1
|
Çolak NG, Eken NT, Ülger M, Frary A, Doğanlar S. Mapping of quantitative trait loci for the nutritional value of fresh market tomato. Funct Integr Genomics 2023; 23:121. [PMID: 37039853 DOI: 10.1007/s10142-023-01045-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 03/27/2023] [Accepted: 03/28/2023] [Indexed: 04/12/2023]
Abstract
The incidence of many diseases, such as cancer, cardiovascular diseases, and diabetes, is associated with malnutrition and an unbalanced daily diet. Vegetables are an important source of vitamins and essential compounds for human health. As a result, such metabolites have increasingly become the focus of breeding programs. Tomato is one of the most popular components of our daily diet. Therefore, the improvement of tomato's nutritional quality is an important goal. In the present study, we performed targeted metabolic profiling of an interspecific Solanum pimpinellifolium × S. lycopersicum inbred backcross line (IBL) population and identified quantitative trait loci responsible for the nutritional value of tomato. Transgressive segregation was apparent for many of the nutritional compounds such that some IBLs had extremely high levels of various amino acids and vitamins compared to their parents. A total of 117 QTLs for nutritional traits including 62 QTLs for amino acids, 18 QTLs for fatty acids, 12 QTLs for water-soluble vitamins, and 25 QTLs for fat-soluble vitamins were identified. Moreover, almost 24% of identified QTLs were confirmed in previous studies, and 40 possible gene candidates were found for 18 identified QTLs. These findings can help breeders to improve the nutritional value of tomato.
Collapse
Affiliation(s)
- Nergiz Gürbüz Çolak
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir, 35430, Turkey
- Plant Science and Technology Application and Research Center, Izmir Institute of Technology, İzmir, 35430, Turkey
| | - Neslihan Tek Eken
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir, 35430, Turkey
| | - Mehmet Ülger
- MULTI Tarım Seed Company, Antalya, 07112, Turkey
| | - Anne Frary
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir, 35430, Turkey
| | - Sami Doğanlar
- Department of Molecular Biology and Genetics, Faculty of Science, Izmir Institute of Technology, İzmir, 35430, Turkey.
- Plant Science and Technology Application and Research Center, Izmir Institute of Technology, İzmir, 35430, Turkey.
| |
Collapse
|
2
|
Qu W, Song X, Li G, Hou J, Han Y, Ye P, Zhang HE, Chen C, Chen Y, Wang E. Profiling and discovery of volatile marker compounds for Ginseng berries with different growth years by HS-SPME-GC-MS. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2022. [DOI: 10.1016/j.cjac.2022.100208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
|
3
|
Li D, Dierschke T, Roden S, Chen K, Bowman JL, Chang C, Van de Poel B. A transporter of 1-aminocyclopropane-1-carboxylic acid affects thallus growth and fertility in Marchantia polymorpha. THE NEW PHYTOLOGIST 2022; 236:2103-2114. [PMID: 36151927 DOI: 10.1111/nph.18510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Accepted: 09/01/2022] [Indexed: 06/16/2023]
Abstract
In seed plants, 1-aminocyclopropane-1-carboxylic acid (ACC) is the precursor of the plant hormone ethylene but also has ethylene-independent signaling roles. Nonseed plants produce ACC but do not efficiently convert it to ethylene. In Arabidopsis thaliana, ACC is transported by amino acid transporters, LYSINE HISTIDINE TRANSPORTER 1 (LHT1) and LHT2. In nonseed plants, LHT homologs have been uncharacterized. Here, we isolated an ACC-insensitive mutant (Mpain) that is defective in ACC uptake in the liverwort Marchantia polymorpha. Mpain contained a frameshift mutation (1 bp deletion) in the MpLHT1 coding sequence, and was complemented by expression of a wild-type MpLHT1 transgene. Additionally, ACC insensitivity was re-created in CRISPR/Cas9-Mplht1 knockout mutants. We found that MpLHT1 can also transport l-hydroxyproline and l-histidine. We examined the physiological functions of MpLHT1 in vegetative growth and reproduction based on mutant phenotypes. Mpain and Mplht1 plants were smaller and developed fewer gemmae cups compared to wild-type plants. Mplht1 mutants also had reduced fertility, and archegoniophores displayed early senescence. These findings reveal that MpLHT1 serves as an ACC and amino acid transporter in M. polymorpha and has diverse physiological functions. We propose that MpLHT1 contributes to homeostasis of ACC and other amino acids in M. polymorpha growth and reproduction.
Collapse
Affiliation(s)
- Dongdong Li
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, 3001, Leuven, Belgium
- Department of Cell Biology and Molecular Genetics, University of Maryland, Bioscience Research Building, College Park, MD, 20742, USA
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, 310058, Hangzhou, China
| | - Tom Dierschke
- School of Biological Sciences, Monash University, 3800, Melbourne, Vic., Australia
| | - Stijn Roden
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, 3001, Leuven, Belgium
| | - Kunsong Chen
- College of Agriculture and Biotechnology, Zhejiang University, Zijingang Campus, 310058, Hangzhou, China
| | - John L Bowman
- School of Biological Sciences, Monash University, 3800, Melbourne, Vic., Australia
| | - Caren Chang
- Department of Cell Biology and Molecular Genetics, University of Maryland, Bioscience Research Building, College Park, MD, 20742, USA
| | - Bram Van de Poel
- Division of Crop Biotechnics, Department of Biosystems, University of Leuven, 3001, Leuven, Belgium
- KU Leuven Plant Institute (LPI), University of Leuven, 3001, Leuven, Belgium
| |
Collapse
|
4
|
Feng ZQ, Wang X, Li T, Wang XF, Li HF, You CX. Genome-wide identification and comparative analysis of genes encoding AAPs in apple (Malus × domestica Borkh.). Gene X 2022; 832:146558. [PMID: 35569773 DOI: 10.1016/j.gene.2022.146558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/10/2022] [Accepted: 05/06/2022] [Indexed: 11/27/2022] Open
Abstract
Amino acid permeases (AAPs) play important roles in plant amino acid transport and nitrogen metabolism. In this study, we carried a comprehensive analysis for apple genes encoding AAPs using bioinformatics and molecular biology. Eleven MdAAPs were identified by a genome-wide search and comparative genomic analysis revealed relatively conserved gene composition, transmembrane characteristics, and protein structures. Phylogenetic tree construction and analysis of the conserved motifs of MdAAPs and AtAAPs showed that AAPs can be classified into three groups (I, II, and III). We compared the promoters of the identified genes and did gene functional annotation and qRT-PCR and found a relationship between apple AAPs and nitrogen deficiency. The expression profile data implied that MdAAPs exhibit diversified distributions and functions in different tissues.
Collapse
Affiliation(s)
- Zi-Quan Feng
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xun Wang
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Tong Li
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an 271018, Shandong, China
| | - Hui-Feng Li
- Shandong Institue of Pomology, Taian, Shandong 271018, China
| | - Chun-Xiang You
- State Key Laboratory of Crop Biology, National Research Center for Apple Engineering and Technology, Collaborative Innovation Center of Fruit & Vegetable Quality and Efficient Production, Shandong Agricultural University, Tai'an 271018, Shandong, China.
| |
Collapse
|
5
|
Genome-Wide Identification and Functional Analysis of Lysine Histidine Transporter (LHT) Gene Families in Maize. Genet Res (Camb) 2022; 2022:2673748. [PMID: 35528221 PMCID: PMC9064515 DOI: 10.1155/2022/2673748] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 11/18/2022] Open
Abstract
Amino acid transporters (AATs) are essential membrane proteins that transfer amino acids across cells. They are necessary for plant growth and development. The lysine histidine transporter (LHT) gene family in maize (Zea mays) has not yet been characterized. According to sequence composition and phylogenetic placement, this study found 15 LHT genes in the maize genome. The ZmLHT genes are scattered across the plasma membrane. The study also analyzed the evolutionary relationships, gene structures, conserved motifs, 3D protein structure, a transmembrane domain, and gene expression of the 15 LHT genes in maize. Comprehensive analyses of ZmLHT gene expression profiles revealed distinct expression patterns in maize LHT genes in various tissues. This study's extensive data will serve as a foundation for future ZmLHT gene family research. This study might make easier to understand how LHT genes work in maize and other crops.
Collapse
|
6
|
Liber M, Duarte I, Maia AT, Oliveira HR. The History of Lentil ( Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions. FRONTIERS IN PLANT SCIENCE 2021; 12:628439. [PMID: 33841458 PMCID: PMC8030269 DOI: 10.3389/fpls.2021.628439] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/15/2021] [Indexed: 05/06/2023]
Abstract
Protein-rich legumes accompanied carbohydrate-rich cereals since the beginning of agriculture and yet their domestication history is not as well understood. Lentil (Lens culinaris Medik. subsp. culinaris) was first cultivated in Southwest Asia (SWA) 8000-10,000 years ago but archeological evidence is unclear as to how many times it may have been independently domesticated, in which SWA region(s) this may have happened, and whether wild species within the Lens genus have contributed to the cultivated gene pool. In this study, we combined genotyping-by-sequencing (GBS) of 190 accessions from wild (67) and domesticated (123) lentils from the Old World with archeological information to explore the evolutionary history, domestication, and diffusion of lentils to different environments. GBS led to the discovery of 87,647 single-nucleotide polymorphisms (SNPs), which allowed us to infer the phylogeny of genus Lens. We confirmed previous studies proposing four groups within it. The only gene flow detected was between cultivated varieties and their progenitor (L. culinaris subsp. orientalis) albeit at very low levels. Nevertheless, a few putative hybrids or naturalized cultivars were identified. Within cultivated lentil, we found three geographic groups. Phylogenetics, population structure, and archeological data coincide in a scenario of protracted domestication of lentils, with two domesticated gene pools emerging in SWA. Admixed varieties are found throughout their range, suggesting a relaxed selection process. A small number of alleles involved in domestication and adaptation to climatic variables were identified. Both novel mutation and selection on standing variation are presumed to have played a role in adaptation of lentils to different environments. The results presented have implications for understanding the process of plant domestication (past), the distribution of genetic diversity in germplasm collections (present), and targeting genes in breeding programs (future).
Collapse
Affiliation(s)
- Marta Liber
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
- Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
| | - Isabel Duarte
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, Portugal
| | - Ana Teresa Maia
- Department of Biomedical Sciences and Medicine (DCBM), Universidade do Algarve, Faro, Portugal
- Centre for Biomedical Research (CBMR), Universidade do Algarve, Faro, Portugal
- Algarve Biomedical Center (ABC), Universidade do Algarve, Faro, Portugal
| | - Hugo R. Oliveira
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior (ICArEHB), Universidade do Algarve, Faro, Portugal
- *Correspondence: Hugo R. Oliveira,
| |
Collapse
|
7
|
Li W, Chen Y, Ye M, Wang D, Chen Q. Evolutionary history of the heat shock protein 90 (Hsp90) family of 43 plants and characterization of Hsp90s in Solanum tuberosum. Mol Biol Rep 2020; 47:6679-6691. [PMID: 32780253 DOI: 10.1007/s11033-020-05722-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/02/2020] [Indexed: 01/12/2023]
Abstract
Heat shock protein 90 genes/proteins (Hsp90s) are related to the stress resistance found in various plant species. These proteins affect the growth and development of plants and have important effects on the plants under various stresses (cold, drought and salt) in the environment. In this study, we identified 334 Hsp90s from 43 plant species, and Hsp90s were found in all species. Phylogenetic tree and conserved domain database analysis of all Hsp90s showed three independent clades. The analysis of motifs, gene duplication events, and the expression data from PGSC website revealed the gene structures, evolution relationships, and expression patterns of the Hsp90s. In addition, analysis of the transcript levels of the 7 Hsp90s in potato (Solanum tuberosum) under low temperature and high temperature stresses showed that these genes were related to the temperature stresses. Especially StHsp90.2 and StHsp90.4, under high or low temperature conditions, the expression levels in leaves, stems, or roots were significantly up-regulated. Our findings revealed the evolution of the Hsp90s, which had guiding significance for further researching the precise functions of the Hsp90s.
Collapse
Affiliation(s)
- Wan Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Yue Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Minghui Ye
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Dongdong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
| | - Qin Chen
- College of Food Science and Engineering, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
| |
Collapse
|