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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (11): 2797-2812.doi: 10.3724/SP.J.1006.2022.14199

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

Genome-wide identification and expression analysis of BBX gene family in potato (Solanum tuberosum L.)

MA Wen-Jing1(), LIU Zhen1, LI Zhi-Tao1, ZHU Jin-Yong1, LI Hong-Yang1, CHEN Li-Min1, SHI Tian-Bin1, ZHANG Jun-Lian2, LIU Yu-Hui1,*()   

  1. 1College of Agronomy, Gansu Agricultural University / State Key Laboratory of Aridland Crop Science / Gansu Provincial Key Laboratory of Crop Improvement and Germplasm Enhancement, Lanzhou 730070, Gansu, China
    2College of Horticulture, Gansu Agricultural University, Lanzhou 730070, Gansu, China
  • Received:2021-10-26 Accepted:2022-02-25 Online:2022-11-12 Published:2022-03-24
  • Contact: LIU Yu-Hui E-mail:810774875@qq.com;lyhui@gsau.edu.cn
  • Supported by:
    The Program for Innovation Ability Improvement of the Higher Education Institutions of Gansu Province(2020A-056);The National Natural Science Foundation of China(31860398);The Fuxi Talent Project of Gansu Agricultural University(Gaufx-02Y04);The China Agriculture Research System of MOF and MARA(马铃薯);The China Agriculture Research System of MOF and MARA(CARS-09-P14);The Scientific Research Startup Funds for Openly-recruited Doctors Agricultural University(GAU-KYQD-2020-11)

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Abstract:

The B-box (BBX) gene family is a type of zinc finger protein transcription factor that plays an important role in the growth and development of plants. In this study, 30 potato BBXs family members (StBBXs) were identified, and their physical and chemical properties, chromosomal location, gene structure, protein conserved domains, gene repetition events, expression patterns, and protein interaction network were analyzed. The results showed that 30 StBBXs were unevenly distributed on 11 chromosomes. According to their gene structures and phylogenetic characteristics, 30 StBBXs were divided into 5 subclasses. Collinearity analysis indicated that there were 15 pairs BBX genes which were orthologous to potato (Solanum tuberosum) and Arabidopsis. We analyzed the relative expression profiles of StBBX genes in different tissues of double haploid (DM) potato, as well as under abiotic stresses and hormone treatments by RNA-seq downloaded from the PGSC (Potato Genome Sequencing Consortium) database. In addition, to explore the relative expression patterns of the StBBX genes in these tissues, we performed RNA-seq on the tuber skin and flesh of three potato varieties with different colors and analyzed their correlations with the expression of key genes for anthocyanin synthesis. Furthermore, the protein interaction network of StBBXs which differentially expressed in color tuber tissues was constructed using String database. These results provide a theoretical basis for further understanding the StBBX gene family, further function of StBBX genes in abiotic stress tolerance and anthocyanin biosynthesis in potato, and StBBX genes in potato might be related to abiotic stress responses and anthocyanin biosynthesis.

Key words: potato, BBX genes family, abiotic stress, anthocyanin biosynthesis, expression analysis

Fig. 1

Tubers of three potato varieties with different colors"

Table 1

Primers for qPCR study"

基因名称
Gene name		 正向引物
Forward primer (5°-3°)		 反向引物
Reverse primer (5°-3°)
StEF-1α ATTGGAAACGGATATGCTCCA TCCTTACCTGAACGCCTGTCA
PG0011378 ATCATCAGCAGCAGCAGCAAGAG TCACGGTCACAGGTAAAACAGAGC
PG0029365 CGTCGGCATGAGCGGTTTCC TCATCATCAGCAGCATCAGCATCG
PG0027475 CGGTGGAATCGGTCGTGAAGTC CGTGGTCGTGGTCATGGTTGTG
PG0027017 GCAAGGACTGTGACGAAGCAATTC GCTCAAGGCTACACGGATTCCAG
PG0026311 GACTCCGCCTCCGCCAGATC GACTCCGCTTCCGCTTCTTCTTC
PG0026181 TGGAGGAGAGTGAGAGCGTGAATG GCGGTGGAGGCGTCGTATTTG
PG0025024 GGTGCGTTCGGTGAGTTCTTCC CCTTACTCGCTTCCACGGAGATG
PG0013753 GTCATCAACTCCGCCTCCACAG CATTCGTCACGCATTCGTTCAAAG

Fig. 2

Evolutionary tree of BBXs gene family in Arabidopsis and potato The red circles represents StBBXs, and the blue triangles represent AtBBXs."

Table 2

Physicochemical properties and subcellular localization of StBBX genes family"

基因名称
Gene name		 氨基酸长度 Amino acid
length		 相对分子量
Molecular weight
(kD)		 等电点
Point isoelectric (pI)		 亚细胞定位
Subcellular localization		 染色体定位 Chromosome
localization		 亚组分类
Class of
subgroup
PG0003625 551 44,860.59 5.26 细胞核Nuclear Chr02 BBX IV
PG0022345 575 46,990.87 5.27 细胞核Nuclear Chr02 BBX V
PG1010056 1220 100,730.6 5.05 细胞核Nuclear Chr02 BBX I
PG0007061 899 74,980.43 5.12 细胞核Nuclear Chr07 BBX IV
PG0017411 1238 102,001 5.08 细胞核Nuclear Chr07 BBX II
PG0026169 395 32,108.31 5.34 细胞核Nuclear Chr07 BBX V
PG0026181 776 61,856.12 5.18 细胞核Nuclear Chr07 BBX V
PG0027475 1160 96,517.16 5.04 细胞核Nuclear Chr07 BBX I
PG0003109 641 52,158.76 5.22 细胞核Nuclear Chr01 BBX IV
PG0030958 761 64,412.27 5.20 细胞核Nuclear Chr01 BBX IV
PG0001263 1271 104,574.6 5.09 细胞核Nuclear Chr05 BBX II
PG0005325 1244 102,491.8 5.07 细胞核Nuclear Chr05 BBX II
PG0014566 1346 108,627.7 5.10 细胞核Nuclear Chr05 BBX III
PG0025414 1364 112,088.5 5.05 细胞核Nuclear Chr05 BBX II
PG0013178 341 27,626.76 5.50 细胞核Nuclear Chr12 BBX II
PG0013753 623 49,919.71 5.25 细胞核Nuclear Chr12 BBX V
PG0019025 902 75,119.83 5.12 细胞核Nuclear Chr12 BBX IV
PG0028818 1229 100,908.6 5.09 细胞核Nuclear Chr12 BBX II
PG0029365 1076 88,519.16 5.07 细胞核Nuclear Chr12 BBX I
PG0029426 995 83,207.43 5.13 细胞核Nuclear Chr12 BBX IV
PG0011378 1142 94,480.42 5.11 细胞核Nuclear Chr12 BBX II
PG0005633 1208 97,557.49 5.11 细胞核Nuclear Chr03 BBX III
PG0026515 782 65,781.32 5.15 细胞核Nuclear Chr06 BBX V
PG0027017 704 58,425.39 5.17 细胞核Nuclear Chr06 BBX IV
PG0026311 1046 85,660.46 5.06 细胞核Nuclear Chr08 BBX I
PG0025024 701 57,480.47 5.21 细胞核Nuclear Chr10 BBX V
PG0003711 899 75,536.97 5.15 细胞核Nuclear Chr04 BBX IV
PG0005997 1472 122,076 5.03 细胞核Nuclear Chr04 BBX V
PG0007749 1694 137,183.7 5.08 细胞核Nuclear Chr04 BBX III
PG2010056 1244 102,374.8 5.05 细胞核Nuclear Chr02 BBX I

Fig. 3

Evolutionary relationship, gene structure, and conserved motif analysis of StBBX genes family A: StBBXs evolutionary tree. B: exon/intron structure of StBBXs. The blue boxes represent exons, and the black lines of the same length represent introns. The upstream/downstream area is indicated by a red box. The numbers 0, 1, and 2 indicate the splicing stage of introns. C: the distribution of conserved motifs in StBBX.s 10 different colored boxes represent 10 different motifs."

Fig. 4

BBX genes family repeat events The red line indicates that there is homology between StBBX genes and AtBBX genes, and the chromosome number is displayed at the bottom of each chromosome."

Fig. 5

Relative expression levels of StBBXs in different tissues The relative expression level of 30 StBBXs is 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 levels of StBBXs under different abiotic stresses and different hormone treatments The logarithm with the base of 2 is taken for the expression of 30 StBBXs for standardized treatment. Color blocks of different colors represent the expression levels of genes under abiotic stress and hormone treatment."

Fig. 7

Relative expression levels of StBBXs in different potato skins and flesh The relative expression levels of 30 StBBXs are taken as the logarithm with base 2 for standardization, the color patches of different colors indicate the relative expression levels of genes in different color potato skins and flesh."

Fig. 8

Correlation analysis of the anthocyanin content of StBBXs in different parts of colored potatoes * and ** mean significant correlation at the 0.05 and 0.01 probability levels, respectively."

Fig. 9

Relative expression analysis of eight StBBX genes in white and color potato skin and potato flesh Relative expression analysis of eight StBBXs genes in white and colored potato skins and flesh. XDS, LTS, and HMS represent the potato skins of “Xindaping”, “Hongmei”, and “Heimeiren”, respectively. XDF, LTF, and HMF represent the potato fleshes of “Xindaping”, “Hongmei”, and “Heimeiren”, respectively."

Fig. 10

StBBX proteins interaction network Red circles indicate StBBXs candidate genes, yellow circles indicate genes related to anthocyanin synthesis. Blue lines indicate composite scores ≥ 400, purple lines indicate composite scores ≥ 700, and red lines indicate composite scores ≥ 900."

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