
BvABF5	ACTACCTAGGACGCTTAGTCA	54.2	GTGATCTCCCCAAGTGTCTG	55.4
BvABF6	CTGTGTGATAAGCCCAATTCG	53.8	AATTCATTGTGGTAAGCCTGT	51.5
BvACTIN	ACTGGTATTGTGCTTGACTC	51.9	ATGAGATAATCAGTGAGATC	44.8

基因名称 Gene name	正向引物 Forward primer sequence （5′-3′）	溶解温度 Melting temperature （℃）	反向引物 Reverse primer sequence （5′-3′）	溶解温度 Melting temperature （℃）
BvABF1	GCCGAATACCTTGCTTGATGCT	58.2	GAATTTCCGCATCCTCGCCAT	58.4
BvABF2	CTCAATTGGCAGTTTCAACCAC	54.7	CTCAACAGTCTTCTCGACCAC	55.4
BvABF3	CTGGAGTTGGAAGTTGTCCAATA	54.3	AGCATGGCGTTTTCTTTCGTT	49.3
BvABF4	AATGCACAATTAAAGCAAGCC	51.6	GCCCTGCTTAGTATTACCTGT	54.0
BvABF5	ACTACCTAGGACGCTTAGTCA	54.2	GTGATCTCCCCAAGTGTCTG	55.4
BvABF6	CTGTGTGATAAGCCCAATTCG	53.8	AATTCATTGTGGTAAGCCTGT	51.5
BvACTIN	ACTGGTATTGTGCTTGACTC	51.9	ATGAGATAATCAGTGAGATC	44.8

基因名称 Gene name	基因号 Gene ID	位置 Locus	CDS （bp）	蛋白长度 Protein length （aa）	MW （kDa）	pI	GRAVY	亚细胞定位 Subcellular localization
BvABF1	Bv1_011670_nwdc	Bvchr1.sca004：3786136..3794120（-）	813	270	29.49	5.55	-0.607	细胞核Nucleus
BvABF2	Bv3_064480_rnwf	Bvchr3.sca011：690504..695203（-）	1002	333	36.54	9.27	-0.807	细胞核Nucleus
BvABF3	Bv6_134230_aref	Bvchr6.sca003：2686565..2693985（+）	723	240	26.69	9.35	-0.697	细胞核Nucleus
BvABF4	Bv7_159570_afnu	Bvchr7.sca001：3838771..3848492（-）	1356	451	49.19	8.30	-0.793	细胞核Nucleus
BvABF5	Bv7_169340_mcdu	Bvchr7.sca021：1716062..1720374（-）	1470	489	51.59	9.49	-0.655	细胞核Nucleus
BvABF6	Bv9_207080_uszh	Bvchr9.sca010：874741..883695（+）	795	264	29.46	6.92	-0.653	细胞核Nucleus

基因名称 Gene name	基因号 Gene ID	位置 Locus	CDS （bp）	蛋白长度 Protein length （aa）	MW （kDa）	pI	GRAVY	亚细胞定位 Subcellular localization
BvABF1	Bv1_011670_nwdc	Bvchr1.sca004：3786136..3794120（-）	813	270	29.49	5.55	-0.607	细胞核Nucleus
BvABF2	Bv3_064480_rnwf	Bvchr3.sca011：690504..695203（-）	1002	333	36.54	9.27	-0.807	细胞核Nucleus
BvABF3	Bv6_134230_aref	Bvchr6.sca003：2686565..2693985（+）	723	240	26.69	9.35	-0.697	细胞核Nucleus
BvABF4	Bv7_159570_afnu	Bvchr7.sca001：3838771..3848492（-）	1356	451	49.19	8.30	-0.793	细胞核Nucleus
BvABF5	Bv7_169340_mcdu	Bvchr7.sca021：1716062..1720374（-）	1470	489	51.59	9.49	-0.655	细胞核Nucleus
BvABF6	Bv9_207080_uszh	Bvchr9.sca010：874741..883695（+）	795	264	29.46	6.92	-0.653	细胞核Nucleus

基序Motif	序列长度Sequence length （aa）	基序序列Motif sequence
Motif 1	49	VDKVVERRQKRMIKNRESAARSRARKQAYTVELESEVSQLEEENEELRK
Motif 2	45	RQVSIYSLTLDEFQNTLGGLGKDFGSMNMDEFLKNIWTAEENQSV
Motif 3	26	SLPRQGSLTLPRHLSRKTVDEVWREI
Motif 4	24	PKRZATLGEMTLEDFLVKAGVVRE
Motif 5	12	KYQLRRTSSAPF
Motif 6	10	PPPHQHPPHH
Motif 7	11	MTAFIDGHHNP
Motif 8	6	FFAFDN
Motif 9	6	NHIDEN
Motif 10	9	TKECFKQQM