1
|
Su Y, Fang J, Zeeshan Ul Haq M, Yang W, Yu J, Yang D, Liu Y, Wu Y. Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Peanut ( Arachis hypogea L.) Revealed Its Crucial Role in Growth and Multiple Stress Tolerance. PLANTS (BASEL, SWITZERLAND) 2024; 13:2077. [PMID: 39124195 PMCID: PMC11313903 DOI: 10.3390/plants13152077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2024] [Revised: 07/20/2024] [Accepted: 07/24/2024] [Indexed: 08/12/2024]
Abstract
Casparian strip membrane domain proteins (CASPs), regulating the formation of Casparian strips in plants, serve crucial functions in facilitating plant growth, development, and resilience to abiotic stress. However, little research has focused on the characteristics and functions of AhCASPs in cultivated peanuts. In this study, the genome-wide identification and expression analysis of the AhCASPs gene family was performed using bioinformatics and transcriptome data. Results showed that a total of 80 AhCASPs members on 20 chromosomes were identified and divided into three subclusters, which mainly localized to the cell membrane. Ka/Ks analysis revealed that most of the genes underwent purifying selection. Analysis of cis elements suggested the possible involvement of AhCASPs in hormonal and stress responses, including GA, MeJA, IAA, ABA, drought, and low temperature. Moreover, 20 different miRNAs for 37 different AhCASPs genes were identified by the psRNATarget service. Likewise, transcriptional analysis revealed key AhCASPs responding to various stresses, hormonal processing, and tissue types, including 33 genes in low temperature and drought stress and 41 genes in tissue-specific expression. These results provide an important theoretical basis for the functions of AhCASPs in growth, development, and multiple stress resistance in cultivated peanuts.
Collapse
Affiliation(s)
- Yating Su
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jieyun Fang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Muhammad Zeeshan Ul Haq
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Wanli Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Jing Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Dongmei Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| | - Ya Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
- Key Laboratory for Quality Regulation of Tropical Horticultural Crops of Hainan Province, Hainan University, Haikou 570228, China
| | - Yougen Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), School of Tropical Agriculture and Forestry, Hainan University, Sanya 572025, China
| |
Collapse
|
2
|
Su Y, Zeeshan Ul Haq M, Liu X, Li Y, Yu J, Yang D, Wu Y, Liu Y. A Genome-Wide Identification and Expression Analysis of the Casparian Strip Membrane Domain Protein-like Gene Family in Pogostemon cablin in Response to p-HBA-Induced Continuous Cropping Obstacles. PLANTS (BASEL, SWITZERLAND) 2023; 12:3901. [PMID: 38005798 PMCID: PMC10675793 DOI: 10.3390/plants12223901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Casparian strip membrane domain protein-like (CASPL) genes are key genes for the formation and regulation of the Casparian strip and play an important role in plant abiotic stress. However, little research has focused on the members, characteristics, and biological functions of the patchouli PatCASPL gene family. In this study, 156 PatCASPL genes were identified at the whole-genome level. Subcellular localization predicted that 75.6% of PatCASPL proteins reside on the cell membrane. A phylogenetic analysis categorized PatCASPL genes into five subclusters alongside Arabidopsis CASPL genes. In a cis-acting element analysis, a total of 16 different cis-elements were identified, among which the photo-responsive element was the most common in the CASPL gene family. A transcriptome analysis showed that p-hydroxybenzoic acid, an allelopathic autotoxic substance, affected the expression pattern of PatCASPLs, including a total of 27 upregulated genes and 30 down-regulated genes, suggesting that these PatCASPLs may play an important role in the regulation of patchouli continuous cropping obstacles by affecting the formation and integrity of Casparian strip bands. These results provided a theoretical basis for exploring and verifying the function of the patchouli PatCASPL gene family and its role in continuous cropping obstacles.
Collapse
Affiliation(s)
- Yating Su
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Muhammad Zeeshan Ul Haq
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
| | - Xiaofeng Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Yang Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Jing Yu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Dongmei Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Yougen Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| | - Ya Liu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Danzhou 571737, China
| |
Collapse
|
3
|
Cui Z, Liu S, Ge C, Shen Q, Zhang S, Ma H, Liu R, Zhao X, Liu R, Li P, Wang H, Wu Q, Pang C, Chen J. Genome-wide association study reveals that GhTRL1 and GhPIN8 affect cotton root development. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3161-3176. [PMID: 35965278 DOI: 10.1007/s00122-022-04177-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 07/06/2022] [Indexed: 06/15/2023]
Abstract
Two regions located at chromosome A05 and D04 were found to be significantly associated with 0-0.5 mm and 0.5-2 mm diameter roots, respectively, and two candidate genes related to root development were identified. Roots absorb water and nutrients, and play an important role in plant growth. However, there are few genetic developmental studies on cotton root structural traits. In this study, we used 200 upland cotton (Gossypium hirsutum L.) varieties to analyze the phenotypic variation of 43 traits. A total of 2001 related single-nucleotide polymorphism (SNP) sites located within or near 1046 genes were detected through a genome-wide association study (GWAS). The 32 root traits were linked to SNPs that corresponded to 317 nonrepetitive genes. For SNPs associated with root length and 0-0.5 mm diameter root traits, a significant peak appeared on chromosome A05 (between 21.91 and 22.24 Mb). For SNPs associated with root surface area, root volume and 0.5-2 mm diameter root traits, a significant peak appeared on chromosome D04 (between 7.35 and 7.70 Mb). Within these two key regions, SNPs were detected in the promoter and coding regions of two candidate genes, GhTRL1-A05 and GhPIN8-D04. The expression levels of these two genes also changed significantly according to transcriptome sequencing and quantitative real-time PCR (qRT-PCR). After silencing the GhTRL1 and GhPIN8 genes via virus-induced gene silencing (VIGS), we found that the plants expressing TRV2::GhTRL1 and TRV2::GhPIN8 had a reduced root length, surface area. Moreover, the contents of cis-12-oxo-phytodienoic acid (cis-OPDA), isopentenyl adenosine (iPR) and cis-zeatin (cZ) in the roots of the plants expressing TRV2::GhTRL1 decreased. This study contributes to the cultivation and improvement of cotton varieties.
Collapse
Affiliation(s)
- Ziqian Cui
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Shaodong Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Changwei Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Qian Shen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Siping Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Huijuan Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruihua Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Xinhua Zhao
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Ruida Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Pengzhen Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Hongchen Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Qidi Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
| | - Chaoyou Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
- Institute of Economic Crops, Xinjiang Academy of Agricultural Sciences, Ürümqi, China.
| | - Jing Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China.
- Zhengzhou Research Station, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China.
| |
Collapse
|
4
|
Zhou T, Wang N, Wang Y, Zhang XL, Li BG, Li W, Su JJ, Wang CX, Zhang A, Ma XF, Li ZH. Nucleotide Evolution, Domestication Selection, and Genetic Relationships of Chloroplast Genomes in the Economically Important Crop Genus Gossypium. FRONTIERS IN PLANT SCIENCE 2022; 13:873788. [PMID: 35498673 PMCID: PMC9051515 DOI: 10.3389/fpls.2022.873788] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Gossypium hirsutum (upland cotton) is one of the most economically important crops worldwide, which has experienced the long terms of evolution and domestication process from wild species to cultivated accessions. However, nucleotide evolution, domestication selection, and the genetic relationship of cotton species remain largely to be studied. In this study, we used chloroplast genome sequences to determine the evolutionary rate, domestication selection, and genetic relationships of 72 cotton genotypes (36 cultivated cotton accessions, seven semi-wild races of G. hirsutum, and 29 wild species). Evolutionary analysis showed that the cultivated tetraploid cotton genotypes clustered into a single clade, which also formed a larger lineage with the semi-wild races. Substitution rate analysis demonstrated that the rates of nucleotide substitution and indel variation were higher for the wild species than the semi-wild and cultivated tetraploid lineages. Selection pressure analysis showed that the wild species might have experienced greater selection pressure, whereas the cultivated cotton genotypes underwent artificial and domestication selection. Population clustering analysis indicated that the cultivated cotton accessions and semi-wild races have existed the obviously genetic differentiation. The nucleotide diversity was higher in the semi-wild races compared with the cultivated genotypes. In addition, genetic introgression and gene flow occurred between the cultivated tetraploid cotton and semi-wild genotypes, but mainly via historical rather than contemporary gene flow. These results provide novel molecular mechanisms insights into the evolution and domestication of economically important crop cotton species.
Collapse
Affiliation(s)
- Tong Zhou
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Ning Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yuan Wang
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Xian-Liang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Bao-Guo Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Jun-Ji Su
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Cai-Xiang Wang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Ai Zhang
- Gansu Provincial Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, China
| | - Zhong-Hu Li
- Shaanxi Key Laboratory for Animal Conservation, Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| |
Collapse
|