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Qiao K, Lv J, Hao J, Zhao C, Fan S, Ma Q. Identification of cotton PIP5K genes and role of GhPIP5K9a in primary root development. Gene 2024; 921:148532. [PMID: 38705423 DOI: 10.1016/j.gene.2024.148532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 04/24/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
Phosphatidylinositol 4 phosphate 5-kinase (PIP5K) is crucial for the phosphatidylinositol (PI) signaling pathway. It plays a significant role in plant growth and development, as well as stress response. However, its effects on cotton are unknown. This study identified PIP5K genes from four cotton species and conducted bioinformatic analyses, with a particular emphasis on the functions of GhPIP5K9a in primary roots. The results showed that cotton PIP5Ks were classified into four subgroups. Analysis of gene structure and motif composition showed obvious conservation within each subgroup. Synteny analysis suggested that the PIP5K gene family experienced significant expansion due to both whole-genome duplication (WGD) and segmental duplication. Transcriptomic data analysis revealed that the majority of GhPIP5K genes had the either low or undetectable levels of expression. Moreover, GhPIP5K9a is highly expressed in the root and was located in plasmalemma. Suppression of GhPIP5K9a transcripts resulted in longer primary roots, longer primary root cells and increased auxin polar transport-related genes expression, and decreased abscisic acid (ABA) content, indicating that GhPIP5K9a negatively regulates cotton primary root growth. This study lays the foundation for further exploration of the role of the PIP5K genes in cotton.
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Affiliation(s)
- Kaikai Qiao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China
| | - Jiaoyan Lv
- Anyang Academy of Agricultural Sciences, Anyang 455000, China
| | - Juxin Hao
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
| | - Chenglong Zhao
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
| | - Shuli Fan
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China; National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.
| | - Qifeng Ma
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research of Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China; Western Agricultural Research Center, Chinese Academy of Agricultural Sciences, Changji 831100, China.
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Ling P, Ju J, Zhang X, Wei W, Luo J, Li Y, Hai H, Shang B, Cheng H, Wang C, Zhang X, Su J. The Silencing of GhPIP5K2 and GhPIP5K22 Weakens Abiotic Stress Tolerance in Upland Cotton ( Gossypium hirsutum). Int J Mol Sci 2024; 25:1511. [PMID: 38338791 PMCID: PMC10855785 DOI: 10.3390/ijms25031511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 02/12/2024] Open
Abstract
Phosphatidylinositol 4-phosphate 5-kinases (PIP5Ks), essential enzymes in the phosphatidylinositol signaling pathway, are crucial for the abiotic stress responses and the overall growth and development of plants. However, the GhPIP5Ks had not been systematically studied, and their function in upland cotton was unknown. This study identified a total of 28 GhPIP5Ks, and determined their chromosomal locations, gene structures, protein motifs and cis-acting elements via bioinformatics analysis. A quantitative real-time PCR (qRT‒PCR) analysis showed that most GhPIP5Ks were upregulated under different stresses. A virus-induced gene silencing (VIGS) assay indicated that the superoxide dismutase (SOD), peroxidase (POD), and catalase (CAT) activities were significantly decreased, while malondialdehyde (MDA) content were significantly increased in GhPIP5K2- and GhPIP5K22-silenced upland cotton plants under abiotic stress. Furthermore, the expression of the stress marker genes GhHSFB2A, GhHSFB2B, GhDREB2A, GhDREB2C, GhRD20-1, GhRD29A, GhBIN2, GhCBL3, GhNHX1, GhPP2C, GhCBF1, GhSnRK2.6 and GhCIPK6 was significantly decreased in the silenced plants after exposure to stress. These results revealed that the silencing of GhPIP5K2 and GhPIP5K22 weakened the tolerance to abiotic stresses. These discoveries provide a foundation for further inquiry into the actions of the GhPIP5K gene family in regulating the response and resistance mechanisms of cotton to abiotic stresses.
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Affiliation(s)
- Pingjie Ling
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Jisheng Ju
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Xueli Zhang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Wei Wei
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Jin Luo
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Ying Li
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Han Hai
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Bowen Shang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Hongbo Cheng
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Caixiang Wang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
| | - Xianliang Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (CAAS), Anyang 455000, China
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
| | - Junji Su
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (P.L.); (J.J.); (X.Z.); (W.W.); (J.L.); (Y.L.); (H.H.); (B.S.); (H.C.); (C.W.)
- Western Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Changji 831100, China
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Wang Z, Wang Z, Li X, Chen Z, Liu Y, Zhang F, Dai Q, Yu Q, Li N. Identification and Analysis of the Expression of the PIP5K Gene Family in Tomatoes. Int J Mol Sci 2023; 25:159. [PMID: 38203328 PMCID: PMC10778592 DOI: 10.3390/ijms25010159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/12/2024] Open
Abstract
To explore the function of phosphatidylinositol 4-phosphate 5-kinase (PIP5K) in tomatoes, members of the tomato PIP5K family were identified and characterized using bioinformatic methods, and their expression patterns were also analyzed under salt stress and in different tissues. Twenty-one PIP5K members-namely, SlPIP5K1-SlPIP5K21-were identified from ten chromosomes, and these were divided into three groups according to a phylogenetic analysis. Further bioinformatic analysis showed four pairs of collinear relationships and fragment replication events among the SlPIP5K family members. To understand the possible roles of the SlPIP5Ks, a cis-acting element analysis was conducted, which indicated that tomato PIP5Ks could be associated with plant growth, hormones, and stress responses. We further validated the results of the in silico analysis by integrating RNA-seq and qRT-PCR techniques for salt- and hormone-treated tomato plants. Our results showed that SlPIP5K genes exhibited tissue- and treatment-specific patterns, and some of the SlPIP5Ks exhibited significantly altered expressions after our treatments, suggesting that they might be involved in these stresses. We selected one of the SlPIP5Ks that responded to our treatments, SlPIP5K2, to further understand its subcellular localization. Our results showed that SlPIP5K2 was located on the membrane. This study lays a foundation for the analysis of the biological functions of the tomato SlPIP5K genes and can also provide a theoretical basis for the selection and breeding of new tomato varieties and germplasm innovation, especially under salt stress.
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Affiliation(s)
- Zepeng Wang
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zhongyu Wang
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Xianguo Li
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Zhaolong Chen
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yuxiang Liu
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Fulin Zhang
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
- College of Horticulture, Xinjiang Agricultural University, Urumqi 830052, China
| | - Qi Dai
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Qinghui Yu
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
| | - Ning Li
- 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; (Z.W.); (Z.W.); (X.L.); (Z.C.); (Y.L.); (F.Z.); (Q.D.)
- The State Key Laboratory of Genetic Improvement and Germplasm Innovation of Crop Resistance in Arid Desert Regions (Preparation), Urumqi 830091, China
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He L, Fan Y, Zhang Z, Wei X, Yu J. Identifying Genes Associated with Female Flower Development of Phellodendron amurense Rupr. Using a Transcriptomics Approach. Genes (Basel) 2023; 14:661. [PMID: 36980934 PMCID: PMC10048520 DOI: 10.3390/genes14030661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 03/09/2023] Open
Abstract
Phellodendron amurense Rupr., a species of Rutaceae, is a nationally protected and valuable medicinal plant. It is generally considered to be dioecious. With the discovery of monoecious P. amurense, the phenomenon that its sex development is regulated by epigenetics has been revealed, but the way epigenetics affects the sex differentiation of P. amurense is still unclear. In this study, we investigated the effect of DNA methylation on the sexual development of P. amurense. The young inflorescences of male plants were treated with the demethylation agent 5-azaC, and the induced female flowers were obtained. The induced female flowers’ morphological functions and transcriptome levels were close to those of normally developed plants. Genes associated with the development of female flowers were studied by comparing the differences in transcriptome levels between the male and female flowers. Referring to sex-related genes reported in other plants, 188 candidate genes related to the development of female flowers were obtained, including sex-regulating genes, genes related to the formation and development of sexual organs, genes related to biochemical pathways, and hormone-related genes. RPP0W, PAL3, MCM2, MCM6, SUP, PIN1, AINTEGUMENTA, AINTEGUMENTA-LIKE6, AGL11, SEUSS, SHI-RELATED SEQUENCE 5, and ESR2 were preliminarily considered the key genes for female flower development. This study has demonstrated that epigenetics was involved in the sex regulation of P. amurense, with DNA methylation as one of its regulatory modes. Moreover, some candidate genes related to the sexual differentiation of P. amurense were obtained with analysis. These results are of great significance for further exploring the mechanism of sex differentiation of P. amurense and studying of sex differentiation of plants.
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Wang H, Coulman B, Bai Y, Tarˈan B, Biligetu B. Genetic diversity and local adaption of alfalfa populations (Medicago sativa L.) under long-term grazing. Sci Rep 2023; 13:1632. [PMID: 36717619 DOI: 10.1038/s41598-023-28521-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 01/19/2023] [Indexed: 02/01/2023] Open
Abstract
Genomic information on alfalfa adaptation to long-term grazing is useful for alfalfa genetic improvement. In this study, 14 alfalfa populations were collected from long-term grazing sites (> 25 years) across four soil zones in western Canada. Alfalfa cultivars released between 1926 and 1980 were used to compare degree of genetic variation of the 14 populations. Six agro-morphological and three nutritive value traits were evaluated from 2018 to 2020. The genotyping-by-sequencing (GBS) data of the alfalfa populations and environmental data were used for genotype-environment association (GEA). Both STRUCTURE and UPGMA based on 19,853 SNPs showed that the 14 alfalfa populations from long-term grazing sites had varying levels of parentages from alfalfa sub-species Medicago sativa and M. falcata. The linear regression of STRUCTURE membership probability on phenotypic data indicated genetic variations of forage dry matter yield, spring vigor and plant height were low, but genetic variations of regrowth, fall plant height, days to flower and crude protein were still high for the 14 alfalfa populations from long-term grazing sites. The GEA identified 31 SNPs associated with 13 candidate genes that were mainly associated with six environmental factors of. Candidate genes underlying environmental factors were associated with a variety of proteins, which were involved in plant responses to abiotic stresses, i.e., drought, cold and salinity-alkali stresses.
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Liu H, Wang Q, Xie L, Xu K, Zhang F, Ruan X, Li L, Tan G. Genome-wide identification of cystathionine beta synthase genes in wheat and its relationship with anther male sterility under heat stress. Front Plant Sci 2022; 13:1061472. [PMID: 36589045 PMCID: PMC9795209 DOI: 10.3389/fpls.2022.1061472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Cystathionine beta synthase (CBS) domains containing proteins (CDCPs) plays an important role in plant development through regulation of the thioredoxin system, as well as its ability to respond to biotic and abiotic stress conditions. Despite this, no systematic study has examined the wheat CBS gene family and its relation to high temperature-induced male sterility. In this study, 66 CBS family members were identified in the wheat genome, and their gene or protein sequences were used for subsequent analysis. The TaCBS gene family was found to be unevenly distributed on 21 chromosomes, and they were classified into four subgroups according to their gene structure and phylogeny. The results of collinearity analysis showed that there were 25 shared orthologous genes between wheat, rice and Brachypodium distachyon, and one shared orthologous gene between wheat, millet and barley. The cis-regulatory elements of the TaCBS were related to JA, IAA, MYB, etc. GO and KEGG pathway analysis identified these TaCBS genes to be associated with pollination, reproduction, and signaling and cellular processes, respectively. A heatmap of wheat plants based on transcriptome data showed that TaCBS genes were expressed to a higher extent in spikelets relative to other tissues. In addition, 29 putative tae-miRNAs were identified, targeting 41 TaCBS genes. Moreover, qRT-PCR validation of six TaCBS genes indicated their critical role in anther development, as five of them were expressed at lower levels in heat-stressed male sterile anthers than in Normal anthers. Together with anther phenotypes, paraffin sections, starch potassium iodide staining, and qRT-PCR data, we hypothesized that the TaCBS gene has a very important connection with the heat-stressed sterility process in wheat, and these data provide a basis for further insight into their relationship.
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Affiliation(s)
- Hongzhan Liu
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Qi Wang
- School of Network Engineering, Zhoukou Normal University, Zhoukou, Henan, China
| | - Liuyong Xie
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Kedong Xu
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Fuli Zhang
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Institute of Plant Protection and Edible Mushrooms, Zhoukou Academy of Agricultural Sciences, Zhoukou, Henan, China
| | - Xianle Ruan
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
| | - Lili Li
- College of Life Science and Agronomy, Zhoukou Normal University, Zhoukou, Henan, China
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
| | - Guangxuan Tan
- Key Laboratory of Plant Genetics and Molecular Breeding, Zhoukou Normal University, Zhoukou, Henan, China
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