Browsing by Author "Zhang, Ailing"

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    Pangenomic analysis identifies structural variation associated with heat tolerance in pearl millet
    Yan, Haidong; Sun, Min; Zhang, Zhongren; Jin, Yarong; Zhang, Ailing; Lin, Chuang; Wu, Bingchao; He, Min; Xu, Bin; Wang, Jing; Qin, Peng; Mendieta, John Pablo; Nie, Gang; Wang, Jianping; Jones, Chris S. S.; Feng, Guangyan; Srivastava, Rakesh K. K.; Zhang, Xinquan; Bombarely, Aureliano; Luo, Dan; Jin, Long; Peng, Yuanying; Wang, Xiaoshan; Ji, Yang; Tian, Shilin; Huang, Linkai (Nature Portfolio, 2023-03)
    Pearl millet is an important cereal crop worldwide and shows superior heat tolerance. Here, we developed a graph-based pan-genome by assembling ten chromosomal genomes with one existing assembly adapted to different climates worldwide and captured 424,085 genomic structural variations (SVs). Comparative genomics and transcriptomics analyses revealed the expansion of the RWP-RK transcription factor family and the involvement of endoplasmic reticulum (ER)-related genes in heat tolerance. The overexpression of one RWP-RK gene led to enhanced plant heat tolerance and transactivated ER-related genes quickly, supporting the important roles of RWP-RK transcription factors and ER system in heat tolerance. Furthermore, we found that some SVs affected the gene expression associated with heat tolerance and SVs surrounding ER-related genes shaped adaptation to heat tolerance during domestication in the population. Our study provides a comprehensive genomic resource revealing insights into heat tolerance and laying a foundation for generating more robust crops under the changing climate. A graph-based pan-genome constructed using de novo genome assemblies of ten pearl millet accessions adapted to different climates worldwide identifies structural variations and their contribution to heat tolerance in pearl millet.
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    Transcriptional Changes in Pearl Millet Leaves under Heat Stress
    Huang, Dejun; Sun, Min; Zhang, Ailing; Chen, Jishan; Zhang, Jian; Lin, Chuang; Zhang, Huan; Lu, Xiaowen; Wang, Xiaoshan; Yan, Haidong; Tang, Jianan; Huang, Linkai (MDPI, 2021-10-28)
    High-temperature stress negatively affects the growth and development of plants, and therefore threatens global agricultural safety. Cultivating stress-tolerant plants is the current objective of plant breeding programs. Pearl millet is a multi-purpose plant, commonly used as a forage but also an important food staple. This crop is very heat-resistant and has a higher net assimilation rate than corn under high-temperature stress. However, the response of heat resistant pearl millet has so far not been studied at the transcriptional level. In this study, transcriptome sequencing of pearl millet leaves exposed to different lengths of heat treatment (1 h, 48 h and 96 h) was conducted in order to investigate the molecular mechanisms of the heat stress response and to identify key genes related to heat stress. The results showed that the amount of heat stress-induced DEGs in leaves differs with the length of exposure to high temperatures. The highest value of DEGs (8286) was observed for the group exposed to heat stress for 96 h, while the other two treatments showed lower DEGs values of 4659 DEGs after 1 h exposure and 3981 DEGs after 48 h exposure to heat stress. The DEGs were mainly synthesized in protein folding pathways under high-temperature stress after 1 h exposure. Moreover, a large number of genes encoding ROS scavenging enzymes were activated under heat stress for 1 h and 48 h treatments. The flavonoid synthesis pathway of pearl millet was enriched after heat stress for 96 h. This study analyzed the transcription dynamics under short to long-term heat stress to provide a theoretical basis for the heat resistance response of pearl millet.
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    Transcriptome analysis of heat stress and drought stress in pearl millet based on Pacbio full-length transcriptome sequencing
    Sun, Min; Huang, Dejun; Zhang, Ailing; Khan, Imran; Yan, Haidong; Wang, Xiaoshan; Zhang, Xinquan; Zhang, Jian; Huang, Linkai (2020-07-08)
    Background Heat and drought are serious threats for crop growth and development. As the sixth largest cereal crop in the world, pearl millet can not only be used for food and forage but also as a source of bioenergy. Pearl millet is highly tolerant to heat and drought. Given this, it is considered an ideal crop to study plant stress tolerance and can be used to identify heat-resistant genes. Results In this study, we used Pacbio sequencing data as a reference sequence to analyze the Illumina data of pearl millet that had been subjected to heat and drought stress for 48 h. By summarizing previous studies, we found 26,299 new genes and 63,090 new transcripts, and the number of gene annotations increased by 20.18%. We identified 2792 transcription factors and 1223 transcriptional regulators. There were 318 TFs and 149 TRs differentially expressed under heat stress, and 315 TFs and 128 TRs were differentially expressed under drought stress. We used RNA sequencing to identify 6920 genes and 6484 genes differentially expressed under heat stress and drought stress, respectively. Conclusions Through Pacbio sequencing, we have identified more new genes and new transcripts. On the other hand, comparing the differentially expressed genes under heat tolerance with the DEGs under drought stress, we found that even in the same pathway, pearl millet responds with a different protein.