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Min D, Shi W, Dehshiri MM, Gou Y, Li W, Zhang K, Zhou M, Li B. The molecular phylogenetic position of Harpagocarpus (Polygonaceae) sheds new light on the infrageneric classification of Fagopyrum. PHYTOKEYS 2023; 220:109-126. [PMID: 37251612 PMCID: PMC10209611 DOI: 10.3897/phytokeys.220.97667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 01/19/2023] [Indexed: 05/31/2023]
Abstract
In the context of the molecular phylogeny of Polygonaceae, the phylogenetic positions of most genera and their relationships have been resolved. However, the monotypic genus Harpagocarpus has never been included in any published molecular phylogenetic studies. In the present study, we adopt a two-step approach to confirm the phylogenetic placement of Harpagocarpus using two datasets: (1) a concatenated dataset of three chloroplast DNA (cpDNA) regions (matK, rbcL and trnL-F) for Polygonaceae and (2) a combined cpDNA dataset of five sequences (accD, matK, psbA-trnH, rbcL and trnL-F) for Fagopyrum. Our analyses confirm the previous hypothesis based on morphological, anatomical and palynological investigations that Harpagocarpus is congeneric with Fagopyrum and further reveal that H.snowdenii (≡ F.snowdenii) is sister to the woody buckwheat F.tibeticum. Within Fagopyrum, three highly supported clades were discovered and the first sectional classification was proposed to accommodate them: sect. Fagopyrum comprises the two domesticated common buckwheat (F.esculentum and F.tataricum) and their wild relatives (F.esculentumsubsp.ancestrale, F.homotropicum and F.dibotrys) which are characterised by having large corymbose inflorescences and achenes greatly exceeding the perianth; sect. Tibeticum, including F.snowdenii and F.tibeticum, is characterised by the achene having appurtenances along the ribs, greatly exceeding the perianth and the perianth accrescent in fruit; sect. Urophyllum contains all other species of which the achenes were completely enclosed in the perianth. This study is very helpful to understand the phylogeny of the Fagopyrum and sheds light on the future study of taxonomy, biogeography, diversification and character evolution of the genus.
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Affiliation(s)
- Daozhang Min
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, ChinaJiangxi Agricultural UniversityNanchangChina
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina
- The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, ChinaThe Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, ChinaJiangxi Agricultural UniversityNanchangChina
| | - Mohammad Mehdi Dehshiri
- Department of Biology, Borujerd Branch, Islamic Azad University, Borujerd, IranIslamic Azad UniversityBorujerdIran
| | - Yuting Gou
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina
| | - Wei Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, ChinaInstitute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingChina
| | - Bo Li
- Research Centre of Ecological Sciences, College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, ChinaXinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina
- The Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, ChinaThe Specimen Museum of Xinjiang Institute of Ecology and Geography, Chinese Academy of SciencesUrumqiChina
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Li QJ, Liu Y, Wang AH, Chen QF, Wang JM, Peng L, Yang Y. Plastome comparison and phylogenomics of Fagopyrum (Polygonaceae): insights into sequence differences between Fagopyrum and its related taxa. BMC PLANT BIOLOGY 2022; 22:339. [PMID: 35831794 PMCID: PMC9281083 DOI: 10.1186/s12870-022-03715-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/23/2022] [Indexed: 05/09/2023]
Abstract
BACKGROUND Fagopyrum (Polygonaceae) is a small plant lineage comprised of more than fifteen economically and medicinally important species. However, the phylogenetic relationships of the genus are not well explored, and the characteristics of Fagopyrum chloroplast genomes (plastomes) remain poorly understood so far. It restricts the comprehension of species diversity in Fagopyrum. Therefore, a comparative plastome analysis and comprehensive phylogenomic analyses are required to reveal the taxonomic relationship among species of Fagopyrum. RESULTS In the current study, 12 plastomes were sequenced and assembled from eight species and two varieties of Fagopyrum. In the comparative analysis and phylogenetic analysis, eight previously published plastomes of Fagopyrum were also included. A total of 49 plastomes of other genera in Polygonaceae were retrieved from GenBank and used for comparative analysis with Fagopyrum. The variation of the Fagopyrum plastomes is mainly reflected in the size and boundaries of inverted repeat/single copy (IR/SC) regions. Fagopyrum is a relatively basal taxon in the phylogenomic framework of Polygonaceae comprising a relatively smaller plastome size (158,768-159,985 bp) than another genus of Polygonaceae (158,851-170,232 bp). A few genera of Polygonaceae have nested distribution of the IR/SC boundary variations. Although most species of Fagopyrum show the same IRb/SC boundary with species of Polygonaceae, only a few species show different IRa/SC boundaries. The phylogenomic analyses of Fagopyrum supported the cymosum and urophyllum groups and resolved the systematic position of subclades within the urophyllum group. Moreover, the repeat sequence types and numbers were found different between groups of Fagopyrum. The plastome sequence identity showed significant differences between intra-group and inter-group. CONCLUSIONS The deletions of intergenic regions cause a short length of Fagopyrum plastomes, which may be the main reason for plastome size diversity in Polygonaceae species. The phylogenomic reconstruction combined with the characteristics comparison of plastomes supports grouping within Fagopyrum. The outcome of these genome resources may facilitate the taxonomy, germplasm resources identification as well as plant breeding of Fagopyrum.
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Affiliation(s)
- Qiu-Jie Li
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yu Liu
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - An-Hu Wang
- Panxi Crops Research and Utilization Key Laboratory of Sichuan Province, Xichang University, Xichang, 615013, China
| | - Qing-Fu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, China
| | - Jian-Mei Wang
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Lu Peng
- College of Life Sciences, Sichuan University, Chengdu, 610065, China
| | - Yi Yang
- College of Life Sciences, Sichuan University, Chengdu, 610065, China.
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Zhang LL, He Y, Sheng F, Hu YF, Song Y, Li W, Chen J, Zhang J, Zou L. Towards a better understanding of Fagopyrum dibotrys: a systematic review. Chin Med 2021; 16:89. [PMID: 34530893 PMCID: PMC8447528 DOI: 10.1186/s13020-021-00498-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 08/30/2021] [Indexed: 01/12/2023] Open
Abstract
Fagopyrum dibotrys (F. dibotrys) (D.Don) H.Hara is a well-known edible herbal medicine in Asian countries. It has been widely used for the treatment of lung diseases, swelling, etc., and is also an important part of many Chinese medicine prescriptions. At present, more than 100 compounds have been isolated and identified from F. dibotrys, and these compounds can be primarily divided into flavonoids, phenols, terpenes, steroids, and fatty acids. Flavonoids and phenolic compounds are considered to be the main active ingredients of F. dibotrys. Previous pharmacological studies have shown that F. dibotrys possesses anti-inflammatory, anti-cancer, anti-oxidant, anti-bacterial, and anti-diabetic activities. Additional studies on functional genes have led to a better understanding of the metabolic pathways and regulatory factors related with the flavonoid active ingredients in F. dibotrys. In this paper, we systemically reviewed the research advances on the phytochemistry and pharmacology of F. dibotrys, as well as the functional genes related to the synthesis of active ingredients, aiming to promote the development and utilization of F. dibotrys.
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Affiliation(s)
- Le-Le Zhang
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Yan He
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Feiya Sheng
- School of Basic Medical Sciences, Chengdu University, Chengdu, China.
| | - Ying-Fan Hu
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Yu Song
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China
| | - Wei Li
- School of Basic Medical Sciences, Chengdu University, Chengdu, China
| | - Jiarong Chen
- Affiliated Hospital of Chengdu University, Chengdu, China
| | - Jinming Zhang
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Liang Zou
- Key Laboratory of Coarse Cereal Processing of Ministry of Agriculture and Rural Affairs, Chengdu University, Chengdu, China.
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Sohn HB, Kim SJ, Hong SY, Park SG, Oh DH, Lee S, Nam HY, Nam JH, Kim YH. Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources. PLoS One 2021; 16:e0250786. [PMID: 34081692 PMCID: PMC8174720 DOI: 10.1371/journal.pone.0250786] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/14/2021] [Indexed: 11/18/2022] Open
Abstract
Tartary buckwheat (Fagopyrum tataricum Gartn.) is a highly functional crop that is poised to be the target of many future breeding efforts. The reliable ex situ conservation of various genetic resources is essential for the modern breeding of tartary buckwheat varieties. We developed PCR-based co-dominant insertion/deletion (InDel) markers to discriminate tartary buckwheat genetic resources. First, we obtained the whole genome from 26 accessions across a superscaffold-scale reference genome of 569.37 Mb for tartary buckwheat cv. "Daegwan 3-7." Next, 171,926 homogeneous and 53,755 heterogeneous InDels were detected by comparing 26 accessions with the "Daegwan 3-7" reference sequence. Of these, 100 candidate InDels ranging from 5-20 bp in length were chosen for validation, and 50 of them revealed polymorphisms between the 26 accessions and "Daegwan 3-7." The validated InDels were further tested through the assessment of their likelihood to give rise to a single or a few PCR products in 50 other accessions, covering most tartary buckwheat genome types. The major allele frequencies ranged from 0.5616 at the TB42 locus to 0.9863 at the TB48 locus, with the average PIC value of 0.1532 with a range of 0.0267-0.3712. To create a user-friendly system, the homology of the genotypes between and among the accessions were visualized in both one- (1D) and two-dimensional (2D) barcode types by comparing amplicon polymorphisms with the reference variety, "Daegwan 3-7." A phylogenetic tree and population structure of the 76 accessions according to amplicon polymorphisms for the 50 InDel markers corresponded to those using non-synonymous single nucleotide polymorphism variants, indicating that the barcode system based on the 50 InDels was a useful tool to improve the reliability of identification of tartary buckwheat accessions in the germplasm stocks.
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Affiliation(s)
- Hwang-Bae Sohn
- Highland Agriculture Research Institute, National Institute of Crop Science, Pyeongchang, Gangwon-do, Republic of Korea
| | - Su-Jeong Kim
- Highland Agriculture Research Institute, National Institute of Crop Science, Pyeongchang, Gangwon-do, Republic of Korea
| | - Su-Young Hong
- Highland Agriculture Research Institute, National Institute of Crop Science, Pyeongchang, Gangwon-do, Republic of Korea
| | - Sin-Gi Park
- TheragenEtex Bio Institute, TherageneEtex Inc., Suwon, Gyeonggi-do, Republic of Korea
| | - Dong-Ha Oh
- Department of Biological Science, Louisiana State University, Baton Rouge, LA, United States of America
| | - Sunghoon Lee
- EONE-DIAGNOMICS Genome Center Co. Ltd., Incheon, Republic of Korea
| | - Hwa Yeun Nam
- Highland Agriculture Research Institute, National Institute of Crop Science, Pyeongchang, Gangwon-do, Republic of Korea
| | - Jung Hwan Nam
- Highland Agriculture Research Institute, National Institute of Crop Science, Pyeongchang, Gangwon-do, Republic of Korea
| | - Yul-Ho Kim
- Highland Agriculture Research Institute, National Institute of Crop Science, Pyeongchang, Gangwon-do, Republic of Korea
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Zhang K, He M, Fan Y, Zhao H, Gao B, Yang K, Li F, Tang Y, Gao Q, Lin T, Quinet M, Janovská D, Meglič V, Kwiatkowski J, Romanova O, Chrungoo N, Suzuki T, Luthar Z, Germ M, Woo SH, Georgiev MI, Zhou M. Resequencing of global Tartary buckwheat accessions reveals multiple domestication events and key loci associated with agronomic traits. Genome Biol 2021; 22:23. [PMID: 33430931 PMCID: PMC7802136 DOI: 10.1186/s13059-020-02217-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 12/03/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Tartary buckwheat (Fagopyrum tataricum) is a nutritionally balanced and flavonoid-rich crop plant that has been in cultivation for 4000 years and is now grown globally. Despite its nutraceutical and agricultural value, the characterization of its genetics and its domestication history is limited. RESULTS Here, we report a comprehensive database of Tartary buckwheat genomic variation based on whole-genome resequencing of 510 germplasms. Our analysis suggests that two independent domestication events occurred in southwestern and northern China, resulting in diverse characteristics of modern Tartary buckwheat varieties. Genome-wide association studies for important agricultural traits identify several candidate genes, including FtUFGT3 and FtAP2YT1 that significantly correlate with flavonoid accumulation and grain weight, respectively. CONCLUSIONS We describe the domestication history of Tartary buckwheat and provide a detailed resource of genomic variation to allow for genomic-assisted breeding in the improvement of elite cultivars.
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Affiliation(s)
- Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Ming He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Yu Fan
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Hui Zhao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Bin Gao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Keli Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Faliang Li
- Research Station of Alpine Crop, Xichang Institute of Agricultural Sciences, Liangshan, 616150 Sichuan China
| | - Yu Tang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, 58083 Guangdong China
| | - Tao Lin
- College of Horticulture, China Agricultural University, Beijing, 100083 China
| | - Muriel Quinet
- Groupe de Recherche en Physiologie Végétale (GRPV), Earth and Life Institute-Agronomy (ELI-A), Université catholique de Louvain, Croix du Sud 45, boîte L7.07.13, B-1348 Louvain-la-Neuve, Belgium
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, Prague 6, Czech Republic
| | - Vladimir Meglič
- Agricultural Institute of Slovenia, Hacquetova ulica, Ljubljana, Slovenia
| | - Jacek Kwiatkowski
- Department of Plant Breeding and Seed Production, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10-724 Olsztyn, Poland
| | - Olga Romanova
- N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), Bol’shaya Morskaya, 42-44, St. Petersburg, Russia 190000
| | - Nikhil Chrungoo
- Department of Botany, North Eastern Hill University, Shillong, 793022 India
| | - Tatsuro Suzuki
- Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization, Suya 2421, Koshi, Kumamoto 861-1192 Japan
| | - Zlata Luthar
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Mateja Germ
- Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, SI-1000 Ljubljana, Slovenia
| | - Sun-Hee Woo
- Department of Crop Science, Chungbuk National University, Cheong-ju, Republic of Korea
| | - Milen I. Georgiev
- Group of Plant Cell Biotechnology and Metabolomics, The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Plovdiv, Bulgaria
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 107, Ziyuan North Building, Xueyuan South Road No. 80, Haidian District, Beijing, 100081 China
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Matsui K, Yasui Y. Genetic and genomic research for the development of an efficient breeding system in heterostylous self-incompatible common buckwheat (Fagopyrum esculentum). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1641-1653. [PMID: 32152716 DOI: 10.1007/s00122-020-03572-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/22/2020] [Indexed: 06/10/2023]
Abstract
Common buckwheat (Fagopyrum esculentum Moench; 2n = 2x = 16) is an annual crop that is cultivated widely around the world and contains an abundance of nutrients and bioactive compounds. However, the yield of buckwheat is low compared to that of other major crops, and it contains proteins that cause allergic reactions in some people. Much research has aimed to improve or eliminate these undesirable traits, and some major advances have recently been made. Here, we review recent advances in buckwheat breeding materials, tools, and methods, including the development of self-compatible lines, genetic maps, a buckwheat genome database, and an efficient breeding strategy. We also describe emerging breeding methods for high-value lines.
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Affiliation(s)
- Katsuhiro Matsui
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 3-1-3, Tsukuba, Ibaraki, 305-8518, Japan.
- Graduate School of Life and Environmental Science, University of Tsukuba, Kannondai 3-1-3, Tsukuba, Ibaraki, 305-8518, Japan.
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto, 606-8501, Japan
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Ohsako T, Li C. Classification and systematics of the Fagopyrum species. BREEDING SCIENCE 2020; 70:93-100. [PMID: 32351308 PMCID: PMC7180149 DOI: 10.1270/jsbbs.19028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/16/2019] [Indexed: 05/09/2023]
Abstract
Fagopyrum (Polygonaceae) is a small genus including less than 30 species, mostly endemic to southern China. The genus includes two cultivated species, common buckwheat F. esculentum and Tartary buckwheat F. tataricum. Fagopyrum is clearly distinguished from other genus in Polygonaceae by the central position of embryo in achene. The genus is divided into two major groups, namely the cymosum group and the urophyllum group, based on morphological characters and molecular systematics. In the last three decades the number of species in the genus has doubled by the discovery of new species by Japanese and Chinese groups. Most of them are revealed to be included in the urophyllum group based on morphological and molecular genetic analyses. Molecular systematic surveys have also detected inappropriate treatment of some non-Fagopyrum species as new species or combination in the genus.
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Affiliation(s)
- Takanori Ohsako
- Laboratory of Plant Resource Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, 74 Kitainayazuma, Seika, Kyoto 619-0244, Japan
- Corresponding author (e-mail: )
| | - Chengyun Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Heilongtan, Kunming, Yunnan 650201, China
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Matsui K, Yasui Y. Buckwheat heteromorphic self-incompatibility: genetics, genomics and application to breeding. BREEDING SCIENCE 2020; 70:32-38. [PMID: 32351302 PMCID: PMC7180150 DOI: 10.1270/jsbbs.19083] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Accepted: 07/07/2019] [Indexed: 06/10/2023]
Abstract
Common buckwheat (Fagopyrum esculentum Moench 2n = 2x = 16) is an outcrossing crop with heteromorphic self-incompatibility due to its distylous flowers, called pin and thrum. In pin plants, a long style is combined with short stamens and small pollen grains; in thrum plants, a short style is combined with long stamens and large pollen grains. Both the intra-morph self-incompatibility and flower morphology are controlled by a single genetic locus named the S locus; thrum plants are heterozygous (Ss) and pin plants are homozygous recessive (ss) at this locus. Self-incompatibility is an obstacle for establishing pure lines and fixation of agronomically useful genes. Elucidation of the molecular mechanism of heterostylous self-incompatibility of common buckwheat has continued for a quarter of a century. Recent advances in genomic and transcriptomic analyses using next-generation sequencing have made it possible to determine the genomic region harboring the buckwheat S locus and to identify novel genes at this locus. In this review, we summarize the current knowledge on buckwheat heterostyly gained from conventional and molecular genetics and genomics. We also discuss the application of these studies to breeding of common buckwheat.
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Affiliation(s)
- Katsuhiro Matsui
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518, Japan
- Graduate School of Life and Environmental Science, University of Tsukuba, Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518, Japan
| | - Yasuo Yasui
- Graduate School of Agriculture, Kyoto University, Sakyou-ku, Kyoto 606-8502, Japan
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psbE-psbL and ndhA Intron, the Promising Plastid DNA Barcode of Fagopyrum. Int J Mol Sci 2019; 20:ijms20143455. [PMID: 31337110 PMCID: PMC6678665 DOI: 10.3390/ijms20143455] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/03/2019] [Accepted: 07/10/2019] [Indexed: 01/09/2023] Open
Abstract
Buckwheat is an important functional food material with high nutritional value. However, it is still a difficult task for the taxonomy studies of wild buckwheat that are only based on morphology. In order to demonstrate the most efficient DNA barcode in the phylogenetic research of buckwheat, promote the investigation of wild buckwheat, and also reveal the phylogenetic relationship between Fagopyrum species, psbE-psbL and ndhA intron were validated here, which previously have been proved to be promising DNA barcode candidates for phylogenetic studies in genera Fagopyrum. Meanwhile, ndhA intron + psbE-psbL and matK + psbE-psbL could distinguish the relationship between species clearly. Combining the results of morphology and molecular markers, we suggested the buckwheat species should be divided into two subgroups, one subgroup consisted of F. tataricum, F. esculentum, F. cymosum and its related wild species, and the other subgroup included other wild buckwheat species. Our results could fulfill molecular markers of taxonomy research in genera Fagopyrum, promote wild buckwheat species identification, and assist in the use of wild buckwheat resources in the future. Additionally, the phylogenetic relationship revealed here could provide valuable information for molecular breeding of buckwheat and provide reference for inter-species hybridization.
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Wang X, Zhou T, Bai G, Zhao Y. Complete chloroplast genome sequence of Fagopyrum dibotrys: genome features, comparative analysis and phylogenetic relationships. Sci Rep 2018; 8:12379. [PMID: 30120274 PMCID: PMC6098159 DOI: 10.1038/s41598-018-30398-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Accepted: 07/30/2018] [Indexed: 12/18/2022] Open
Abstract
Fagopyrum dibotrys, belongs to Polygonaceae family, is one of national key conserved wild plants of China with important medicinal and economic values. Here, the complete chloroplast (cp) genome sequence of F. dibotrys is reported. The cp genome size is 159,919 bp with a typical quadripartite structure and consisting of a pair of inverted repeat regions (30,738 bp) separated by large single copy region (85,134 bp) and small single copy region (13,309 bp). Sequencing analyses indicated that the cp genome encodes 131 genes, including 80 protein-coding genes, 28 tRNA genes and 4 rRNA genes. The genome structure, gene order and codon usage are typical of angiosperm cp genomes. We also identified 48 simple sequence repeats (SSR) loci, fewer of them are distributed in the protein-coding sequences compared to the noncoding regions. Comparison of F. dibotrys cp genome to other Polygonaceae cp genomes indicated the inverted repeats (IRs) and coding regions were more conserved than single copy and noncoding regions, and several variation hotspots were detected. Coding gene sequence divergence analyses indicated that five genes (ndhK, petL rpoC2, ycf1, ycf2) were subject to positive selection. Phylogenetic analysis among 42 species based on cp genomes and 50 protein-coding genes indicated a close relationship between F. dibotrys and F. tataricum. In summary, the complete cp genome sequence of F. dibotrys reported in this study will provide useful plastid genomic resources for population genetics and pave the way for resolving phylogenetic relationships of order Caryophyllales.
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Affiliation(s)
- Xumei Wang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China.
| | - Tao Zhou
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, 710061, China
| | - Guoqing Bai
- Shaanxi Engineering Research Centre for Conservation and Utilization of Botanical Resources, Xi'an Botanical Garden of Shaanxi Province, Xi'an, 710061, China
| | - Yuemei Zhao
- College of Biopharmaceutical and Food Engineering, Shangluo University, Shangluo, 726000, China
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Wang CL, Ding MQ, Zou CY, Zhu XM, Tang Y, Zhou ML, Shao JR. Comparative Analysis of Four Buckwheat Species Based on Morphology and Complete Chloroplast Genome Sequences. Sci Rep 2017; 7:6514. [PMID: 28747666 PMCID: PMC5529468 DOI: 10.1038/s41598-017-06638-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 06/15/2017] [Indexed: 11/09/2022] Open
Abstract
Buckwheat is a nutritional and economically crop belonging to Polygonaceae, Fagopyrum. To better understand the mutation patterns and evolution trend in the chloroplast (cp) genome of buckwheat, and found sufficient number of variable regions to explore the phylogenetic relationships of this genus, two complete cp genomes of buckwheat including Fagopyrum dibotrys (F. dibotrys) and Fagopyrum luojishanense (F. luojishanense) were sequenced, and other two Fagopyrum cp genomes were used for comparative analysis. After morphological analysis, the main difference among these buckwheat were height, leaf shape, seeds and flower type. F. luojishanense was distinguishable from the cultivated species easily. Although the F. dibotrys and two cultivated species has some similarity, they different in habit and component contents. The cp genome of F. dibotrys was 159,320 bp while the F. luojishanense was 159,265 bp. 48 and 61 SSRs were found in F. dibotrys and F. luojishanense respectively. Meanwhile, 10 highly variable regions among these buckwheat species were located precisely. The phylogenetic relationships among four Fagopyrum species based on complete cp genomes was showed. The results suggested that F. dibotrys is more closely related to Fagopyrum tataricum. These data provided valuable genetic information for Fagopyrum species identification, taxonomy, phylogenetic study and molecular breeding.
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Affiliation(s)
- Cheng-Long Wang
- School of Life Sciences, Sichuan Agricultural University, Yaan, Sichuan, 625014, China
| | - Meng-Qi Ding
- School of Life Sciences, Sichuan Agricultural University, Yaan, Sichuan, 625014, China.,Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chen-Yan Zou
- School of Life Sciences, Sichuan Agricultural University, Yaan, Sichuan, 625014, China
| | - Xue-Mei Zhu
- School of Resources and Environment, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Yu Tang
- Department of Tourism Culture, Sichuan Higher Institute of Cuisine, Chengdu, Sichuan, 610072, China
| | - Mei-Liang Zhou
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Ji-Rong Shao
- School of Life Sciences, Sichuan Agricultural University, Yaan, Sichuan, 625014, China.
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12
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Thiyagarajan K, Vitali F, Tolaini V, Galeffi P, Cantale C, Vikram P, Singh S, De Rossi P, Nobili C, Procacci S, Del Fiore A, Antonini A, Presenti O, Brunori A. Genomic Characterization of Phenylalanine Ammonia Lyase Gene in Buckwheat. PLoS One 2016; 11:e0151187. [PMID: 26990297 PMCID: PMC4798664 DOI: 10.1371/journal.pone.0151187] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Accepted: 02/24/2016] [Indexed: 01/05/2023] Open
Abstract
Phenylalanine Ammonia Lyase (PAL) gene which plays a key role in bio-synthesis of medicinally important compounds, Rutin/quercetin was sequence characterized for its efficient genomics application. These compounds possessing anti-diabetic and anti-cancer properties and are predominantly produced by Fagopyrum spp. In the present study, PAL gene was sequenced from three Fagopyrum spp. (F. tataricum, F. esculentum and F. dibotrys) and showed the presence of three SNPs and four insertion/deletions at intra and inter specific level. Among them, the potential SNP (position 949th bp G>C) with Parsimony Informative Site was selected and successfully utilised to individuate the zygosity/allelic variation of 16 F. tataricum varieties. Insertion mutations were identified in coding region, which resulted the change of a stretch of 39 amino acids on the putative protein. Our Study revealed that autogamous species (F. tataricum) has lower frequency of observed SNPs as compared to allogamous species (F. dibotrys and F. esculentum). The identified SNPs in F. tataricum didn't result to amino acid change, while in other two species it caused both conservative and non-conservative variations. Consistent pattern of SNPs across the species revealed their phylogenetic importance. We found two groups of F. tataricum and one of them was closely related with F. dibotrys. Sequence characterization information of PAL gene reported in present investigation can be utilized in genetic improvement of buckwheat in reference to its medicinal value.
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Affiliation(s)
- Karthikeyan Thiyagarajan
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
- Bioversity International, 00054, Maccarese (Fiumicino), Italy
| | - Fabio Vitali
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Valentina Tolaini
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Patrizia Galeffi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Cristina Cantale
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Prashant Vikram
- Genetic Resource Program, International Center for Maize and Wheat Improvement, El Batan, Texcoco, Mexico
| | - Sukhwinder Singh
- Genetic Resource Program, International Center for Maize and Wheat Improvement, El Batan, Texcoco, Mexico
| | - Patrizia De Rossi
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Chiara Nobili
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Silvia Procacci
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Antonella Del Fiore
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Alessandro Antonini
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Ombretta Presenti
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
| | - Andrea Brunori
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), UTAGRI- INN, Via Anguillarese, 301, 00123 Rome, Italy
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13
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Phylogenetic relationship of four new species related to southwestern Sichuan Fagopyrum based on morphological and molecular characterization. BIOCHEM SYST ECOL 2014. [DOI: 10.1016/j.bse.2014.09.024] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Mendler-Drienyovszki N, Cal AJ, Dobránszki J. Progress and prospects for interspecific hybridization in buckwheat and the genus Fagopyrum. Biotechnol Adv 2013; 31:1768-75. [PMID: 24055817 DOI: 10.1016/j.biotechadv.2013.09.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/09/2013] [Accepted: 09/11/2013] [Indexed: 11/28/2022]
Abstract
Cultivated buckwheat, such as common (Fagopyrum esculentum Moench.) and tartary (Fagopyrum tataricum (L.) Gaertn.) buckwheat, is one of the most versatile crops for forage and food and has several benefits for human health. Interspecific hybridization between Fagopyrum species is of great importance to improvement of buckwheat. Hybridization would allow the transfer of agronomical beneficial characteristics from wild Fagopyrum species, including self-pollination and increased fertility, frost tolerance, and higher content of beneficial compounds. However, conventional breeding methods are only partially applicable because of the self-incompatibility and incompatibility barriers between different species. Present review summarizes the morphology of self-incompatibility, the genetic and cellular basis of incompatibility between different Fagopyrum species. In many interspecific crosses hybrid embryos are aborted after successful pollination due to post-zygotic incompatibility. The use of in vitro embryo rescue after interspecific hybridization has been successful in circumventing breeding barriers between Fagopyrum species. Methods applied successfully for the construction of interspecific hybrids are discussed in detail.
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Affiliation(s)
- Nóra Mendler-Drienyovszki
- Research Institute of Nyíregyháza, Research Institutes and Study Farm, Centre for Agricultural and Applied Economic Sciences, University of Debrecen, Nyíregyháza, P.O. Box 12, H-4400, Hungary.
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15
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Tian X, Luo J, Wang A, Mao K, Liu J. On the origin of the woody buckwheat Fagopyrum tibeticum (=Parapteropyrum tibeticum) in the Qinghai-Tibetan Plateau. Mol Phylogenet Evol 2011; 61:515-20. [PMID: 21798359 DOI: 10.1016/j.ympev.2011.07.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2011] [Revised: 06/20/2011] [Accepted: 07/05/2011] [Indexed: 10/17/2022]
Abstract
Here we tested whether 'insular woodiness', a striking evolutionary pattern that commonly occurs on islands, has also appeared in QTP continental endemics. Parapteropyrum, a monotypic shrubby genus occurring in the central QTP, has been previously placed in the tribe Atraphaxideae of the family Polygonaceae, while all the other woody species of this tribe mainly occur in western and central Asia. We studied sequence variations of nuclear ITS (internal transcribed spacer) and cp (chloroplast) DNA (rbcL and accD) of this genus and the other ten genera. The constructed phylogenies based on ITS, cpDNA or a combination of both datasets, suggest that the woody Parapteropyrum is nested within and most likely evolved from the herbaceous Fagopyrum. We propose that the large-scale uplift of the QTP not only promoted continental species radiation, but also the secondary feature of woodiness in a few herbaceous lineages in response to strong selection pressures, similar to those acting on island flora. In addition, the confirmation of Parapteropyrum within Fagopyrum highlights its potential use as a new, perennial source of buckwheat.
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Affiliation(s)
- Xinmin Tian
- Molecular Ecology Group, Key Laboratory of Arid and Grassland Ecology, Lanzhou University, Lanzhou 730000, Gansu, PR China
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16
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Logacheva MD, Kasianov AS, Vinogradov DV, Samigullin TH, Gelfand MS, Makeev VJ, Penin AA. De novo sequencing and characterization of floral transcriptome in two species of buckwheat (Fagopyrum). BMC Genomics 2011; 12:30. [PMID: 21232141 PMCID: PMC3027159 DOI: 10.1186/1471-2164-12-30] [Citation(s) in RCA: 124] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Accepted: 01/13/2011] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Transcriptome sequencing data has become an integral component of modern genetics, genomics and evolutionary biology. However, despite advances in the technologies of DNA sequencing, such data are lacking for many groups of living organisms, in particular, many plant taxa. We present here the results of transcriptome sequencing for two closely related plant species. These species, Fagopyrum esculentum and F. tataricum, belong to the order Caryophyllales--a large group of flowering plants with uncertain evolutionary relationships. F. esculentum (common buckwheat) is also an important food crop. Despite these practical and evolutionary considerations Fagopyrum species have not been the subject of large-scale sequencing projects. RESULTS Normalized cDNA corresponding to genes expressed in flowers and inflorescences of F. esculentum and F. tataricum was sequenced using the 454 pyrosequencing technology. This resulted in 267 (for F. esculentum) and 229 (F. tataricum) thousands of reads with average length of 341-349 nucleotides. De novo assembly of the reads produced about 25 thousands of contigs for each species, with 7.5-8.2× coverage. Comparative analysis of two transcriptomes demonstrated their overall similarity but also revealed genes that are presumably differentially expressed. Among them are retrotransposon genes and genes involved in sugar biosynthesis and metabolism. Thirteen single-copy genes were used for phylogenetic analysis; the resulting trees are largely consistent with those inferred from multigenic plastid datasets. The sister relationships of the Caryophyllales and asterids now gained high support from nuclear gene sequences. CONCLUSIONS 454 transcriptome sequencing and de novo assembly was performed for two congeneric flowering plant species, F. esculentum and F. tataricum. As a result, a large set of cDNA sequences that represent orthologs of known plant genes as well as potential new genes was generated.
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Affiliation(s)
- Maria D Logacheva
- Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
- Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
| | - Artem S Kasianov
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Dmitriy V Vinogradov
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
| | - Tagir H Samigullin
- Department of Evolutionary Biochemistry, A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail S Gelfand
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
- Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vsevolod J Makeev
- V.A. Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- N.I Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- State Scientific Institute of Genetics and Selection of Industrial Microorganisms, GosNIIgenetika, Moscow, Russia
| | - Aleksey A Penin
- Evolutionary Genomics Laboratory, Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Moscow, Russia
- A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Science, Moscow, Russia
- Department of Genetics, Biological faculty, M.V. Lomonosov Moscow State University, Moscow, Russia
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17
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Ma KH, Kim NS, Lee GA, Lee SY, Lee JK, Yi JY, Park YJ, Kim TS, Gwag JG, Kwon SJ. Development of SSR markers for studies of diversity in the genus Fagopyrum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1247-54. [PMID: 19680622 DOI: 10.1007/s00122-009-1129-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 07/28/2009] [Indexed: 05/15/2023]
Abstract
The numbers of SSR markers and their utilization have not been determined and investigated as extensively in Fagopyrum species as compared to other crop species. The current report presents 136 new SSR markers in Fagopyrum esculentum ssp. esculentum and their application to related species in the genus Fagopyrum. Of the 136 SSRs, 10 polymorphic SSR markers were utilized in a genetic diversity analysis of a common buckwheat population consisting of 41 accessions of diverse origin. The study showed observed (H(O)) and expected (H(E)) heterozygosities ranging from 0.071 to 0.924 (mean = 0.53) and from 0.073 to 0.902 (mean = 0.412), respectively. Forty-one of the 136 SSRs amplified sequences in other Fagopyrum species, including the cymosum and urophyllum groups. The phylogenetic relationships revealed using the SSRs was consistent with results obtained using other marker systems, with one exception. The sequence and diversity information obtained using these new SSRs and their cross-transferability to related Fagopyrum species will increase our understanding of genetic structures and species relationships within the Fagopyrum genus.
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Affiliation(s)
- Kyung-Ho Ma
- National Agrobiodiversity Center, National Academy of Agricultural Science, RDA, 88-20, Seodun-Dong, Suwon, Gyunggi-do 441-707, Korea
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18
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Yang YX, Wu W, Zheng YL, Yang WT, Cai QR. Genetic diversity of storage proteins in cultivated buckwheat. Pak J Biol Sci 2008; 11:1662-8. [PMID: 18819616 DOI: 10.3923/pjbs.2008.1662.1668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Prolamin and albumn variations of the storage proteins in 76 cultivated buckwheat accessions (55 accessions of Fagopyrum tataricum, 21 accessions of F. esculentum) from 7 countries were characterized by A-PAGE and SDS-PAGE, respectively, for the purpose of evaluating the genetic diversity of cultivated buckwheat at the level of proteins. A total of 18 prolamin bands were detected, among which 88.89 % bands were polymorphic. The number of albumn bands based on SDS-PAGE observed in accessions ranged from 4 to 10. Most intense bands were in the range of molecular weights from 29 to 97.2 kDa. The average of genetic similarity coefficient based on prolamin bands was 0.784 (in F. tataricum and F. esculentum were 0.892 and 0.681, respectively), while on prolamin and albumn bands was 0.742 (in F. tataricum and F. esculentum were 0.864 and 0.633, respectively). Accessions of F. tataricum and F. esculentum showed significant interspecific variation in the A-PAGE and SDS-PAGE profile of the storage proteins. The cluster analysis indicated that all the accessions could be divided into 3 groups and 3 subgroups. The genetic variations among cultivated buckwheat accessions were associated with their geographic origins in some degree.
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Affiliation(s)
- Yu-Xia Yang
- Agronomy College, Sichuan Agricultural University, Yaan, Sichuan 625014, China
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19
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Kawasaki M, Ohnishi O. Two distinct groups of natural populations of Fagopyrum urophyllum (Bur. et Franch.) Gross revealed by the nucleotide sequence of a noncoding region in chloroplast DNA. Genes Genet Syst 2006; 81:323-32. [PMID: 17159293 DOI: 10.1266/ggs.81.323] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Fagopyrum urophyllum is a cross-pollinating perennial woody shrub species belonging to the urophyllum group of Fagopyrum. Natural populations of F. urophyllum were morphologically classified into two distinct groups, the Dali group and the Kunming group without exception. This grouping was verified by molecular phylogeny based on the nucleotide sequence of chloroplast DNA. The reproductive isolation found between the two groups was almost perfect as the distribution of two groups did not overlap each other. The net nucleotide substitution rate (Da) between the two groups was at the same level as between two distinct species. These data suggests that the two groups should be classified into distinct species if future studies on F. urophyllum confirm complete reproductive isolation and no ambiguously classified populations in the border area of the central Yunnan province of China.
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Affiliation(s)
- Mitsuyo Kawasaki
- Plant Germ Plasm Institute, Graduate School of Agriculture, Kyoto University, Mukoh, Japan.
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20
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Fukunaga K, Ichitani K, Taura S, Sato M, Kawase M. Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces. Hereditas 2006; 142:38-44. [PMID: 16970610 DOI: 10.1111/j.1601-5223.2005.01905.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
We determined the sequence of ribosomal DNA (rDNA) intergenic spacer (IGS) of foxtail millet isolated in our previous study, and identified subrepeats in the polymorphic region. We also developed a PCR-based method for identifying rDNA types based on sequence information and assessed 153 accessions of foxtail millet. Results were congruent with our previous works. This study provides new findings regarding the geographical distribution of rDNA variants. This new method facilitates analyses of numerous foxtail millet accessions. It is helpful for typing of foxtail millet germplasms and elucidating the evolution of this millet.
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MESH Headings
- Base Sequence
- DNA, Intergenic/chemistry
- DNA, Intergenic/genetics
- DNA, Plant/chemistry
- DNA, Plant/genetics
- DNA, Plant/isolation & purification
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- Molecular Sequence Data
- Polymerase Chain Reaction
- Polymorphism, Restriction Fragment Length
- Repetitive Sequences, Nucleic Acid/genetics
- Sequence Alignment
- Sequence Analysis, DNA/methods
- Setaria Plant/classification
- Setaria Plant/genetics
- Species Specificity
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Affiliation(s)
- Kenji Fukunaga
- Laboratory of Crop Evolution, Faculty of Agriculture, Kyoto University, Mukoh, Japan.
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21
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Konishi T, Yasui Y, Ohnishi O. Original birthplace of cultivated common buckwheat inferred from genetic relationships among cultivated populations and natural populations of wild common buckwheat revealed by AFLP analysis. Genes Genet Syst 2005; 80:113-9. [PMID: 16172523 DOI: 10.1266/ggs.80.113] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The genetic relationships among seven cultivated populations and eight natural populations of wild common buckwheat were analyzed using amplified fragment length polymorphism (AFLP). The genetic distance was estimated for each pair of the 15 populations based on the AFLP data, and a phylogenetic tree was constructed using the neighbor-joining (NJ) method based on the genetic distance. All the cultivated populations were grouped in a cluster. The natural populations were grouped into two clusters composed of (1) the Sanjiang group (three populations from eastern Tibet and one population from Adong village of Yunnan province) and (2) two populations from Yunnan province and two populations from Sichuan province. The Sanjiang group is more closely related to cultivated populations. These results indicate that the direct ancestor of common buckwheat was natural populations of wild common buckwheat from the Sanjiang area.
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Affiliation(s)
- Takehiko Konishi
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Muko, Japan.
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22
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FUKUNAGA KENJI, ICHITANI KATSUYUKI, TAURA SATORU, SATO MUNEHARU, KAWASE MAKOTO. Ribosomal DNA intergenic spacer sequence in foxtail millet, Setaria italica (L.) P. Beauv. and its characterization and application to typing of foxtail millet landraces. Hereditas 2005. [DOI: 10.1111/j.2005.0018-0661.01905.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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23
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Hirao T, Imai S, Sawada H, Shiomi N, Hachimura S, Kato H. PCR method for detecting trace amounts of buckwheat (Fagopyrum spp.) in food. Biosci Biotechnol Biochem 2005; 69:724-31. [PMID: 15849410 DOI: 10.1271/bbb.69.724] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Buckwheat often causes severe allergic reactions, even when its ingestion level is extremely low. Therefore, buckwheat is listed in several countries as a common food allergen. In addition to common buckwheat and Tartarian buckwheat that are cultivated and consumed widely, wild buckwheat may be potentially allergenic. Food containing undeclared buckwheat poses a risk to patients with the buckwheat allergy. We describe in this report a PCR method to detect buckwheat DNA by using primers corresponding to the internal transcribed spacer region and the 5.8S rRNA gene. The method is buckwheat-specific and compatible with both cultivated and wild buckwheat of the Fagopyrum spp. Its sensitivity was sufficient to detect 1 ppm (w/w) of buckwheat DNA spiked in wheat DNA. This method should benefit food manufacturers, clinical doctors, and allergic patients by providing information on the presence of buckwheat contamination in food.
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Affiliation(s)
- Takashi Hirao
- Somatech Center, House Foods Corporation, chiba 284-0033, Japan.
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24
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Yasui Y, Wang Y, Ohnishi O, Campbell CG. Amplified fragment length polymorphism linkage analysis of common buckwheat (Fagopyrum esculentum) and its wild self-pollinated relative Fagopyrum homotropicum. Genome 2005; 47:345-51. [PMID: 15060587 DOI: 10.1139/g03-126] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Common buckwheat (Fagopyrum esculentum) (2n = 2x = 16) and Fagopyrum homotropicum (2n = 2x = 16) were mated in an interspecific cross and amplified fragment length polymorphism (AFLP) linkage maps were constructed by analyzing segregation in the F2 population. Six hundred and sixty-nine bands were identified using 20 AFLP primer combinations, of which 462 (69%) segregated in the F2 population. The map of F. esculentum has eight linkage groups with 223 markers covering a total of 508.3 cM. The map of F. homotropicum has eight linkage groups with 211 markers covering 548.9 cM. There was one to one correspondence of the esculentum and homotropicum linkage groups. Three morphological markers, distylous self-incompatibility, shattering habit, and winged seed, were located on the AFLP map. Distylous self-incompatibility and shattering habit are tightly linked to each other (1.3 cM) and are located near the center of linkage group 1. Winged seed is located on linkage group 4.
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Affiliation(s)
- Yasuo Yasui
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Muko, Japan.
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25
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Matsui K, Tetsuka T, Nishio T, Hara T. Heteromorphic incompatibility retained in self-compatible plants produced by a cross between common and wild buckwheat. THE NEW PHYTOLOGIST 2003; 159:701-708. [PMID: 33873587 DOI: 10.1046/j.1469-8137.2003.00840.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
• Common buckwheat (Fagopyrum esculentum) is a dimorphic self-incompatible plant with either a pin or a thrum flower. It is considered that self-incompatibility, flower morphology, and pollen size are governed by the S supergene. • Here, we produced self-compatible buckwheat lines by an interspecific cross between F. esculentum and F. homotropicum with embryo rescue. • The flower morphology of these lines was long homostyle and pollen size was similar to that of thrum. Pollen size of F1 plants produced by a cross between a pin plant and the self-compatible plant was similar to that of the self-compatible line and segregated together with flower morphology without exception. The pollen tubes of the self-compatible plants were compatible with styles of the pin plants but incompatible with the styles of thrum plants. However, the pollen tubes of pin flowers were incompatible with the styles of self-compatible plants, but the pollen tubes of thrum flowers were compatible with the styles of self-compatible plants. • These results indicate that the self-compatibility allele, Sh , retains heteromorphic incompatibility and suggest that the Sh allele was derived from recombination in the S supergene.
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Affiliation(s)
- K Matsui
- National Agricultural Research Center for Kyushu Okinawa region, Nishigoshi, Kumamoto 861-1192, Japan
| | - T Tetsuka
- National Agricultural Research Center for Kyushu Okinawa region, Nishigoshi, Kumamoto 861-1192, Japan
| | - T Nishio
- Laboratory of Plant Breeding and Genetics, Tohoku University, Aoba-ku, Sendai 981-8555, Japan
| | - T Hara
- National Agricultural Research Center for Kyushu Okinawa region, Nishigoshi, Kumamoto 861-1192, Japan
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Nishimoto Y, Ohnishi O, Hasegawa M. Topological incongruence between nuclear and chloroplast DNA trees suggesting hybridization in the urophyllum group of the genus Fagopyrum (Polygonaceae). Genes Genet Syst 2003; 78:139-53. [PMID: 12773814 DOI: 10.1266/ggs.78.139] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We performed phylogenetic analyses of Fagopyrum species in the urophyllum group based on nucleotide sequences of two nuclear genes, FLORICAULA/LEAFY (FLO/LFY) and AGAMOUS (AG), and three segments of chloroplast DNA (cpDNA), rbcL-accD, trnK intron, and trnC-rpoB spacer. The FLO/LFY and AG sequences turned out to be phylogenetically more informative at the intrageneric level than the cpDNA sequences. Congruence among these gene trees, inferred by a maximum-likelihood (ML) method, demonstrated that topologies were partially incongruent between the nuclear and chloroplast DNA phylogenies. The nuclear DNA sequence data supported a monophyletic relation of F. statice, F. gilesii, and F. jinshaense, whereas the former two species formed another monophyletic relation with the F. capillatum-F. gracilipes-F. gracilipedoides-F. rubifolium clade excluding F. jinshaense in the synthetic cpDNA phylogeny. In addition, two divergent sequences of FLO/LFY were found in F. rubifolium (tetraploid). One of these was sister to F. gracilipedoides and another was sister to F. statice, and a monophyletic relation of these two genes was rejected by a bootstrap analysis. These results suggest that hybridization may have occurred during diversification of Fagopyrum species in the urophyllum group, and that F. rubifolium is possibly allotetraploid species.
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Affiliation(s)
- Yuriko Nishimoto
- Department of Biosystems Science, School of Advanced Studies, The Graduate University for Advanced Studies.
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Ohsako T, Yamane K, Ohnishi O. Two new Fagopyrum (Polygonaceae) species, F. gracilipedoides and F. jinshaense from Yunnan, China. Genes Genet Syst 2002; 77:399-408. [PMID: 12589075 DOI: 10.1266/ggs.77.399] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Two new Fagopyrum (Polygonaceae) species, F. gracilipedoides and F. jinshaense, are described. Fagopyrum gracilipedoides was only found at Baoshan village, Lijiang district, Yunnan province, China. This species resembles the weedy species, F. gracilipes in morphology but they differ in both mating system and ploidy level; F. gracilipedoides is a heterostylous self-incompatible diploid species (2n = 16), whereas F. gracilipes is a self-compatible tetraploid species (2n = 32). Fagopyrum jinshaense was found along the Jinsha River valley near the border of Sichuan, Yunnan, and Tibet in China. Fagopyrum jinshaense is morphologically similar to F. gilesii, but they differ in the morphology of their inflorescences. Fagopyrum jinshaense has long spike-like inflorescences, whereas F. gilesii has a compact head-like one. Both F. jinshaense and F. gilesii are self-incompatible with heterostylous flowers and are diploid. Interspecific crosses between the two new species and already known species in the urophyllum group of Fagopyrum resulted in the production of self- and cross-sterile hybrids in the species combinations attempted. These results indicated that both new species are reproductively isolated from other Fagopyrum species. Molecular phylogenetic analysis based on the nucleotide sequence of the trnK gene intron in chloroplast DNA revealed the following points: 1) F. gracilipedoides, F. rubifolium and F. gracilipes / F. capillatum showed a trifurcating relationship and 2) F. jinshaense formed a clade with F. pleioramosum, F. callanthum, and F. macrocarpum, and was only distantly related to F. gilesii. In the clade of F. capillatum, F. gracilipes, F. gracilipedoides and F. rubifolium, the breakdown of self-incompatibility accompanying genome duplication seems to have occurred twice independently.
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Tsukatani N, Aii J, Miyabe Y, Shimizu K, Adachi T, Yabuya T. Identification of Somatic Hybrids between Iris ensata Thunb. and I. germanica L. by Designing Species-specific Primers of ITS Regions of Nuclear rDNA. CYTOLOGIA 2002. [DOI: 10.1508/cytologia.67.361] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - J. Aii
- Japan Science and Technology Corporation, Domestic Research Fellow, National Institute of Agrobiological Resources
| | - Y. Miyabe
- Division of Biotechnology and Biochemistry, Faculty of Agriculture, Miyazaki University
| | - K. Shimizu
- Laboratory of Ornamental Horticulture and Floriculture, Faculty of Agriculture, Kagoshima University
| | - T. Adachi
- Laboratory of Plant Genes and Physiology, Graduate School of Agriculture and Biological Science, Osaka Prefecture University
| | - T. Yabuya
- Division of Biotechnology and Biochemistry, Faculty of Agriculture, Miyazaki University
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Ohsako T, Ohnishi O. Intra- and interspecific phylogeny of wild Fagopyrum (Polygonaceae) species based on nucleotide sequences of noncoding regions in chloroplast DNA. AMERICAN JOURNAL OF BOTANY 2000; 87:573-582. [PMID: 10766729 DOI: 10.2307/2656601] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The intra- and interspecific phylogeny of Fagopyrum (Polygonaceae) species was studied using nucleotide sequence data from two noncoding regions in chloroplast DNA, the trnK (UUU) intron and the trnC (GCA)-rpoB spacer. Thirty-seven accessions of ten species and two unidentified samples in the urophyllum group of Fagopyrum were analyzed. Both of the studied regions showed high variability, including nucleotide substitutions, insertion/deletions, and inversions. Separate parsimony analyses of the two regions generated phylogenies that were largely consistent with each other. A single most parsimonious tree derived from the combined data of the two regions suggested that (1) either F. statice or F. leptopodum was derived from the ancestor more than once, (2) F. gracilipes, a tetraploid species, has recently been derived from diploid ancestor and rapidly spread out to its present distribution areas, and (3) F. pleioramosum, F. macrocarpum, and F. callianthum, three newly discovered species endemic to the upper Min River valley, differentiated from their common ancestral species in the present distribution area.
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Affiliation(s)
- T Ohsako
- Plant Germ-Plasm Institute, Faculty of Agriculture, Kyoto University, Mozume-cho, Muko, 617-0001 Japan
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