Genome and transcriptome analysis provide insights into the genetics and breeding of Salix suchowensis growth traits. Liu, W., Gu, S., Zhu, M., Han, Y., Dai, X., Wu, H., Yin, T., Guo, L., Feng, L., Zan, Y., & Liu, J. New Forests, 56(6):63, October, 2025. ![Genome and transcriptome analysis provide insights into the genetics and breeding of Salix suchowensis growth traits [link]](https://bibbase.org/img/filetypes/link.svg "link")
Paper doi abstract bibtex Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.
@article{liu_genome_2025,
title = {Genome and transcriptome analysis provide insights into the genetics and breeding of {Salix} suchowensis growth traits},
volume = {56},
issn = {1573-5095},
url = {https://doi.org/10.1007/s11056-025-10132-7},
doi = {10.1007/s11056-025-10132-7},
abstract = {Shrub willow species (Salix sp.) are ideal for cultivation as bioenergy source and can serve as effective models for genetic research due to their rapid growth rates. Understanding the genetic basis of growth traits in willows can enhance the development of high-quality cultivars. In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. This study provides valuable insights into the genetic regulatory mechanisms underlying key growth traits in S. suchowensis and establishes a genomic prediction model to facilitate the rapid genetic improvement of the species.},
language = {en},
number = {6},
urldate = {2025-11-07},
journal = {New Forests},
author = {Liu, Wei and Gu, Shaobo and Zhu, Mingjia and Han, Yu and Dai, Xiaogang and Wu, Huaitong and Yin, Tongming and Guo, Linjie and Feng, Landi and Zan, Yanjun and Liu, Jianquan},
month = oct,
year = {2025},
keywords = {Breeding prediction, Ground diameter, Plant height, QTL, QTL-by-environment interactions, Salix suchowensis},
pages = {63},
}
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In this study, we performed genome-wide association studies (GWAS), expression quantitative trait locus (eQTL) mapping, and transcriptome-wide association analyses to investigate the genetic basis of plant height (Height) and ground diameter (GD) in a full-sib population of Salix suchowensis derived from eight parental lines, which were phenotyped across three sites in southwest China. We identified 15 quantitative trait loci (QTLs) associated with Height and 10 QTLs associated with GD. Furthermore, we identified 938 eQTLs influencing the expression of 685 genes, including a trans-eQTL hub, as well as eight co-expression modules correlated with Height and GD. Transcriptome-wide association studies (TWAS) revealed five genes linked to Height and three genes associated with GD. By jointly modeling genetic variations and environmental factors, we developed a multi-site predictive model that outperformed the genomic best linear unbiased prediction. 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