Combining Transcriptome Analysis and Comparative Genomics to Identify Key Components of the Lignin Biosynthesis Gene Network in <i>Sorghum bicolor</i>
Hao Niu,
Yanbo Wang,
Ruizhen Liu,
Xiaoqiang Cheng,
Yao Wang,
Yubin Wang,
Xin Lv,
Fangfang Fan,
Lan Ju,
Jianqiang Chu,
Haisheng Yan,
Hongru Wang,
Hetan Chang,
Yancong Zhang,
Yongfu Tao,
Junai Ping
Affiliations
Hao Niu
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Yanbo Wang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Ruizhen Liu
College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China
Xiaoqiang Cheng
College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China
Yao Wang
College of Agriculture, Shanxi Agricultural University, Jinzhong 030801, China
Yubin Wang
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Xin Lv
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Fangfang Fan
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Lan Ju
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Jianqiang Chu
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Haisheng Yan
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Hongru Wang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Hetan Chang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Yancong Zhang
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Yongfu Tao
Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
Junai Ping
Institute of Sorghum, Shanxi Agricultural University, Jinzhong 030600, China
Sorghum is a versatile crop that serves as a major source of food, feed, fodder and biofuel globally. Lignin content in sorghum affects multiple important traits, including lodging resistance, forage digestibility and the efficiency of bioenergy production. However, the genetic regulation of lignin content in sorghum remains poorly understood. In this study, we combined transcriptomic and comparative genomic approaches to uncover the genetic network underlying lignin biosynthesis in sorghum. Through comparative genomic analysis, we identified 104 candidate genes involved in lignin biosynthesis. Transcriptome analysis of four sorghum accessions with contrasting lignin contents identified 6132 differentially expressed genes with an enrichment of genes related to phenylpropanoid biosynthesis and cell wall biogenesis. The 104 lignin biosynthesis candidates were significantly enriched (p-value < 0.01) in these differentially expressed genes, with most differentially expressed candidate genes related to monolignol biosynthesis and polymerization being up-regulated in high-lignin accessions. These up-regulated genes are related to all key enzymes involved in lignin biosynthesis, suggesting that the elevated lignin content in these accessions results from a collective increase in enzyme activity. Sequence analysis revealed a significant reduction in genetic diversity across lignin biosynthesis genes in cultivated sorghum compared to wild sorghum. Moreover, selection signals during domestication were identified in 30 lignin biosynthesis genes, 22 of which were differentially expressed, further supporting the functional relevance of these differentially expressed genes in lignin biosynthesis. Overall, our findings uncover the lignin biosynthesis gene network in sorghum and offer potential targets for future functional studies and trait manipulation.
