Integrated single-molecule real-time sequencing and RNA sequencing reveal the molecular mechanisms of salt tolerance in a novel synthesized polyploid genetic bridge between maize and its wild relatives

BMC Genomics

Research

Ping Zhang¹  Yan Li²  Mingjun Cheng³  Yang Li⁴  Xu Yan⁵  Muhammad Zafar Iqbal⁶  Ruyu He⁶  Yunfeng Zhong⁶  Tingzhao Rong⁶  Yang Zhou⁶  Yibo Zhang⁶  Xingyu Wang⁶  Qiangqiang Ma⁶  Yingzheng Li⁶  Qilin Tang⁶  Jianmei He⁶  Xiaofeng Li⁶ 

[1]Chengdu Research Base of Giant Panda Breeding, 61130, Chengdu, China

[2]Crop Research Institute, Sichuan Academy of Agricultural Sciences, 611041, Chengdu, China

[3]Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, 610041, Chengdu, China

[4]Mianyang Teachers’ College School of Urban and Rural Construction and Planning, 621000, Mianyany, China

[5]Sericulture Research Institute, Sichuan Academy of Agricultural Sciences, 637000, Nanchong, China

[6]Sichuan Agricultural University, 611130, Chengdu, China

关键词: SMRT-sequencing;    RNA-sequencing;    Zea mays;    Tripsacum dactyloides;    Zea perennis;    Genetic bridge;    Salt tolerance;   

DOI  :  10.1186/s12864-023-09148-0

 received in 2022-10-16, accepted in 2023-01-23,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundTripsacum dactyloides (2n = 4x = 72) and Zea perennis (2n = 4x = 40) are tertiary gene pools of Zea mays L. and exhibit many abiotic adaptations absent in modern maize, especially salt tolerance. A previously reported allopolyploid (hereafter referred to as MTP, 2n = 74) synthesized using Zea mays, Tripsacum dactyloides, and Zea perennis has even stronger salt tolerance than Z. perennis and T. dactyloides. This allopolyploid will be a powerful genetic bridge for the genetic improvement of maize. However, the molecular mechanisms underlying its salt tolerance, as well as the key genes involved in regulating its salt tolerance, remain unclear.ResultsSingle-molecule real-time sequencing and RNA sequencing were used to identify the genes involved in salt tolerance and reveal the underlying molecular mechanisms. Based on the SMRT-seq results, we obtained 227,375 reference unigenes with an average length of 2300 bp; most of the unigenes were annotated to Z. mays sequences (76.5%) in the NR database. Moreover, a total of 484 and 1053 differentially expressed genes (DEGs) were identified in the leaves and roots, respectively. Functional enrichment analysis of DEGs revealed that multiple pathways responded to salt stress, including “Flavonoid biosynthesis,” “Oxidoreductase activity,” and “Plant hormone signal transduction” in the leaves and roots, and “Iron ion binding,” “Acetyl-CoA carboxylase activity,” and “Serine-type carboxypeptidase activity” in the roots. Transcription factors, such as those in the WRKY, B3-ARF, and bHLH families, and cytokinin negatively regulators negatively regulated the salt stress response. According to the results of the short time series-expression miner analysis, proteins involved in “Spliceosome” and “MAPK signal pathway” dynamically responded to salt stress as salinity changed. Protein–protein interaction analysis revealed that heat shock proteins play a role in the large interaction network regulating salt tolerance.ConclusionsOur results reveal the molecular mechanism underlying the regulation of MTP in the response to salt stress and abundant salt-tolerance-related unigenes. These findings will aid the retrieval of lost alleles in modern maize and provide a new approach for using T. dactyloides and Z. perennis to improve maize.

【 授权许可】

CC BY   
© The Author(s) 2023

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