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. 2022 Dec 31;45(1):311-326.
doi: 10.3390/cimb45010022.

BSR and Full-Length Transcriptome Approaches Identified Candidate Genes for High Seed Ratio in Camellia vietnamensis

Bing-Qing Hao  1   2   3 , Hong-Ze Liao  4 , Ying-Ying Xia  2   3 , Dong-Xue Wang  2   3 , Hang Ye  2   3
Affiliations

BSR and Full-Length Transcriptome Approaches Identified Candidate Genes for High Seed Ratio in Camellia vietnamensis

Bing-Qing Hao et al. Curr Issues Mol Biol. .

Abstract

(1) Background: C. vietnamensis is very suitable for growth in the low hilly areas of southern subtropical regions. Under appropriate conditions, the oil yield of C. vietnamensis can reach 1125 kg/ha (the existing varieties can reach 750 kg/ha). Moreover, the fruit of C. vietnamensis is large and the pericarp is thick (>5 cm). Therefore, a high seed ratio has become the main target economic trait for the breeding of C. vietnamensis. (2) Methods: A half-sibling population of C. vietnamensis plants with a combination of high and low seed ratios was constructed by crossing a C. vietnamensis female parent. Bulked segregant RNA analysis and full-length transcriptome sequencing were performed to determine the molecular mechanisms underlying a high seed ratio. (3) Results: Seed ratio is a complex quantitative trait with a normal distribution, which is significantly associated with four other traits of fruit (seed weight, seed number, fruit diameter, and pericarp thickness). Two candidate regions related to high seed ratio (HSR) were predicted. One spanned 140.8−148.4 Mb of chromosome 2 and was associated with 97 seed-yield-related candidate genes ranging in length from 278 to 16,628 bp. The other spanned 35.3−37.3 Mb on chromosome 15 and was associated with 38 genes ranging in length from 221 to 16,928 bp. Using the full-length transcript as a template, a total of 115 candidate transcripts were obtained, and 78 transcripts were predicted to be functionally annotated. The DEGs from two set pairs of cDNA sequencing bulks were enriched to cytochrome p450 CYP76F14 (KOG0156; GO:0055114, HSR4, HSR7), the gibberellin phytohormone pathway (GO:0016787, HSR5), the calcium signaling pathway (GO:0005509, HSR6), the polyubiquitin-PPAR signaling pathway (GO:0005515, HSR2, HSR3), and several main transcription factors (bZIP transcription factor, HSR1) in C. vietnamensis.

Keywords: Camellia vietnamensis; bulked segregant RNA analysis; full-lengthtranscriptome sequencing; high seed ratio.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Normal distribution of seed ratio in C. vietnamensis population.
Figure 2
Figure 2
Phenotypic data (A) and architecture (B) of high- and low-seed-ratio C. vietnamensis fruits. (1) Architecture of high-seed-ratio fruit; (2) Architecture of low-seed-ratio fruit. Asterisks indicate significant differences: * p < 0.05 and ** p < 0.01.
Figure 3
Figure 3
The enriched GO and KEGG terms of the differential expression of transcripts. (A) The enriched GO terms of the differential expression of transcripts. (B) The enriched KEGG terms of the differential expression of transcripts.
Figure 4
Figure 4
Distribution of variant loci in two seed ratio bulks of C. vietnamensis on C. oleifera var. chromosomes.
Figure 5
Figure 5
Distribution of ED association values of two bulks of C. vietnamensis on C. oleifera var. chromosomes. Note: the horizontal coordinates are the chromosome names, the different-colored dots represent the ED values of each SNP locus, the black line is the fitted ED value, and the red dashed line represents the significance association threshold. The higher the ED value, the better the association effect of the point.
Figure 6
Figure 6
The enriched GO terms in the molecular function, cellular component, and biological process categories.
Figure 7
Figure 7
The enriched KEGG terms.
Figure 8
Figure 8
Analysis of the expression of genes associated with high seed ratio. HSR: high seed ratio.
See this image and copyright information in PMC

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