1
|
Cheng M, Zheng J, Cui K, Luo X, Yang T, Pan Z, Zhou Y, Chen S, Chen Y, Wang H, Zhang R, Yao M, Li H, He R. Transcriptomics integrated with metabolomics provides a new strategy for mining key genes in response to low temperature stress in Helictotrichon virescens. Int J Biol Macromol 2023:125070. [PMID: 37244338 DOI: 10.1016/j.ijbiomac.2023.125070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 04/24/2023] [Accepted: 05/22/2023] [Indexed: 05/29/2023]
Abstract
H. virescens is a perennial herbaceous plant with highly tolerant to cold weather, but the key genes that respond to low temperature stress still remain unclear. Hence, RNA-seq was performed using leaves of H. virescens treated at 0 °C and 25 °C for 12 h, 36 h, and 60 h, respectively, and a total of 9416 DEGs were significantly enriched into seven KEGG pathways. The LC-QTRAP platform was performed using leaves of H. virescens leaves at 0 °C and 25 °C for 12 h, 36 h, and 60 h, respectively, and a total of 1075 metabolites were detected, which were divided into 10 categories. Additionally, 18 major metabolites, two key pathways, and six key genes were mined using a multi-omics analytical strategy. The RT-PCR results showed that with the extension of treatment time, the expression levels of key genes in the treatment group gradually increased, and the difference between the treatment group and the control group was extremely significant. Notably, the functional verification results showed that the key genes positively regulated cold tolerance of H. virescens. These results can lay a foundation for the in-depth analysis of the mechanism of response of perennial herbs to low temperature stress.
Collapse
Affiliation(s)
- Mingjun Cheng
- Institute of Qinghai-tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Junjun Zheng
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kuoshu Cui
- Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Xuan Luo
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Tao Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zeyang Pan
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shiyong Chen
- Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China; College of Animal and Veterinary Sciences, Southwest Minzu University, Chengdu 610041, China
| | - Youjun Chen
- Institute of Qinghai-tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Hui Wang
- Institute of Qinghai-tibetan Plateau, Southwest Minzu University, Chengdu 610041, China; Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Ruizhen Zhang
- Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Mingjiu Yao
- Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Hongquan Li
- Sichuan ZoigeAlpine Wetland Ecosystem National Observationand Research Station, Southwest Minzu University, Chengdu 610041, China
| | - Ruyu He
- Maize Research Institute, Sichuan Agricultural University, Chengdu 611130, China.
| |
Collapse
|
2
|
He RY, Zheng JJ, Chen Y, Pan ZY, Yang T, Zhou Y, Li XF, Nan X, Li YZ, Cheng MJ, Li Y, Li Y, Yan X, Iqbal MZ, He JM, Rong TZ, Tang QL. QTL-seq and transcriptomic integrative analyses reveal two positively regulated genes that control the low-temperature germination ability of MTP-maize introgression lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:116. [PMID: 37093290 DOI: 10.1007/s00122-023-04362-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 04/06/2023] [Indexed: 05/03/2023]
Abstract
KEY MESSAGE Two candidate genes (ZmbZIP113 and ZmTSAH1) controlling low-temperature germination ability were identified by QTL-seq and integrative transcriptomic analyses. The functional verification results showed that two candidate genes positively regulated the low-temperature germination ability of IB030. Low-temperature conditions cause slow maize (Zea mays L.) seed metabolism, resulting in slow seedling emergence and irregular seedling emergence, which can cause serious yield loss. Thus, improving a maize cultivar's low-temperature germination ability (LTGA) is vital for increasing yield production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant of cold stress and can thus be used to improve the LTGA of maize. In a previous study, the genetic bridge MTP was constructed (from maize, T. dactyloides, and Z. perennis) and used to obtain a highly LTGA maize introgression line (IB030) by backcross breeding. In this study, IB030 (Strong-LTGA) and Mo17 (Weak-LTGA) were selected as parents to construct an F2 offspring. Additionally, two major QTLs (qCS1-1 and qCS10-1) were mapped. Then, RNA-seq was performed using seeds of IB030 and the recurrent parent B73 treated at 10 °C for 27 days and 25 °C for 7 days, respectively, and two candidate genes (ZmbZIP113 and ZmTSAH1) controlling LTGA were located using QTL-seq and integrative transcriptomic analyses. The functional verification results showed that the two candidate genes positively regulated LTGA of IB030. Notably, homologous cloning showed that the source of variation in both candidate genes was the stable inheritance of introgressed alleles from Z. perennis. This study was thus able to analyze the LTGA mechanism of IB030 and identify resistance genes for genetic improvement in maize, and it proved that using MTP genetic bridge confers desirable traits or phenotypes of Z. perennis and tripsacum essential to maize breeding systems.
Collapse
Affiliation(s)
- Ru-Yu He
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jun-Jun Zheng
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Chen
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ze-Yang Pan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Tao Yang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yang Zhou
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Feng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xinyi Nan
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ying-Zheng Li
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ming-Jun Cheng
- Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu, 610041, China
| | - Yan Li
- Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, China
| | - Yang Li
- Mianyang Teacher's College, Mianyang, 621000, Sichuan, China
| | - Xu Yan
- Sericultural Research Institute, Sichuan Academy of Agricultural Sciences, Nanchong, 637000, Sichuan, China
| | - Muhammad-Zafar Iqbal
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jian-Mei He
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Ting-Zhao Rong
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qi-Lin Tang
- Maize Research Institute, Sichuan Agricultural University, Chengdu, 611130, China.
| |
Collapse
|