Genome-wide Identification of the BvATGs Genes Family in Sugar Beet （Beta vulgaris L.） and Analysis of Their Expression Pattern under Salt Stress

doi:10.13560/j.cnki.biotech.bull.1985.2025-0504

Abstract

Abstract:

Objective Autophagy is a crucial degradation pathway for maintaining cellular homeostasis and plays an essential role in plant responses to abiotic stress. In this study, autophagy-related genes (ATGs) were identified and characterized in sugar beet (Beta vulgaris L.), and their expression patterns under salt stress were analyzed to provide a theoretical basis for understanding their potential functions in stress responses. Method Members of the BvATGs gene family were identified from the sugar beet genome using bioinformatics methods, and the physicochemical properties, chromosomal distribution, phylogenetic relationships, gene structures, conserved motifs, cis-acting regulatory elements, and collinearity were analyzed. RT-qPCR was used to analyze the expression patterns of these genes under salt stress. The subcellular localization of BvATG4 and BvATG6a-1 was determined through transient transformation of Arabidopsisthaliana protoplasts mediated by PEG. Furthermore, the overexpression vectors for BvATG4 and BvATG6a-1 were constructed and genetically transformed into A.thaliana. Result A total of 51 BvATGs genes were identified and classified into 20 subfamilies in sugar beet. Among them, 48 BvATGs were unevenly distributed across nine chromosomes, while the other three genes (BvATG1a, BvATG1d and BvATG1k) were not mapped onto chromosomes. The BvATGs genes in the same subfamily had similar gene structures and conserved domains. The number of amino acids encoding BvATGs genes was 84-2 467 aa, and the molecular weight was 10.21-277.30 kD, most of which were hydrophilic proteins. Approximately 88.2% of the BvATGs members were localized to the cytoplasm, nucleus and chloroplast. Intraspecific collinearity analysis showed that there were 3 pairs of homologous genes of BvATGs, and interspecific collinearity showed that there were 9 pairs and 30 pairs of homologous genes of BvATGs in rice (Oryza sativa) and A. thaliana, respectively. A large number of light-responsive, hormone-responsive and stress-responsive elements were found in the promoter regions of the BvATGs genes. The RT-qPCR analysis showed that the expressions of 12 BvATG genes in the shoots and roots were up-regulated to varying degrees under salt stress. BvATG4 was primarily localized in the nucleus and cytoplasm, while BvATG6a-1 was mainly localized in the cytoplasm and endoplasmic reticulum. Compared to wild-type A. thaliana, the relative expressions of BvATG4 and BvATG6a-1 genes in the transgenic lines significantly increased. Conclusion A total of 51 BvATGs family members are identified at the whole genome of sugar beet in this study. Among those, 12 genes are differentially induced and up-regulated under salt stress. BvATG4 is localized in the nucleus and cytoplasm, while BvATG6a-1 is localized in the cytoplasm and endoplasmic reticulum. Further, BvATG4 and BvATG6a-1 are introduced into A. thaliana, and transgenic lines with high expression (OE4 and OE2) are obtained, respectively. This study establishs a theoretical basis for identification and utilization of salt-tolerant genetic resources in sugar beet.

Key words: sugar beet, bioinformatics, autophagy, autophagy-related genes, salt stress, expression analysis, subcellular localization

REN Yun-er, WU Guo-qiang, CHENG Bin, WEI Ming. Genome-wide Identification of the BvATGs Genes Family in Sugar Beet （Beta vulgaris L.） and Analysis of Their Expression Pattern under Salt Stress[J]. Biotechnology Bulletin, 2026, 42(1): 184-197.

Figures/Tables 10

References 47

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基因名称 Gene name	上游引物 Forward primer sequence （5′‒3′）	下游引物 Reverse primer sequence （5′‒3′）
BvACTIN	ACTGGTATTGTGCTTGACTC	ATGAGATAATCAGTGAGATC
BvATG1e	CAATCTGTCTGGCTTATTCGATG	CGCTCGAAGTTTAGCAACCC
BvATG1h	TTTGCCGGAACACCTTAGACA	CCTTAGCACCATCATATCCCT
BvATG3	CCATGCTCGCAAAACGGTA	GTCAACTTCTGGCTCAACCC
BvATG4	TCGTCGTCAACTAGGGCTTC	CTCCTCCGAACGATGCTCA
BvATG6a-1	GTCTCCCTAAAGTTCCGGTTG	TTTACAGGCCCAAACAGGT
BvATG8b	CCTACTGGAGCAATCATGTCT	CTCCACAGCAAGATACCCGAA
BvATG8c	GCTCCAACATCCTCTCGAAC	TGCCCCACAGTTAAATCAGC
BvATG8d	TCCTGAGAAAGCCATATTCGT	TAGCAATGCACCTCAATCCAA
BvATG8e	TGCCAAGTATCCTGATCGAGT	ATATAAATAGAGCTTTGCCCGGAG
BvATG10	CCTCTCTTCACTTCCCACGA	TTGCAGGATCAATACGCTCT
BvATG16-2	CAGTGCAGCTTATGATCGAAC	CAAAGCCGGAGATTCCCAT
BvATG20c	TCCCGAGATTTCCACTACTGC	AAGGATCGAAACATAGCGTCA

基因名称 Gene name	上游引物 Forward primer sequence （5′‒3′）	下游引物 Reverse primer sequence （5′‒3′）
BvACTIN	ACTGGTATTGTGCTTGACTC	ATGAGATAATCAGTGAGATC
BvATG1e	CAATCTGTCTGGCTTATTCGATG	CGCTCGAAGTTTAGCAACCC
BvATG1h	TTTGCCGGAACACCTTAGACA	CCTTAGCACCATCATATCCCT
BvATG3	CCATGCTCGCAAAACGGTA	GTCAACTTCTGGCTCAACCC
BvATG4	TCGTCGTCAACTAGGGCTTC	CTCCTCCGAACGATGCTCA
BvATG6a-1	GTCTCCCTAAAGTTCCGGTTG	TTTACAGGCCCAAACAGGT
BvATG8b	CCTACTGGAGCAATCATGTCT	CTCCACAGCAAGATACCCGAA
BvATG8c	GCTCCAACATCCTCTCGAAC	TGCCCCACAGTTAAATCAGC
BvATG8d	TCCTGAGAAAGCCATATTCGT	TAGCAATGCACCTCAATCCAA
BvATG8e	TGCCAAGTATCCTGATCGAGT	ATATAAATAGAGCTTTGCCCGGAG
BvATG10	CCTCTCTTCACTTCCCACGA	TTGCAGGATCAATACGCTCT
BvATG16-2	CAGTGCAGCTTATGATCGAAC	CAAAGCCGGAGATTCCCAT
BvATG20c	TCCCGAGATTTCCACTACTGC	AAGGATCGAAACATAGCGTCA

引物用途 Primer purpose	引物名称 Primer name	引物序列 Primer sequence （5′‒3′）
基因克隆 Gene clone	BvATG4-F-Xho I	GAGGACACGCTCGAGATGAAGAACTTGTTTGAGAGTGCTGG
	BvATG4-R-Sma I	CTTTGTAATCCCCGGGGAGGAGTTGCCATTCGTCCTCTTG
	BvATG6a-1-F-Xho I	TTTGGAGAGGACACGCTCGAGATGAAGGAGAAGCAGCTTG
	BvATG6a-1-R-Sma I	TCATCTTTGTAATCCCCGGGTTGACCAGATGGAAATCGAG
转基因拟南芥PCR检测 Transgenic A. thaliana PCR detection	35S-F	GACGCACAATCCCACTATCC
	BvATG4-R	GAGGAGTTGCCATTCGTCCTCTTG
	BvATG6a-1-R	TTGACCAGATGGAAATCGAG
内参基因 Refenrence gene	AtUBQ10-F	AGATCCAGGACAAGGAAGGTATTC
内参基因 Refenrence gene	AtUBQ10-R	CGCAGGACCAAGTGAAGAGTAG
亚细胞定位 Subcellular localization	BvATG4-F-Hind III	GGACAGCCCAAGCTTATGAAGAACTTGTTTGAGAGTGCTGG
	BvATG4-R-Nco I	TTGCTCACCATGGATCCGAGGAGTTGCCATTCGTCCTCTTG
	BvATG6a-1-F-Hind III	CATGGAGGCCAGTGAATTCATGAAGGAGAAGCAGCTTGATG
	BvATG6a-1-R-Nco I	TCGAGCTCGATGGATCCTTGACCAGATGGAAATCGAGAATC

引物用途 Primer purpose	引物名称 Primer name	引物序列 Primer sequence （5′‒3′）
基因克隆 Gene clone	BvATG4-F-Xho I	GAGGACACGCTCGAGATGAAGAACTTGTTTGAGAGTGCTGG
	BvATG4-R-Sma I	CTTTGTAATCCCCGGGGAGGAGTTGCCATTCGTCCTCTTG
	BvATG6a-1-F-Xho I	TTTGGAGAGGACACGCTCGAGATGAAGGAGAAGCAGCTTG
	BvATG6a-1-R-Sma I	TCATCTTTGTAATCCCCGGGTTGACCAGATGGAAATCGAG
转基因拟南芥PCR检测 Transgenic A. thaliana PCR detection	35S-F	GACGCACAATCCCACTATCC
	BvATG4-R	GAGGAGTTGCCATTCGTCCTCTTG
	BvATG6a-1-R	TTGACCAGATGGAAATCGAG
内参基因 Refenrence gene	AtUBQ10-F	AGATCCAGGACAAGGAAGGTATTC
内参基因 Refenrence gene	AtUBQ10-R	CGCAGGACCAAGTGAAGAGTAG
亚细胞定位 Subcellular localization	BvATG4-F-Hind III	GGACAGCCCAAGCTTATGAAGAACTTGTTTGAGAGTGCTGG
	BvATG4-R-Nco I	TTGCTCACCATGGATCCGAGGAGTTGCCATTCGTCCTCTTG
	BvATG6a-1-F-Hind III	CATGGAGGCCAGTGAATTCATGAAGGAGAAGCAGCTTGATG
	BvATG6a-1-R-Nco I	TCGAGCTCGATGGATCCTTGACCAGATGGAAATCGAGAATC