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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (10): 2533-2545.doi: 10.3724/SP.J.1006.2022.14183

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

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

JIA Xiao-Xia1,2(), QI En-Fang1,2, MA Sheng1,2, HUANG Wei1,2, ZHENG Yong-Wei1,2, BAI Yong-Jie1,2, WEN Guo-Hong1,2,*()   

  1. 1Potato Research Institute of Gansu Academy of Agricultural Sciences / Gansu Engineering Laboratory of Potato Germplasm resources Innovation, Lanzhou 730070, Gansu, China
    2National Germplasm Resources Agricultural Experimental Station, Weiyuan 748201, Gansu, China
  • Received:2021-10-11 Accepted:2022-01-05 Online:2022-10-12 Published:2022-02-09
  • Contact: WEN Guo-Hong E-mail:jiaxx0601@163.com;251580436@qq.com
  • Supported by:
    Key Project of Natural Science Foundation of Gansu Province(21JR7RA728);Science and Technology Support Program of Gansu Academy of Agricultural Sciences(2020GAAS16);Special Project of Biotechnology Breeding of Gansu Academy of Agricultural Sciences(2020GAAS10);National Natural Science Foundation of China(31560412);National Natural Science Foundation of China(31860401);China Agriculture Research System of MOF and MARA(CARS-09-P06)

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Abstract:

As a key signalling molecule, abscisic acid (ABA) extensively regulates plant growth and development, and stress response processes through its core signalling pathway PYLs-PP2Cs-SnRK2s. As a core component of ABA signalling transduction, PYLs protein plays an irreplaceable role. In order to explore the evolution and expression pattern of PYL (PYR/PYL/RCARs) genes in potato, 17 PYL genes were identified from the whole potato genome ‘DM-v 6.1’, and their distribution, protein physical and chemical properties, system evolution, structural characteristics, and the relative expression patterns were analysed. The results showed that the 17 StPYL genes were unevenly distributed on 8 chromosomes, with amino acids of 163-231 aa, isoelectric points of 4.5-8.6, and relative molecular weights of 18.71-25.29 kD. According to the gene structure and protein phylogenetic characteristics, the members of the StPYL family were divided into three subgroups. Motif 1 existed in all genes in this family, indicating that it was relatively conserved in the evolution of StPYLs. Gene expression patterns showed that the members of the StPYL family had obvious tissue expression specificity, and except for the up-regulation of StPYL1 under exogenous hormones (BAP, ABA, and IAA) and abiotic stress (high temperature, salt and drought), the rest of the StPYL genes were functionally differentiated and their relative expression patterns were different under different stresses. The results of this study lay a theoretical foundation for further elucidating the function of StPYLs gene in potato.

Key words: potato, PYL gene family, abscisic acid (ABA), gene expression analysis

Table 1

Genes and primers used for qRT-PCR expression verification"

基因编号
Gene ID		 正向引物
Forward primer (5′-3′)		 反向引物
Reverse primer (5′-3′)
EF1α ATTGGAAACGGATATGCTCCA TCCTTACCTGAACGCCTGTCA
Soltu.DM.05G022460 TCCTCAAGAGCTGCCACG GCCGCCGACTATACTAATGC
Soltu.DM.10G022490 CTCCCGTCTCCACCGTATG CCCCACCAACAACGCTAAA
Soltu.DM.03G013340 CGTCATTAGTTTCAGCGTCATC CGTTTCTTCCTTTGTATTCCCT
Soltu.DM.10G019340 CAATCCCACCAATCACTACAGC TTTGTACGCTTGAGGGTTGTC
Soltu.DM.02G024820 ATCGAACCTGTTTATCCTCCTG AAATAGCCATCTGGCAAGTCA
Soltu.DM.02G001580 TGAAGACGATGTTTTCCCAGAC TGAAGGCAGTGAAGCGGTAT
Soltu.DM.04G027470 GCATTGCTTCCTCCTCATTACT TGAACTCTTCTGCCCTATCCC
Soltu.DM.01G033740 GTTGCCTGACGGGACATTT CATATCCTTGGACCAGCATTAA

Table 2

Sequence characteristics of PYL genes family members in potato"

基因名称
Gene name		 基因编号
Gene ID		 染色体定位
Chromosome localization		 亚组分类Subgroup 氨基酸数量
Number of amino acids (aa)		 等电点
Isoelectric point (pI)		 相对分子量
Molecular
weight (kD)
StPYL1 Soltu.DM.01G034800 Chr.01: 74327768-74330316 I 186 6.30 20.79
StPYL2 Soltu.DM.03G013340 Chr.03: 35693624-35694662 II 201 5.95 22.16
StPYL3 Soltu.DM.03G022780 Chr.03: 47692175-47694992 I 185 5.61 20.96
StPYL4 Soltu.DM.05G022460 Chr.05: 50931814-50932956 II 208 7.15 22.89
StPYL5 Soltu.DM.06G010300 Chr.06: 31336857-31338048 II 218 6.40 23.99
StPYL6 Soltu.DM.06G018570 Chr.06: 45115651-45116827 III 213 4.98 23.72
StPYL7 Soltu.DM.08G013560 Chr.08: 39726166-39727508 III 188 6.65 21.08
StPYL8 Soltu.DM.08G014660 Chr.08: 41607872-41608584 I 183 4.93 20.17
StPYL9 Soltu.DM.08G014670 Chr.08: 41614500-41615633 I 176 4.50 19.78
StPYL10 Soltu.DM.08G014680 Chr.08: 41634425-41635105 I 163 5.32 18.71
StPYL11 Soltu.DM.08G022790 Chr.08: 52187476-52188465 III 231 5.12 25.29
StPYL12 Soltu.DM.08G028930 Chr.08: 58181068-58185195 I 189 6.75 21.57
StPYL13 Soltu.DM.09G009100 Chr.09: 10398942-10400047 II 214 8.60 23.39
StPYL14 Soltu.DM.10G019340 Chr.10: 50673639-50674710 II 207 7.10 22.82
StPYL15 Soltu.DM.10G022490 Chr.10: 54650751-54652125 II 213 6.79 23.49
StPYL16 Soltu.DM.12G004400 Chr.12: 3523014-3524941 III 190 5.12 21.24
StPYL17 Soltu.DM.12G008390 Chr.12: 7357759-7362992 I 181 5.97 20.68

Fig. 1

Phylogenetic relationships, gene structure, and conserved motifs analysis of StPYLs A: the phylogenetic tree of StPYLs; B: the structure of StPYLs gene; C: the distribution of conserved motifs in StPYLs."

Fig. 2

Phylogenic tree of PYL gene family At: Arabidopsis thaliana; St: Solanum tubersum; Bn: Brassica napus L.; Os: Oryza sativa."

Fig. 3

PYLs genes promoter sequence binding transcription factor in potato"

Table 3

Evolution selection pressure information of StPYL, AtPYL, and OsPYL"

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
1 AtPYL1 StPYL11 0.252113 2.46901 0.102111
2 AtPYL10 StPYL1 0.209896 2.62041 0.0801006
3 AtPYL10 StPYL3 0.203876 3.47713 0.0586336
4 AtPYL2 StPYL16 0.199507 3.38436 0.0589498
5 AtPYL2 StPYL7 0.202235 3.41170 0.0592768
6 AtPYL4 StPYL14 0.277640 3.19545 0.0868861
7 AtPYL4 StPYL15 0.251724 3.78848 0.0664447
8 AtPYL5 StPYL2 0.337324 3.20802 0.10515
9 AtPYL5 StPYL5 0.358874 3.08254 0.116422
10 AtPYL6 StPYL14 0.391640 2.85503 0.137175
11 AtPYL6 StPYL2 0.335979 3.04837 0.110216
12 AtPYL6 StPYL5 0.310522 3.18218 0.0975815
13 AtPYL7 StPYL1 0.228439 2.12794 0.107352
14 AtPYL7 StPYL12 0.214102 3.49394 0.0612782
15 AtPYL8 StPYL1 0.148691 4.52157 0.0328847
16 AtPYL8 StPYL12 0.176819 3.71724 0.0475675
17 AtPYL8 StPYL3 0.130553 4.14104 0.0315267
18 AtPYL9 StPYL1 0.163537 1.84526 0.0886251
19 AtPYR1 StPYL11 0.196102 1.34623 0.145668
20 AtPYR1 StPYL6 0.204242 3.81927 0.0534767
21 OsPYL1 StPYL11 0.347476 3.45055 0.100702
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
22 OsPYL12 StPYL1 0.330709 2.89213 0.114348
23 OsPYL12 StPYL12 0.285345 2.94688 0.0968295
24 OsPYL4 StPYL13 0.347064 3.44965 0.100609
25 OsPYL4 StPYL5 0.355825 3.12683 0.113797
26 OsPYL5 StPYL13 0.362471 3.22157 0.112514
27 OsPYL5 StPYL14 0.360063 3.06688 0.117404
28 OsPYL5 StPYL5 0.356826 3.18746 0.111947
29 OsPYL6 StPYL13 0.384219 3.18292 0.120713
30 OsPYL6 StPYL14 0.376110 3.09537 0.121507
31 OsPYL6 StPYL5 0.359420 3.20874 0.112013
32 OsPYL7 StPYL1 0.364590 3.24765 0.112262
33 OsPYL7 StPYL3 0.321310 3.17375 0.10124
34 OsPYL8 StPYL12 0.273630 2.71313 0.100854

Fig. 4

Heat map of the relative expression level of StPYLs genes under different stresses"

Fig. 5

Expression pattern of StPYLs genes in different tissues (A) and under different drought stress conditions (B) In Fig. 5-B, T75-1, T75-2, and T75-3 represent three biological replicates of 75%-80%; T65-1, T65-2, and T65-3 represent three biological replicates of 65%-70%; T55-1, T55-2, and T55-3 represent three biological replicates of 55%-60%; T45-1, T45-2, and T45-3 represent three biological replicates of 45%-50%."

Table 4

FPKM value of different genes under different drought stress"

基因名称
Gene name		 处理Treatment
T75 T65 T55 T45
StPYL1 82.75±3.26 b 105.73±9.28 a 110.58±13.47 a 101.73±7.90 a
StPYL3 84.46±3.52 a 73.15±4.16 a 73.57±2.17 a 78.06±3.83 a
StPYL12 11.47±2.07 a 15.16±1.26 a 12.43±0.29 a 15.89±2.72 a
StPYL17 38.49±6.22 a 39.70±0.44 a 34.52±1.45 a 27.13±4.26 a
StPYL8 1.53±0.46 ab 1.96±0.04 a 0.99±0.19 b 0.97±0.16 b
StPYL9 2.72±0.32 a 2.91±0.33 a 3.17±0.52 a 3.07±0.09 a
StPYL10 0.46±0.09 b 0.70±0.11 a 0.53±0.15 b 0.52±0.13 b
StPYL2 72.03±3.26 a 58.73±1.45 b 28.23±2.78 c 21.69±5.01 c
StPYL4 17.93±5.37 a 14.44±1.41 a 6.24±1.51 b 5.11±2.19 b
StPYL5 25.90±2.86 a 26.34±4.12 a 17.34±3.35 b 14.46±3.55 b
StPYL13 4.07±0.43 a 2.94±0.48 ab 2.87±0.27 ab 2.54±0.45 b
基因名称
Gene name		 处理Treatment
T75 T65 T55 T45
StPYL14 22.86±2.94 a 18.82±1.06 ab 15.00±1.31 bc 9.44±1.92 c
StPYL15 146.99±4.30 a 121.88±7.18 b 105.61±8.19 b 66.12±9.62 c
StPYL6 40.26±5.09 a 48.10±0.99 a 44.86±3.91 a 48.78±3.15 a
StPYL11 1.00±0.08 c 1.42±0.04 ab 1.47±0.11 a 1.10±0.14 bc
StPYL7 1.68±0.28 b 2.03±0.34 a 1.12±0.20 b 1.14±0.28 b
StPYL16 0 0 0 0

Fig. 6

Validation of RNA-seq data by qRT-PCR A: the relative expression levels of differentially expressed genes in T75 vs T45 and T75 vs T55 groups under drought stress. Data from qRT-PCR are means of three replicates, and bars represent standard errors. B: the correlation between qRT-PCR and RNA-seq."

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