1
|
Ye H, Wang Y, Liu H, Lei D, Li H, Gao Z, Feng X, Han M, Qie Q, Zhou H. The Phylogeography of Deciduous Tree Ulmus macrocarpa (Ulmaceae) in Northern China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1334. [PMID: 38794406 PMCID: PMC11125379 DOI: 10.3390/plants13101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/08/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024]
Abstract
Disentangling how climate oscillations and geographical events significantly influence plants' genetic architecture and demographic history is a central topic in phytogeography. The deciduous ancient tree species Ulmus macrocarpa is primarily distributed throughout Northern China and has timber and horticultural value. In the current study, we studied the phylogenic architecture and demographical history of U. macrocarpa using chloroplast DNA with ecological niche modeling. The results indicated that the populations' genetic differentiation coefficient (NST) value was significantly greater than the haplotype frequency (GST) (p < 0.05), suggesting that U. macrocarpa had a clear phylogeographical structure. Phylogenetic inference showed that the putative chloroplast haplotypes could be divided into three groups, in which the group Ⅰ was considered to be ancestral. Despite significant genetic differentiation among these groups, gene flow was detected. The common ancestor of all haplotypes was inferred to originate in the middle-late Miocene, followed by the haplotype overwhelming diversification that occurred in the Quaternary. Combined with demography pattern and ecological niche modeling, we speculated that the surrounding areas of Shanxi and Inner Mongolia were potential refugia for U. macrocarpa during the glacial period in Northern China. Our results illuminated the demography pattern of U. macrocarpa and provided clues and references for further population genetics investigations of precious tree species distributed in Northern China.
Collapse
Affiliation(s)
- Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Yiling Wang
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Dingfan Lei
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Haochen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Zhimei Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xiaolong Feng
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Mian Han
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Qiyang Qie
- School of Life Sciences, Shanxi Normal University, Taiyuan 030031, China
| | - Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province (Institute of Botany of Shaanxi Province), Xi'an 710061, China
| |
Collapse
|
2
|
Ma J, Zuo D, Zhang X, Li H, Ye H, Zhang N, Li M, Dang M, Geng F, Zhou H, Zhao P. Genome-wide identification analysis of the 4-Coumarate: CoA ligase (4CL) gene family expression profiles in Juglans regia and its wild relatives J. Mandshurica resistance and salt stress. BMC PLANT BIOLOGY 2024; 24:211. [PMID: 38519917 PMCID: PMC10960452 DOI: 10.1186/s12870-024-04899-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/11/2024] [Indexed: 03/25/2024]
Abstract
Persian walnut (Juglans regia) and Manchurian walnut (Juglans mandshurica) belong to Juglandaceae, which are vulnerable, temperate deciduous perennial trees with high economical, ecological, and industrial values. 4-Coumarate: CoA ligase (4CL) plays an essential function in plant development, growth, and stress. Walnut production is challenged by diverse stresses, such as salinity, drought, and diseases. However, the characteristics and expression levels of 4CL gene family in Juglans species resistance and under salt stress are unknown. Here, we identified 36 Jr4CL genes and 31 Jm4CL genes, respectively. Based on phylogenetic relationship analysis, all 4CL genes were divided into three branches. WGD was the major duplication mode for 4CLs in two Juglans species. The phylogenic and collinearity analyses showed that the 4CLs were relatively conserved during evolution, but the gene structures varied widely. 4CLs promoter region contained multiply cis-acting elements related to phytohormones and stress responses. We found that Jr4CLs may be participated in the regulation of resistance to anthracnose. The expression level and some physiological of 4CLs were changed significantly after salt treatment. According to qRT-PCR results, positive regulation was found to be the main mode of regulation of 4CL genes after salt stress. Overall, J. mandshurica outperformed J. regia. Therefore, J. mandshurica can be used as a walnut rootstock to improve salt tolerance. Our results provide new understanding the potential functions of 4CL genes in stress tolerance, offer the theoretical genetic basis of walnut varieties adapted to salt stress, and provide an important reference for breeding cultivated walnuts for stress tolerance.
Collapse
Affiliation(s)
- Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Dongjun Zuo
- College of Life and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Xuedong Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Haochen Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Nijing Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Meng Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Fangdong Geng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China
| | - Huijuan Zhou
- Xi'an Botanical Garden of Shaanxi Province, Institute of Botany of Shaanxi Province, Shaanxi Academy of Science, Xi'an, Shaanxi, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi, 710069, China.
| |
Collapse
|
3
|
Li M, Ou M, He X, Ye H, Ma J, Liu H, Yang H, Zhao P. DNA methylation role in subgenome expression dominance of Juglans regia and its wild relative J. mandshurica. PLANT PHYSIOLOGY 2023; 193:1313-1329. [PMID: 37403190 DOI: 10.1093/plphys/kiad394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 06/07/2023] [Accepted: 06/12/2023] [Indexed: 07/06/2023]
Abstract
Subgenome expression dominance plays a crucial role in the environmental adaptation of polyploids. However, the epigenetic molecular mechanism underlying this process has not been thoroughly investigated, particularly in perennial woody plants. Persian walnut (Juglans regia) and its wild relative, Manchurian walnut (Juglans mandshurica), are woody plants of great economic importance and are both paleopolyploids that have undergone whole-genome duplication events. In this study, we explored the characteristics of subgenome expression dominance in these 2 Juglans species and examined its epigenetic basis. We divided their genomes into dominant subgenome (DS) and submissive subgenome (SS) and found that the DS-specific genes might play critical roles in biotic stress response or pathogen defense. We comprehensively elucidated the characteristics of biased gene expression, asymmetric DNA methylation, transposable elements (TEs), and alternative splicing (AS) events of homoeologous gene pairs between subgenomes. The results showed that biased expression genes (BEGs) in 2 Juglans species were mainly related to external stimuli response, while non-BEGs were related to complexes that might be involved in signal transduction. DS genes had higher expression and more AS events while having less DNA methylation and TEs than homoeologous genes from the SS in the 2 Juglans species. Further studies showed that DNA methylation might contribute to the biased expression of gene pairs by modifying LTR/TIR/nonTIR TEs and improving the AS efficiency of corresponding precursor mRNAs in a particular context. Our study contributes to understanding the epigenetic basis of subgenome expression dominance and the environmental adaptation of perennial woody plants.
Collapse
Affiliation(s)
- Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Mengwei Ou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Xiaozhou He
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Jiayu Ma
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Huijuan Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, Shaanxi 710069, China
| |
Collapse
|
4
|
Shi N, Yang Z, Miao K, Tang L, Zhou N, Xie P, Wen G. Comparative analysis of the medicinal plant Polygonatum kingianum (Asparagaceae) with related verticillate leaf types of the Polygonatum species based on chloroplast genomes. FRONTIERS IN PLANT SCIENCE 2023; 14:1202634. [PMID: 37680362 PMCID: PMC10482041 DOI: 10.3389/fpls.2023.1202634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 07/06/2023] [Indexed: 09/09/2023]
Abstract
Background Polygonatum kingianum has been widely used as a traditional Chinese medicine as well as a healthy food. Because of its highly variable morphology, this medicinal plant is often difficult to distinguish from other related verticillate leaf types of the Polygonatum species. The contaminants in P. kingianum products not only decrease the products' quality but also threaten consumer safety, seriously inhibiting the industrial application of P. kingianum. Methods Nine complete chloroplast (cp) genomes of six verticillate leaf types of the Polygonatum species were de novo assembled and systematically analyzed. Results The total lengths of newly sequenced cp genomes ranged from 155,437 to 155,977 bp, including 86/87 protein-coding, 38 tRNA, and 8 rRNA genes, which all exhibited well-conserved genomic structures and gene orders. The differences in the IR/SC (inverted repeats/single-copy) boundary regions and simple sequence repeats were detected among the verticillate leaf types of the Polygonatum cp genomes. Comparative cp genomes analyses revealed that a higher similarity was conserved in the IR regions than in the SC regions. In addition, 11 divergent hotspot regions were selected, providing potential molecular markers for the identification of the Polygonatum species with verticillate leaf types. Phylogenetic analysis indicated that, as a super barcode, plastids realized a fast and efficient identification that clearly characterized the relationships within the verticillate leaf types of the Polygonatum species. In brief, our results not only enrich the data on the cp genomes of the genus Polygonatum but also provide references for the P. kingianum germplasm resource protection, herbal cultivation, and drug production. Conclusion This study not only accurately identifies P. kingianum species, but also provides valuable information for the development of molecular markers and phylogenetic analyses of the Polygonatum species with verticillate leaf types.
Collapse
Affiliation(s)
- Naixing Shi
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Zefen Yang
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| | - Ke Miao
- Chinese Academy of Sciences (CAS) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lilei Tang
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Nian Zhou
- Chinese Academy of Sciences (CAS) Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Pingxuan Xie
- College of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Guosong Wen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China
| |
Collapse
|
5
|
Zhu X, Tang J, Jiang H, Yang Y, Chen Z, Zou R, Xu A, Luo Y, Deng Z, Wei X, Chai S. Genomic evidence reveals high genetic diversity in a narrowly distributed species and natural hybridization risk with a widespread species in the genus Geodorum. BMC PLANT BIOLOGY 2023; 23:317. [PMID: 37316828 DOI: 10.1186/s12870-023-04285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023]
Abstract
BACKGROUND Understanding genetic diversity is a core issue in conservation genetics. However, previous genetic diversity evaluations of narrowly distributed species have rarely used closely related widespread species as a reference. Furthermore, identifying natural hybridization signals between narrowly and widely distributed sympatric species is of great importance for the development of species conservation programs. METHODS In this study, population genotyping by sequencing (GBS) was performed for a narrowly distributed species, Geodorum eulophioides (endemic and endangered in Southwest China), and a widespread species, G. densiflorum. A total of 18,490 high-quality single nucleotide polymorphisms (SNPs) were identified at the whole-genome level. RESULTS The results showed that the nucleotide diversity and heterozygosity of G. eulophioides were significantly higher than those of G. densiflorum, confirming that narrowly distributed species can still preserve high genetic diversity. Consistent with taxonomic boundaries, all sampled individuals from the two species were divided into two genetic clusters and showed high genetic differentiation between species. However, in a sympatric population, a few G. eulophioides individuals were detected with genetic components from G. densiflorum, suggesting potential interspecific natural hybridization. This hypothesis was supported by Treemix analysis and hand-hybridization trials. Invasion of the habitat of G. eulophioides invasion by G. densiflorum under anthropogenic disturbance may be the main factor causing interspecific hybridization. CONCLUSIONS Therefore, reducing or avoiding habitat disturbance is a key measure to protect the G. eulophioides populations. This study provides valuable information for future conservation programs for narrowly distributed species.
Collapse
Affiliation(s)
- Xianliang Zhu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Jianmin Tang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Haidu Jiang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Yishan Yang
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Zongyou Chen
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Rong Zou
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
| | - Aizhu Xu
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China
- College of Tourism and Landscape Architecture, Guilin University of Technology, Guilin, Guangxi, 541006, China
| | - Yajin Luo
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Zhenhai Deng
- Yachang Orchid National Nature Reserve Management Center, Baise, Guangxi, 533209, China
| | - Xiao Wei
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
| | - Shengfeng Chai
- Guangxi Key Laboratory of Plant Functional Phytochemicals and Sustainable Utilization, Guangxi Institute of Botany, Guangxi Zhuang Autonomous Region and Chinese Academy of Sciences, Guilin, 541006, China.
| |
Collapse
|
6
|
Gao XF, Xiong XH, Boufford DE, Gao YD, Xu B, Zhang C. Phylogeny of the Diploid Species of Rubus (Rosaceae). Genes (Basel) 2023; 14:1152. [PMID: 37372332 DOI: 10.3390/genes14061152] [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: 04/25/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/29/2023] Open
Abstract
Rubus L. (Rosaceae, Rosoideae) contains around 700 species distributed on all continents except Antarctica, with the highest species diversity in temperate to subtropical regions of the northern hemisphere. The taxonomy of Rubus is challenging due to the frequency of polyploidy, hybridization and apomixis. Previous studies mostly sampled sparsely and used limited DNA sequence data. The evolutionary relationships between infrageneric taxa, therefore, remain to be further clarified. In the present study, genotyping by sequencing (GBS) reduced-representation genome sequencing data from 186 accessions representing 65 species, 1 subspecies and 17 varieties of Rubus, with emphasis on diploid species, were used to infer a phylogeny using maximum likelihood and maximum parsimony methods. The major results were as follows: (1) we confirmed or reconfirmed the polyphyly or paraphyly of some traditionally circumscribed subgenera, sections and subsections; (2) 19 well-supported clades, which differed from one another on molecular, morphological and geographical grounds, were identified for the species sampled; (3) characteristics such as plants with dense bristles or not, leaves leathery or papyraceous, number of carpels, instead of inflorescences paniculate or not, aggregate fruits and leaves abaxially tomentose or not, may be of some use in classifying taxa whose drupelets are united into a thimble-shaped aggregate fruit that falls in its entirety from the dry receptacle; and (4) a preliminary classification scheme of diploid species of Rubus is proposed based on our results combined with those from previous phylogenetic analyses.
Collapse
Affiliation(s)
- Xin-Fen Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Xian-Hua Xiong
- College of Life Science and Biotechnology, Mianyang Teachers' College, Mianyang 621000, China
| | - David E Boufford
- Harvard University Herbaria, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Yun-Dong Gao
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Bo Xu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| | - Cheng Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, China
| |
Collapse
|
7
|
Luo X, Zhou H, Cao D, Yan F, Chen P, Wang J, Woeste K, Chen X, Fei Z, An H, Malvolti M, Ma K, Liu C, Ebrahimi A, Qiao C, Ye H, Li M, Lu Z, Xu J, Cao S, Zhao P. Domestication and selection footprints in Persian walnuts (Juglans regia). PLoS Genet 2022; 18:e1010513. [PMID: 36477175 PMCID: PMC9728896 DOI: 10.1371/journal.pgen.1010513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/07/2022] [Indexed: 12/12/2022] Open
Abstract
Walnut (Juglans) species are economically important hardwood trees cultivated worldwide for both edible nuts and high-quality wood. Broad-scale assessments of species diversity, evolutionary history, and domestication are needed to improve walnut breeding. In this study, we sequenced 309 walnut accessions from around the world, including 55 Juglans relatives, 98 wild Persian walnuts (J. regia), 70 J. regia landraces, and 86 J. regia cultivars. The phylogenetic tree indicated that J. regia samples (section Dioscaryon) were monophyletic within Juglans. The core areas of genetic diversity of J. regia germplasm were southwestern China and southern Asia near the Qinghai-Tibet Plateau and the Himalayas, and the uplift of the Himalayas was speculated to be the main factor leading to the current population dynamics of Persian walnut. The pattern of genomic variation in terms of nucleotide diversity, linkage disequilibrium, single nucleotide polymorphisms, and insertions/deletions revealed the domestication and selection footprints in Persian walnut. Selective sweep analysis, GWAS, and expression analysis further identified two transcription factors, JrbHLH and JrMYB6, that influence the thickness of the nut diaphragm as loci under selection during domestication. Our results elucidate the domestication and selection footprints in Persian walnuts and provide a valuable resource for the genomics-assisted breeding of this important crop.
Collapse
Affiliation(s)
- Xiang Luo
- College of Agriculture, Henan University, Kaifeng, Henan, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- Xi’an Botanical Garden of Shaanxi Province, Xi’an, China
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
| | - Da Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Xin Chen
- Shandong Institute of Pomology, National Germplasm Repository of Walnut and Chestnut, Tai’an, China
| | - Zhangjun Fei
- Boyce Thompson Institute for Plant Research, US Department of Agriculture (USDA) Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, New York, United States of America
| | - Hong An
- Bioinformatics and Analytics Core, University of Missouri, Columbia, Missouri, United States of America
| | - Maria Malvolti
- Research Institute on Terrestrial Ecosystems, National Research Council, Porano, Terni, Italy
| | - Kai Ma
- Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Chaobin Liu
- Laboratory of Functional Plant Biology, Department of Biology, Ghent University, Ghent, Belgium
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, Indiana, United States of America
| | - Chengkui Qiao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Mengdi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
| | - Zhenhua Lu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Jiabao Xu
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
- * E-mail: (JX); (SC); (PZ)
| | - Shangying Cao
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
- * E-mail: (JX); (SC); (PZ)
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, Shaanxi, China
- * E-mail: (JX); (SC); (PZ)
| |
Collapse
|
8
|
Ha YH, Gil HY, Kim SC, Choi K, Kim JH. Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing. Sci Rep 2022; 12:16262. [PMID: 36171257 PMCID: PMC9519971 DOI: 10.1038/s41598-022-20513-z] [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: 05/17/2022] [Accepted: 09/14/2022] [Indexed: 11/09/2022] Open
Abstract
This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.
Collapse
Affiliation(s)
- Young-Ho Ha
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea.,Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea
| | - Hee-Young Gil
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Sang-Chul Kim
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Kyung Choi
- Division of Forest Biodiversity, Korea National Arboretum, Pocheon, Gyeonggi-do, 11186, Republic of Korea
| | - Joo-Hwan Kim
- Department of Life Science, Gachon University, Seongnam, Gyeonggi-do, 13120, Republic of Korea.
| |
Collapse
|
9
|
Wang J, Ye H, Zhou H, Chen P, Liu H, Xi R, Wang G, Hou N, Zhao P. Genome-wide association analysis of 101 accessions dissects the genetic basis of shell thickness for genetic improvement in Persian walnut (Juglans regia L.). BMC PLANT BIOLOGY 2022; 22:436. [PMID: 36096735 PMCID: PMC9469530 DOI: 10.1186/s12870-022-03824-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Understanding the underlying genetic mechanisms that drive phenotypic variations is essential for enhancing the efficacy of crop improvement. Persian walnut (Juglans regia L.), which is grown extensively worldwide, is an important economic tree fruit due to its horticultural, medicinal, and material value. The quality of the walnut fruit is related to the selection of traits such as thinner shells, larger filling rates, and better taste, which is very important for breeding in China. The complex quantitative fruit-related traits are influenced by a variety of physiological and environmental factors, which can vary widely between walnut genotypes. RESULTS For this study, a set of 101 Persian walnut accessions were re-sequenced, which generated a total of 906.2 Gb of Illumina sequence data with an average read depth of 13.8× for each accession. We performed the genome-wide association study (GWAS) using 10.9 Mb of high-quality single-nucleotide polymorphisms (SNPs) and 10 agronomic traits to explore the underlying genetic basis of the walnut fruit. Several candidate genes are proposed to be involved in walnut characteristics, including JrPXC1, JrWAKL8, JrGAMYB, and JrFRK1. Specifically, the JrPXC1 gene was confirmed to participate in the regulation of secondary wall cellulose thickening in the walnut shell. CONCLUSION In addition to providing considerable available genetic resources for walnut trees, this study revealed the underlying genetic basis involved in important walnut agronomic traits, particularly shell thickness, as well as providing clues for the improvement of genetic breeding and domestication in other perennial economic crops.
Collapse
Affiliation(s)
- Jiangtao Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hang Ye
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
- College of Forestry, Northwest A&F University, Yangling, 712100, China
| | - Pengpeng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Hengzhao Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Ruimin Xi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Gang Wang
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China
| | - Na Hou
- Guizhou Academy of Forestry, Guiyang, 550005, Guizhou, China.
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| |
Collapse
|
10
|
Huang X, Coulibaly D, Tan W, Ni Z, Shi T, Li H, Hayat F, Gao Z. The analysis of genetic structure and characteristics of the chloroplast genome in different Japanese apricot germplasm populations. BMC PLANT BIOLOGY 2022; 22:354. [PMID: 35864441 PMCID: PMC9306182 DOI: 10.1186/s12870-022-03731-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/04/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Chloroplast (cp) genomes are generally considered to be conservative and play an important role in population diversity analysis in plants, but the characteristics and diversity of the different germplasm populations in Japanese apricot are still not clear. RESULTS A total of 146 cp genomes from three groups of wild, domesticated, and bred accessions of Japanese apricot were sequenced in this study. The comparative genome analysis revealed that the 146 cp genomes were divided into 41 types, and ranged in size from 157,886 to 158,167 bp with a similar structure and composition to those of the genus Prunus. However, there were still minor differences in the cp genome that were mainly caused by the contraction and expansion of the IR region, and six types of SSR in which mono-nucleotide repeats were the most dominant type of repeats in the cp genome. The genes rpl33 and psbI, and intergenic regions of start-psbA, rps3-rpl22, and ccsA-ndhD, showed the highest nucleotide polymorphism in the whole cp genome. A total of 325 SNPs were detected in the 146 cp genomes, and more than 70% of the SNPs were in region of large single-copy (LSC). The SNPs and haplotypes in the cp genome indicated that the wild group had higher genetic diversity than the domesticated and bred groups. In addition, among wild populations, Southwest China, including Yunnan, Tibet, and Bijie of Guizhou, had the highest genetic diversity. The genetic relationship of Japanese apricot germplasm resources in different regions showed a degree of correlation with their geographical distribution. CONCLUSION Comparative analysis of chloroplast genomes of 146 Japanese apricot resources was performed to analyze the used to explore the genetic relationship and genetic diversity among Japanese apricot resources with different geographical distributions, providing some reference for the origin and evolution of Japanese apricot.
Collapse
Affiliation(s)
- Xiao Huang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Daouda Coulibaly
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhaojun Ni
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Ting Shi
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Hantao Li
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Faisal Hayat
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| | - Zhihong Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu China
| |
Collapse
|
11
|
Bai Q, He B, Cai Y, Lian H, Zhang Q, Liang D, Wang Y. Genetic Diversity and Population Structure of Schima superba From Southern China. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.879512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The tree Schima superba is important for afforestation and fire prevention in southern China. The wood of this tree can also be used for furniture and buildings. However, the lack of genetic background and genomic information for this species has lowered wood yield speed and quality improvement. Here, we aimed to discover genome-wide single nucleotide polymorphisms (SNPs) in 302 S. superba germplasms collected from southern China and to use these SNPs to investigate the population structure. Using genotyping by sequencing, a total of 785 high-quality SNP markers (minor allele frequency [MAF] ≥ 0.05) were identified from 302 accessions collected from seven geographical locations. Population structure analyses and principal coordinate analyses (PCoAs) indicated that these germplasm resources can be clearly separated into different populations. The S. superba accessions originating from Yunnan (YN) and Guangxi (GX) fell into the same population, separate from the accessions originating from Guangdong (GD), which indicated that these two regions should be regarded as major provenances of this species. In addition, two independent core germplasm sets with abundant genetic polymorphisms were constructed to support the breeding work. The identification of SNP markers, analyses of population genetics, and construction of core germplasm sets will greatly promote the molecular breeding work of S. superba.
Collapse
|
12
|
Jafari O, Zeinalabedini M, Robledo D, Fernandes JMO, Hedayati AA, Arefnezhad B. Genotyping-by-Sequencing Reveals the Impact of Restocking on Wild Common Carp Populations of the Southern Caspian Basin. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.872176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Understanding the population structure and level of genetic diversity of wild populations is fundamental for appropriate stock management and species conservation. The common carp (Cyprinus carpio) is one of the most important bony fish throughout the Southern coastline of the Caspian Sea, but captures of this species have seen a dramatic reduction during the last decade. As a consequence, a restocking program has been put in place to maintain C. carpio populations, but its impact is not clear. In the present study, the population structure and genetic diversity of C. carpio in the Southern Caspian basin was determined using 17,828 single-nucleotide polymorphism (SNP) markers. A total of 117 individuals collected from four different locations in the southern Caspian basin and a farm were genotyped by genotyping-by-sequencing. The overall Fst obtained was 0.04, indicating a low level of differentiation between populations, and most genetic diversity was attributed to within population variation (97%). The low Fst values suggest that frequent migration events between different locations occur, and three migration events were inferred in the present study. However, each population still showed a distinct genetic profile, which allowed distinguishing the origin of the fish. This indicates that the ongoing restocking program is maintaining the differences between populations to some extent. Nonetheless, high inbreeding and low heterozygosity were detected in all populations, suggesting that additional conservation efforts are required to protect C. carpio populations in the Southern coast of the Caspian Sea.
Collapse
|
13
|
Zhang WP, Cao L, Lin XR, Ding YM, Liang Y, Zhang DY, Pang EL, Renner SS, Bai WN. Dead-End Hybridization in Walnut Trees Revealed by Large-Scale Genomic Sequence Data. Mol Biol Evol 2022; 39:msab308. [PMID: 34687315 PMCID: PMC8760940 DOI: 10.1093/molbev/msab308] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Although hybridization plays a large role in speciation, some unknown fraction of hybrid individuals never reproduces, instead remaining as genetic dead-ends. We investigated a morphologically distinct and culturally important Chinese walnut, Juglans hopeiensis, suspected to have arisen from hybridization of Persian walnut (J. regia) with Asian butternuts (J. cathayensis, J. mandshurica, and hybrids between J. cathayensis and J. mandshurica). Based on 151 whole-genome sequences of the relevant taxa, we discovered that all J. hopeiensis individuals are first-generation hybrids, with the time for the onset of gene flow estimated as 370,000 years, implying both strong postzygotic barriers and the presence of J. regia in China by that time. Six inversion regions enriched for genes associated with pollen germination and pollen tube growth may be involved in the postzygotic barriers that prevent sexual reproduction in the hybrids. Despite its long-recurrent origination and distinct traits, J. hopeiensis does not appear on the way to speciation.
Collapse
Affiliation(s)
- Wei-Ping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lei Cao
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xin-Rui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Ya-Mei Ding
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yu Liang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Er-Li Pang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Susanne S Renner
- Department of Biology, Washington University, Saint Louis, MO, USA
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
14
|
Xi J, Lv S, Zhang W, Zhang J, Wang K, Guo H, Hu J, Yang Y, Wang J, Xia G, Fan G, Wang X, Xiao L. Comparative plastomes of Carya species provide new insights into the plastomes evolution and maternal phylogeny of the genus. FRONTIERS IN PLANT SCIENCE 2022; 13:990064. [PMID: 36407576 PMCID: PMC9667483 DOI: 10.3389/fpls.2022.990064] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 09/21/2022] [Indexed: 05/03/2023]
Abstract
Carya, in the Juglandiodeae subfamily, is to a typical temperate-subtropical forest-tree genus for studying the phylogenetic evolution and intercontinental disjunction between eastern Asia (EA) and North America (NA). Species of the genus have high economic values worldwide for their high-quality wood and the rich healthy factors of their nuts. Although previous efforts based on multiple molecular markers or genome-wide SNPs supported the monophyly of Carya and its two EA and NA major subclades, the maternal phylogeny of Carya still need to be comprehensively evaluated. The variation of Carya plastome has never been thoroughly characterized. Here, we novelly present 19 newly generated plastomes of congeneric Carya species, including the recently rediscovered critically endangered C. poilanei. The overall assessment of plastomes revealed highly conservative in the general structures. Our results indicated that remarkable differences in several plastome features are highly consistent with the EA-NA disjunction and showed the relatively diverse matrilineal sources among EA Carya compared to NA Carya. The maternal phylogenies were conducted with different plastome regions and full-length plastome datasets from 30 plastomes, representing 26 species in six genera of Juglandoideae and Myrica rubra (as root). Six out of seven phylogenetic topologies strongly supported the previously reported relationships among genera of Juglandoideae and the two subclades of EA and NA Carya, but displayed significant incongruencies between species within the EA and NA subclades. The phylogenetic tree generated from full-length plastomes demonstrated the optimal topology and revealed significant geographical maternal relationships among Carya species, especially for EA Carya within overlapping distribution areas. The full-length plastome-based phylogenetic topology also strongly supported the taxonomic status of five controversial species as separate species of Carya. Historical and recent introgressive hybridization and plastid captures might contribute to plastome geographic patterns and inconsistencies between topologies built from different datasets, while incomplete lineage sorting could account for the discordance between maternal topology and the previous nuclear genome data-based phylogeny. Our findings highlight full-length plastomes as an ideal tool for exploring maternal relationships among the subclades of Carya, and potentially in other outcrossing perennial woody plants, for resolving plastome phylogenetic relationships.
Collapse
Affiliation(s)
- Jianwei Xi
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Saibin Lv
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Weiping Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jingbo Zhang
- Department of Biological Sciences, St. John’s University - Queens, NY, United States
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
| | - Ketao Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Haobing Guo
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Jie Hu
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Yang Yang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Jianhua Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guohua Xia
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
| | - Guangyi Fan
- The Beijing Genomics Institute (BGI) -Qingdao, The Beijing Genomics Institute (BGI)-Shenzhen, Qingdao, China
| | - Xinwang Wang
- Pecan Breeding and Genetics, Southern Plains Agricultural Research Center, USDA-ARS, College Station, TX, United States
| | - Lihong Xiao
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, China
- *Correspondence: Lihong Xiao, ; Jingbo Zhang,
| |
Collapse
|
15
|
Sun Z, Zhao M, Zuo L, Zhou S, Fan F, Jia Q, Xue L, Li H, Kang J, Zhang X. Rapid qualitative profiling and quantitative analysis of Juglandis Mandshuricae Cortex and seven flavonoids by ultra-high performance liquid chromatography-quadrupole/orbitrap high-resolution mass spectrometry. J Sep Sci 2021; 45:518-528. [PMID: 34784088 DOI: 10.1002/jssc.202100658] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 01/13/2023]
Abstract
Juglandis Mandshuricae Cortex is the bark of Juglans mandshurica Maxim., which has been used as a folk medicine plant in China and India. In this study, an ultra-high performance liquid chromatography-quadrupole/orbitrap high-resolution mass spectrometry method was developed to clarify and quantify the chemical profiling of Juglandis Mandshuricae Cortex rapidly. A total of 113 compounds were characterized. Among them, seven flavonoids were simultaneously quantified in 15 min, including myricetin, myricetrin, taxifolin, kaempferol, quercetin, quercitrin, and naringenin. The method was validated for accuracy, precision, and the limits of detection and quantification. All calibration curves showed a good linear relationship (r > 0.9990) within test ranges. The intra- and inter-day relative standard deviations were less than 2.16%. Accuracy validation showed that the recovery was between 95.6% and 101.3% with relative standard deviation values below 2.85%. The validated method was successfully applied to determine the contents of seven flavones in Juglandis Mandshuricae Cortex from seven sources and the contents of these places were calculated respectively. This method provides a theoretical basis for further developing the medicinal value of Juglandis Mandshuricae Cortex.
Collapse
Affiliation(s)
- Zhi Sun
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Mengfan Zhao
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Lihua Zuo
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Shengnan Zhou
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P. R. China
| | - Feng Fan
- Department of Neurointerventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Qingquan Jia
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Lianping Xue
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Hanbing Li
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, P. R. China
| | - Jian Kang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| | - Xiaojian Zhang
- Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, P. R. China
| |
Collapse
|
16
|
Zhou H, Hu Y, Ebrahimi A, Liu P, Woeste K, Zhao P, Zhang S. Whole genome based insights into the phylogeny and evolution of the Juglandaceae. BMC Ecol Evol 2021; 21:191. [PMID: 34674641 PMCID: PMC8529855 DOI: 10.1186/s12862-021-01917-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 09/22/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes. RESULTS We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. CONCLUSIONS A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).
Collapse
Affiliation(s)
- Huijuan Zhou
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yiheng Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peiliang Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
17
|
Zhou H, Hu Y, Ebrahimi A, Liu P, Woeste K, Zhao P, Zhang S. Whole genome based insights into the phylogeny and evolution of the Juglandaceae. BMC Ecol Evol 2021. [PMID: 34674641 DOI: 10.21203/rs.3.rs-495294/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
BACKGROUND The walnut family (Juglandaceae) contains commercially important woody trees commonly called walnut, wingnut, pecan and hickory. Phylogenetic relationships and diversification within the Juglandaceae are classic and hot scientific topics that have been elucidated by recent fossil, morphological, molecular, and (paleo) environmental data. Further resolution of relationships among and within genera is still needed and can be achieved by analysis of the variation of chloroplast, mtDNA, and nuclear genomes. RESULTS We reconstructed the backbone phylogenetic relationships of Juglandaceae using organelle and nuclear genome data from 27 species. The divergence time of Juglandaceae was estimated to be 78.7 Mya. The major lineages diversified in warm and dry habitats during the mid-Paleocene and early Eocene. The plastid, mitochondrial, and nuclear phylogenetic analyses all revealed three subfamilies, i.e., Juglandoideae, Engelhardioideae, Rhoipteleoideae. Five genera of Juglandoideae were strongly supported. Juglandaceae were estimated to have originated during the late Cretaceous, while Juglandoideae were estimated to have originated during the Paleocene, with evidence for rapid diversification events during several glacial and geological periods. The phylogenetic analyses of organelle sequences and nuclear genome yielded highly supported incongruence positions for J. cinerea, J. hopeiensis, and Platycarya strobilacea. Winged fruit were the ancestral condition in the Juglandoideae, but adaptation to novel dispersal and regeneration regimes after the Cretaceous-Paleogene boundary led to the independent evolution of zoochory among several genera of the Juglandaceae. CONCLUSIONS A fully resolved, strongly supported, time-calibrated phylogenetic tree of Juglandaceae can provide an important framework for studying classification, diversification, biogeography, and comparative genomics of plant lineages. Our addition of new, annotated whole chloroplast genomic sequences and identification of their variability informs the study of their evolution in walnuts (Juglandaceae).
Collapse
Affiliation(s)
- Huijuan Zhou
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Yiheng Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Aziz Ebrahimi
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peiliang Liu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, 715 West State Street, West Lafayette, 47907, Indiana, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, Shaanxi, China.
| | - Shuoxin Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| |
Collapse
|
18
|
Yang YY, Qu XJ, Zhang R, Stull GW, Yi TS. Plastid phylogenomic analyses of Fagales reveal signatures of conflict and ancient chloroplast capture. Mol Phylogenet Evol 2021; 163:107232. [PMID: 34129935 DOI: 10.1016/j.ympev.2021.107232] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Revised: 05/21/2021] [Accepted: 06/10/2021] [Indexed: 11/17/2022]
Abstract
Plastid phylogenomic analyses have shed light on many recalcitrant relationships across the angiosperm Tree of Life and continue to play an important role in plant phylogenetics alongside nuclear data sets given the utility of plastomes for revealing ancient and recent introgression. Here we conduct a plastid phylogenomic study of Fagales, aimed at exploring contentious relationships (e.g., the placement of Myricaceae and some intergeneric relationships in Betulaceae, Juglandaceae, and Fagaceae) and dissecting conflicting phylogenetic signals across the plastome. Combining 102 newly sequenced samples with publically available plastomes, we analyzed a dataset including 256 species and 32 of the 34 total genera of Fagales, representing the largest plastome-based study of the order to date. We find strong support for a sister relationship between Myricaceae and Juglandaceae, as well as strongly supported conflicting signal for alternative generic relationships in Betulaceae and Juglandaceae. These conflicts highlight the sensitivity of plastid phylogenomic analyses to genic composition, perhaps due to the prevalence of uninformative loci and heterogeneity in signal across different regions of the plastome. Phylogenetic relationships were geographically structured in subfamily Quercoideae, with Quercus being non-monophyletic and its sections forming clades with co-distributed Old World or New World genera of Quercoideae. Compared against studies based on nuclear genes, these results suggest extensive introgression and chloroplast capture in the early diversification of Quercus and Quercoideae. This study provides a critical plastome perspective on Fagales phylogeny, setting the stage for future studies employing more extensive data from the nuclear genome.
Collapse
Affiliation(s)
- Ying-Ying Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Xiao-Jian Qu
- Shandong Provincial Key Laboratory of Plant Stress Research, College of Life Sciences, Shandong Normal University, Jinan, Shangdong 250014, China
| | - Rong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China
| | - Gregory W Stull
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| | - Ting-Shuang Yi
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650201, China; CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.
| |
Collapse
|
19
|
Fort A, Linderhof C, Coca-Tagarro I, Inaba M, McHale M, Cascella K, Potin P, Guiry MD, Sulpice R. A sequencing-free assay for foliose Ulva species identification, hybrid detection and bulk biomass characterisation. ALGAL RES 2021. [DOI: 10.1016/j.algal.2021.102280] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
|
20
|
Yan F, Xi RM, She RX, Chen PP, Yan YJ, Yang G, Dang M, Yue M, Pei D, Woeste K, Zhao P. Improved de novo chromosome-level genome assembly of the vulnerable walnut tree Juglans mandshurica reveals gene family evolution and possible genome basis of resistance to lesion nematode. Mol Ecol Resour 2021; 21:2063-2076. [PMID: 33817972 DOI: 10.1111/1755-0998.13394] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 03/15/2021] [Accepted: 03/29/2021] [Indexed: 12/12/2022]
Abstract
Manchurian walnut (Juglans mandshurica Maxim.) is a synonym of J. cathayensis, a diploid, vulnerable, temperate deciduous tree valued for its wood and nut. It is also valued as a rootstock for Juglans regia because of its reported tolerance of lesion nematode. Reference genomes are available for several Juglans species, our goal was to produce a de novo, chromosome-level assembly of the J. mandshurica genome. Here, we reported an improved assembly of J. mandshurica with a contig N50 size of 6.49 Mb and a scaffold N50 size of 36.1 Mb. The total genome size was 548 Mb encoding 29,032 protein coding genes which were annotated. The collinearity analysis showed that J. mandshurica and J. regia originated from a common ancestor, with both species undergoing two WGD events. A genomic comparison showed that J. mandshurica was missing 1657 genes found in J. regia, and J. mandshurica includes 2827 genes not found in of the J. regia genome. The J. mandshurica contained 1440 unique paralogues that were highly enriched for flavonoid biosynthesis, phenylpropanoid biosynthesis, and plant-pathogen interaction. Four gene families related to disease resistance notable contraction (rapidly evolving; LEA, WAK, PPR, and PR) in J. mandshurica compared to eight species. JmaPR10 and JmaPR8 contained three orthologous gene pairs with J. regia that were highly expressed in root bark. JmaPR10 is a strong candidate gene for lesion nematodes resistance in J. mandshurica. The J. mandshurica genome should be a useful resource for study of the evolution, breeding, and genetic variation in walnuts (Juglans).
Collapse
Affiliation(s)
- Feng Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Rui-Min Xi
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Rui-Xue She
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Peng-Peng Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Yu-Jie Yan
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Ge Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Meng Dang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| | - Ming Yue
- Xi'an Botanical Garden of Shaanxi Province, Xi'an, China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Keith Woeste
- Department of Forestry and Natural Resources, USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Purdue University, West Lafayette, IN, USA
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, China
| |
Collapse
|
21
|
Levin RA, Miller JS. Molecular signatures of long-distance oceanic dispersal and the colonization of Pacific islands in Lycium carolinianum. AMERICAN JOURNAL OF BOTANY 2021; 108:694-710. [PMID: 33811320 DOI: 10.1002/ajb2.1626] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/24/2020] [Indexed: 06/12/2023]
Abstract
PREMISE Long-distance dispersal has been important in explaining the present distributions of many plant species. Despite being infrequent, such dispersal events have considerable evolutionary consequences, because bottlenecks during colonization can result in reduced genetic diversity. We examined the phylogeographic history of Lycium carolinianum, a widespread taxon that ranges from southeastern North America to several Pacific islands, with intraspecific diversity in sexual and mating systems. METHODS We used Bayesian, likelihood, and coalescent approaches with nuclear and plastid sequence data and genome-wide single nucleotide polymorphisms to reconstruct the dispersal history of this species. We also compared patterns of genetic variation in mainland and island populations using single nucleotide polymorphisms and allelic diversity at the S-RNase mating system gene. RESULTS Lycium carolinianum is monophyletic and dispersed once from the North American mainland, colonizing the Pacific islands ca. 40,100 years ago. This dispersal was accompanied by a loss of genetic diversity in SNPs and the S-RNase locus due to a colonization bottleneck and the loss of self-incompatibility. Additionally, we documented at least two independent transitions to gynodioecy: once following the colonization of the Hawaiian Islands and loss of self-incompatibility, and a second time associated with polyploidy in the Yucatán region of Mexico. CONCLUSIONS Long-distance dispersal via fleshy, bird dispersed fruits best explains the unusually widespread distribution of L. carolinianum. The collapse of diversity at the S-RNase locus in island populations suggests that self-fertilization may have facilitated the subsequent colonization of Pacific islands following a single dispersal from mainland North America.
Collapse
Affiliation(s)
- Rachel A Levin
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
| | - Jill S Miller
- Department of Biology, Amherst College, Amherst, Massachusetts, 01002, USA
| |
Collapse
|
22
|
Luan F, Wang Z, Yang Y, Ji Y, Lv H, Han K, Liu D, Shang X, He X, Zeng N. Juglans mandshurica Maxim.: A Review of Its Traditional Usages, Phytochemical Constituents, and Pharmacological Properties. Front Pharmacol 2021; 11:569800. [PMID: 33551795 PMCID: PMC7858255 DOI: 10.3389/fphar.2020.569800] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 12/04/2020] [Indexed: 12/20/2022] Open
Abstract
Juglans mandshurica Maxim., also known as “Manchurian walnut” (Chinese) and “Onigurumi” (Japanese), is a medicinal plant widely distributed in Western and Central Asia, especially in China. It has been traditionally used to treat cancer, gastric ulcers, diarrhea, dysentery, dermatosis, uterine prolapse, and leukopenia. To date, more than 400 constituents including quinones (e.g. naphthoquinones, anthraquinones, naphthalenones, tetralones), phenolics, flavonoids, triterpenoids, coumarins, lignans, phenylpropanoids, diarylheptanoids, and steroids, were isolated and structurally identified from different plant parts of J. mandshurica. Among them, quinones, phenolics, triterpenoids, and diarylheptanoids, as the major bioactive substances, have been extensively studied and displayed significant bioactivity. Previous studies have demonstrated that J. mandshurica and a few of its active components exhibit a wide range of pharmacologically important properties, such as antitumor, immunomodulatory, anti-inflammatory, neuroprotective, anti-diabetic, antiviral, antimicrobial, and anti-melanogenesis activities. However, many investigations on biological activities were mainly based on crude extracts of this plant, and the major bioactive ingredients responsible for these bioactivities have not been well identified. Further in vitro and in vivo studies on the mechanisms of action of the pure bioactive compounds, and more elaborate toxicity studies as well as clinical studies are needed to ensure safety and effectiveness of the plant for human use. Taken together, the present review will provide some specific useful suggestions guide to further investigations and applications of this plant in the preparation of medicines and functional foods.
Collapse
Affiliation(s)
- Fei Luan
- Department of Pharmacology, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China.,Department of Clinical Pharmacy, Shaanxi Provincial Hospital of Tuberculosis Prevention and Treatment, Xi'an, China
| | - Ziyan Wang
- Department of Clinical Pharmacy, Shaanxi Provincial Hospital of Tuberculosis Prevention and Treatment, Xi'an, China
| | - Yan Yang
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Yafei Ji
- Department of Pharmacology, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Haizhen Lv
- Department of Clinical Pharmacy, Shaanxi Provincial Hospital of Tuberculosis Prevention and Treatment, Xi'an, China
| | - Keqing Han
- Department of Clinical Pharmacy, Shaanxi Provincial Hospital of Tuberculosis Prevention and Treatment, Xi'an, China
| | - Daoheng Liu
- Department of Clinical Pharmacy, Shaanxi Provincial Hospital of Tuberculosis Prevention and Treatment, Xi'an, China
| | - Xiaofei Shang
- Key Laboratory of Veterinary Pharmaceutical Development of Ministry of Agriculture, Key Laboratory of New Animal Drug Project, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xirui He
- Department of Bioengineering, Zhuhai Campus of Zunyi Medical University, Zhuhai, China
| | - Nan Zeng
- Department of Pharmacology, College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| |
Collapse
|
23
|
Jin Y, Zhang Z, Xi Y, Yang Z, Xiao Z, Guan S, Qu J, Wang P, Zhao R. Identification and Functional Verification of Cold Tolerance Genes in Spring Maize Seedlings Based on a Genome-Wide Association Study and Quantitative Trait Locus Mapping. FRONTIERS IN PLANT SCIENCE 2021; 12:776972. [PMID: 34956272 PMCID: PMC8696014 DOI: 10.3389/fpls.2021.776972] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/19/2021] [Indexed: 05/13/2023]
Abstract
Maize (Zea mays L.) is a tropical crop, and low temperature has become one of the main abiotic stresses for maize growth and development, affecting many maize growth processes. The main area of maize production in China, Jilin province, often suffers from varying degrees of cold damage in spring, which seriously affects the quality and yield of maize. In the face of global climate change and food security concerns, discovering cold tolerance genes, developing cold tolerance molecular markers, and creating cold-tolerant germplasm have become urgent for improving maize resilience against these conditions and obtaining an increase in overall yield. In this study, whole-genome sequencing and genotyping by sequencing were used to perform genome-wide association analysis (GWAS) and quantitative trait locus (QTL) mapping of the two populations, respectively. Overall, four single-nucleotide polymorphisms (SNPs) and 12 QTLs were found to be significantly associated with cold tolerance. Through joint analysis, an intersection of GWAS and QTL mapping was found on chromosome 3, on which the Zm00001d002729 gene was identified as a potential factor in cold tolerance. We verified the function of this target gene through overexpression, suppression of expression, and genetic transformation into maize. We found that Zm00001d002729 overexpression resulted in better cold tolerance in this crop. The identification of genes associated with cold tolerance contributes to the clarification of the underlying mechanism of this trait in maize and provides a foundation for the adaptation of maize to colder environments in the future, to ensure food security.
Collapse
Affiliation(s)
- Yukun Jin
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, Novogene Co., Ltd, Beijing, China
| | - Yongjing Xi
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
| | - Zhou Yang
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
| | - Zhifeng Xiao
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
| | - Shuyan Guan
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
| | - Jing Qu
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
| | - Piwu Wang
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
- *Correspondence: Piwu Wang, Rengui Zhao,
| | - Rengui Zhao
- Joint Laboratory of International Cooperation in Modern Agriculture Technology of Ministry of Education, Plant Biotechnology Center, Jilin Agricultural University, Changchun, China
- *Correspondence: Piwu Wang, Rengui Zhao,
| |
Collapse
|
24
|
Zhang CY, Ling Low S, Song YG, Nurainas, Kozlowski G, Li L, Zhou SS, Tan YH, Cao GL, Zhou Z, Meng HH, Li J. Shining a light on species delimitation in the tree genus Engelhardia Leschenault ex Blume (Juglandaceae). Mol Phylogenet Evol 2020; 152:106918. [PMID: 32738292 DOI: 10.1016/j.ympev.2020.106918] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 07/16/2020] [Accepted: 07/21/2020] [Indexed: 10/23/2022]
Abstract
Enhanced efficacy in species delimitation is critically important in biology given the pending biodiversity crisis under global warming and anthropogenic activity. In particular, delineation of traditional classifications in view of the complexity of species requires an integrative approach to effectively define species boundaries, and this is a major focus of systematic biology. Here, we explored species delimitation of Engelhardia in tropical and subtropical Asia. In total, 716 individuals in 71 populations were genotyped using five chloroplast regions, one nuclear DNA region (nrITS), and 11 nuclear simple sequence repeats (nSSR). Phylogenetic trees were constructed and relationships among species were assessed. Molecular analyses were then combined with 14 morphological characteristics of 720 specimens to further explore the species boundaries of Engelhardia. Integrating phylogenetic and morphological clusters provided well-resolved relationships to delineate seven species. The results suggested that: first, that E. fenzelii, E. roxburghiana, E. hainanensis, E. apoensis, and E. serrata are distinct species; second, E. spicata var. spicata, E. spicata var. aceriflora, E. spicata var. colebrookeana, and E. rigida should be combined under E. spicata and treated as a species complex; third, E. serrata var. cambodica should be raised to species level and named E. villosa. We illuminated that bias thresholds determining the cluster number for delimiting species boundaries were substantially reduced when morphological data were incorporated. Our results urge caution when using the concepts of subspecies and varieties in order to prevent confusion, particularly with respect to species delimitation for tropical and subtropical species. In some cases, re-ranking or combining subspecies and/or varieties may enable more accurate species delimitation.
Collapse
Affiliation(s)
- Can-Yu Zhang
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shook Ling Low
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla 666303, China
| | - Yi-Gang Song
- Shanghai Chenshan Plant Science Research Center, Chinese Academy of Sciences, Shanghai 201602, China; Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Nurainas
- Department of Biology, Faculty of Math. & Nat. Sci. Andalas University, Padang 25163, West Sumatra, Indonesia
| | - Gregor Kozlowski
- Department of Biology and Botanic Garden, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Lang Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Shi-Shun Zhou
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar
| | - Yun-Hong Tan
- Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China
| | - Guan-Long Cao
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhuo Zhou
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Hong-Hu Meng
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar.
| | - Jie Li
- Plant Phylogenetics and Conservation Group, Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Kunming 650023, China; Southeast Asia Biodiversity Research Institute, Chinese Academy of Sciences, Nay Pyi Taw 05282, Myanmar; Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Mengla 666303, China.
| |
Collapse
|
25
|
Ramírez-Reyes T, Blair C, Flores-Villela O, Piñero D, Lathrop A, Murphy R. Phylogenomics and molecular species delimitation reveals great cryptic diversity of leaf-toed geckos (Phyllodactylidae: Phyllodactylus), ancient origins, and diversification in Mexico. Mol Phylogenet Evol 2020; 150:106880. [PMID: 32512192 DOI: 10.1016/j.ympev.2020.106880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 05/25/2020] [Accepted: 06/01/2020] [Indexed: 10/24/2022]
Abstract
We utilize the efficient GBS technique to obtain thousands of nuclear loci and SNPs to reconstruct the evolutionary history of Mexican leaf-toed geckos (Phyllodactylus). Through the incorporation of unprecedented sampling for this group of geckos, in combination with genomic data analysis, we generate mostly consistent phylogenetic hypotheses using two approaches: supermatrix and coalescent-based inference. All topologies depict three, mutually exclusive major clades. Clade I comprises P. bordai and all species closer to P. bordai than to any other Phyllodactylus. Clade II comprises P. nocticolus and all species closer to P. nocticolus than to any other Phyllodactylus. Clade III comprises P. tuberculosus and all species closer to P. tuberculosus than to any other Phyllodactylus. Analyses estimate the age for the most recent common ancestor of Phyllodactylus in the Eocene (~43 mya), and the ancestors of each major clade date to the Eocene-Oligocene transition (32-36 mya). This group includes one late-Eocene lineage (P. bordai), Oligocene lineages (P. paucituberculatus, P. delcampi), but also topological patterns that indicate a recent radiation occurred during the Pleistocene on islands in the Gulf of California. The wide spatial and temporal scale indicates a complex and unique biogeographic history for each major clade. The 33 species delimited by BPP and stepping-stone BFD*coalescent based genomic approaches reflect this history. This diversity delimited for Mexican leaf-toed geckos demonstrates a vast underestimation in the number of species based on morphological data alone.
Collapse
Affiliation(s)
- Tonatiuh Ramírez-Reyes
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Circuito de Posgrados, Ciudad Universitaria, Coyoacán, 04510 Ciudad de México, Mexico; Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510 Ciudad de México, Mexico; Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, 04510 Ciudad de México, Mexico.
| | - Christopher Blair
- Department of Biological Sciences, New York City College of Technology, The City University of New York, 285 Jay Street, Brooklyn, NY 11201, USA; Biology PhD Program, CUNY Graduate Center, 365 5th Ave., New York, NY 10016, USA
| | - Oscar Flores-Villela
- Museo de Zoología, Facultad de Ciencias, Universidad Nacional Autónoma de México, Circuito Exterior de CU, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Daniel Piñero
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad Universitaria, Apartado Postal 70-275, 04510 Ciudad de México, Mexico
| | - Amy Lathrop
- Royal Ontario Museum, Centre for Biodiversity and Conservation Biology, Toronto, Ontario, Canada
| | - Robert Murphy
- Royal Ontario Museum, Centre for Biodiversity and Conservation Biology, Toronto, Ontario, Canada; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Kunming, China
| |
Collapse
|
26
|
Trouern-Trend AJ, Falk T, Zaman S, Caballero M, Neale DB, Langley CH, Dandekar AM, Stevens KA, Wegrzyn JL. Comparative genomics of six Juglans species reveals disease-associated gene family contractions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 102:410-423. [PMID: 31823432 DOI: 10.1111/tpj.14630] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Accepted: 11/01/2019] [Indexed: 06/10/2023]
Abstract
Juglans (walnuts), the most speciose genus in the walnut family (Juglandaceae), represents most of the family's commercially valuable fruit and wood-producing trees. It includes several species used as rootstock for their resistance to various abiotic and biotic stressors. We present the full structural and functional genome annotations of six Juglans species and one outgroup within Juglandaceae (Juglans regia, J. cathayensis, J. hindsii, J. microcarpa, J. nigra, J. sigillata and Pterocarya stenoptera) produced using BRAKER2 semi-unsupervised gene prediction pipeline and additional tools. For each annotation, gene predictors were trained using 19 tissue-specific J. regia transcriptomes aligned to the genomes. Additional functional evidence and filters were applied to multi-exonic and mono-exonic putative genes to yield between 27 000 and 44 000 high-confidence gene models per species. Comparison of gene models to the BUSCO embryophyta dataset suggested that, on average, genome annotation completeness was 85.6%. We utilized these high-quality annotations to assess gene family evolution within Juglans, and among Juglans and selected Eurosid species. We found notable contractions in several gene families in J. hindsii, including disease resistance-related wall-associated kinase (WAK), Catharanthus roseus receptor-like kinase (CrRLK1L) and others involved in abiotic stress response. Finally, we confirmed an ancient whole-genome duplication that took place in a common ancestor of Juglandaceae using site substitution comparative analysis.
Collapse
Affiliation(s)
| | - Taylor Falk
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Sumaira Zaman
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - Madison Caballero
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| | - David B Neale
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Charles H Langley
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
| | - Abhaya M Dandekar
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Kristian A Stevens
- Department of Evolution and Ecology, University of California Davis, Davis, CA, USA
- Department of Computer Science, University of California Davis, Davis, CA, USA
| | - Jill L Wegrzyn
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA
| |
Collapse
|
27
|
Hao DC, Xiao PG. Pharmaceutical resource discovery from traditional medicinal plants: Pharmacophylogeny and pharmacophylogenomics. CHINESE HERBAL MEDICINES 2020; 12:104-117. [PMID: 36119793 PMCID: PMC9476761 DOI: 10.1016/j.chmed.2020.03.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/11/2019] [Accepted: 09/25/2019] [Indexed: 01/25/2023] Open
Abstract
The worldwide botanical and medicinal culture diversity are astonishing and constitute a Pierian spring for innovative drug R&D. Here, the latest awareness and the perspectives of pharmacophylogeny and pharmacophylogenomics, as well as their expanding utility in botanical drug R&D, are systematically summarized and highlighted. Chemotaxonomy is based on the fact that closely related plants contain the same or similar chemical profiles. Correspondingly, it is better to combine morphological characters, DNA markers and chemical markers in the inference of medicinal plant phylogeny. Medicinal plants within the same phylogenetic groups may have the same or similar therapeutic effects, thus forming the core of pharmacophylogeny. Here we systematically review and comment on the versatile applications of pharmacophylogeny in (1) looking for domestic resources of imported drugs, (2) expanding medicinal plant resources, (3) quality control, identification and expansion of herbal medicines, (4) predicting the chemical constituents or active ingredients of herbal medicine and assisting in the identification and determination of chemical constituents, (5) the search for new drugs sorting out, and (6) summarizing and improving herbal medicine experiences, etc. Such studies should be enhanced within the context of deeper investigations of molecular biology and genomics of traditional medicinal plants, phytometabolites and metabolomics, and ethnomedicine-based pharmacological activity, thus enabling the sustainable conservation and utilization of traditional medicinal resources.
Collapse
Affiliation(s)
- Da-cheng Hao
- Biotechnology Institute, School of Environment and Chemical Engineering, Dalian Jiaotong University, Dalian 116028, China
- Corresponding author.
| | - Pei-gen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Beijing 100193, China
| |
Collapse
|
28
|
Sun Y, Hou N, Woeste K, Zhang C, Yue M, Yuan X, Zhao P. Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China. Ecol Evol 2019; 9:14154-14166. [PMID: 31938510 PMCID: PMC6953554 DOI: 10.1002/ece3.5850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/07/2022] Open
Abstract
Southwestern (SW) China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that influences the genetic structure of the resident populations of plants and animals. Iron walnut (Juglans regia subsp. sigillata) is a deciduous tree species endemic to this region of China and cultivated there for its edible nuts. We sampled 36 iron walnut populations from locations throughout the species' range in SW China and genotyped a total of 765 individuals at five chloroplast DNA regions and 22 nuclear microsatellite loci. Species distribution models were produced to predict the evolution and historical biogeography of iron walnut and to estimate the impacts of climate oscillations and orographic environments on the species' demography. Our results indicated that J. regia subsp. sigillata had relatively low genetic diversity, high interpopulation genetic differentiation, and asymmetric interpopulation gene flow. Based on DIYABC analysis, we identified two lineages of J. sigillata in southwestern China. The lineages (subpopulations) diverge during the last glacial period (~1.34 Ma). Southwestern China was a glacial refuge during the last glacial period, but increasingly colder and arid climates might have fostered the fragmentation of J. regia subsp. sigillata within this refugium. Finally, we found that recent habitat fragmentation has led to a reduction in population connectivity and increased genetic differentiation by genetic drift in isolated populations. Our results support a conclusion that geological and climatic factors since the Miocene triggered the differentiation, evolutionary origin, and range shifts of J. sigillata in the studied region.
Collapse
Affiliation(s)
- Yi‐Wei Sun
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Na Hou
- Guizhou Academy of ForestryGuiyangChina
| | - Keith Woeste
- Department of Forestry and Natural ResourcesUSDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC)Purdue UniversityWest LafayetteINUSA
| | - Chuchu Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
- Xi'an Botanical Garden of Shaanxi ProvinceXi'anChina
| | - Xiao‐Ying Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| |
Collapse
|
29
|
Liu S, Cornille A, Decroocq S, Tricon D, Chague A, Eyquard JP, Liu WS, Giraud T, Decroocq V. The complex evolutionary history of apricots: Species divergence, gene flow and multiple domestication events. Mol Ecol 2019; 28:5299-5314. [PMID: 31677192 DOI: 10.1111/mec.15296] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 10/28/2019] [Accepted: 10/31/2019] [Indexed: 12/31/2022]
Abstract
Domestication is an excellent model to study diversification and this evolutionary process can be different in perennial plants, such as fruit trees, compared to annual crops. Here, we inferred the history of wild apricot species divergence and of apricot domestication history across Eurasia, with a special focus on Central and Eastern Asia, based on microsatellite markers and approximate Bayesian computation. We significantly extended our previous sampling of apricots in Europe and Central Asia towards Eastern Asia, resulting in a total sample of 271 cultivated samples and 306 wild apricots across Eurasia, mainly Prunus armeniaca and Prunus sibirica, with some Prunus mume and Prunus mandshurica. We recovered wild Chinese species as genetically differentiated clusters, with P. sibirica being divided into two clusters, one possibly resulting from hybridization with P. armeniaca. Central Asia also appeared as a diversification centre of wild apricots. We further revealed at least three domestication events, without bottlenecks, that gave rise to European, Southern Central Asian and Chinese cultivated apricots, with ancient gene flow among them. The domestication event in China possibly resulted from ancient hybridization between wild populations from Central and Eastern Asia. We also detected extensive footprints of recent admixture in all groups of cultivated apricots. Our results thus show that apricot is an excellent model for studying speciation and domestication in long-lived perennial fruit trees.
Collapse
Affiliation(s)
- Shuo Liu
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France.,Liaoning Institute of Pomology, Yingkou City, China
| | - Amandine Cornille
- GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - David Tricon
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France
| | - Aurélie Chague
- UMR BFP, INRA-Université de Bordeaux, Villenave d'Ornon, France
| | | | | | - Tatiana Giraud
- Ecologie Systematique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay, France
| | | |
Collapse
|
30
|
Gene Introgression among Closely Related Species in Sympatric Populations: A Case Study of Three Walnut (Juglans) Species. FORESTS 2019. [DOI: 10.3390/f10110965] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Gene introgression usually results from natural hybridization occurring among closely related species in sympatric populations. In this study, we discussed two rare and frequent gene flow phenomena between three species of Juglans plants and analyzed the possible causes for the difference. We collected 656 individuals from 40 populations of Persian walnut (Juglans regia L.), Chinese walnut (J. cathayensis Dode), and Iron walnut (J. sigillata Dode) that were genotyped at 17 expressed sequence tag simple sequence repeat (EST-SSR) loci to analyze the introgressions between J. regia and J. cathayensis, and J. regia and J. sigillata. Our study compared the spatial patterns of expected heterozygosity (HE), allelic richness (Rs), and private allele richness (PAR) so as to vividly infer the biogeographic history of related species of Juglans in the two regions. The results of the PCoA, UPGMA, and STRUCTURE analyses showed that all J. regia and J. sigillata populations clustered into one group, and the J. cathayensis populations clustered into the other group. The results of the historical gene flow analysis indicated that J. regia and J. sigillata have no genetic barriers, and the directional gene flow is mainly from J. regia to J. sigillata. For the three species of Juglans, all the above results indicated that gene flow was common among the same group of Juglans, and only rare and low-level gene flow appeared in distinct groups. Therefore, our study revealed multiple phenomena of gene flow and introgression among closely related species in sympatric populations, thereby providing a theoretical basis for the genetic evolution of the genus Juglans.
Collapse
|
31
|
Ge Y, Dong X, Wu B, Wang N, Chen D, Chen H, Zou M, Xu Z, Tan L, Zhan R. Evolutionary analysis of six chloroplast genomes from three Persea americana ecological races: Insights into sequence divergences and phylogenetic relationships. PLoS One 2019; 14:e0221827. [PMID: 31532782 PMCID: PMC6750585 DOI: 10.1371/journal.pone.0221827] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2019] [Accepted: 08/15/2019] [Indexed: 11/19/2022] Open
Abstract
Chloroplasts significantly influence species phylogenies because of their maternal inheritance and the moderate evolutionary rate of their genomes. Avocado, which is a member of the family Lauraceae, has received considerable attention from botanists, likely because of its position as a basal angiosperm. However, there is relatively little avocado genomic information currently available. In this study, six complete avocado chloroplast genomes from three ecological races were assembled to examine the sequence diversity among the three avocado ecological races. A comparative genomic analysis revealed that 515 simple sequence repeat loci and 176 repeats belonging to four other types were polymorphic across the six chloroplast genomes. Three highly variable regions (trnC-GCA-petN, petN-psbM, and petA-psbJ) were identified as highly informative markers. A phylogenetic analysis based on 79 common protein-coding genes indicated that the six examined avocado accessions from three ecological races form a monophyletic clade. The other three genera belonging to the Persea group clustered to form a sister clade with a high bootstrap value. These chloroplast genomes provide important genetic information for future attempts at identifying avocado races and for the related biological research.
Collapse
Affiliation(s)
- Yu Ge
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xiangshu Dong
- College of Agriculture, Yunnan University, Yunnan, China
| | - Bin Wu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Nan Wang
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Di Chen
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Haihong Chen
- College of Agriculture, Guangxi Vocational and Technical College, Nanning, China
| | - Minghong Zou
- South Subtropical Crops Research Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Zining Xu
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Lin Tan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail: (LT); (RZ)
| | - Rulin Zhan
- Haikou Experimental Station, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- * E-mail: (LT); (RZ)
| |
Collapse
|
32
|
Luo X, Liu J. Transcriptome Analysis of Acid-Responsive Genes and Pathways Involved in Polyamine Regulation in Iron Walnut. Genes (Basel) 2019; 10:E605. [PMID: 31405132 PMCID: PMC6723594 DOI: 10.3390/genes10080605] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 08/07/2019] [Accepted: 08/07/2019] [Indexed: 02/07/2023] Open
Abstract
We reported changes in the co-regulated mRNA expression in iron walnut (Juglans sigillata) in response to soil pH treatments and identified mRNAs specific to acidic soil conditions. Phenotypic and physiological analyses revealed that iron walnut growth was greater for the pH 4-5 and pH 5-6 treatments than for the pH 3-4 and pH 6-7 treatments. A total of 2768 differentially expressed genes were detected and categorized into 12 clusters by Short Time-series Expression Miner (STEM). The 994 low-expression genes in cluster III and 255 high-expression genes in cluster X were classified as acid-responsive genes on the basis of the relationships between phenotype, physiology, and STEM clustering, and the two gene clusters were analyzed by a maximum likelihood (ML) evolutionary tree with the greatest log likelihood values. No prominent sub-clusters occurred in cluster III, but three occurred in cluster X. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated that acid-responsive genes were related primarily to arginine biosynthesis and the arginine/proline metabolism pathway, implying that polyamine accumulation may enhance iron walnut acid stress tolerance. Overall, our results revealed 1249 potentially acid-responsive genes in iron walnut, indicating that its response to acid stress involves different pathways and activated genes.
Collapse
Affiliation(s)
- Xiaomei Luo
- College of Forestry, Sichuan Agricultural University, Huimin Road 211 in Wenjiang District, Chengdu 611130, China.
| | - Juncheng Liu
- College of Forestry, Sichuan Agricultural University, Huimin Road 211 in Wenjiang District, Chengdu 611130, China
| |
Collapse
|
33
|
Zhang BW, Xu LL, Li N, Yan PC, Jiang XH, Woeste KE, Lin K, Renner SS, Zhang DY, Bai WN. Phylogenomics Reveals an Ancient Hybrid Origin of the Persian Walnut. Mol Biol Evol 2019; 36:2451-2461. [PMID: 31163451 DOI: 10.1093/molbev/msz112] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 04/13/2019] [Accepted: 04/16/2019] [Indexed: 01/25/2023] Open
Abstract
Abstract
Persian walnut (Juglans regia) is cultivated worldwide for its high-quality wood and nuts, but its origin has remained mysterious because in phylogenies it occupies an unresolved position between American black walnuts and Asian butternuts. Equally unclear is the origin of the only American butternut, J. cinerea. We resequenced the whole genome of 80 individuals from 19 of the 22 species of Juglans and assembled the genome of its relatives Pterocarya stenoptera and Platycarya strobilacea. Using phylogenetic-network analysis of single-copy nuclear genes, genome-wide site pattern probabilities, and Approximate Bayesian Computation, we discovered that J. regia (and its landrace J. sigillata) arose as a hybrid between the American and the Asian lineages and that J. cinerea resulted from massive introgression from an immigrating Asian butternut into the genome of an American black walnut. Approximate Bayesian Computation modeling placed the hybrid origin in the late Pliocene, ∼3.45 My, with both parental lineages since having gone extinct in Europe.
Collapse
Affiliation(s)
- Bo-Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lin-Lin Xu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Nan Li
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Peng-Cheng Yan
- Beijing Key Laboratory of Cloud Computing Key Technology and Application, Beijing Computing Center, Beijing, China
| | - Xin-Hua Jiang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Keith E Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Susanne S Renner
- Department of Biology, Systematic Botany and Mycology, University of Munich (LMU), Munich, Germany
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
34
|
Genome-Wide Identification and Transcriptional Expression Profiles of the F-box Gene Family in Common Walnut (Juglans regia L.). FORESTS 2019. [DOI: 10.3390/f10030275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The common walnut (or Persian walnut), Juglans regia L., is an economically important temperate tree species valued for both its edible nut and high-quality wood. F-box gene family members are involved in plant development, which includes regulating plant development, reproduction, cellular protein degradation, response to biotic and abiotic stresses, and flowering. However, in common walnut (J. regia), there are no reports about the F-box gene family. Here, we report a genome-wide identification of J. regia F-box genes and analyze their phylogeny, duplication, microRNA, pathway, and transcriptional expression profile. In this study, 74 F-box genes were identified and clustered into three groups based on phylogenetic analysis and eight subfamilies based on special domains in common walnut. These common walnut F-box genes are distributed on 31 different pseudo-chromosomes. The gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and microRNA profiles showed that the F-box gene family might play a critical role in the flowering of common walnut. The expressions were significantly higher in female flowers and male flowers compared with leaf and hull tissues at a transcriptome level. The results revealed that the expressions of the F-box gene in female flowers were positively correlated with male flowers, but there was no correlation between any other tissue combinations in common walnut. Our results provided insight into the general characteristics of the F-box genes in common walnut.
Collapse
|
35
|
Zhou YY, Guo S, Wang Y, Song HJ, Gao HR, Zhang XJ, Sun YP, Liu Y, Yang BY, Kuang HX. α-Tetralone glycosides from the green walnut husks of Juglans mandshurica Maxim. and their cytotoxic activities. Nat Prod Res 2019; 34:1805-1813. [PMID: 30676067 DOI: 10.1080/14786419.2018.1561681] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Five new α-tetralone glycosides, juglanbiosides A-E (1-5), together with an α-tetralone derivative (15) and nine known 1,4-naphthoquinones (6-14) were isolated from the 95% EtOH extract of green walnut husks of Juglans mandshurica Maxim. Their structures were elucidated by comprehensive spectroscopic methods (1H, 13C NMR, DEPT, HSQC, HMBC, CD, HR-ESI-MS). In vitro cytotoxicities of all the isolated compounds were evaluated against BGC-823, HCT-15 and K562 cancer cell lines.[Formula: see text].
Collapse
Affiliation(s)
- Yuan-Yuan Zhou
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Shuang Guo
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Ying Wang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hong-Juan Song
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hui-Rui Gao
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Xiao-Juan Zhang
- Academic research department, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yan-Ping Sun
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yan Liu
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Bing-You Yang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| | - Hai-Xue Kuang
- College of Pharmacy, Heilongjiang University of Chinese Medicine, Harbin, China
| |
Collapse
|
36
|
Luo Z, Brock J, Dyer JM, Kutchan T, Schachtman D, Augustin M, Ge Y, Fahlgren N, Abdel-Haleem H. Genetic Diversity and Population Structure of a Camelina sativa Spring Panel. FRONTIERS IN PLANT SCIENCE 2019; 10:184. [PMID: 30842785 PMCID: PMC6391347 DOI: 10.3389/fpls.2019.00184] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/05/2019] [Indexed: 05/20/2023]
Abstract
There is a need to explore renewable alternatives (e.g., biofuels) that can produce energy sources to help reduce the reliance on fossil oils. In addition, the consumption of fossil oils adversely affects the environment and human health via the generation of waste water, greenhouse gases, and waste solids. Camelina sativa, originated from southeastern Europe and southwestern Asia, is being re-embraced as an industrial oilseed crop due to its high seed oil content (36-47%) and high unsaturated fatty acid composition (>90%), which are suitable for jet fuel, biodiesel, high-value lubricants and animal feed. C. sativa's agronomic advantages include short time to maturation, low water and nutrient requirements, adaptability to adverse environmental conditions and resistance to common pests and pathogens. These characteristics make it an ideal crop for sustainable agricultural systems and regions of marginal land. However, the lack of genetic and genomic resources has slowed the enhancement of this emerging oilseed crop and exploration of its full agronomic and breeding potential. Here, a core of 213 spring C. sativa accessions was collected and genotyped. The genotypic data was used to characterize genetic diversity and population structure to infer how natural selection and plant breeding may have affected the formation and differentiation within the C. sativa natural populations, and how the genetic diversity of this species can be used in future breeding efforts. A total of 6,192 high-quality single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing (GBS) technology. The average polymorphism information content (PIC) value of 0.29 indicate moderate genetic diversity for the C. sativa spring panel evaluated in this report. Population structure and principal coordinates analyses (PCoA) based on SNPs revealed two distinct subpopulations. Sub-population 1 (POP1) contains accessions that mainly originated from Germany while the majority of POP2 accessions (>75%) were collected from Eastern Europe. Analysis of molecular variance (AMOVA) identified 4% variance among and 96% variance within subpopulations, indicating a high gene exchange (or low genetic differentiation) between the two subpopulations. These findings provide important information for future allele/gene identification using genome-wide association studies (GWAS) and marker-assisted selection (MAS) to enhance genetic gain in C. sativa breeding programs.
Collapse
Affiliation(s)
- Zinan Luo
- U.S. Arid Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, United States
- *Correspondence: Zinan Luo, Hussein Abdel-Haleem,
| | - Jordan Brock
- Department of Biology, Washington University in St. Louis, St. Louis, MO, United States
| | - John M. Dyer
- U.S. Arid Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, United States
| | - Toni Kutchan
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Daniel Schachtman
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE, United States
| | - Megan Augustin
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Yufeng Ge
- Department of Biological and Agricultural Engineering, University of Nebraska, Lincoln, NE, United States
| | - Noah Fahlgren
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Hussein Abdel-Haleem
- U.S. Arid Land Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Maricopa, AZ, United States
- *Correspondence: Zinan Luo, Hussein Abdel-Haleem,
| |
Collapse
|
37
|
Chen L, Dong R, Ma Q, Zhang Y, Xu S, Ning D, Chen Q, Pei D. Precocious genotypes and homozygous tendency generated by self-pollination in walnut. BMC PLANT BIOLOGY 2018; 18:323. [PMID: 30509158 PMCID: PMC6278120 DOI: 10.1186/s12870-018-1549-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 11/21/2018] [Indexed: 06/01/2023]
Abstract
BACKGROUND Observations of precocious (early bearing) genotypes of walnut (Juglans regia L.) under natural conditions encouraged us to study the origin and genetic control of these fascinating traits. RESULTS In this study, the self-fertility, progeny performance, and simple sequence repeat (SSR) locus variation of iron walnut (Juglans sigillata Dode), an ecotype of J. regia, were investigated. The average self-pollinated fruit set rate of J. sigillata cv. 'Dapao' (DP) was 7.0% annually from 1979 to 1982. The average germination rate of self-pollinated seeds was 45.2% during the 4-year period. Most progeny had inbreeding depression. Nine representative self-pollinated progeny (SP1-SP9), with special or typical traits of DP, were selected. SP1-SP4 were precocious because they initiated flowers as early as 2 years after germination, compared to the 7-10-yr period that is typical of DP. SP9 had not flowered since 1980. Twelve SSR markers were used to analyze the SP and DP. The genome of SP had a tendency toward high levels of homozygosity. The high levels of homozygosity reported in 18 additional precocious walnut genotypes complemented the results of this study. CONCLUSIONS These results provide evidence of precocious phenotypes and genomes with high levels of homozygosity that might be generated from self-pollinating walnut. This suggests that self-pollination might facilitate the generation of unique homozygous parents for subsequent use in walnut-breeding programs. The results also indicate that more attention should be focused on adequate management of precocious walnut to avoid early depression in the production of nuts.
Collapse
Affiliation(s)
- Lingna Chen
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
- Research Institute of Resources Insects, Chinese Academy of Forestry, Kunming, 650233 Yunnan China
| | - Runquan Dong
- Yunnan Academy of Forestry, Kunming, 650204 Yunnan China
| | - Qingguo Ma
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| | - Yu Zhang
- Yunnan Academy of Forestry, Kunming, 650204 Yunnan China
| | - Shizhong Xu
- Dali Forest Resource Management Station, Dali, 671000 Yunnan China
| | - Delu Ning
- Yunnan Academy of Forestry, Kunming, 650204 Yunnan China
| | - Qin Chen
- Yunnan Academy of Forestry, Kunming, 650204 Yunnan China
| | - Dong Pei
- State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091 China
| |
Collapse
|
38
|
Population Structure, Genetic Diversity, and Gene Introgression of Two Closely Related Walnuts (Juglans regia and J. sigillata) in Southwestern China Revealed by EST-SSR Markers. FORESTS 2018. [DOI: 10.3390/f9100646] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The common walnut (Juglans regia L.) and iron walnut (J. sigillata Dode) are well-known economically important species cultivated for their edible nuts, high-quality wood, and medicinal properties and display a sympatric distribution in southwestern China. However, detailed research on the genetic diversity and introgression of these two closely related walnut species, especially in southwestern China, are lacking. In this study, we analyzed a total of 506 individuals from 28 populations of J. regia and J. sigillata using 25 EST-SSR markers to determine if their gene introgression was related to sympatric distribution. In addition, we compared the genetic diversity estimates between them. Our results indicated that all J. regia populations possess slightly higher genetic diversity than J. sigillata populations. The Geostatistical IDW technique (HO, PPL, NA and PrA) revealed that northern Yunnan and Guizhou provinces had high genetic diversity for J. regia while the northwestern Yunnan province had high genetic diversity for J. sigillata. AMOVA analysis revealed that significant genetic variation was mainly distributed within population as 73% in J. regia and 76% in J. sigillata. The genetic differentiation (FST) was 0.307 between the two walnut species (p < 0.0001), which was higher than FST values within populations (J. regia FST = 0.265 and J. sigillata FST = 0.236). However, the STRUCTURE analysis of the J. regia and J. sigillata populations revealed two genetic clusters in which gene introgression exists, therefore, the boundary of separation between these two walnut species is not clear. Moreover, these results were validated by NJ and UPGMA analysis with additional conformation from the PCoA. Based on the SSR data, our results indicate that J. sigillata is an ecotype of J. regia. Taken together, these results reveal novel information on population genetics and provide specific geographical regions containing high genetic diversity of the Juglans species sampled, which will assist in future conservation management.
Collapse
|
39
|
Feng X, Zhou H, Zulfiqar S, Luo X, Hu Y, Feng L, Malvolti ME, Woeste K, Zhao P. The Phytogeographic History of Common Walnut in China. FRONTIERS IN PLANT SCIENCE 2018; 9:1399. [PMID: 30298084 PMCID: PMC6160591 DOI: 10.3389/fpls.2018.01399] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 09/03/2018] [Indexed: 05/16/2023]
Abstract
Common walnut (Juglans regia L.) is an economically important hardwood tree species cultivated worldwide for its high quality wood and edible nuts. It is generally accepted that after the last glaciation J. regia survived and grew in almost completely isolated stands in Asia, and that ancient humans dispersed walnuts across Asia and into new habitats via trade and cultural expansion. The history of common walnut in China is a matter of debate, however. We estimated the genetic diversity and spatial genetic structure of 31 walnut populations sampled across its Chinese range using 22 microsatellite markers (13 neutral and 9 non-neutral). Using historical data and population genetic analysis, including approximate Bayesian analysis (ABC), we reconstructed the demographic history of J. regia in China. The genetic data indicated the likely presence of J. regia in glacial refugia in the Xinjiang province (Northwest China), Northeastern China (Beijing, Shandong, and Changbai Mountains), Central China (Qinling and Baishan Mountains and Xi'an), and Southwestern China (Tibet, Yunnan, Guizhou, and Sichuan provinces). Based on DIY-ABC analysis, we identified three ancient lineages of J. regia in China. Two lineages (subpopulation A and subpopulation B+C) diverged about 2.79 Mya, while Southwestern China, and Qinling and Baishan Mountains lineages diverged during the Quaternary glaciations (about 1.13 Mya). Remnants of these once-distinct genetic clusters of J. regia may warrant ecological management if they are to be retained as in situ resources. A population size expansion in Northeastern China was detected in the last five centuries. The present distribution of walnut in China resulted from the combined effects of expansion/contraction from multiple refugia after the Last Glacial Maximum and later human exploitation.
Collapse
Affiliation(s)
- Xiaojia Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Huijuan Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Saman Zulfiqar
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Xiang Luo
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, China
| | - Yiheng Hu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Li Feng
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| | - Maria E. Malvolti
- Institute of Agro-environmental and Forest Biology, Consiglio Nazionale delle Ricerche, Terni, Italy
| | - Keith Woeste
- USDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC), Department of Forestry and Natural Resources, Purdue University, West Lafayette, IN, United States
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an, China
| |
Collapse
|