Mining candidate genes associated with growth traits in Schima superba using eQTL and WGCNA

LU Yaojia, YULUO Zhuoma, CHENG Yuhang, WANG Yunpeng, TANG Xinghao, SHAO Wen, ZHOU Zhichun, ZHANG Rui

Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 0

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南京林业大学学报（自然科学版）
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Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 0 DOI: 10.12302/j.issn.1000-2006.202604021

Mining candidate genes associated with growth traits in Schima superba using eQTL and WGCNA

  • LU Yaojia1,2, YULUO Zhuoma1, CHENG Yuhang1, WANG Yunpeng3, TANG Xinghao4, SHAO Wen5, ZHOU Zhichun1, ZHANG Rui1,*
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Abstract

【Objective】The formation of tree height and diameter at breast height in Schima superba is regulated by complex molecular networks. This study aimed to identify the genes and loci associated with these growth traits, thereby providing precise targets for the breeding of fast-growing trees. 【Method】A total of 186 individuals representing 24 provenances from 18-year-old S. superba plantations were used in this study. Phenotypic traits, including tree height and diameter at breast height, were measured, and cambium and secondary xylem tissues were collected for transcriptome sequencing. Weighted gene co-expression network analysis (WGCNA) and expression quantitative trait locus (eQTL) mapping were combined to identify genetic loci and candidate genes significantly associated with tree height and diameter at breast height, and to further clarify their regulatory networks. 【Result】A total of 30 786 eQTLs were identified at the whole-genome level, regulating the expression of 7 224 genes. Compared with distant eQTLs, local eQTLs showed higher significance and explained a greater proportion of the variation in gene expression. WGCNA identified 16 co-expression modules. Among them, the black module was significantly positively correlated with both tree height and diameter at breast height (r = 0.47 and 0.43, p < 0.01), while the green module was significantly negatively correlated with these traits (r = -0.51 and -0.46, p < 0.01). Integrative analysis of WGCNA and eQTL revealed that Ssu10G00379 (SsuMYB152), a MYB3R transcription factor, was associated with both a local eQTL (SNP_chr10_4859354) and a distant eQTL interval, indicating that it is an important regulatory node linking genetic variation to tree height. Higher expression of this gene was significantly associated with the A genotype at SNP_chr10_4859354 (p = 9.64 × 10-9) and was extremely significantly positively correlated with higher tree height (r = 0.40, p < 1.2 × 10-8). Taking SsuMYB152 as the core gene, 87 candidate genes significantly associated with microtubule movement, cell morphogenesis, plant hormone signaling and MAPK signaling pathway were identified (r > 0.6, FDR < 0.01). The interaction network showed that SsuMYB152 was closely connected with several genes involved in cell cycle and growth development, including CYCB1-2, CYCB2-4, CDKB1-2, UBC20, KIN12B, KIN13B, and TAN. 【Conclusion】The A genotype of the local eQTL locus SNP_chr10_4859354 was associated with higher expression of SsuMYB152, and the higher expression of this gene was significantly correlated with increased tree height (r = 0.40, p < 1.2 × 10-8). This gene was also affected by a distant eQTL and served as a key regulatory node linking genetic variation to tree height.

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Schima superba / MYB / eQTLs / WGCNA / tree height / genetic improvement

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LU Yaojia, YULUO Zhuoma, CHENG Yuhang, WANG Yunpeng, TANG Xinghao, SHAO Wen, ZHOU Zhichun, ZHANG Rui. Mining candidate genes associated with growth traits in Schima superba using eQTL and WGCNA[J]. Journal of Nanjing Forestry University (Natural Sciences Edition）. 0 https://doi.org/10.12302/j.issn.1000-2006.202604021

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