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A total of 171 possible PoHSP20s were identified through bidirectional blast alignment using TBtools in the P. ostii genome, but 22 do not contain the conserved domain after submitting to NCBI-CDD database for ACD verification. 149 PoHSP20s were finally obtained and named according to their chromosomal location (Fig. 1, Supplemental Table S1). A total of 142 PoHSP20s were randomly distributed on five chromosomes, while, the other seven were unclassified. It indicated that these PoHSP20s contain 62−831 amino acids with predicted molecular weights of 7.00−94.11 kDa. The putative isoelectric point ranges from 4.62 to 9.37. The grand average of hydropathicity (GRAVY) of all genes is negative, indicating that these PoHSP20s are hydrophilic. Sub-cell localization prediction results showed that 112 PoHSP20s were mainly localized in the cytoplasm, and the others were in the golgi apparatus, nucleus, chloroplast, mitochondrion, vacuole, extra-cell and peroxisome (Supplemental Table S1).
Figure 1.
Chromosomal locations of PoHSP20s on P. ostii chromosomes. The genes in red were also identified in the transcriptome of flower bud of P. ostii, the genes marked in blue were used for association analysis.
Phylogenetic analysis of PoHSP20s
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In order to clarify the evolutionary relationship and grouping characteristics, a phylogenetic tree was generated from 149 PoHSP20s together with 19, 23 and 53 related proteins from A. thaliana, O. sativa, G. max, respectively (Fig. 2), which demonstrated high homology. The 149 PoHSP20s were divided into 10 subfamilies, including CI, CII, CIII, CV and CVII (cytoplasm or nucleus), MI and MII (mitochondria), P (plastid), Po (peroxysome), and ER (endoplasmic reticulum). Within each subfamily, CI has the highest number of members (51), followed by CIII (29), CII (24), Po (10), ER (9), MI (8), CVII (7), P (4), CV (1), and MII (1). The remaining five PoHSP20s could not be clustered into any subfamily, and were clustered into the unknown group, namely, UN1 (1) and UN3 (4). Most of the PoHSP20s were classified into CI, CII, CIII, CV and CVII, which were putatively located in cytoplasm or nucleus indicating their similar or conserved function.
Figure 2.
The phylogenetic tree of HSP20s from A. thaliana, O. sativa, G. max and P. ostii. It was constructed using the ML method with 1,000 bootstrap replications. The colors indicate the different subfamilies, the stars indicate the genes for association analysis.
Gene structure and motif analysis of PoHSP20s
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Among the PoHSP20s, 40 (26.85%) were intronless, 36 (24.16%), 22 (14.77%), 22 (14.77%) and 29 (19.46%) had one, two, three, and four or more introns, respectively. A total of 10 motifs were found, and the length of these conserved motifs varied from 15 to 29 amino acids (Fig. 3; Supplemental Table S2). Based on NCBI-CDD database, the motifs 1−5 together consisted of a highly conserved complete ACD. Among the 149 PoHSP20s, the motif 1, motif 2, motif 3, motif 4 and motif 5 was shared by 113, 60, 117, 52 and 76 members. While, 31 PoHSP20s (20.8%) contained the combination of motifs 1−5, others PoHSP20s lacked the complete five motifs.
Figure 3.
Phylogenetic relationship, gene structure and conserved motif analysis of PoHSP20s. (a) The phylogenetic tree of 149 PoHSP20s. The unrooted neighbor-joining phylogenetic tree was constructed with MEGA11 using full-length amino acid sequences with 1,000 bootstrap replicates. (b) Exon/intron organization of PoHSP20s. Green and yellow box represents CDS and untranslated regions (UTR), and the black lines indicate introns, respectively. The length of sequence can be inferred by the scale at the bottom. (c) The distribution of conserved motifs in PoHSP20s. Ten putative motifs are indicated in different colored boxes, refer to Supplemental Table S2 for details.
Expression patterns of the PoHSP20s in flower bud with 5-carpels and polycarpels at three developmental stages
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In order to further characterize the expression profiles of PoHSP20s, 38 differentially expressed PoHSP20s were obtained and grouped into four clusters based on the transcriptome of flower bud with 5-carpels and polycarpels at three developmental stages (Fig. 4). In conclusion, members of cluster I showed higher expression levels in Pa than that of 5a, while, for cluster III, it demonstrated an opposite trend in Pc and 5c, which suggests a possibly different function.
Figure 4.
Expression profiles of PoHSP20s in flower buds at different developmental stages of P. ostii with various carpels. Stage a, sepals and a few petal primordia appeared; stage b, stamen primordia initiated; stage c, carpel primordia initiated. 5, plants with five carpels; P, plants with more than 5 carpels (6−8 carpels). The stars indicate the genes for association analysis.
Sequence variation analysis of PoHSP89 and PoHSP133
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Based on the expression pattern and SNPs provided by the transcriptome, two PoHSP20s (PoHSP89 and PoHSP133) of cluster I were identified for further cloning and association analysis. In total, we obtained the coding sequences of 215 and 265 ones in 271 tree peony cultivars, respectively. After removing the unmatched parts at both ends, the sequence of 461 bp long for PoHSP89 and 421 bp long for PoHSP133 were used for subsequent analysis. The sequences of PoHSP89 in 215 cultivars were detected, 37 SNPs with an average of 1 SNP per 12 bp, while, 32 SNPs were obtained in 265 cultivars with an average of 1 SNP per 13 bp. Among the SNPs, 18 for PoHSP89 and 14 for PoHSP133 occurred with a frequency higher than 5%, respectively, and 13 out of the 18 loci for PoHSP89 and 6 of 14 for PoHSP133 exhibited synonymous mutation, while the remaining ones contained non-synonymous mutation (Supplemental Table S3). The nucleotide polymorphism values of π and θ for PoHSP89 and PoHSP133 were 0.01795, 0.00799 and 0.01488, 0.01259, respectively.
Linkage disequilibrium and population structure analysis
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Further, linkage disequilibrium analysis was performed on the high-frequency polymorphic loci of PoHSP89 and PoHSP133 (Fig. 5a, b). There were two block regions in PoHSP89, one containing three loci (21, 42, and 101 bp) and the other containing two loci (403 and 429 bp). The average R2 value between different loci was 0.30. R2 value between locus 342 and 403 was higher than 0.80, indicating a strong linkage between them. In addition, seven pairs of loci reached an R2 value of 0.70. For PoHSP133, only the linkage between locus 34 and 216 was strong with an R2 value greater than 0.80. A block region was found between locus 373 and 374 with an R2 value of 0.67.
Figure 5.
Linkage disequilibrium and population structure of associated populations. (a), (b) Linkage disequilibrium analysis of PoHSP89 and PoHSP133, respectively. Different colors indicate standard (D'/LOD) values, from white to red, the value increased; the value in the box indicates R2 and was magnified 100 times. (c) Variation tendency of ΔK. (d) Population structure of associated group when K = 3.
Population structure analysis is an important way to determine the kinship and taxon classification among different cultivars. Based on the SNPs of PoHSP89 and PoHSP133, the population structure was analyzed. It showed that the ΔK value was the largest at K = 3, thus the tested cultivars could be mainly divided into three groups (Fig. 5c, d).
Association analysis between candidate genes and floral organ number
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Association analysis was performed between SNPs of PoHSP89 and PoHSP133 and floral organ number, and a total of 7 and 19 pairs of association combinations were identified, respectively, which explained the phenotypic variation by 1.79% to 4.06%, and 1.92% to 12.37%, respectively. In total, there were 9, 3, 14 SNPs associated with CN, PeN and SN, respectively. For PoHSP89, SNP on the locus 121 associated with CN has the highest R2 value (4.06%), others' were all lower than 3.00%. For PoHSP133, the R2 value of 15 pairs of association combinations were higher than 3.00%, among which SNP on the locus 237 associated with SN had the highest value (12.37%), followed by locus 34 associated with SN (9.16%) and CN (7.03%), locus 374 associated with SN (6.78%) and locus 216 associated with CN (6.51%) (Table 1).
Table 1. Associated combinations of PoHSP89 and PoSHP133 with flower organ number.
No. Trait Gene Locus SNP/Indel p value R2/% 1 CN PoHSP89 121 A/G 0.0028 4.06 2 CN PoHSP89 225 T/C 0.0199 2.48 3 CN PoHSP89 393 C/T 0.0484 1.79 4 PeN PoHSP89 436 A/G 0.0236 2.31 5 SN PoHSP89 342 A/C 0.0411 1.88 6 SN PoHSP89 402 A/G 0.0191 2.46 7 SN PoHSP89 403 T/C 0.0361 1.97 8 CN PoHSP133 5 C/A 0.0084 3.54 9 CN PoHSP133 34 G/A 0.0000 7.03 10 CN PoHSP133 150 C/T 0.0028 3.31 11 CN PoHSP133 216 T/G 0.0000 6.51 12 CN PoHSP133 237 A/G 0.0016 3.69 13 CN PoHSP133 374 G/T 0.0007 4.22 14 PeN PoHSP133 237 A/G 0.0008 3.87 15 PeN PoHSP133 373 C/T 0.0166 2.02 16 SN PoHSP133 5 C/A 0.0264 2.74 17 SN PoHSP133 34 G/A 0.0000 9.16 18 SN PoHSP133 150 C/T 0.0001 5.75 19 SN PoHSP133 210 G/A 0.0242 1.92 20 SN PoHSP133 216 T/G 0.0002 5.26 21 SN PoHSP133 218 G/A 0.0026 3.41 22 SN PoHSP133 219 C/T 0.0012 3.92 23 SN PoHSP133 237 A/G 0.0000 12.37 24 SN PoHSP133 373 C/T 0.0002 5.34 25 SN PoHSP133 374 G/T 0.0000 6.78 26 SN PoHSP133 393 C/A 0.0084 2.62 Phenotypic variation of significantly associated loci was further analyzed. It demonstrated that these cultivars with genotype GA at locus 121 of PoHSP89 had 26.24% higher CN than that of genotype GG. The SNPs had two alleles at the locus 34 and 216 of PoHSP133, and the average of CN associated with allele G was significantly different from the other allele and increased by 24.00% for locus 34 and decreased by 23.00% for locus 216, respectively (Fig. 6). The cultivars with allele G at the locus 34, 237 and 374 of PoHSP133 showed significantly higher SN than that of other alleles, and increased by 39.50% for locus 34, 47.43% for locus 237 and 32.93% for locus 374, respectively (Fig. 6).
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All data generated or analyzed during this study are included in this published article and its supplementary information files.
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About this article
Cite this article
Peng L, Song W, Tan W, Liu Z, Wang X, et al. 2023. Integration of genome-wide identification, transcriptome and association analysis of HSP20 gene family to revealing genetic basis of floral organ number-related traits in tree peony. Ornamental Plant Research 3:22 doi: 10.48130/OPR-2023-0022
Integration of genome-wide identification, transcriptome and association analysis of HSP20 gene family to revealing genetic basis of floral organ number-related traits in tree peony
- Received: 02 November 2023
- Accepted: 15 December 2023
- Published online: 26 December 2023
Abstract: The HSP20 family is the major member of heat shock proteins that are essential components involved in plant growth, development, and stress response, but little is known about tree peony (Paeonia suffruticosa). In this study, genome-wide analysis combining HSP20 gene family expression analysis of tree peony transcriptome was conducted, and the association between SNPs of HSP20s and flower organ number-related traits was analyzed. A total of 149 members were identified in the P. ostii genome, and divided into 10 subfamilies, most of which were classified into cytoplasm or nucleus. Interestingly, their protein sequences were highly conserved, mainly containing motif 1 or 3. In addition, a total of 38 deferentially expressed HSP20s were identified from transcriptome of flower buds with 5-carpels and polycarpels of P. ostii plants at three developmental stages, among which PoHSP89 and PoHSP133 were further cloned from 271 cultivars for association analysis. It indicated that seven or 19 pairs of associated combinations were obtained with the number of carpel, petal, stamen in PoHSP89 and PoHSP133, which could explain the phenotypic variation by 1.79% to 4.06%, and 1.92% to 12.37%, respectively. It will provide a valuable basis for clarifying the phylogenetic relationship to understand their biological function within the HSP20 gene family, and the identified candidate genes and their corresponding associated SNP loci would reveal the genetic basis on floral organ number variation and be useful for molecular marker-assisted breeding of tree peony in view to improving ornamental traits and yields.
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Key words:
- HSP20 /
- Tree peony /
- Association study /
- Floral organ number variation