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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (12): 2348-2361.doi: 10.3724/SP.J.1006.2021.04268

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide identification and expression analysis of potato GAUT gene family

NIU Na1,2(), LIU Zhen2, HUANG Peng-Xiang2,3, ZHU Jin-Yong1,2, LI Zhi-Tao1,2, MA Wen-Jing1,2, ZHANG Jun-Lian2,3, BAI Jiang-Ping1,2,*(), LIU Yu-Hui1,2,*()   

  1. 1College of Agronomy, Gansu Agricultural University, Lanzhou 730070, Gansu, China
    2Gansu Provincial Key Laboratory of Arid Land Crop Science / Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, Gansu, China
    3College of Horticulture, Gansu Agricultural University, Lanzhou 730070, Gansu, China
  • Received:2020-12-09 Accepted:2021-04-14 Online:2021-12-12 Published:2021-06-03
  • Contact: BAI Jiang-Ping,LIU Yu-Hui E-mail:2413748774@qq.com;baijp@gsau.edu.cn;lyhui@gsau.edu.cn
  • Supported by:
    National Natural Science Foundation of China(31860398);Program for Innovation Foundation of the Higher Education Institutions of Gansu Province(2020A-056);Gansu Science Foundation for Distinguished Young Scholars(17JR5RA138);Program for Longyuan Youth Innovation Team of Gansu Province(LRYCT-2020-1)

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Abstract:

Galacturonyltransferases (GAUTs) are enzymes responsible for catalyzing glycosylation reactions and play an important role in the growth and development of plant. In this study, GAUT genes family members in potato (StGAUT) were identified, and their physical and chemical characteristics, distribution on chromosomes, gene structure, conserved motifs, gene duplication events, and expression patterns were analyzed. The results showed that a total of 41 StGAUTs were identified and distributed extensively and unevenly on 10 chromosomes. According to their structural and phylogenetic protein features, these 41 StGAUT genes were divided into four subclasses. Collinearity analysis indicated that 12 pairs of StGAUTs were segmental duplication genes, and these gene pairs evolved under purifying selection. RNA-seq data of different tissues and abiotic stresses were used to analyze tissue-specific and abiotic stress-responses of the StGAUT genes in doubled monoploid potato (DM). Results revealed that StGAUT genes might be involved in anthocyanin biosynthesis in three different-colored potato cultivars based on RNA-seq data. The results provide valuable information regarding further functional elucidation of StGAUT genes in potato.

Key words: potato (Solanum tuberosum L.), galacturonyltransferase, the relative expression level, anthocyanin biosynthesis

Table 1

Primers for qPCR used in this study"

基因名称
Gene name		 正向引物
Forward sequence (5°-3°)		 反向引物
Reverse sequence (5°-3°)
StEF-1α GGTCGTGTTGAGACTGGTGTGATC GCTTCGTGGTGCATCTCTACAGAC
PG0024800 ACAGAGTATTCGCTTGGCAGGTTC CTTCCATCCGGCAGCCTCTAAAC
PG0024782 CATTGGAGTGGAGGTGGCAAACC TGCAAATCATATCGAGCCCAGAGC
PG0020103
PG0000827		 CTGATCTCGGCGTCGGAATTACAC
AAGCTCCAGCATTCCGCAACG		 AGCCAGAACCAATGAACGGTGATC
CGGAGGTAAGGGGAGGAGTAATCG
PG0003522 GCCGTTGATGGTGAAGTTGAAGC GCCGCCGATGGAGCAGTTATG
PG0001444 CAGACAGTTGCCTTCACCAGAGC GGCAGCCAGGATGTTGTCAGTG
PG0001396 GGGAAACCTTGGGTCAGGCTTG CATCGCTCTTCGCTCTTGATCGTC
PG0001388 ACTTGCATCGGTCATTGGTGTCAC TAAGCGGCGTAGGCATTCACAAG

Fig. 1

Genomic distributions of StGAUT genes on 12 potato chromosomes"

Fig. 2

Phylogenic classification of GAUTs between Arabidopsis and potato The different subgroups were marked with different colors. The blue rounds represent StGAUTs genes, and the red stars represent AtGAUTs genes."

Table 2

Physicochemical properties and subcellular location of StGAUT gene family"

基因名称
Gene name		 染色体定位Chromosome
localization		 亚组
分类Subgroup		 氨基酸长度Amino acid
length		 等电点
Point isoelectric (pI)		 相对分子量
Molecular
weight (kD)		 亚细胞定位
Subcellular localization
PG0025139 ch02 C III 533 9.30 60,619.92 线粒体 Mitochondrial
PG0003522 ch02 C II 337 5.48 38,646.39 细胞外 Extracellular
PG0015490 ch02 C II 327 5.52 37,560.90 细胞外 Extracellular
PG0001183 ch02 C I 285 5.77 31,985.75 细胞膜 Plasma membrane
PG0001388 ch02 C IV 547 8.47 63,223.59 线粒体 Mitochondrial
PG0001396 ch02 C I 365 8.84 42,038.75 细胞膜 Plasma membrane
PG0010088 ch02 C I 345 6.24 38,390.78 细胞膜 Plasma membrane
PG0001444 ch02 C III 534 9.09 60,404.61 线粒体 Mitochondrial
PG0004427 ch00 C III 423 9.04 48,777.15 线粒体 Mitochondrial
PG2003179 ch07 C IV 597 9.33 68,386.80 线粒体 Mitochondrial
PG0017341 ch07 C III 545 7.36 61,040.35 细胞膜 Plasma membrane
PG0019228 ch07 C III 533 9.10 60,862.53 线粒体 Mitochondrial
PG0018996 ch01 C II 555 8.84 65,196.17 细胞核 Nuclear
基因名称
Gene name		 染色体定位Chromosome
localization		 亚组
分类Subgroup		 氨基酸长度Amino acid
length		 等电点
Point isoelectric (pI)		 相对分子量
Molecular
weight (kD)		 亚细胞定位
Subcellular localization
PG0046135 ch01 C II 321 6.02 36,737.36 细胞质 Cytoplasmic
PG0018997 ch01 C II 504 8.56 58,979.96 细胞质 Cytoplasmic
PG0000010 ch01 C IV 688 9.46 78,276.85 线粒体 Mitochondrial
PG0005216 ch01 C II 336 6.02 38,507.42 细胞质 Cytoplasmic
PG0012098 ch01 C III 90 10.39 10,714.47 线粒体 Mitochondrial
PG0024782 ch01 C I 353 9.26 40,529.85 细胞膜 Plasma membrane
PG0014677 ch01 C IV 680 8.34 78,728.64 细胞核 Nuclear
PG0023500 ch05 C II 533 8.96 60,350.47 细胞膜 Plasma membrane
PG0000827 ch05 C I 351 8.64 40,823.85 细胞膜 Plasma membrane
PG0022608 ch05 C I 385 8.32 44,667.17 细胞膜 Plasma membrane
PG0019367 ch12 C I 116 9.45 13,445.85 细胞膜 Plasma membrane
PG0007896 ch12 C IV 579 9.00 66,706.29 线粒体 Mitochondrial
PG0014637 ch06 C I 350 8.68 40,382.78 细胞膜 Plasma membrane
PG0011872 ch06 C II 465 8.68 52,580.83 细胞膜 Plasma membrane
PG0020103 ch06 C IV 557 9.23 63,946.48 线粒体 Mitochondrial
PG0003843 ch09 C I 356 8.63 40,860.88 细胞外 Extracellular
PG0027950 ch09 C IV 288 7.21 32,817.57 细胞膜 Plasma membrane
PG0031840 ch09 C I 353 9.02 40,214.14 细胞膜 Plasma membrane
PG0024623 ch09 C IV 536 6.95 62,348.31 细胞膜 Plasma membrane
PG0027227 ch04 C IV 678 9.26 77,430.93 细胞核 Nuclear
PG0016880 ch04 C I 351 5.99 39,345.05 细胞膜 Plasma membrane
PG0008016 ch04 C II 579 8.70 67,676.72 细胞质 Cytoplasmic
PG0024824 ch04 C IV 534 9.18 61,816.85 细胞膜 Plasma membrane
PG0008015 ch04 C II 564 9.02 66,085.84 细胞核 Nuclear
PG0011479 ch04 C II 533 9.05 60,263.41 细胞膜 Plasma membrane
PG0024800 ch04 C II 648 6.24 75,006.44 细胞质 Cytoplasmic
PG0014401 ch10 C III 533 6.58 60,586.97 细胞质 Cytoplasmic
PG0010264 ch10 C IV 635 9.24 72,635.34 线粒体 Mitochondrial

Fig. 3

Phylogenetic relationships, gene structure, and conserved motifs analysis of StGAUT A: the phylogenetic tree of StGAUT. B: exon/intron structure of StGAUT gene; the blue boxes indicate exons, the black lines of the same length indicates the intron, the upstream/downstream area is indicated by a red box, the numbers 0, 1, and 2 represent the splicing phase of the intron. C: the distribution of conserved motifs in StGAUT; the 10 different colored boxes represent 10 different motifs."

Fig. 4

Segmental replication events of StGAUT genes The gray lines indicate all the same linear blocks in the potato genome, and the red lines indicate the segmental repeats of StGAUT genes."

Table 3

Ka/Ks ratios of tandemly and segmentally duplicated StGAUT"

序号
No.		 基因1
Gene 1		 基因2
Gene 2		 非同义替换率
Ka		 同义替换率
Ks		 非同义替换率/同义替换率
Ka/Ks		 P值
P-value		 类型
Type
1 PG0001396 PG0022608 0.946754 1.20121 0.788168 4.76E-08 片段重复Segmental repeat
2 PG0024782 PG0031840 0.291121 3.40619 0.0854681 0 片段重复Segmental repeat
3 PG0003843 PG0014637 0.121239 1.39384 0.0869818 1.54E-98 片段重复Segmental repeat
4 PG0010088 PG0016880 0.179392 4.47249 0.0401102 0 片段重复Segmental repeat
5 PG0001183 PG0010088 0.0740382 2.24318 0.0330059 2.71E-125 片段重复Segmental repeat
6 PG0011479 PG0023500 0.103092 0.542081 0.190177 1.53E-47 片段重复Segmental repeat
7 PG0005216 PG0046135 0.264587 3.85123 0.0687019 0 片段重复Segmental repeat
8 PG0003522 PG0015490 0.103439 1.30535 0.0792418 1.55E-87 片段重复Segmental repeat
9 PG0014401 PG0019228 0.077988 0.755095 0.103282 3.94E-89 片段重复Segmental repeat
10 PG0001444 PG0025139 0.0574037 0.557829 0.102906 6.74E-66 片段重复Segmental repeat
11 PG0020103 PG0027950 0.957665 1.1718 0.817262 1.33E-05 片段重复Segmental repeat
12 PG0007896 PG2003179 0.172114 0.703844 0.244535 2.81E-54 片段重复Segmental repeat

Fig. 5

Relative expression profiles of StGAUT genes in different tissues The relative expression levels of 41 StGAUT genes are taken as the logarithm with base 2 for standardization, and the color patches of different colors indicate the relative expression levels of genes in different tissues."

Fig. 6

Relative expression profiles of StGAUT under salt, drought, and heat stress The relative expression profiles of StGAUT genes under salt, mannitol, and heat stress in DM potato. The log2 mean of each gene FPKM is used to draw a color scale."

Fig. 7

Relative expression profile of StGAUT genes in different potato skin and potato flesh colours The relative expression levels of 41 StGAUT genes ars taken as the logarithm with base 2 for standardization, and the color patches of different colors indicate the expression levels of genes in different color potato skin and flesh. XDS, HMS, and LTS represent the white skin of the white potato cultivar (Xindaping), the purple skin of the purple potato cultivar (Heimeiren), and the red skin of the red potato cultivar (Lingtianhongmei), respectively. XDF, HMF, and LTF represent the white flesh of Xindaping, the purple flesh of Heimeiren, and the red flesh of Lingtianhongmei, respectively."

Fig. 8

Relative expression profile of eight StGAUT genes in white and pigmented skin and flesh XDS, HMS, and LTS represent the white skin of the white potato cultivar (Xindaping), the purple skin of the purple potato cultivar (Heimeiren), and the red skin of the red potato cultivar (Lingtianhongmei), respectively. XDF, HMF, and LTF represent the white flesh of Xindaping, the purple flesh of Heimeiren, and the red flesh of Lingtianhongmei, respectively."

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