1
|
Li Y, Zhang X, He K, Song X, Yu J, Guo Z, Xu M. Isolation and Identification of Bacillus subtilis LY-1 and Its Antifungal and Growth-Promoting Effects. Plants (Basel) 2023; 12:4158. [PMID: 38140485 PMCID: PMC10747398 DOI: 10.3390/plants12244158] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 11/29/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023]
Abstract
Peanut root rot, caused by Fusarium spp., is a devastating fungal disease. As part of a program to obtain a biocontrol agent to control peanut root rot in the field, a bacterial strain LY-1 capable of inhibiting the growth of the fungus in vitro was isolated from rhizosphere soil samples collected from wild mint by agar disk dilution and dual-culture assay. Strain LY-1 was identified as Bacillus subtilis based on morphological characteristics, 16S rDNA, and gyrA sequence analyses. The bacterial suspension and cell-free culture filtrate of LY-1 could significantly inhibit the growth of Fusarium oxysporum, Fusarium proliferatum and Fusarium solani, but volatile organic compounds from the cultures had only a weak effect on mycelial growth. The percentage inhibition of 20% concentration of the cell-free culture filtrate of LY-1 on conidium production of each of the three Fusarium species was greater than 72.38%, and the percentage inhibition by the culture filtration on the germination of conidia of the three species was at least 62.37%. The production of extracellular enzyme activity by LY-1 was studied in functional assays, showing protease, cellulase, amylase, chitinase, and β-1,3-glucanase activity, while LY-1 contained a gene encoding iturin, an antifungal lipopeptide. In addition, under pot culture in a greenhouse, culture filtrate of LY-1 significantly promoted the growth of peanut, increasing the fresh and dry mass of the plant by 30.77% and 27.27%, respectively, in comparison with the no-filtrate control. The culture filtrate of LY-1 increased the resistance of peanut plants to F. oxysporum, with the biocontrol efficiency reaching 44.71%. In conclusion, B. subtilis LY-1, a plant-growth-promoting rhizobacterium, was able to protect peanuts from Fusarium spp. infection.
Collapse
Affiliation(s)
- Ying Li
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Xia Zhang
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Kang He
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Xinying Song
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Jing Yu
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Zhiqing Guo
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| | - Manlin Xu
- Shandong Peanut Research Institute, Qingdao 266100, China; (Y.L.); (X.Z.); (K.H.); (X.S.); (J.Y.); (Z.G.)
- National Engineering Research Center for Peanut, Qingdao 266100, China
| |
Collapse
|
2
|
Wei R, Shang R, Cheng K, Wang S, Yuan X, Wu J, Yu Z. Phylogenetic analysis and molecular characterization of the co-infection of the new variant of the porcine epidemic diarrhea virus and the novel porcine kobuvirus isolated from piglets with diarrhea. Braz J Microbiol 2023; 54:2527-2534. [PMID: 37344656 PMCID: PMC10484880 DOI: 10.1007/s42770-023-01025-y] [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: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 06/23/2023] Open
Abstract
Porcine epidemic diarrhea virus (PEDV) is a virus that can cause diarrhea in pigs, resulting in significant economic losses to the pig industry. The mutation of the virus and its co-infection with other enteroviruses leads to poor control of PEDV infection. In this study, we found that the diarrhea outbreak in a pig farm in Shandong Province was mainly caused by PEDV infection. Through high-throughput sequencing, we also detected one other diarrhea-related virus (porcine kobuvirus). In the phylogenetic analysis and molecular characterization of the detected PEDV S gene and PKV, it was found that the S gene of the PEDV strain detected in this study (named SD22-2) had more mutations than the CV777 strain. The highest homology between PKV (named SD/2022/China) detected in this study and other strains was only 89.66%. Based on polyprotein, we divided SD/2022/China strains into a new grouping (designated group 4) and detected recombination signals. In summary, SD22-2 detected in this study is a new PEDV variant strain, and SD/2022/China strain might be a novel PKV strain. We also found the co-infection of the new PEDV variant and the novel PKV isolated from piglets with diarrhea. Our data suggested the importance of continuous surveillance of PEDV and PKV.
Collapse
Affiliation(s)
- Ran Wei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Rui Shang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Kaihui Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Song Wang
- Medical Integration and Practice Center, Shandong University, Jinan, 250012, China
| | - Xiaoyuan Yuan
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Jiaqiang Wu
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Zhijun Yu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| |
Collapse
|
3
|
Li G, Sun X, Zhu X, Wu B, Hong H, Xin Z, Xin X, Peng J, Jiang S. Selection and Validation of Reference Genes in Virus-Infected Sweet Potato Plants. Genes (Basel) 2023; 14:1477. [PMID: 37510381 PMCID: PMC10379385 DOI: 10.3390/genes14071477] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/13/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Quantitative real-time PCR (qRT-PCR) in sweet potatoes requires accurate data normalization; however, there are insufficient studies on appropriate reference genes for gene expression analysis. We examined variations in the expression of eight candidate reference genes in the leaf and root tissues of sweet potatoes (eight nonvirus-infected or eight virus-infected samples). Parallel analyses with geNorm, NormFinder, and Best-Keeper show that different viral infections and origin tissues affect the expression levels of these genes. Based on the results of the evaluation of the three software, the adenosine diphosphate-ribosylation factor is suitable for nonvirus or virus-infected sweet potato leaves. Cyclophilin and ubiquitin extension proteins are suitable for nonvirus-infected sweet potato leaves. Phospholipase D1 alpha is suitable for virus-infected sweet potato leaves. Actin is suitable for roots of nonvirus-infected sweet potatoes. Glyceraldehyde-3-phosphate dehydrogenase is suitable for virus-infected sweet potato roots. The research provides appropriate reference genes for further analysis in leaf and root samples of viruses in sweet potatoes.
Collapse
Affiliation(s)
- Guangyan Li
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaohui Sun
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiaoping Zhu
- Shandong Provincial Key Laboratory for Biology of Vegetable Diseases and Insect Pests, College of Plant Protection, Shandong Agricultural University, Taian 271018, China
| | - Bin Wu
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hao Hong
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhimei Xin
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Xiangqi Xin
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Jiejun Peng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| | - Shanshan Jiang
- Shandong Key Laboratory of Plant Virology, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, Jinan 250100, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agroproducts, Key Laboratory of Biotechnology in Plant Protection of MARA and Zhejiang Province, Institute of Plant Virology, Ningbo University, Ningbo 315211, China
| |
Collapse
|
4
|
Zhou Y, Zhao C, Du T, Li A, Qin Z, Zhang L, Dong S, Wang Q, Hou F. Overexpression of 9- cis-Epoxycarotenoid Dioxygenase Gene, IbNCED1, Negatively Regulates Plant Height in Transgenic Sweet Potato. Int J Mol Sci 2023; 24:10421. [PMID: 37445599 DOI: 10.3390/ijms241310421] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 06/08/2023] [Accepted: 06/16/2023] [Indexed: 07/15/2023] Open
Abstract
Plant height is one of the key agronomic traits for improving the yield of sweet potato. Phytohormones, especially gibberellins (GAs), are crucial to regulate plant height. The enzyme 9-cis-epoxycarotenoid dioxygenase (NCED) is the key enzyme for abscisic acid (ABA) biosynthesis signalling in higher plants. However, its role in regulating plant height has not been reported to date. Here, we cloned a new NCED gene, IbNCED1, from the sweet potato cultivar Jishu26. This gene encoded the 587-amino acid polypeptide containing an NCED superfamily domain. The expression level of IbNCED1 was highest in the stem and the old tissues in the in vitro-grown and field-grown Jishu26, respectively. The expression of IbNCED1 was induced by ABA and GA3. Overexpression of IbNCED1 promoted the accumulation of ABA and inhibited the content of active GA3 and plant height and affected the expression levels of genes involved in the GA metabolic pathway. Exogenous application of GA3 could rescue the dwarf phenotype. In conclusion, we suggest that IbNCED1 regulates plant height and development by controlling the ABA and GA signalling pathways in transgenic sweet potato.
Collapse
Affiliation(s)
- Yuanyuan Zhou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Chunling Zhao
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Taifeng Du
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Aixian Li
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Zhen Qin
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Liming Zhang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Shunxu Dong
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Qingmei Wang
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Fuyun Hou
- Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| |
Collapse
|
5
|
Wei R, Shang R, Cheng K, Wang S, Wu J, Yu Z. A novel recombinant porcine sapovirus infection in piglets with diarrhea in Shandong Province, China, 2022. Braz J Microbiol 2023; 54:1309-1314. [PMID: 37036658 PMCID: PMC10235293 DOI: 10.1007/s42770-023-00963-x] [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: 11/29/2022] [Accepted: 04/03/2023] [Indexed: 04/11/2023] Open
Abstract
Sapporo virus (SaV) is an emerging enteric virus causing acute gastroenteritis in animals. Here, we found a novel porcine SaV (PoSaV) strain (named SD2202) from the piglets with diarrhea in China in 2022. The highest nucleotide homology of SD2202 with other PoSaV strains is only 90.67%, and there are four amino acids insertion in the viral capsid protein and minor structural protein compared to other PoSaV; furthermore, we found that SD2202 belongs to a new GIII genogroup clade (GIII-6 clade). Interestingly, we found that SD2202 may be an intra-genogroup recombinant strain. Taken together, we found a novel PoSaV implicated in the piglet diarrhea epidemic and emphasized the importance of continuous surveillance of PoSaV.
Collapse
Affiliation(s)
- Ran Wei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Rui Shang
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Kaihui Cheng
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Song Wang
- Medical Integration and Practice Center, Shandong University, Jinan, 250012, China
| | - Jiaqiang Wu
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Zhijun Yu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
| |
Collapse
|
6
|
Zhao Q, Liu L, Huang T, Tian Y, Guo X, Liu C, Huang B, Chen Q. Complete genomic analysis of rabbit rotavirus G3P[22] in China. Arch Virol 2023; 168:129. [PMID: 37004683 DOI: 10.1007/s00705-023-05740-7] [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] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/20/2023] [Indexed: 04/04/2023]
Abstract
A rabbit rotavirus Z3171 isolate from diarrheic rabbits was identified and sequenced. The genotype constellation of Z3171 is G3-P[22]-I2-R3-C3-M3-A9-N2-T1-E3-H3, which is different from the constellation observed in previously characterized LRV strains. However, the genome of Z3171 differed substantially from those of the rabbit rotavirus strains N5 and Rab1404 in terms of both gene content and gene sequence. Our study suggests that either a reassortment event occurred between human and rabbit rotavirus strains or there are undetected genotypes circulating in the rabbit population. This is the first report of detection of a G3P[22] RVA strain in rabbits in China.
Collapse
Affiliation(s)
- Qiaoya Zhao
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, Jiangsu Province, China
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Liping Liu
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Tao Huang
- College of Veterinary Medicine, Southwest University, 402460, Chongqing, China
| | - Ye Tian
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Xiaozhen Guo
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Cunxia Liu
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China
| | - Bing Huang
- Institute of Poultry Sciences, Shandong Academy of Agricultural Sciences, 250023, Jinan, Shandong Province, China.
| | - Qiusheng Chen
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, 210095, Nanjing, Jiangsu Province, China.
| |
Collapse
|
7
|
Chen P, Li HQ, Li XY, Zhou XH, Zhang XX, Zhang AS, Liu QZ. Transcriptomic analysis provides insight into defensive strategies in response to continuous cropping in strawberry (Fragaria × ananassa Duch.) plants. BMC Plant Biol 2022; 22:476. [PMID: 36203126 PMCID: PMC9540695 DOI: 10.1186/s12870-022-03857-6] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Strawberries are an important economic fruit crop world-wide. In strawberry cultivation, continuous cropping (CC) can seriously threaten yield and quality. However, our understanding of the gene expression changes in response to CC and during subsequent defense processes is limited. In this study, we analyzed the impact of CC on the transcriptome of strawberry roots using RNA-Seq technology to elucidate the effect of CC and the subsequent molecular changes. RESULTS We found that CC significantly affects the growth of strawberry plants. The transcriptome analysis identified 136 differentially expressed genes (DEGs), including 49 up-regulated and 87 down-regulated DEGs. A Gene Ontology (GO) analysis indicated that the up-regulated DEGs were mainly assigned to defense-related GO terms, and most down-regulated DEGs were assigned to nutrient-related GO terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the responsive DEGs were classified in a large number of important biological pathways, such as phenylalanine metabolism, starch and sucrose metabolism, phenylpropanoid biosynthesis, glutathione metabolism and plant-pathogen interaction. We also found that four WRKY transcription factors and three peroxidase genes involved in plant defense pathways were up-regulated in the roots of strawberry plants subjected to CC. CONCLUSION Several unigenes involved in plant defense processes, such as CNGCs, WRKY transcription factors, PR1, and peroxidase genes with highly variable expression levels between non-CC and CC treatments may be involved in the regulation of CC in strawberry. These results indicate that strawberry roots reallocate development resources to defense mechanisms in response to CC. This study will further deepen our understanding of the fundamental regulatory mechanisms of strawberry resource reallocation in response to CC.
Collapse
Affiliation(s)
- Peng Chen
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
- Laboratory of Entomology and Nematology, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| | - He-qin Li
- Shandong Provincial Key Laboratory of Dryland Technology, College of Agronomy, Qingdao Agricultural University, 266109 Qingdao, China
| | - Xing-yue Li
- Institute of Plant Protection, Sichuan Academy of Agricultural Science, 610066 Chengdu, China
| | - Xian-hong Zhou
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
| | - Xiu-xia Zhang
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
| | - An-sheng Zhang
- Key Laboratory of Natural Enemies Insects, Ministry of Agriculture and Rural Affairs, Shandong Provincial Engineering Technology Research Center on Biocontrol of Crop Diseases and Insect Pest, Institute of Plant Protection, Shandong Academy of Agricultural Sciences, 250100 Jinan, China
| | - Qi-zhi Liu
- Laboratory of Entomology and Nematology, College of Plant Protection, China Agricultural University, 100193 Beijing, China
| |
Collapse
|
8
|
Zi Y, Cheng D, Li H, Guo J, Ju W, Wang C, Humphreys DG, Liu A, Cao X, Liu C, Liu J, Zhao Z, Song J. Effects of the different waxy proteins on starch biosynthesis, starch physicochemical properties and Chinese noodle quality in wheat. Mol Breed 2022; 42:23. [PMID: 37309456 PMCID: PMC10248619 DOI: 10.1007/s11032-022-01292-x] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
Abstract
Noodles are an important food in Asia. Wheat starch is the most important component in Chinese noodles. Loss of the waxy genes leads to lower activity of starch synthesis enzymes and decreased amylose content that further affects starch properties and noodle quality. To study the effects of different waxy (Wx) protein subunits on starch biosynthesis and processing quality, the high-yielding wheat cultivar Jimai 22 was treated with the mutagen ethyl methane sulfonate (EMS) to produce a population of Wx lines and chosen 7 Wx protein combinations. The amylose content increased but swelling power decreased as the number of Wx proteins increased. Both GBSS activity and gene expression were the lowest for the waxy mutant, followed by the mutants with 1 Wx protein. The combinations of these mutant alleles lead to reductions in both RNA expression and protein levels. Noodles made from materials with 2 Wx protein subunits had the highest score, which agreed with peak viscosity. The influence of the Wx-B1 protein on amylose synthesis and noodle quality was the highest, whereas the influence of Wx-A1 protein was the lowest. Mutants with lower amylose content caused by the absence of 1 subunit, especially the Wx-B1 subunit, had superior noodle quality. Additionally, the identified mutant lines can be used as intermediate materials to improve wheat quality. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01292-x.
Collapse
Affiliation(s)
- Yan Zi
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Dungong Cheng
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Haosheng Li
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jun Guo
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Wei Ju
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Canguo Wang
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - D. G. Humphreys
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, K.W. Neatby Building, 960 Carling Avenue, Ottawa, K1A 06C ON UK
| | - Aifeng Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Xinyou Cao
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Cheng Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jianjun Liu
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Zhendong Zhao
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| | - Jianmin Song
- National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100 Shandong China
| |
Collapse
|
9
|
Wang P, Shi S, Ma J, Song H, Zhang Y, Gao C, Zhao C, Zhao S, Hou L, Lopez-Baltazar J, Fan S, Xia H, Wang X. Global Methylome and gene expression analysis during early Peanut pod development. BMC Plant Biol 2018; 18:352. [PMID: 30545288 PMCID: PMC6293580 DOI: 10.1186/s12870-018-1546-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 11/20/2018] [Indexed: 05/21/2023]
Abstract
BACKGROUND Early peanut pod development is an important process of peanut reproductive development. Modes of DNA methylation during early peanut pod development are still unclear, possibly because its allotetraploid genome may cause difficulty for the methylome analysis. RESULTS To investigate the functions of the dynamic DNA methylation during the early development of the peanut pod, global methylome and gene expression analyses were carried out by Illumina high throughput sequencing. A novel mapping strategy of reads was developed and used for methylome and gene expression analysis. Differentially methylated genes, such as nodulin, cell number regulator-like protein, and senescence-associated genes, were identified during the early developmental stages of the peanut pod. The expression levels of gibberellin-related genes changed during this period of pod development. From the stage one (S1) gynophore to the stage two (S2) gynophore, the expression levels of two key methyltransferase genes, DRM2 and MET1, were up-regulated, which may lead to global DNA methylation changes between these two stages. The differentially methylated and expressed genes identified in the S1, S2, and stage 3 (S3) gynophore are involved in different biological processes such as stem cell fate determination, response to red, blue, and UV light, post-embryonic morphogenesis, and auxin biosynthesis. The expression levels of many genes were co-related by their DNA methylation levels. In addition, our results showed that the abundance of some 24-nucleotide siRNAs and miRNAs were positively associated with DNA methylation levels of their target loci in peanut pods. CONCLUSION A novel mapping strategy of reads was described and verified in this study. Our results suggest that the methylated modes of the S1, S2, and S3 gynophore are different. The methylation changes that were identified during early peanut pod development provide useful information for understanding the roles of epigenetic regulation in peanut pod development.
Collapse
Affiliation(s)
- Pengfei Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Shandong Academy of Grape, Jinan, 250100 People’s Republic of China
| | - Suhua Shi
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Junjie Ma
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
| | - Hui Song
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Ye Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chao Gao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | - Chuanzhi Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Shuzhen Zhao
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Lei Hou
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
| | | | - Shoujin Fan
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Han Xia
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
| | - Xingjun Wang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences; Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and Physiology, Jinan, 250100 People’s Republic of China
- Life Science College of Shandong Normal University, Jinan, 250014 People’s Republic of China
- Life Science College of Shandong University, Jinan, 250100 People’s Republic of China
| |
Collapse
|
10
|
Wang X, Xu P, Yin L, Ren Y, Li S, Shi Y, Alcock TD, Xiong Q, Qian W, Chi X, Pandey MK, Varshney RK, Yuan M. Genomic and Transcriptomic Analysis Identified Gene Clusters and Candidate Genes for Oil Content in Peanut (Arachis hypogaea L.). Plant Mol Biol Report 2018; 36:518-529. [PMID: 30100671 PMCID: PMC6061501 DOI: 10.1007/s11105-018-1088-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Peanut (Arachis hypogaea), a major source of vegetable oil in many Asian countries, has become an integral part of human diet globally due to its high nutritional properties and option to consume in different forms. In order to meet the demand of vegetable oil, many peanut breeding programs of China have intensified their efforts in increasing oil content in newly bred varieties for reducing the import of edible oils in China. In this context, transcriptome sequencing data generated on 49 peanut cultivars were analyzed to identify candidate genes and develop molecular markers for seed oil content across multiple environments. Transcriptome analysis identified 5458 differentially expressed genes (DEGs) including 2243 positive DEGs and 3215 negative DEGs involved in oil synthesis process. Genome-wide association study identified 48 significant insertion/deletion (InDel) markers associated with seed oil content across five environments. A comparative genomics and transcriptomics analysis detected a total of 147 common gene clusters located in 17 chromosomes. Interestingly, an InDel cluster associated with seed oil content on A03 chromosome was detected in three different environments. Candidate genes identified on A03 form a haplotype, in which variable alleles were found to be different in oil content in an independent population. This locus is important for understanding the genetic control of peanut oil content and may be useful for marker-assisted selection in peanut breeding programs.
Collapse
Affiliation(s)
- Xiaohua Wang
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Ping Xu
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Liang Yin
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yan Ren
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Shuangling Li
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Yanmao Shi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Thomas D. Alcock
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD UK
| | - Qing Xiong
- College of Computer and Information Science, Southwest University, Chongqing, 400715 China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400715 China
| | - Xiaoyuan Chi
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| | - Manish K. Pandey
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Rajeev K. Varshney
- International Crops Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Mei Yuan
- Key Laboratory for Peanut Biology, Genetics and Breeding, Ministry of Agriculture, Shandong Peanut Research Institute, Qingdao, 266100 China
| |
Collapse
|