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Huang D, Niu S, Bai D, Zhao Z, Li C, Deng X, Wang Y. Analysis of population structure and genetic diversity of Camellia tachangensis in Guizhou based on SNP markers. Mol Biol Rep 2024; 51:715. [PMID: 38824248 PMCID: PMC11144125 DOI: 10.1007/s11033-024-09632-0] [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: 12/04/2023] [Accepted: 05/10/2024] [Indexed: 06/03/2024]
Abstract
BACKGROUND Camellia tachangensis F. C. Zhang is a five-compartment species in the ovary of tea group plants, which represents the original germline of early differentiation of some tea group plants. METHODS AND RESULTS In this study, we analyzed single-nucleotide polymorphisms (SNPs) at the genome level, constructed a phylogenetic tree, analyzed the genetic diversity, and further investigated the population structure of 100 C. tachangensis accessions using the genotyping-by-sequencing (GBS) method. A total of 91,959 high-quality SNPs were obtained. Population structure analysis showed that the 100 C. tachangensis accessions clustered into three groups: YQ-1 (Village Group), YQ-2 (Forest Group) and YQ-3 (Transition Group), which was further consistent with the results of phylogenetic analysis and principal component analyses (PCA). In addition, a comparative analysis of the genetic diversity among the three populations (Forest, Village, and Transition Groups) detected the highest genetic diversity in the Transition Group and the highest differentiation between Forest and Village Groups. CONCLUSIONS C. tachangensis plants growing in the forest had different genetic backgrounds from those growing in villages. This study provides a basis for the effective protection and utilization of C. tachangensis populations and lays a foundation for future C. tachangensis breeding.
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Grants
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (2021YFD1200203-1) Project of the National key R & D plan
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (32060700) Projectofthe National Science Foundation, in PR China·
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (2023009) the National Guidance Foundation for Local Science and Technology Development of China
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (Construction Technology Contract [2023] ·48-21) Guiyang Science and Technology Plan Project
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- (KY [20211·042) Project of the key filed project of Natural Science Foundation of Guizhou Provincial Department of education
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- ([2021] General 126) Science and Technology Plan Project of Guizhou province, in PR China
- Project of the National key R & D plan
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Affiliation(s)
- Dejun Huang
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Suzhen Niu
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China.
- Institute of Agro-Bioengineering, Guizhou university, Xueshi Road, Guiyang, Guizhou, China.
| | - Dingchen Bai
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Zhifei Zhao
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Caiyun Li
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Xiuling Deng
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
| | - Yihan Wang
- Institute of Tea, Guizhou university, Jiaxiu South Road, Guiyang, Guizhou, China
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Dong X, Shi L, Bao S, Fu H, You Y, Ren Y, Wang J, Li Q, Chen Z. Leaf traits of prickly ash and its correlation with ecological and geographical factors of origin. Sci Rep 2024; 14:6276. [PMID: 38491102 PMCID: PMC10943195 DOI: 10.1038/s41598-024-56962-x] [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: 01/26/2024] [Accepted: 03/13/2024] [Indexed: 03/18/2024] Open
Abstract
The morphological, physiological, and biochemical characteristics of leaves result from the long-term adaptation of plants to their environment and are closely related to plant growth and development. In this study, 37 prickly ash germplasm resources from 18 production areas were utilized as the subjects of research. Logistic equations, principal component analysis, and cluster analysis were employed to comprehensively evaluate the leaf traits of prickly ash germplasm resources, with an analysis of their correlation with ecological and geographical factors in the production areas. The results showed that the leaf traits of prickly ash germplasms of different origins are substantially different and diverse. The coefficient of variation for the 14 leaf traits was greater than 10%. The coefficient of variation of the compound leaflet number was the highest among all the considered leaf traits, and the coefficient of variation of leaf thickness was the lowest, at 49.86% and 11.37%, respectively. The leaf traits of the prickly ash germplasm originating from Chongqing in Yongchuan, Chongqing in Rongchang, and Yunnan in Honghe ranked highest, whereas the leaf traits of the prickly ash germplasm from Henan in Jiaozuo, Gansu in Tianshui, and Shanxi in Yuncheng ranked lowest. The results of the correlation analysis showed that among the ecological and geographical factors of the origins, latitude had the strongest correlation with the leaf traits of the prickly ash germplasm. As latitude increased, the leaves of prickly ash gradually decreased in size, weight, and leaf shape index. The factor with the second strongest correlation was temperature. The leaves of the prickly ash germplasm originating from warmer climate areas were larger and heavier than those from areas with colder climates. Altitude and longitude did not significantly affect the leaf traits of the prickly ash germplasm, but at similar latitudes, the leaves of the prickly ash germplasm in high-altitude areas were smaller, and the leaves of the prickly ash germplasm in low-altitude areas were larger. These findings can provide valuable references for breeding and the sustainable utilization of new varieties of prickly ash resources.
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Affiliation(s)
- Xixi Dong
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Lin Shi
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Shuqin Bao
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Hao Fu
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
- Geological Team 607, Chongqing Geological and Mineral Exploration and Development Bureau, Chongqing, 401300, China
| | - Yuming You
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Yun Ren
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Jichun Wang
- College of Agronomy and Biotechnology, Southwest University, Beibei, Chongqing, 400715, China
| | - Qiang Li
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
| | - Zexiong Chen
- Chongqing Key Laboratory for Germplasm Innovation for Special Aromatic Spice Plants, Institute of Special Plants, College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.
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Wang Y, Zhang X, Yang J, Chen B, Zhang J, Li W, Du H, Geng S. Optimized Pepper Target SNP-Seq Applied in Population Structure and Genetic Diversity Analysis of 496 Pepper ( Capsicum spp.) Lines. Genes (Basel) 2024; 15:214. [PMID: 38397204 PMCID: PMC10887817 DOI: 10.3390/genes15020214] [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: 01/04/2024] [Revised: 01/26/2024] [Accepted: 02/02/2024] [Indexed: 02/25/2024] Open
Abstract
Peppers are a major vegetable crop worldwide. With the completion of additional genome assemblies, a multitude of single-nucleotide polymorphisms (SNPs) can be utilized for population structure and genetic diversity analysis. In this study, we used target SNP-sequencing as a new high-throughput sequencing technology, screening out 425 perfect SNPs for analyzing the genetic diversity and population structure among 496 pepper lines from five pepper species in China and abroad. The perfect SNP panel exhibited commendable discriminative ability, as indicated by the average values of polymorphism information content, observed heterozygosity, minor allele frequency, and genetic diversity, which were 0.346, 0.011, 0.371, and 0.449, respectively. Based on phylogenetic, population structure, and principal component analyses, 484 C. annuum lines were divided into four subpopulations according to the shape of fruit: blocky fruit, wide-horn fruit, narrow-horn fruit, and linear fruit. These subpopulations displayed clear clustering with minimal or no overlap. Moreover, F statistic (Fst) analysis revealed considerable distinctions among these subpopulations. Additionally, we established a set of 47 core SNPs that could effectively differentiate among all pepper lines. This core SNP set could precisely classify the C. annuum lines into four distinct fruit-shape groups. The blocky and narrow-horn fruit subpopulations displayed the lowest and highest genetic diversity, respectively. This study highlights the importance of fruit shape as a crucial trait in pepper breeding. Moreover, this work indicates the immense potential of optimized target SNP technology in the addition of foreground markers of important traits to improve molecular breeding efficiency, and demonstrates its broad application prospects in the genetic analysis and variety identification of peppers.
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Affiliation(s)
- Yihao Wang
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (Y.W.); (B.C.)
| | - Xiaofen Zhang
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (X.Z.); (J.Y.); (J.Z.)
| | - Jingjing Yang
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (X.Z.); (J.Y.); (J.Z.)
| | - Bin Chen
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (Y.W.); (B.C.)
- Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing 100097, China
| | - Jian Zhang
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (X.Z.); (J.Y.); (J.Z.)
- Key Laboratory of Biology and Genetics Improvement of Horticultural Crops (North China), Beijing 100097, China
| | - Wenyue Li
- Henan OULAND Seed Industry Co., Ltd., Zhengzhou 450003, China;
| | - Heshan Du
- National Engineering Research Center for Vegetables, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (X.Z.); (J.Y.); (J.Z.)
| | - Sansheng Geng
- State Key Laboratory of Vegetable Biobreeding, Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Science, Beijing 100097, China; (Y.W.); (B.C.)
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Deng Y, He Z, Li Y, Ye M, Xiang L. Six Express Sequence Tag-Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species. Curr Issues Mol Biol 2023; 45:7183-7196. [PMID: 37754238 PMCID: PMC10529843 DOI: 10.3390/cimb45090454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag-simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.
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Affiliation(s)
- Yangchuan Deng
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Zhoujian He
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Yanlin Li
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Meng Ye
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing 100700, China
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He Z, Lei Y, Gong W, Ye M, Luo X. Karyotype and Phylogenetic Relationship Analysis of Five Varieties and Cultivars of Zanthoxylum armatum Based on Oligo-FISH. Genes (Basel) 2023; 14:1459. [PMID: 37510363 PMCID: PMC10379346 DOI: 10.3390/genes14071459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/12/2023] [Accepted: 07/14/2023] [Indexed: 07/30/2023] Open
Abstract
Green prickly ash (Zanthoxylum armatum) has edible and medicinal value and is an economically significant plant in many countries. Z. armatum has many cultivars and varieties with similar phenotypes that are difficult to distinguish via traditional methods. In this study, we utilized oligo-FISH to distinguish five varieties and cultivars of Z. armatum on the basis of three oligonucleotide probes of 5S rDNA, (AG3T3)3, and (GAA)6. Karyotype analysis of the five varieties and cultivars of Z. armatum showed that the Z. armatum 'Tengjiao' karyotype formula was 2n = 2x = 98m with karyotype type 1C and an arm ratio of 4.3237, including two pairs of 5S rDNA signals and five pairs of (GAA)6 signals. The karyotype formula of Z. armatum 'Youkangtengjiao' was 2n = 2x = 128m + 8sm with karyotype type 2B and an arm ratio of 3.5336, including three pairs of 5S rDNA signals and 17 pairs of (GAA)6 signals. The karyotype formula of Z. armatum var. novemfolius was 2n = 2x = 134m + 2sm with karyotype type 1C and an arm ratio of 5.5224, including two pairs of 5S rDNA signals and eight pairs of (GAA)6 signals. The karyotype formula of Z. armatum 'YT-03' was 2n = 2x = 2M + 128m + 4sm + 2st with karyotype type 2C and an arm ratio of 4.1829, including three pairs of 5S rDNA signals and nine pairs of (GAA)6 signals. The karyotype formula of Z. armatum 'YT-06' was 2n = 2x = 126m + 10sm with cytotype 2B and an arm ratio of 3.3011, including three pairs of 5S rDNA signals and two pairs of (GAA)6 signals. The five varieties and cultivars of Z. armatum had (AG3T3)3 signals on all chromosomes. The chromosomal symmetry of Z. armatum 'Tengjiao' was high, whereas the chromosomal symmetry of Z. armatum 'YT-03' was low, with the karyotypes of the five materials showing a trend toward polyploid evolution. The phylogenetic relationship between Z. armatum 'Tengjiao' and Z. armatum var. novemfolius was the closest, while that between Z. armatum 'YT-03' and Z. armatum 'YT-06' was closer than with Z. armatum 'Youkangtengjiao' according to oligo-FISH. The results provided a karyotype profile and a physical map that contributes to the distinction of varieties and cultivars of Z. armatum and provides strategies for distinguishing other cultivated species.
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Affiliation(s)
- Zhoujian He
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Yuting Lei
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Wei Gong
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Meng Ye
- College of Forestry, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaomei Luo
- National Forestry and Grassland Administration Key Laboratory of Forest Resources Conservation and Ecological Safety on the Upper Reaches of the Yangtze River & Forestry Ecological Engineering in the Upper Reaches of the Yangtze River Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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α-Linolenic Acid Inhibits RANKL-Induced Osteoclastogenesis In Vitro and Prevents Inflammation In Vivo. Foods 2023; 12:foods12030682. [PMID: 36766210 PMCID: PMC9914290 DOI: 10.3390/foods12030682] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 02/09/2023] Open
Abstract
Inflammation is an important risk factor for bone-destroying diseases. Our preliminary research found that Zanthoxylum bungeanum seed oil (ZBSO) is abundant in unsaturated fatty acids and could inhibit osteoclastogenesis in receptor activator of nuclear factor κB ligand (RANKL)-induced RAW264.7 cells. However, the key constituents in ZBSO in the prevention of osteoclastogenesis and its possible mechanism related to inflammation are still unclear. Therefore, in this study, oleic acid (OA), linoleic acid (LA), palmitoleic acid (PLA), and alpha-linolenic acid (ALA) in ZBSO, havingthe strongest effect on RANKL-induced osteoclastogenesis, were selected by a tartrate-resistant acid phosphatase (TRAP) staining method. Furthermore, the effects of the selected fatty acids on anti-inflammation and anti-osteoclastogenesis in vitro and in vivo were assessed using RT-qPCR. Among the four major unsaturated fatty acids we tested, ALA displayed the strongest inhibitory effect on osteoclastogenesis. The increased expression of free fatty acid receptor 4 (FFAR4) and β-arrestin2 (βarr2), as well as the decreased expression of nuclear factor-kappa B (NF-κB), tumor necrosis factor-α (TNF-α), nuclear factor of activated T-cells c1 (NFATc1), and tartrate-resistant acid phosphatase (TRAP) in RAW264.7 cells after ALA treatment were observed. Moreover, in ovariectomized osteoporotic rats with ALA preventive intervention, we found that the expression of TNF-α, interleukin-6 (IL-6), interleukin-1β (IL-1β), NFATc1, and TRAP were decreased, while with the ALA therapeutic intervention, downregulated expression of NF-κB, NFATc1, TRAP, and transforming growth factor beta-activated kinase 1 (TAK1) were noticed. These results indicate that ALA, as the major unsaturated fatty acid in ZBSO, could inhibit RANKL-induced osteoclastogenesis via the FFAR4/βarr2 signaling pathway and could prevent inflammation, suggesting that ZBSO may be a promising potential natural product of unsaturated fatty acids and a dietary supplement for the prevention of osteoclastogenesis and inflammatory diseases.
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Hu L, Xu Z, Fan R, Wang G, Wang F, Qin X, Yan L, Ji X, Meng M, Sim S, Chen W, Hao C, Wang Q, Zhu H, Zhu S, Xu P, Zhao H, Lindsey K, Daniell H, Wendel JF, Jin S. The complex genome and adaptive evolution of polyploid Chinese pepper (Zanthoxylum armatum and Zanthoxylum bungeanum). PLANT BIOTECHNOLOGY JOURNAL 2023; 21:78-96. [PMID: 36117410 PMCID: PMC9829393 DOI: 10.1111/pbi.13926] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 07/28/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Zanthoxylum armatum and Zanthoxylum bungeanum, known as 'Chinese pepper', are distinguished by their extraordinary complex genomes, phenotypic innovation of adaptive evolution and species-special metabolites. Here, we report reference-grade genomes of Z. armatum and Z. bungeanum. Using high coverage sequence data and comprehensive assembly strategies, we derived 66 pseudochromosomes comprising 33 homologous phased groups of two subgenomes, including autotetraploid Z. armatum. The genomic rearrangements and two whole-genome duplications created large (~4.5 Gb) complex genomes with a high ratio of repetitive sequences (>82%) and high chromosome number (2n = 4x = 132). Further analysis of the high-quality genomes shed lights on the genomic basis of involutional reproduction, allomones biosynthesis and adaptive evolution in Chinese pepper, revealing a high consistent relationship between genomic evolution, environmental factors and phenotypic innovation. Our study provides genomic resources and new insights for investigating diversification and phenotypic innovation in Chinese pepper, with broader implications for the protection of plants under severe environmental changes.
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Affiliation(s)
- Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Zhongping Xu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Rui Fan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Guanying Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Fuqiu Wang
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Xiaowei Qin
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Lin Yan
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Xunzhi Ji
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Minghui Meng
- State Key Laboratory of Grassland and Agro‐Ecosystems, School of Life SciencesLanzhou UniversityLanzhouChina
| | | | - Wei Chen
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Chaoyun Hao
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Qinghuang Wang
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural SciencesWanningChina
- Ministry of Agriculture Key Laboratory of Genetic Resources Utilization of Spice and Beverage CropsWanningChina
- Key Laboratory of Genetic Improvement and Quality Regulation for Tropical Spice and Beverage Crops of Hainan ProvinceWanningChina
| | - Huaguo Zhu
- College of Biology and Agricultural ResourcesHuanggang Normal UniversityHuanggangHubeiChina
| | - Shu Zhu
- Jinjiaohong Spice Research InstituteJinjiaohong Agricultural Technology Group CorporationNanjingChina
| | - Pan Xu
- State Key Laboratory of Grassland and Agro‐Ecosystems, School of Life SciencesLanzhou UniversityLanzhouChina
| | - Hui Zhao
- Hainan Key Laboratory for Biosafety Monitoring and Molecular Breeding in Off‐Season Reproduction RegionsHaikouChina
- Sanya Research Institute of Chinese Academy of Tropical Agricultural SciencesSanyaChina
| | | | - Henry Daniell
- Department of Biochemistry, School of Dental MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Jonathan F. Wendel
- Department Ecology, Evolution, and Organismal BiologyIowa State UniversityAmesIowaUSA
| | - Shuangxia Jin
- National Key Laboratory of Crop Genetic ImprovementHuazhong Agricultural UniversityWuhanChina
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8
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Hui W, Zheng H, Fan J, Wang J, Saba T, Wang K, Wu J, Wu H, Zhong Y, Chen G, Gong W. Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum. BMC Genomics 2022; 23:652. [PMID: 36104767 PMCID: PMC9472409 DOI: 10.1186/s12864-022-08863-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Background Multiprotein bridging factor 1 (MBF1) is a crucial transcriptional coactivator in animals, plants, and some microorganisms, that plays a necessary role in growth development and stress tolerance. Zanthoxylum armatum is an important perennial plant for the condiments and pharmaceutical industries, whereas the potential information in the genes related to stress resistance remains poorly understood in Z. armatum. Results Herein, six representative species were selected for use in a genome-wide investigation of the MBF1 family, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Citrus sinensis, Ginkgo biloba, and Z. armatum. The results showed that the MBF1 genes could be divided into two groups: Group I contained the MBF1a and MBF1b subfamilies, and group II was independent of the MBF1c subfamily.. Most species have at least two different MBF1 genes, and MBF1c is usually an essential member. The three ZaMBF1 genes were respectively located on ZaChr26, ZaChr32, and ZaChr4 of Zanthoxylum chromosomes. The collinearity were occurred between three ZaMBF1 genes, and ZaMBF1c showed the collinearity between Z. armatum and both P. trichocarpa and C. sinensis. Moreover, many cis-elements associated with abiotic stress and phytohormone pathways were detected in the promoter regions of MBF1 of six representative species. The ERF binding sites were the most abundant targets in the sequences of the ZaMBF1 family, and some transcription factor sites related to floral differentiation were also identified in ZaMBF1c, such as MADS, LFY, Dof, and AP2. ZaMBF1a was observed to be very highly expressed in 25 different samples except in the seeds, and ZaMBF1c may be associated with the male and female floral initiation processes. In addition, expression in all the ZaMBF1 genes could be significantly induced by water-logging, cold stress, ethephon, methyl jasmonate, and salicylic acid treatments, especially in ZaMBF1c. Conclusion The present study carried out a comprehensive bioinformatic investigation related to the MBF1 family in six representative species, and the responsiveness of ZaMBF1 genes to various abiotic stresses and phytohormone inductions was also revealed. This work not only lays a solid foundation to uncover the biological roles of the ZaMBF1 family in Z. armatum, but also provides some broad references for conducting the MBF1 research in other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08863-4.
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Hu H, He B, Ma L, Chen X, Han P, Luo Y, Liu Y, Fei X, Wei A. Physiological and transcriptome analyses reveal the photosynthetic response to drought stress in drought-sensitive (Fengjiao) and drought-tolerant (Hanjiao) Zanthoxylum bungeanum cultivars. FRONTIERS IN PLANT SCIENCE 2022; 13:968714. [PMID: 36186061 PMCID: PMC9524374 DOI: 10.3389/fpls.2022.968714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/12/2022] [Indexed: 06/16/2023]
Abstract
As an important economical plant, Zanthoxylum bungeanum is widely cultivated in arid and semi-arid areas. The studies associated with photosynthesis under drought stress were widely carried out, but not yet in Z. bungeanum. Here, the photosynthesis of two Z. bungeanum cultivars (FJ, Z. bungeanum cv. "Fengjiao"; HJ, Z. bungeanum cv. "Hanjiao") was analyzed under drought stress using physiological indicators and transcriptome data. Drought decreased stomatal aperture and stomatal conductance (Gsw), reduced transpiration rate (E) and sub-stomatal CO2 concentration (Ci), and lowered chlorophyll and carotenoid content, which reduced the net photosynthetic rate (Pn) of Z. bungeanum. The higher photosynthetic rate in HJ stemmed from its higher chlorophyll content, larger stomatal aperture and Gsw, and higher Ci. Weighted gene co-expression network analysis (WGCNA) identified several ABA signal transduction genes (PYL4, PYL9, and PYR1), LCH-encoding genes (LHCB4.3), and chlorophyll metabolism genes (CRD1, PORA, and CHLH). Additionally, seven transcription factor genes were identified as important factors regulating photosynthesis under drought conditions. In general, a photosynthetic response model under drought stress was built firstly in Z. bungeanum, and the key genes involved in photosynthesis under drought stress were identified. Therefore, the results in our research provide important information for photosynthesis under drought and provided key clues for future molecular breeding in Z. bungeanum.
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Affiliation(s)
- Haichao Hu
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
| | - Beibei He
- College of Horticulture, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
| | - Lei Ma
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
| | - Xin Chen
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
| | - Peilin Han
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
| | - Yingli Luo
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
| | - Yonghong Liu
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
| | - Xitong Fei
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
| | - Anzhi Wei
- College of Forestry, Northwest Agriculture and Forestry University, Xianyang, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Xianyang, Shaanxi, China
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Liu X, He X, Liu Z, Wu P, Tang N, Chen Z, Zhang W, Rao S, Cheng S, Luo C, Xu F. Transcriptome mining of genes in Zanthoxylum armatum revealed ZaMYB86 as a negative regulator of prickly development. Genomics 2022; 114:110374. [PMID: 35489616 DOI: 10.1016/j.ygeno.2022.110374] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/23/2022] [Accepted: 04/22/2022] [Indexed: 01/14/2023]
Abstract
Zanthoxylum armatum DC. is an important economic tree species. Prickle is a type of trichome with special morphology, and there are a lot of prickles on the leaves of Z. armatum, which seriously restricts the development of Z. armatum industry. In this study, the leaves of Z. armatum cv. Zhuye (ZY) and its budding variety 'Rongchangwuci' (WC) (A less prickly mutant variety) at different developmental stages were used as materials, and the transcriptome sequencing data were analyzed. A total of 96,931 differentially expressed genes (DEGs) were identified among the samples, among which 1560 were candidate DEGs that might be involved in hormone metabolism. The contents of JA, auxin and CK phytohormones in ZY leaves were significantly higher than those in WC leaves. Combined with weighted gene co-expression network analysis, eight genes (MYC, IAA, ARF, CRE/AHK, PP2C, ARR-A, AOS and LOX) were identified, including 25 transcripts, which might affect the metabolism of the three hormones and indirectly participate in the formation of prickles. Combining with the proteins successfully reported in other plants to regulate trichome formation, ZaMYB86, a transcription factor of R2R3 MYB family, was identified through local Blast and phylogenetic tree analysis, which might regulate prickle formation of Z. armatum. Overexpression of ZaMYB86 in mutant A. thaliana resulted in the reduction of trichomes in A. thaliana leaves, which further verified that ZaMYB86 was involved in the formation of pickles. Yeast two-hybrid results showed that ZaMYB86 interacted with ZaMYB5. Furthermore, ZaMYB5 was highly homologous to AtMYB5, a transcription factor that regulated trichomes development, in MYB DNA binding domain. Taken together, these results indicated that ZaMYB86 and ZaMYB5 act together to regulate the formation of prickles in Z. armatum. Our findings provided a new perspective for revealing the molecular mechanism of prickly formation.
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Affiliation(s)
- Xiaomeng Liu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Xiao He
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Zhongbing Liu
- School of Horticulture and Landscape, Wuhan University of Bioengineering, Wuhan, China
| | - Peiyin Wu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China
| | - Ning Tang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China
| | - Zexiong Chen
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing 402160, China; Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing 400000, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China; Spice Crops Research Institute, Yangtze University, Jingzhou 434025, Hubei, China.
| | - Shen Rao
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, Hubei, China
| | - Shuiyuan Cheng
- School of Modern Industry for Selenium Science and Engineering, National R&D Center for Se-rich Agricultural Products Processing Technology, Wuhan Polytechnic University, Wuhan 430023, Hubei, China; National Selenium Rich Product Quality Supervision and Inspection Center, Enshi 445000, Hubei, China
| | - Chengrong Luo
- Sichuan Academy of Forestry, Chengdu 610081, Sichuan, China
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, Hubei, China.
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Tian J, Ma Y, Chen Y, Chen X, Wei A. Plant Hormone Response to Low-Temperature Stress in Cold-Tolerant and Cold-Sensitive Varieties of Zanthoxylum bungeanum Maxim. FRONTIERS IN PLANT SCIENCE 2022; 13:847202. [PMID: 35574137 PMCID: PMC9102381 DOI: 10.3389/fpls.2022.847202] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/29/2022] [Indexed: 05/27/2023]
Abstract
Plant growth and survival in nature, its growth process, will be affected by various factors from the environment, among which temperature has a greater impact. In recent years, extreme weather has frequently appeared, and the growth of crops has been increasingly affected by the environment. As an important flavoring and Chinese herbal medicine crop, Zanthoxylum bungeanum is also facing the harm of low-temperature stress. Plant hormones play a vital role in the response of plants to low temperatures. In this study, ultra-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to determine the hormone components of cold-tolerant and cold-sensitive varieties of Z. bungeanum. Combined with chemometric analysis and weighted gene co-expression network analysis (WGCNA), the hormone component differences and hormone response strategies of Z. bungeanum under low-temperature stress were comprehensively studied. The results showed that 45 hormones were detected in Z. bungeanum. Among them, there were 7 kinds of components with high content and were detected in both two varieties. At the late stage of low-temperature stress, the contents of abscisic acid (ABA) and ABA-glucosyl ester (ABA-GE) in Fuguhuajiao (FG) were significantly increased, and the latter served as the storage of the former to supplement the active ABA. Orthogonal partial least squares discriminant analysis (OPLS-DA) found that indole-3-carboxylic acid (ICA), indole-3-carboxaldehyde (ICAld), meta-Topolin riboside (mTR), cis-Zeatin-O-glucoside riboside (cZROG), and N6-isopentenyladenosine (IPR) in FG were the upregulated important difference components, and IPR and 2-methylthio-cis-zeatin riboside (2MeScZR) in Fengxiandahongpao (FX) were the upregulated important difference components. There were common crossing points and independent response pathways in response to low temperature in two varieties. WGCNA analysis found that the main hormone components were associated with multiple metabolic pathways including carbon, fatty acid, amino acid, and sugar metabolism, indicating that hormone regulation plays an important role in the response of Z. bungeanum to low temperature. This study clarified the hormone response mechanism of Z. bungeanum under low-temperature stress and provided a reference and basis for further improving the cold resistance of Z. bungeanum and cultivating new varieties.
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Affiliation(s)
- Jieyun Tian
- College of Forestry, Northwest A&F University, Xianyang, China
| | - Yao Ma
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, China
| | - Yabing Chen
- College of Forestry, Northwest A&F University, Xianyang, China
| | - Xue Chen
- College of Forestry, Northwest A&F University, Xianyang, China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Xianyang, China
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12
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Genome-Wide Identification of the NAC Gene Family in Zanthoxylum bungeanum and Their Transcriptional Responses to Drought Stress. Int J Mol Sci 2022; 23:ijms23094769. [PMID: 35563160 PMCID: PMC9103986 DOI: 10.3390/ijms23094769] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/22/2022] [Accepted: 04/22/2022] [Indexed: 12/13/2022] Open
Abstract
NAC (NAM, ATAF1/2, and CUC2) transcription factors (TFs) are one of the largest plant-specific TF families and play a pivotal role in adaptation to abiotic stresses. The genome-wide analysis of NAC TFs is still absent in Zanthoxylum bungeanum. Here, 109 ZbNAC proteins were identified from the Z. bungeanum genome and were classified into four groups with Arabidopsis NAC proteins. The 109 ZbNAC genes were unevenly distributed on 46 chromosomes and included 4 tandem duplication events and 17 segmental duplication events. Synteny analysis of six species pairs revealed the closely phylogenetic relationship between Z. bungeanum and C. sinensis. Twenty-four types of cis-elements were identified in the ZbNAC promoters and were classified into three types: abiotic stress, plant growth and development, and response to phytohormones. Co-expression network analysis of the ZbNACs revealed 10 hub genes, and their expression levels were validated by real-time quantitative polymerase chain reaction (qRT-PCR). Finally, ZbNAC007, ZbNAC018, ZbNAC047, ZbNAC072, and ZbNAC079 were considered the pivotal NAC genes for drought tolerance in Z. bungeanum. This study represented the first genome-wide analysis of the NAC family in Z. bungeanum, improving our understanding of NAC proteins and providing useful information for molecular breeding of Z. bungeanum.
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13
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Tian J, Tian L, Chen M, Chen Y, Wei A. Low Temperature Affects Fatty Acids Profiling and Key Synthesis Genes Expression Patterns in Zanthoxylum bungeanum Maxim. Int J Mol Sci 2022; 23:ijms23042319. [PMID: 35216434 PMCID: PMC8876529 DOI: 10.3390/ijms23042319] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 02/06/2023] Open
Abstract
Zanthoxylum bungeanum is one of the most important medicinal and edible homologous plants because of its potential health benefits and unique flavors. The chemical components in compositions and contents vary with plant genotype variations and various environmental stress conditions. Fatty acids participate in various important metabolic pathways in organisms to resist biotic and abiotic stresses. To determine the variations in metabolic profiling and genotypes, the fatty acid profiling and key differential genes under low temperature stress in two Z. bungeanum varieties, cold-tolerant (FG) and sensitive (FX), were investigated. Twelve main fatty acids were found in two Z. bungeanum varieties under cold stress. Results showed that the contents of total fatty acids and unsaturated fatty acids in FG were higher than those in FX, which made FG more resistant to low temperature. Based on the result of orthogonal partial least squares discriminant analysis, palmitic acid, isostearic acid, linolenic acid and eicosenoic acid were the important differential fatty acids in FG under cold stress, while isomyristic acid, palmitic acid, isostearic acid, stearic acid, oleic acid, linolenic acid and eicosenoic acid were the important differential fatty acids in FX. Furthermore, fatty acid synthesis pathway genes fatty acyl-ACP thioesterase A (FATA), Delta (8)-fatty-acid desaturase 2 (SLD2), protein ECERIFERUM 3 (CER3), fatty acid desaturase 3 (FAD3) and fatty acid desaturase 5 (FAD5) played key roles in FG, and SLD2, FAD5, 3-oxoacyl-[acyl-carrier-protein] synthase I (KAS I), fatty acyl-ACP thioesterase B (FATB) and acetyl-CoA carboxylase (ACC) were the key genes responding to low temperature in FX. The variation and strategies of fatty acids in two varieties of Z. bungeanum were revealed at the metabolic and molecular level. This work provides a reference for the study of chemical components in plant stress resistance.
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Affiliation(s)
- Jieyun Tian
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.T.); (L.T.); (M.C.); (Y.C.)
- Research Centre for Engineering and Technology of Zanthoxylum, State Forestry Administration, Xianyang 712100, China
| | - Lu Tian
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.T.); (L.T.); (M.C.); (Y.C.)
- Research Centre for Engineering and Technology of Zanthoxylum, State Forestry Administration, Xianyang 712100, China
| | - Ming Chen
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.T.); (L.T.); (M.C.); (Y.C.)
- Research Centre for Engineering and Technology of Zanthoxylum, State Forestry Administration, Xianyang 712100, China
| | - Yabing Chen
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.T.); (L.T.); (M.C.); (Y.C.)
- Research Centre for Engineering and Technology of Zanthoxylum, State Forestry Administration, Xianyang 712100, China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Xianyang 712100, China; (J.T.); (L.T.); (M.C.); (Y.C.)
- Research Centre for Engineering and Technology of Zanthoxylum, State Forestry Administration, Xianyang 712100, China
- Correspondence: ; Tel.: +86-029-8708-2211
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Zhao Z, Song Q, Bai D, Niu S, He Y, Qiao D, Chen Z, Li C, Luo J, Li F. Population structure analysis to explore genetic diversity and geographical distribution characteristics of cultivated-type tea plant in Guizhou Plateau. BMC PLANT BIOLOGY 2022; 22:55. [PMID: 35086484 PMCID: PMC8793275 DOI: 10.1186/s12870-022-03438-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/12/2022] [Indexed: 05/17/2023]
Abstract
BACKGROUND Tea plants originated in southwestern China. Guizhou Plateau is an original center of tea plants, and is rich in germplasm resources. However, the genetic diversity, population structure and distribution characteristics of cultivated-type tea plants in the region are unknown. In this study, we explored the genetic diversity and geographical distribution of cultivated-type tea accessions in Guizhou Plateau. RESULTS We used 112,072 high-quality genotyping-by-sequencing to analyze the genetic diversity, principal components, phylogeny, population structure, and linkage disequilibrium, and develop a core collection of 253 cultivated-type tea plant accessions from Guizhou Plateau. The results showed Genetic diversity of the cultivated-type tea accessions of the Pearl River Basin was significantly higher than that of the cultivated-type tea accessions of the Yangtze River Basin. Three inferred pure groups (CG-1, CG-2 and CG-3) and one inferred admixture group (CG-4), were identified by a population structure analysis, and verified by principal component and phylogenetic analyses. The highest genetic distance and differentiation coefficients were determined for CG-2 vs CG-3. The lower genetic distance and differentiation coefficients were determined for CG-4 vs CG-2 and CG-4 vs CG-3, respectively. We developed a core set and a primary set. The primary and core sets contained 77.0 and 33.6% of all individuals in the initial set, respectively. The primary set may serve as the primary population in genome-wide association studies, while the core collection may serve as the core population in multiple treatment setting studies. CONCLUSIONS The present study demonstrated the genetic diversity and geographical distribution characteristics of cultivated-type tea plants in Guizhou Plateau. Significant differences in genetic diversity and evolutionary direction were detected between the ancient landraces of the Pearl River Basin and the those of the Yangtze River Basin. Major rivers and ancient hubs were largely responsible for the genetic exchange between the Pearl River Basin and the Yangtze River Basin ancient landraces as well as the formation of the ancient hubs evolutionary group. Genetic diversity, population structure and core collection elucidated by this study will facilitate further genetic studies, germplasm protection, and breeding of tea plants.
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Affiliation(s)
- Zhifei Zhao
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Qinfei Song
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dingchen Bai
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Suzhen Niu
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Yingqin He
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Dahe Qiao
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Zhengwu Chen
- lnstitute of Tea Science, Guizhou Academy of Agricultural Sciences, Guiyang, 550006 Guizhou Province PR China
| | - Caiyun Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Jing Luo
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
| | - Fang Li
- College of Tea Science / Tea Engineering Technology Research Center, Guizhou University, Guiyang, 550025 Guizhou Province PR China
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Xu Y, Jia H, Tan C, Wu X, Deng X, Xu Q. Apomixis: genetic basis and controlling genes. HORTICULTURE RESEARCH 2022; 9:uhac150. [PMID: 36072837 PMCID: PMC9437720 DOI: 10.1093/hr/uhac150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 06/27/2022] [Indexed: 05/12/2023]
Abstract
Apomixis is the phenomenon of clonal reproduction by seed. As apomixis can produce clonal progeny with exactly the same genotype as the maternal plant, it has an important application in genotype fixation and accelerating agricultural breeding strategies. The introduction of apomixis to major crops would bring many benefits to agriculture, including permanent fixation of superior genotypes and simplifying the procedures of hybrid seed production, as well as purification and rejuvenation of crops propagated vegetatively. Although apomixis naturally occurs in more than 400 plant species, it is rare among the major crops. Currently, with better understanding of apomixis, some achievements have been made in synthetic apomixis. However, due to prevailing limitations, there is still a long way to go to achieve large-scale application of apomixis to crop breeding. Here, we compare the developmental features of apomixis and sexual plant reproduction and review the recent identification of apomixis genes, transposons, epigenetic regulation, and genetic events leading to apomixis. We also summarize the possible strategies and potential genes for engineering apomixis into crop plants.
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Affiliation(s)
- Yuantao Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Huihui Jia
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Chunming Tan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaomeng Wu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, Hubei 430070, China
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Volatile Oil Profile of Prickly Ash ( Zanthoxylum) Pericarps from Different Locations in China. Foods 2021; 10:foods10102386. [PMID: 34681436 PMCID: PMC8535335 DOI: 10.3390/foods10102386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/29/2021] [Accepted: 10/02/2021] [Indexed: 11/18/2022] Open
Abstract
Volatile oils of prickly ash (Zanthoxylum) pericarps have various potential biological functions with considerable relevance to food, pharmacological, and industrial applications. The volatile profile of oils extracted from prickly ash pericarps obtained from 72 plantations in China was determined by gas chromatography and mass spectrometry. Several chemometric analyses were used to better understand the volatile oil profile differences among different pericarps and to determine the key factors that affected geographical variations in the main volatile constituents of oils. A total of 47 constituents were detected with D-limonene, alfa-myrcene, and linalool as the most abundant. The volatile profile of pericarp oils was significantly affected by prickly ash species and some environmental factors, and the key factors that affected volatile profile variations for different prickly ash species were diverse. Chemometric analyses based on the volatile oil profile could properly distinguish Z. armatum pericarps from other pericarps. This study provides comprehensive information on the volatile oil profile of pericarps from different prickly ash species and different plantations, and it can be beneficial to a system for evaluating of pericarp quality. Moreover, this study speculates on the key environmental factors that cause volatile oil variations for each species, and can help to obtain better prickly ash pericarp volatile oils by improving the cultivated environments.
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Okagu IU, Ndefo JC, Aham EC, Udenigwe CC. Zanthoxylum Species: A Review of Traditional Uses, Phytochemistry and Pharmacology in Relation to Cancer, Infectious Diseases and Sickle Cell Anemia. Front Pharmacol 2021; 12:713090. [PMID: 34603027 PMCID: PMC8479109 DOI: 10.3389/fphar.2021.713090] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/31/2021] [Indexed: 11/24/2022] Open
Abstract
The health benefits and toxicity of plant products are largely dependent on their secondary metabolite contents. These compounds are biosynthesized by plants as protection mechanisms against environmental factors and infectious agents. This review discusses the traditional uses, phytochemical constituents and health benefits of plant species in genus Zanthoxylum with a focus on cancer, microbial and parasitic infections, and sickle cell disease as reported in articles published from 1970 to 2021 in peer-reviewed journals and indexed in major scientific databases. Generally, Z. species are widely distributed in Asia, America and Africa, where they are used as food and for disease treatment. Several compounds belonging to alkaloids, flavonoids, terpenoids, and lignans, among others have been isolated from Z. species. This review discusses the biological activities reported for the plant species and their phytochemicals, including anticancer, antibacterial, antifungal, antiviral, anti-trypanosomal, antimalarial and anti-sickling properties. The safety profiles and suggestions for conservation of the Z. species were also discussed. Taken together, this review demonstrates that Z. species are rich in a wide range of bioactive phytochemicals with multiple health benefits, but more research is needed towards their practical application in the development of functional foods, nutraceuticals and lead compounds for new drugs.
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Affiliation(s)
| | | | - Emmanuel Chigozie Aham
- Department of Biochemistry, University of Nigeria, Nsukka, Nigeria
- Natural Science Unit, School of General Studies, University of Nigeria, Nsukka, Nigeria
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Wang M, Tong S, Ma T, Xi Z, Liu J. Chromosome-level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis. Mol Ecol Resour 2021; 21:2533-2545. [PMID: 34145765 DOI: 10.1111/1755-0998.13449] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Sichuan pepper is a commonly used spice in Asian cuisine. Sanshools and wgx-50/gx-50 isolated from it have been shown to possess a wide spectrum of medicinal properties. Here we generated a chromosome-level genome assembly of one Sichuan pepper species Zanthoxylum armatum characterized by drought tolerance and apomixis. Analyses of functionally related genes suggested that increased gene copy number and expression level of drought-tolerant genes might play an important role in improving drought tolerance of Z. armatum. Moreover, a gene encoding an RWP-RK domain-containing protein was shown to contribute to apomixis in Z. armatum, which was further characterized by overexpression in Arabidopsis thaliana. Furthermore, based on gene homology searching and co-expression patterns of metabolite concentration and gene expressions, we identified a number of candidate genes involved in the biosynthesis of sanshools and wgx-50/gx-50. Taken together, our results yield valuable insights for understanding the evolution of apomixis, drought tolerance, and alkaloid biosynthesis in Z. armatum.
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Affiliation(s)
- Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Institute for Advanced Study, Chengdu University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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Alkylamide Profiling of Pericarps Coupled with Chemometric Analysis to Distinguish Prickly Ash Pericarps. Foods 2021; 10:foods10040866. [PMID: 33921089 PMCID: PMC8071439 DOI: 10.3390/foods10040866] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 01/17/2023] Open
Abstract
Because of extensive cultivation areas, various cultivars, nonstandard naming notations, and morphology similarity among relative cultivars, adulteration and associated business fraud may happen in the marketplaces of prickly ash pericarps due to higher financial gain and high-frequency trading. This study presents variations in the chemical components and contents of different prickly ash species from different plantations. Alkylamide profiling of pericarps derived from Zanthoxylum armatum, Z. bungeanum, and some relative Zanthoxylum species from 72 plantations across China were tested using ultra-performance liquid chromatography. Then, several chemometrics were applied to classify the prickly ash pericarps to reveal potential indicators that distinguish prickly ash pericarps and to identify the key factors that affect pericarp alkylamide profiling. The dominating alkylamides in the prickly ash pericarps were Z. piperitum (ZP)-amide C (0–20.64 mg/g) and ZP-amide D (0–30.43 mg/g). Alkylamide profiling of prickly ash pericarps varied significantly across species and geographical variations. ZP-amide D in prickly ash pericarps was identified as a potential indicator to distinguish prickly ash species. Longitude and aluminum content in soils were identified as key factors that affected alkylamide profiling of prickly ash pericarps. This study provides a useful tool to classify prickly ash species based on pericarp alkylamide profiling and to determine the key influence factors on pericarp alkylamide variations.
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