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Yan P, Xie Z, Feng K, Qiu X, Zhang L, Zhang H. Genetic diversity analysis and fingerprint construction of Korean pine ( Pinus koraiensis) clonal seed orchard. FRONTIERS IN PLANT SCIENCE 2023; 13:1079571. [PMID: 36726668 PMCID: PMC9886227 DOI: 10.3389/fpls.2022.1079571] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 12/29/2022] [Indexed: 06/18/2023]
Abstract
Korean pine is a native tree species in Northeast China. In order to meet the needs of germplasm resource evaluation and molecular marker-assisted breeding of Korean pine, we collected Korean pine clones from 7 populations in Northeast China, analyzed the genetic diversity and genetic structure by SSR molecular marker technology and clustered them to revealed the inter- and intrapopulation differentiation characteristics of each clone. The fingerprint profiles of 161 Korean pine clones were also constructed. 77 alleles were detected for 11 markers, and 18 genotypes were identified on average for each marker. The PIC of the different markers ranged from 0.155-0.855, and the combination of PI and PIsibs for the 11 markers was 3.1 × 10-8 and 1.14 × 10-3, respectively. MANOVA showed that genetic variation existed mainly within populations, accounting for 98% of the total variation. The level of genetic differentiation among populations was low, with an average Nm between populations of 11.036. Genetic diversity is lower in the Lushuihe population and higher in the Tieli population. The 161 Korean pine clones were divided into 4 or 7 populations, and the 7 populations were not clearly distinguished from each other, with only the Lushuihe population showing partial differentiation. There is no significant correlation between the genetic distance of Korean pine populations and the geographical distance of their superior tree sources. This result can provide recommendations for future Korean pine breeding programs. The combination of 11 markers could completely distinguish 161 clones and establish the fingerprint. Genetic diversity of Korean pine clones from the 7 populations was abundant, and the genetic distances of individuals and populations were evenly dispersed. The fingerprint map can be used for the identification of Korean pine clones.
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Affiliation(s)
- Pingyu Yan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Zixiong Xie
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Kele Feng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Xinyu Qiu
- Heilongjiang Academy of Forestry, Harbin, China
| | - Lei Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Hanguo Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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Lee K, Kim IS, Kang KS. Pedigree reconstruction and spatial analysis for genetic testing and selection in a Larix kaempferi (Lamb.) Carrière plantation. BMC PLANT BIOLOGY 2022; 22:152. [PMID: 35346034 PMCID: PMC8962119 DOI: 10.1186/s12870-022-03530-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Larix kaempferi is one of the major timber species in Northeast Asia. Demand for the reforestation of the species is rising in South Korea due to an increase in large timber production and utilization. However, progeny trials for the species have not been explored, making it challenging to foster advanced generations of tree improvement. In the present study, genetic testing and selection for diameter growth were conducted using pedigree reconstruction and phenotypic spatial distribution analysis in a plantation of L. kaempferi. The aim of the present study was to select the superior larch individuals using the pedigree reconstruction and phenotypic spatial distribution to substitute progeny trials. The plantation of seed orchard crops was established in 1990 and one-hundred and eighty-eight trees were selected as the study material. Genetic variation was investigated first to validate its adequacy as breeding material. Genetic testing was carried out using a model considering pedigree information and spatial autoregression of the phenotypes. RESULTS The expected heterozygosity of the mother trees and offspring were 0.672 and 0.681 presenting the corresponding level of genetic variation between two groups. The pedigree reconstruction using maternity analysis assigned one to six progenies to ninety-two candidate mothers. The accuracy of genetic testing was exceedingly increased with the animal model considering AR1 ⊗ AR1 structure compared to the animal model only. The estimated genetic variance of the former was 9.086 whereas that of the latter was 4.9E-5 for DBH. The predicted breeding values of the offspring for DBH were ranged from -5.937 cm to 5.655 cm and the estimated heritability of diameter growth was 0.344. CONCLUSIONS The genetic testing approach based on pedigree reconstruction and phenotypic spatial distribution analysis was considered a useful analytical scheme that could replace or supplement progeny trials.
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Affiliation(s)
- Kyungmi Lee
- Division of Tree Improvement and Biotechnology, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - In-Sik Kim
- Division of Tree Improvement and Biotechnology, Department of Forest Bio-Resources, National Institute of Forest Science, Suwon, 16631, Republic of Korea
| | - Kyu-Suk Kang
- Department of Agriculture, Forestry and Bioresources, College of Agriculture and Life Sciences, Seoul National University, Seoul, 08826, Republic of Korea.
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Genetic Diversity and Population Genetic Structure of Ancient Platycladus orientalis L. (Cupressaceae) in the Middle Reaches of the Yellow River by Chloroplast Microsatellite Markers. FORESTS 2021. [DOI: 10.3390/f12050592] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Ancient trees are famous for their life spans of hundreds or even thousands of years. These trees are rare, a testament to history and are important for scientific research. Platycladus orientalis, with the longest life span and a beautiful trunk, has become the most widely planted tree species and is believed to be sacred in China. Extensive declines in habitat area and quality pose the greatest threats to the loss of genetic diversity of ancient P. orientalis trees in the middle reaches of the Yellow River. Strengthening the protection of P. orientalis genetic resources is of great significance for the long-term development of reasonable conservation and breeding strategies. To better understand the genetic diversity and population structure of P. orientalis, we successfully analyzed four polymorphic chloroplast simple sequence repeat (cpSSR) loci and applied them to diversity and population structure analyses of 202 individuals from 13 populations in the middle reaches of the Yellow River. Based on the cpSSR data, 16 alleles were detected across 202 individuals, and a moderate level of genetic diversity was inferred from the genetic diversity parameters (H = 0.367 and AR = 1.964). The mean pairwise genetic differentiation coefficient (Fst) between populations was 0.153, indicating relatively high genetic population differentiations. Analysis of molecular variance (AMOVA) showed that only 8% of the variation occurred among populations. Structure analysis divided the 13 P. orientalis populations into two groups with no significant geographic population structure, which was consistent with the unweighted pair group method with arithmetic mean (UPGMA) and Mantel test results. These results may indicate that transplanting and cultivation by ancient human activities are the main factors responsible for the revealed pattern of genetic differentiation of ancient P. orientalis populations. Our research is of great significance for the future establishment of protection schemes and scientific breeding of P. orientalis.
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Genome-Wide Variant Identification and High-Density Genetic Map Construction Using RADseq for Platycladus orientalis (Cupressaceae). G3-GENES GENOMES GENETICS 2019; 9:3663-3672. [PMID: 31506321 PMCID: PMC6829139 DOI: 10.1534/g3.119.400684] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Platycladus orientalis is an ecologically important native conifer in Northern China and exotic species in many parts of the world; however, knowledge about the species’ genetics and genome are very limited. The availability of well-developed battery of genetic markers, with large genome coverage, is a prerequisite for the species genetic dissection of adaptive attributes and efficient selective breeding. Here, we present a genome-wide genotyping method with double-digestion restriction site associated DNA sequencing (ddRAD-seq) that is effective in generating large number of Mendelian markers for genome mapping and other genetic applications. Using 139 megagametophytes collected from a single mother tree, we assembled 397,226 loci, of which 108,683 (27.4%) were polymorphic. After stringent filtering for 1:1 segregation ratio and missing rate of <20%, the remaining 23,926 loci (22% of the polymorphic loci) were ordered into 11 linkage groups (LGs) and distributed across 7,559 unique positions, with a total map length of 1,443 cM and an average spacing of 0.2 cM between adjacent unique positions. The 11 LGs correspond to the species’ 11 haploid genome chromosome number. This genetic map is among few high-density maps available for conifers to date, and represents the first genetic map for P. orientalis. The information generated serves as a solid foundation not only for marker-assisted breeding efforts, but also for comparative conifer genomic studies.
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Taheri S, Abdullah TL, Rafii MY, Harikrishna JA, Werbrouck SPO, Teo CH, Sahebi M, Azizi P. De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. Sci Rep 2019; 9:3047. [PMID: 30816255 PMCID: PMC6395698 DOI: 10.1038/s41598-019-39944-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/06/2019] [Indexed: 11/24/2022] Open
Abstract
Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - M Y Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Stefaan P O Werbrouck
- Laboratory of Applied Science In Vitro Plant Biotechnology, Department of Plants and Crops, Faculty of Bioscience Engineering, University Ghent, Valentin Vaerwyckweg 1, BE-9000, Gent, Belgium
| | - Chee How Teo
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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Maruyama TE, Hosoi Y. Progress in Somatic Embryogenesis of Japanese Pines. FRONTIERS IN PLANT SCIENCE 2019; 10:31. [PMID: 30745904 PMCID: PMC6360188 DOI: 10.3389/fpls.2019.00031] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 01/09/2019] [Indexed: 05/23/2023]
Abstract
Somatic embryogenesis (SE) in not only one of the most promising techniques for mass propagation of selected trees, but also is a valuable tool for basic research studies in cell biology and genetic engineering, and it allows the long-term ex situ conservation of genetic resources by cryopreservation techniques. This review reports the most recent progress in SE, protoplast culture, and cryopreservation of four important Japanese pines (Pinus thunbergii, Pinus densiflora, Pinus armandii var. amamiana, and Pinus luchuensis). Induction of embryogenic tissues (ET), embryogenic culture maintenance/proliferation, production of somatic embryos, germination, and conversion to plants are described focusing on the protocols most commonly reported for plant production in Pinus species through to SE.
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Affiliation(s)
- Tsuyoshi E. Maruyama
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research Institute, Tsukuba, Japan
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Hiraoka Y, Fukatsu E, Mishima K, Hirao T, Teshima KM, Tamura M, Tsubomura M, Iki T, Kurita M, Takahashi M, Watanabe A. Potential of Genome-Wide Studies in Unrelated Plus Trees of a Coniferous Species, Cryptomeria japonica (Japanese Cedar). FRONTIERS IN PLANT SCIENCE 2018; 9:1322. [PMID: 30254658 PMCID: PMC6141754 DOI: 10.3389/fpls.2018.01322] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 08/22/2018] [Indexed: 06/08/2023]
Abstract
A genome-wide association study (GWAS) was conducted on more than 30,000 single nucleotide polymorphisms (SNPs) in unrelated first-generation plus tree genotypes from three populations of Japanese cedar Cryptomeria japonica D. Don with genomic prediction for traits of growth, wood properties and male fecundity. Among the assessed populations, genetic characteristics including the extent of linkage disequilibrium (LD) and genetic structure differed and these differences are considered to be due to differences in genetic background. Through population-independent GWAS, several significant SNPs found close to the regions associated with each of these traits and shared in common across the populations were identified. The accuracies of genomic predictions were dependent on the traits and populations and reflected the genetic architecture of traits and genetic characteristics. Prediction accuracies using SNPs selected based on GWAS results were similar to those using all SNPs for several combinations of traits and populations. We discussed the application of genome-wide studies for C. japonica improvement.
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Affiliation(s)
- Yuichiro Hiraoka
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Eitaro Fukatsu
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Kumamoto, Japan
| | - Kentaro Mishima
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Tomonori Hirao
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | | | - Miho Tamura
- Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Miyoko Tsubomura
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
| | - Taiichi Iki
- Tohoku Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Takizawa, Japan
| | - Manabu Kurita
- Kyushu Regional Breeding Office, Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Kumamoto, Japan
| | - Makoto Takahashi
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Hitachi, Japan
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Huang LS, Sun YQ, Jin Y, Gao Q, Hu XG, Gao FL, Yang XL, Zhu JJ, El-Kassaby YA, Mao JF. Development of high transferability cpSSR markers for individual identification and genetic investigation in Cupressaceae species. Ecol Evol 2018; 8:4967-4977. [PMID: 29876074 PMCID: PMC5980425 DOI: 10.1002/ece3.4053] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 02/24/2018] [Accepted: 03/13/2018] [Indexed: 11/18/2022] Open
Abstract
Given the low substitution rate in plastomes, the polymorphic and codominant nature of chloroplast SSRs (cpSSRs) makes them ideal markers, complementing their nuclear counterpart. In Cupressaceae, cpSSRs are mostly paternally inherited, thus, they are useful in mating systems and pollen flow studies. Using e-PCR, 92 SSR loci were identified across six Cupressaceae plastomes, and primers were designed for 26 loci with potential interspecific transferability. The 26 developed cpSSRs were polymorphic in four genera, Platycladus, Sabina, Juniperus, and Cupressus and are suitable for Cupressaceae molecular genetic studies and utilization. We genotyped 192 Platycladus orientalis samples from a core breeding population using 10 of the developed cpSSRs and 10 nuclear SSRs, and these individuals were identified with high confidence. The developed cpSSRs can be used in (1) a marker-assisted breeding scheme, specifically when paternity identification is required, (2) population genetics investigations, and (3) biogeography of Cupressaceae and unraveling the genetic relationships between related species.
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Affiliation(s)
- Li-Sha Huang
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Yan-Qiang Sun
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Yuqing Jin
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Qiong Gao
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Xian-Ge Hu
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
| | - Fu-Ling Gao
- Economic Forest and Seeding Management Station in Henan Province Zhengzhou China
| | - Xiao-Lei Yang
- National Tree Breeding Station for Platycladus orientalis in Jiaxian Forest Farm of Jiaxian County Henan China
| | - Ji-Jun Zhu
- National Tree Breeding Station for Platycladus orientalis in Jiaxian Forest Farm of Jiaxian County Henan China
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences Faculty of Forestry The University of British Columbia Vancouver BC Canada
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design National Engineering Laboratory for Tree Breeding Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants Ministry of Education College of Biological Sciences and Technology Beijing Forestry University Beijing China
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Hou L, Cui Y, Li X, Chen W, Zhang Z, Pang X, Li Y. Genetic Evaluation of Natural Populations of the Endangered Conifer Thuja koraiensis Using Microsatellite Markers by Restriction-Associated DNA Sequencing. Genes (Basel) 2018; 9:E218. [PMID: 29673217 PMCID: PMC5924560 DOI: 10.3390/genes9040218] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 11/16/2022] Open
Abstract
Thuja koraiensis Nakai is an endangered conifer of high economic and ecological value in Jilin Province, China. However, studies on its population structure and conservation genetics have been limited by the lack of genomic data. Here, 37,761 microsatellites (simple sequence repeat, SSR) were detected based on 875,792 de novo-assembled contigs using a restriction-associated DNA (RAD) approach. Among these SSRs, 300 were randomly selected to test for polymorphisms and 96 obtained loci were able to amplify a fragment of expected size. Twelve polymorphic SSR markers were developed to analyze the genetic diversity and population structure of three natural populations. High genetic diversity (mean NA = 5.481, HE = 0.548) and moderate population differentiation (pairwise Fst = 0.048–0.078, Nm = 2.940–4.958) were found in this species. Molecular variance analysis suggested that most of the variation (83%) existed within populations. Combining the results of STRUCTURE, principal coordinate, and neighbor-joining analysis, the 232 individuals were divided into three genetic clusters that generally correlated with their geographical distributions. Finally, appropriate conservation strategies were proposed to protect this species. This study provides genetic information for the natural resource conservation and utilization of T. koraiensis and will facilitate further studies of the evolution and phylogeography of the species.
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Affiliation(s)
- Lu Hou
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yanhong Cui
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Xiang Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Wu Chen
- The Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Zhiyong Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China.
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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Feng S, Zhao L, Liu Z, Liu Y, Yang T, Wei A. De novo transcriptome assembly of Zanthoxylum bungeanum using Illumina sequencing for evolutionary analysis and simple sequence repeat marker development. Sci Rep 2017; 7:16754. [PMID: 29196697 PMCID: PMC5711952 DOI: 10.1038/s41598-017-15911-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/03/2017] [Indexed: 02/04/2023] Open
Abstract
Zanthoxylum, an ancient economic crop in Asia, has a satisfying aromatic taste and immense medicinal values. A lack of genomic information and genetic markers has limited the evolutionary analysis and genetic improvement of Zanthoxylum species and their close relatives. To better understand the evolution, domestication, and divergence of Zanthoxylum, we present a de novo transcriptome analysis of an elite cultivar of Z. bungeanum using Illumina sequencing; we then developed simple sequence repeat markers for identification of Zanthoxylum. In total, we predicted 45,057 unigenes and 22,212 protein coding sequences, approximately 90% of which showed significant similarities to known proteins in databases. Phylogenetic analysis indicated that Zanthoxylum is relatively recent and estimated to have diverged from Citrus ca. 36.5–37.7 million years ago. We also detected a whole-genome duplication event in Zanthoxylum that occurred 14 million years ago. We found no protein coding sequences that were significantly under positive selection by Ka/Ks. Simple sequence repeat analysis divided 31 Zanthoxylum cultivars and landraces into three major groups. This Zanthoxylum reference transcriptome provides crucial information for the evolutionary study of the Zanthoxylum genus and the Rutaceae family, and facilitates the establishment of more effective Zanthoxylum breeding programs.
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Affiliation(s)
- Shijing Feng
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Lili Zhao
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Zhenshan Liu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Tuxi Yang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, 712100, China.
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