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Fan H, Xu J, Ao D, Jia T, Shi Y, Li N, Jing R, Sun D. QTL Mapping of Trichome Traits and Analysis of Candidate Genes in Leaves of Wheat ( Triticum aestivum L.). Genes (Basel) 2023; 15:42. [PMID: 38254932 PMCID: PMC10815787 DOI: 10.3390/genes15010042] [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: 12/01/2023] [Revised: 12/22/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Trichome plays an important role in heat dissipation, cold resistance, water absorption, protection of leaves from mechanical damage, and direct exposure to ultraviolet rays. It also plays an important role in the photosynthesis, transpiration, and respiration of plants. However, the genetic basis of trichome traits is not fully understood in wheat. In this study, wheat DH population (Hanxuan 10 × Lumai 14) was used to map quantitative trait loci (QTL) for trichome traits in different parts of flag leaf at 10 days after anther with growing in Zhao County, Hebei Province, and Taigu County, Shanxi Province, respectively. The results showed that trichome density (TD) was leaf center > leaf tip > leaf base and near vein > middle > edge, respectively, in both environments. The trichome length (TL) was leaf tip > leaf center > leaf base and edge > middle > near vein. Significant phenotypic positive correlations were observed between the trichome-related traits of different parts. A total of 83 QTLs for trichome-related traits were mapped onto 18 chromosomes, and each one accounted for 2.41 to 27.99% of the phenotypic variations. Two QTL hotspots were detected in two marker intervals: AX-95232910~AX-95658735 on 3A and AX-94850949~AX-109507404 on 7D. Six possible candidate genes (TraesCS3A02G406000, TraesCS3A02G414900, TraesCS3A02G440900, TraesCS7D02G145200, TraesCS7D02G149200, and TraesCS7D02G152400) for trichome-related traits of wheat leaves were screened out according to their predicted expression levels in wheat leaves. The expression of these genes may be induced by a variety of abiotic stresses. The results provide the basis for further validation and functional characterization of the candidate genes.
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Affiliation(s)
- Hua Fan
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (H.F.); (J.X.); (D.A.); (T.J.); (Y.S.); (N.L.)
- Experimental Teaching Center, Shanxi Agricultural University, Taigu, Jinzhong 030800, China
| | - Jianchao Xu
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (H.F.); (J.X.); (D.A.); (T.J.); (Y.S.); (N.L.)
| | - Dan Ao
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (H.F.); (J.X.); (D.A.); (T.J.); (Y.S.); (N.L.)
| | - Tianxiang Jia
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (H.F.); (J.X.); (D.A.); (T.J.); (Y.S.); (N.L.)
| | - Yugang Shi
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (H.F.); (J.X.); (D.A.); (T.J.); (Y.S.); (N.L.)
| | - Ning Li
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (H.F.); (J.X.); (D.A.); (T.J.); (Y.S.); (N.L.)
| | - Ruilian Jing
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100000, China;
| | - Daizhen Sun
- College of Agronomy, Shanxi Agricultural University, Taigu, Jinzhong 030800, China; (H.F.); (J.X.); (D.A.); (T.J.); (Y.S.); (N.L.)
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Yang J, Song J, Shilpha J, Jeong BR. Top and Side Lighting Induce Morphophysiological Improvements in Korean Ginseng Sprouts ( Panax ginseng C.A. Meyer) Grown from One-Year-Old Roots. PLANTS (BASEL, SWITZERLAND) 2023; 12:2849. [PMID: 37571002 PMCID: PMC10421474 DOI: 10.3390/plants12152849] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/29/2023] [Accepted: 07/31/2023] [Indexed: 08/13/2023]
Abstract
Nowadays, not only the roots, but also leaves and flowers of ginseng are increasingly popular ingredients in supplements for healthcare products and traditional medicine. The cultivation of the shade-loving crop, ginseng, is very demanding in terms of the light environment. Along with the intensity and duration, light direction is another important factor in regulating plant morphophysiology. In the current study, three lighting directions-top (T), side (S), or top + side (TS)-with an intensity of 30 ± 5 μmol·m-2·s-1 photosynthetic photon flux density (PPFD) were employed. Generally, compared with the single T lighting, the composite lighting direction, TS, was more effective in shaping the ginseng with improved characteristics, including shortened, thick shoots; enlarged, thick leaves; more leaf trichomes; earlier flower bud formation; and enhanced photosynthesis. The single S light resulted in the worst growth parameters and strongly inhibited the flower bud formation, leading to the latest flower bud observation. Additionally, the S lighting acted as a positive factor in increasing the leaf thickness and number of trichomes on the leaf adaxial surface. However, the participation of the T lighting weakened these traits. Overall, the TS lighting was the optimal direction for improving the growth and development traits in ginseng. This preliminary research may provide new ideas and orientations in ginseng cultivation lodging resistance and improving the supply of ginseng roots, leaves, and flowers to the market.
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Affiliation(s)
- Jingli Yang
- Shandong Facility Horticulture Bioengineering Research Center, Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang 262700, China; (J.Y.); (J.S.)
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jinnan Song
- Shandong Facility Horticulture Bioengineering Research Center, Jia Sixie College of Agriculture, Weifang University of Science and Technology, Shouguang 262700, China; (J.Y.); (J.S.)
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jayabalan Shilpha
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea;
| | - Byoung Ryong Jeong
- Department of Horticulture, Division of Applied Life Science (BK21 Four), Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
- Institute of Agriculture and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea;
- Research Institute of Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea
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Zheng H, Yu MY, Han Y, Tai B, Ni SF, Ji RF, Pu CJ, Chen K, Li FQ, Xiao H, Shen Y, Zhou XT, Huang LQ. Comparative Transcriptomics and Metabolites Analysis of Two Closely Related Euphorbia Species Reveal Environmental Adaptation Mechanism and Active Ingredients Difference. FRONTIERS IN PLANT SCIENCE 2022; 13:905275. [PMID: 35712557 PMCID: PMC9194899 DOI: 10.3389/fpls.2022.905275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 05/02/2022] [Indexed: 06/15/2023]
Abstract
Roots of Euphorbia fischeriana and Euphorbia ebracteolata are recorded as the source plant of traditional Chinese medicine "Langdu," containing active ingredients with anticancer and anti-AIDS activity. However, the two species have specific patterns in the graphic distribution. Compared with E. ehracteolata, E. fischeriana distributes in higher latitude and lower temperature areas and might have experienced cold stress adaptation. To reveal the molecular mechanism of environmental adaptation, RNA-seq was performed toward the roots, stems, and leaves of E. fischeriana and E. ehracteolata. A total of 6,830 pairs of putative orthologs between the two species were identified. Estimations of non-synonymous or synonymous substitution rate ratios for these orthologs indicated that 533 of the pairs may be under positive selection (Ka/Ks > 0.5). Functional enrichment analysis revealed that significant proportions of the orthologs were in the TCA cycle, fructose and mannose metabolism, starch and sucrose metabolism, fatty acid biosynthesis, and terpenoid biosynthesis providing insights into how the two closely related Euphorbia species adapted differentially to extreme environments. Consistent with the transcriptome, a higher content of soluble sugars and proline was obtained in E. fischeriana, reflecting the adaptation of plants to different environments. Additionally, 5 primary or secondary metabolites were screened as the biomarkers to distinguish the two species. Determination of 4 diterpenoids was established and performed, showing jolkinolide B as a representative component in E. fischeriana, whereas ingenol endemic to E. ebracteolate. To better study population genetics, EST-SSR markers were generated and tested in 9 species of Euphorbia. A total of 33 of the 68 pairs were screened out for producing clear fragments in at least four species, which will furthermore facilitate the studies on the genetic improvement and phylogenetics of this rapidly adapting taxon. In this study, transcriptome and metabolome analyses revealed the evolution of genes related to cold stress tolerance, biosynthesis of TCA cycle, soluble sugars, fatty acids, and amino acids, consistent with the molecular strategy that genotypes adapting to environment. The key active ingredients of the two species were quantitatively analyzed to reveal the difference in pharmacodynamic substance basis and molecular mechanism, providing insights into rational crude drug use.
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Affiliation(s)
- Han Zheng
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Mu-Yao Yu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Yang Han
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Badalahu Tai
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
- Mongolian Medicine College, Inner Mongolia Minzu University, Tongliao, China
| | - Sheng-Fa Ni
- Anhui University of Science and Technology, Huainan Xinhua Hospital, Huainan, China
| | - Rui-Feng Ji
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chun-Juan Pu
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Kang Chen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Fu-Quan Li
- Hulunbeier Mongolian Medical Hospital, Hulunbeier, China
| | - Hua Xiao
- Hulunbeier Mongolian Medical Hospital, Hulunbeier, China
| | - Ye Shen
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Xiu-Teng Zhou
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Lu-Qi Huang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
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Kosakovsky Pond SL, Wisotsky SR, Escalante A, Magalis BR, Weaver S. Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches. Mol Biol Evol 2021; 38:1184-1198. [PMID: 33064823 PMCID: PMC7947784 DOI: 10.1093/molbev/msaa263] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.
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Affiliation(s)
| | - Sadie R Wisotsky
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Ananias Escalante
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
| | - Brittany Rife Magalis
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.,Emerging Pathogens Institute, University of Florida, Gainesville, FL
| | - Steven Weaver
- Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA
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Shu G, Cao G, Li N, Wang A, Wei F, Li T, Yi L, Xu Y, Wang Y. Genetic variation and population structure in China summer maize germplasm. Sci Rep 2021; 11:8012. [PMID: 33850169 PMCID: PMC8044188 DOI: 10.1038/s41598-021-84732-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 02/17/2021] [Indexed: 02/01/2023] Open
Abstract
Maize (Zea mays L.) germplasm in China Summer maize ecological region (CSM) or central corn-belt of China is diverse but has not been systematically characterized at molecular level. In this study, genetic variation, genome diversity, linkage disequilibrium patterns, population structure, and characteristics of different heterotic groups were studied using 525,141 SNPs obtained by Genotyping-By-Sequencing (GBS) for 490 inbred lines collected from researchers at CSM region. The SNP density is lower near centromere, but higher near telomere region of maize chromosome, the degree of linkage disequilibrium (r2) vary at different chromosome regions. Majority of the inbred lines (66.05%) show pairwise relative kinship near zero, indicating a large genetic diversity in the CSM breeding germplasm. Using 4849 tagSNPs derived from 3618 haplotype blocks, the 490 inbred lines were delineated into 3 supergroups, 6 groups, and 10 subgroups using ADMIXTURE software. A procedure of assigning inbred lines into heterotic groups using genomic data and tag-SNPs was developed and validated. Genome differentiation among different subgroups measured by Fst, and the genetic diversity within each subgroup measured by GD are both large. The share of heterotic groups that have significant North American germplasm contribution: P, SS, IDT, and X, accounts about 54% of the CSM breeding germplasm collection and has increased significantly in the last two decades. Two predominant types of heterotic pattern in CSM region are: M-Reid group × TSPT group, and X subgroup × Local subgroups.
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Affiliation(s)
- Guoping Shu
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001 China
| | - Gangqiang Cao
- grid.207374.50000 0001 2189 3846School of Agricultural Science, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001 China
| | - Niannian Li
- grid.207374.50000 0001 2189 3846School of Agricultural Science, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001 China
| | - Aifang Wang
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001 Henan China
| | - Fang Wei
- grid.207374.50000 0001 2189 3846School of Agricultural Science, Zhengzhou University, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001 China
| | - Ting Li
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001 Henan China
| | - Li Yi
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001 Henan China
| | - Yunbi Xu
- grid.410727.70000 0001 0526 1937Institute of Crop Science, National Key Facility of Crop Gene Resources and Genetic Improvement,Chinese Academy of Agricultural Science, Beijing, 100081 China
| | - Yibo Wang
- Center of Biotechnology, Beijing Lantron Seed, Zhengzhou, 450001 Henan China ,grid.207374.50000 0001 2189 3846Zhengzhou University Graduate Student Training Base at Beijing Lantron Seed, Zhengzhou, 450001 China ,Henan LongPing-Lantron AgriScience & Technology Co., LTD, Zhengzhou, 450001 Henan China
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Wang X, Shen C, Meng P, Tan G, Lv L. Analysis and review of trichomes in plants. BMC PLANT BIOLOGY 2021; 21:70. [PMID: 33526015 PMCID: PMC7852143 DOI: 10.1186/s12870-021-02840-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 01/11/2021] [Indexed: 05/03/2023]
Abstract
BACKGROUND Trichomes play a key role in the development of plants and exist in a wide variety of species. RESULTS In this paper, it was reviewed that the structure and morphology characteristics of trichomes, alongside the biological functions and classical regulatory mechanisms of trichome development in plants. The environment factors, hormones, transcription factor, non-coding RNA, etc., play important roles in regulating the initialization, branching, growth, and development of trichomes. In addition, it was further investigated the atypical regulation mechanism in a non-model plant, found that regulating the growth and development of tea (Camellia sinensis) trichome is mainly affected by hormones and the novel regulation factors. CONCLUSIONS This review further displayed the complex and differential regulatory networks in trichome initiation and development, provided a reference for basic and applied research on trichomes in plants.
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Affiliation(s)
- Xiaojing Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Chao Shen
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China
| | - Pinghong Meng
- Institute of Horticulture, Guizhou Province Academy of Agricultural Sciences, Guiyang, Guizhou, People's Republic of China
| | - Guofei Tan
- Institute of Horticulture, Guizhou Province Academy of Agricultural Sciences, Guiyang, Guizhou, People's Republic of China.
| | - Litang Lv
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guiyang, Guizhou, People's Republic of China.
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Li J, Kim T, Szymanski DB. Multi-scale regulation of cell branching: Modeling morphogenesis. Dev Biol 2018; 451:40-52. [PMID: 30529250 DOI: 10.1016/j.ydbio.2018.12.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 11/29/2018] [Accepted: 12/03/2018] [Indexed: 01/05/2023]
Abstract
Plant growth and development are driven by extended phases of irreversible cell expansion generating cells that increase in volume from 10- to 100-fold. Some specialized cell types define cortical sites that reinitiate polarized growth and generate branched cell morphology. This structural specialization of individual cells has a major importance for plant adaptation to diverse environments and practical importance in agricultural contexts. The patterns of cell shape are defined by highly integrated cytoskeletal and cell wall systems. Microtubules and actin filaments locally define the material properties of a tough outer cell wall to generate complex shapes. Forward genetics, powerful live cell imaging experiments, and computational modeling have provided insights into understanding of mechanisms of cell shape control. In particular, finite element modeling of the cell wall provides a new way to discover which cell wall heterogeneities generate complex cell shapes, and how cell shape and cell wall stress can feedback on the cytoskeleton to maintain growth patterns. This review focuses on cytoskeleton-dependent cell wall patterning during cell branching, and how combinations of multi-scale imaging experiments and computational modeling are being used to unravel systems-level control of morphogenesis.
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Affiliation(s)
- Jing Li
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Taeyoon Kim
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, United States
| | - Daniel B Szymanski
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, United States; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, United States; Department of Agronomy, Purdue University, West Lafayette, IN 47907, United States.
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