1
|
Mei C, Li X, Yan P, Feng B, Mamat A, Wang J, Li N. Identification of Apple Flower Development-Related Gene Families and Analysis of Transcriptional Regulation. Int J Mol Sci 2024; 25:7510. [PMID: 39062752 PMCID: PMC11277112 DOI: 10.3390/ijms25147510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/28/2024] Open
Abstract
Apple (Malus domestica Borkh.) stands out as a globally significant fruit tree with considerable economic importance. Nonetheless, the orchard production of 'Fuji' apples faces significant challenges, including delayed flowering in young trees and inconsistent annual yields in mature trees, ultimately resulting in suboptimal fruit yield due to insufficient flower bud formation. Flower development represents a pivotal process influencing plant adaptation to environmental conditions and is a crucial determinant of successful plant reproduction. The three gene or transcription factor (TF) families, C2H2, DELLA, and FKF1, have emerged as key regulators in plant flowering regulation; however, understanding their roles during apple flowering remains limited. Consequently, this study identified 24 MdC2H2, 6 MdDELLA, and 6 MdFKF1 genes in the apple genome with high confidence. Through phylogenetic analyses, the genes within each family were categorized into three distinct subgroups, with all facets of protein physicochemical properties and conserved motifs contingent upon subgroup classification. Repetitive events between these three gene families within the apple genome were elucidated via collinearity analysis. qRT-PCR analysis was conducted and revealed significant expression differences among MdC2H2-18, MdDELLA1, and MdFKF1-4 during apple bud development. Furthermore, yeast two-hybrid analysis unveiled an interaction between MdC2H2-18 and MdDELLA1. The genome-wide identification of the C2H2, DELLA, and FKF1 gene families in apples has shed light on the molecular mechanisms underlying apple flower bud development.
Collapse
Affiliation(s)
- Chuang Mei
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.M.); (X.L.); (P.Y.); (B.F.); (A.M.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Xianguo Li
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.M.); (X.L.); (P.Y.); (B.F.); (A.M.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Peng Yan
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.M.); (X.L.); (P.Y.); (B.F.); (A.M.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Beibei Feng
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.M.); (X.L.); (P.Y.); (B.F.); (A.M.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Aisajan Mamat
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.M.); (X.L.); (P.Y.); (B.F.); (A.M.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Jixun Wang
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.M.); (X.L.); (P.Y.); (B.F.); (A.M.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Ning Li
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Key Laboratory of Genome Research and Genetic Improvement of Xinjiang Characteristic Fruits and Vegetables, Institute of Horticultural Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, China; (C.M.); (X.L.); (P.Y.); (B.F.); (A.M.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| |
Collapse
|
2
|
Huang S, Shen Z, An R, Jia Q, Wang D, Wei S, Mu J, Zhang Y. Identification and characterization of the plasma membrane H +-ATPase genes in Brassica napus and functional analysis of BnHA9 in salt tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108566. [PMID: 38554537 DOI: 10.1016/j.plaphy.2024.108566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 03/05/2024] [Accepted: 03/25/2024] [Indexed: 04/01/2024]
Abstract
As a primary proton pump, plasma membrane (PM) H+-ATPase plays critical roles in regulating plant growth, development, and stress responses. PM H+-ATPases have been well characterized in many plant species. However, no comprehensive study of PM H+-ATPase genes has been performed in Brassica napus (rapeseed). In this study, we identified 32 PM H+-ATPase genes (BnHAs) in the rapeseed genome, and they were distributed on 16 chromosomes. Phylogenetical and gene duplication analyses showed that the BnHA genes were classified into five subfamilies, and the segmental duplication mainly contributed to the expansion of the rapeseed PM H+-ATPase gene family. The conserved domain and subcellular analyses indicated that BnHAs encoded canonical PM H+-ATPase proteins with 14 highly conserved domains and localized on PM. Cis-acting regulatory element and expression pattern analyses indicated that the expression of BnHAs possessed tissue developmental stage specificity. The 25 upstream open reading frames with the canonical initiation codon ATG were predicted in the 5' untranslated regions of 11 BnHA genes and could be used as potential target sites for improving rapeseed traits. Protein interaction analysis showed that BnBRI1.c associated with BnHA2 and BnHA17, indicating that the conserved activity regulation mechanism of BnHAs may be present in rapeseed. BnHA9 overexpression in Arabidopsis enhanced the salt tolerance of the transgenic plants. Thus, our results lay a foundation for further research exploring the biological functions of PM H+-ATPases in rapeseed.
Collapse
Affiliation(s)
- Shuhua Huang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Zhen Shen
- College of Horticulture, Northwest A&F University, Yangling, 712100, China
| | - Ran An
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Qingli Jia
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Daojie Wang
- Key Laboratory of Plant Stress Biology, State Key Laboratory of Cotton Biology, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Shihao Wei
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China
| | - Jianxin Mu
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China.
| | - Yanfeng Zhang
- Hybrid Rapeseed Research Center of Shaanxi Province, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
3
|
Liu S, Lei C, Zhu Z, Li M, Chen Z, He W, Liu B, Chen L, Li X, Xie Y. Genome-Wide Analysis and Identification of 1-Aminocyclopropane-1-Carboxylate Synthase ( ACS) Gene Family in Wheat ( Triticum aestivum L.). Int J Mol Sci 2023; 24:11158. [PMID: 37446336 DOI: 10.3390/ijms241311158] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/29/2023] [Accepted: 06/30/2023] [Indexed: 07/15/2023] Open
Abstract
Ethylene has an important role in regulating plant growth and development as well as responding to adversity stresses. The 1-aminocyclopropane-1-carboxylate synthase (ACS) is the rate-limiting enzyme for ethylene biosynthesis. However, the role of the ACS gene family in wheat has not been examined. In this study, we identified 12 ACS members in wheat. According to their position on the chromosome, we named them TaACS1-TaACS12, which were divided into four subfamilies, and members of the same subfamilies had similar gene structures and protein-conserved motifs. Evolutionary analysis showed that fragment replication was the main reason for the expansion of the TaACS gene family. The spatiotemporal expression specificity showed that most of the members had the highest expression in roots, and all ACS genes contained W box elements that were related to root development, which suggested that the ACS gene family might play an important role in root development. The results of the gene expression profile analysis under stress showed that ACS members could respond to a variety of stresses. Protein interaction prediction showed that there were four types of proteins that could interact with TaACS. We also obtained the targeting relationship between TaACS family members and miRNA. These results provided valuable information for determining the function of the wheat ACS gene, especially under stress.
Collapse
Affiliation(s)
- Shuqing Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Chao Lei
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Zhanhua Zhu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Mingzhen Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Zhaopeng Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Wei He
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Bin Liu
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Liuping Chen
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Xuejun Li
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Yanzhou Xie
- State Key Laboratory of Crop Stress Biology in Arid Areas and College of Agronomy, Northwest A&F University, Xianyang 712100, China
| |
Collapse
|
4
|
Luo W, Zhao Z, Chen H, Ao W, Lu L, Liu J, Li X, Sun Y. Genome-wide characterization and expression of DELLA genes in Cucurbita moschata reveal their potential roles under development and abiotic stress. FRONTIERS IN PLANT SCIENCE 2023; 14:1137126. [PMID: 36909418 PMCID: PMC9995975 DOI: 10.3389/fpls.2023.1137126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 02/13/2023] [Indexed: 06/18/2023]
Abstract
DELLA gene family plays a key role in regulating plant development and responding to stress. Currently, many DELLA family members have been identified in plants, however, information on DELLA genes in pumpkin (Cucurbita moschata) is scarce. In this study, physical and chemical properties, gene structure cis-regulatory elements and expression of CmoDELLA genes were examined in pumpkin. We found that seven CmoDELLA genes were identified in pumpkin, and they were unevenly classified into five chromosomes. CmoDELLA proteins were relatively unstable and their secondary structures were mainly made up α-helix and random coil. All seven CmoDELLA proteins contained typical DELLA domain and GRAS domain, however, motif numbers between CmoDELLA proteins were unevenly distributed, implying the complex evolution and functional diversification of CmoDELLA proteins. Cis-regulatory elements analysis revealed that CmoDELLA genes might play an essential role in regulating plant growth and development, and response to stress in pumpkin. Transcriptome data in the roots, stems, leaves and fruits demonstrated that CmoDELLA2, CmoDELLA3 and CmoDELLA7 were related to the stems development, CmoDELLA1, CmoDELLA4, CmoDELLA5 and CmoDELLA6 were associated with the fruits development. Furthermore, we found that CmoDELLA1 and CmoDELLA5 were up-regulated under NaCl stress. CmoDELLA1, CmoDELLA2, CmoDELLA3, CmoDELLA5, CmoDELLA6 and CmoDELLA7 were remarkably induced under waterlogging stress. While, all of the 7 CmoDELLA genes showed significantly induced expression under cold stress. The expression patterns under abiotic stress suggested that CmoDELLA genes might mediate the stress response of pumpkin to NaCl, waterlogging and cold, however, the functions of different CmoDELLA genes varied under different stress. Overall, our study provides valuable information for further research about the potential functions and regulatory networks of CmoDELLA genes in pumpkin.
Collapse
Affiliation(s)
- Weirong Luo
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Zhenxiang Zhao
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Hongzhi Chen
- College of Bioengineering, Xinxiang Institute of Engineering, Xinxiang, China
| | - Wenhong Ao
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Lin Lu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Junjun Liu
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Xinzheng Li
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| | - Yongdong Sun
- School of Horticulture and Landscape Architecture, Henan Institute of Science and Technology, Xinxiang, China
- Henan Province Engineering Research Center of Horticultural Plant Resource Utilization and Germplasm Enhancement, Xinxiang, China
| |
Collapse
|
5
|
Zeng D, Si C, Teixeira da Silva JA, Shi H, Chen J, Huang L, Duan J, He C. Uncovering the involvement of DoDELLA1-interacting proteins in development by characterizing the DoDELLA gene family in Dendrobium officinale. BMC PLANT BIOLOGY 2023; 23:93. [PMID: 36782128 PMCID: PMC9926750 DOI: 10.1186/s12870-023-04099-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Gibberellins (GAs) are widely involved in plant growth and development. DELLA proteins are key regulators of plant development and a negative regulatory factor of GA. Dendrobium officinale is a valuable traditional Chinese medicine, but little is known about D. officinale DELLA proteins. Assessing the function of D. officinale DELLA proteins would provide an understanding of their roles in this orchid's development. RESULTS In this study, the D. officinale DELLA gene family was identified. The function of DoDELLA1 was analyzed in detail. qRT-PCR analysis showed that the expression levels of all DoDELLA genes were significantly up-regulated in multiple shoots and GA3-treated leaves. DoDELLA1 and DoDELLA3 were significantly up-regulated in response to salt stress but were significantly down-regulated under drought stress. DoDELLA1 was localized in the nucleus. A strong interaction was observed between DoDELLA1 and DoMYB39 or DoMYB308, but a weak interaction with DoWAT1. CONCLUSIONS In D. officinale, a developmental regulatory network involves a close link between DELLA and other key proteins in this orchid's life cycle. DELLA plays a crucial role in D. officinale development.
Collapse
Affiliation(s)
- Danqi Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Can Si
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | | | - Hongyu Shi
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Chen
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Huang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
| | - Chunmei He
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
| |
Collapse
|
6
|
Hu F, Ye Z, Zhang W, Fang D, Cao J. Decipher the molecular evolution and expression patterns of Cupin family genes in oilseed rape. Int J Biol Macromol 2023; 227:437-452. [PMID: 36549611 DOI: 10.1016/j.ijbiomac.2022.12.150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022]
Abstract
Cupin proteins are involved in plant growth and development as well as in response to various stresses. Here, a total of 173 Cupin genes were identified in Brassica napus, and their molecular evolution and expression patterns were analyzed. These genes were classified into ten groups. Motif and exon-intron structure indicated a high degree of conservation within each group during evolution. BnaCupins were distributed on 19 chromosomes and their expansion is mainly contributed by whole-genome duplication (WGD) and segmental duplication events. BnaCupins have undergone severe purifying selection during a long evolutionary process. Meanwhile, some positive selection sites were identified. Expression patterns and cis-element analysis indicated that BnaCupins play significant roles in plant growth and stress responses. In addition, the expression levels of some BnCupins were significantly altered when treated with different conditions (cold, salt, drought, IAA, ABA, and 6-BA). Some BnaCupin interacting proteins, such as glycosyl hydrolase5 (GHs5), carbohydrate kinase (CHKs), ATP-dependent 6-phosphofructokinase (ATP-PFK), S-adenosylmethionine synthase (S-MAT), and aldolase class II (ALD II), were identified by the protein-protein interaction network. It will contribute to enriching our knowledge of the Cupin gene family in B. napus and provide a basis for further studies of their functions.
Collapse
Affiliation(s)
- Fei Hu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Ziyi Ye
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Weimeng Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Da Fang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China
| | - Jun Cao
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, Jiangsu, China.
| |
Collapse
|
7
|
Sarwar R, Li L, Yu J, Zhang Y, Geng R, Meng Q, Zhu K, Tan XL. Functional Characterization of the Cystine-Rich-Receptor-like Kinases ( CRKs) and Their Expression Response to Sclerotinia sclerotiorum and Abiotic Stresses in Brassica napus. Int J Mol Sci 2022; 24:ijms24010511. [PMID: 36613954 PMCID: PMC9820174 DOI: 10.3390/ijms24010511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/24/2022] [Accepted: 12/24/2022] [Indexed: 12/29/2022] Open
Abstract
Cysteine-rich receptor-like kinases (CRKs) are transmembrane proteins that bind to the calcium ion to regulate stress-signaling and plant development-related pathways, as indicated by several pieces of evidence. However, the CRK gene family hasn’t been inadequately examined in Brassica napus. In our study, 27 members of the CRK gene family were identified in Brassica napus, which are categorized into three phylogenetic groups and display synteny relationship to the Arabidopsis thaliana orthologs. All the CRK genes contain highly conserved N-terminal PKINASE domain; however, the distribution of motifs and gene structure were variable conserved. The functional divergence analysis between BnaCRK groups indicates a shift in evolutionary rate after duplication events, demonstrating that BnaCRKs might direct a specific function. RNA-Seq datasets and quantitative real-time PCR (qRT-PCR) exhibit the complex expression profile of the BnaCRKs in plant tissues under multiple stresses. Nevertheless, BnaA06CRK6-1 and BnaA08CRK8 from group B were perceived to play a predominant role in the Brassica napus stress signaling pathway in response to drought, salinity, and Sclerotinia sclerotiorum infection. Insights gained from this study improve our knowledge about the Brassica napus CRK gene family and provide a basis for enhancing the quality of rapeseed.
Collapse
Affiliation(s)
- Rehman Sarwar
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Lei Li
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Jiang Yu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Yijie Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Rui Geng
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Qingfeng Meng
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Keming Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| |
Collapse
|
8
|
Fang D, Zhang W, Cheng X, Hu F, Ye Z, Cao J. Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species. FRONTIERS IN PLANT SCIENCE 2022; 13:958964. [PMID: 35991428 PMCID: PMC9386158 DOI: 10.3389/fpls.2022.958964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.
Collapse
|
9
|
HSP70 Gene Family in Brassica rapa: Genome-Wide Identification, Characterization, and Expression Patterns in Response to Heat and Cold Stress. Cells 2022; 11:cells11152316. [PMID: 35954158 PMCID: PMC9367284 DOI: 10.3390/cells11152316] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 07/04/2022] [Accepted: 07/17/2022] [Indexed: 02/05/2023] Open
Abstract
Heat shock proteins protect plants from abiotic stress, such as salt, drought, heat, and cold stress. HSP70 is one of the major members of the heat shock protein family. To explore the mechanism of HSP70 in Brassica rapa, we identified 28 putative HSP70 gene family members using state-of-the-art bioinformatics-based tools and methods. Based on chromosomal mapping, HSP70 genes were the most differentially distributed on chromosome A03 and the least distributed on chromosome A05. Ka/Ks analysis revealed that B. rapa evolution was subjected to intense purifying selection of the HSP70 gene family. RNA-sequencing data and expression profiling showed that heat and cold stress induced HSP70 genes. The qRT-PCR results verified that the HSP70 genes in Chinese cabbage (Brassica rapa ssp. pekinensis) are stress-inducible under both cold and heat stress. The upregulated expression pattern of these genes indicated the potential of HSP70 to mitigate environmental stress. These findings further explain the molecular mechanism underlying the responses of HSP70 to heat and cold stress.
Collapse
|
10
|
Sarwar R, Geng R, Li L, Shan Y, Zhu KM, Wang J, Tan XL. Genome-Wide Prediction, Functional Divergence, and Characterization of Stress-Responsive BZR Transcription Factors in B. napus. FRONTIERS IN PLANT SCIENCE 2022; 12:790655. [PMID: 35058951 PMCID: PMC8764130 DOI: 10.3389/fpls.2021.790655] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 12/01/2021] [Indexed: 05/12/2023]
Abstract
BRASSINAZOLE RESISTANT (BZR) are transcriptional factors that bind to the DNA of targeted genes to regulate several plant growth and physiological processes in response to abiotic and biotic stresses. However, information on such genes in Brassica napus is minimal. Furthermore, the new reference Brassica napus genome offers an excellent opportunity to systematically characterize this gene family in B. napus. In our study, 21 BnaBZR genes were distributed across 19 chromosomes of B. napus and clustered into four subgroups based on Arabidopsis thaliana orthologs. Functional divergence analysis among these groups evident the shifting of evolutionary rate after the duplication events. In terms of structural analysis, the BnaBZR genes within each subgroup are highly conserved but are distinctive within groups. Organ-specific expression analyses of BnaBZR genes using RNA-seq data and quantitative real-time polymerase chain reaction (qRT-PCR) revealed complex expression patterns in plant tissues during stress conditions. In which genes belonging to subgroups III and IV were identified to play central roles in plant tolerance to salt, drought, and Sclerotinia sclerotiorum stress. The insights from this study enrich our understanding of the B. napus BZR gene family and lay a foundation for future research in improving rape seed environmental adaptability.
Collapse
Affiliation(s)
- Rehman Sarwar
- School of Food Science and Biological Engineering, Jiangsu University, Zhenjiang, China
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Rui Geng
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Lei Li
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Yue Shan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Ke-Ming Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Jin Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| |
Collapse
|