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Gao Y, Hou H, Cang Q, Sangdan Z, Zhao G, Yuan Y, Feng B. Global Research Trends and Future Directions for Buckwheat as a Smart Crop: A Bibliometric and Content Analysis. Foods 2024; 13:4068. [PMID: 39767010 PMCID: PMC11675993 DOI: 10.3390/foods13244068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2024] [Revised: 12/11/2024] [Accepted: 12/14/2024] [Indexed: 01/11/2025] Open
Abstract
Buckwheat (Fagopyrum esculentum Moench) originates from Central Asia and is widely distributed around the world. It is recognized as a versatile food crop due to its nutritional richness. Conducting a systematic analysis of the literature on buckwheat research can help scientific researchers achieve a better understanding of the current state, hotspots, and trends in this field, thereby promoting the sustainable development of buckwheat. The study retrieved a total of 4512 articles related to buckwheat from the Web of Science Core Collection (WoSCC), involving 104 countries (regions), 3220 institutions, and 12,840 authors. The number of research papers on buckwheat is gradually increasing. China, Japan, Poland, the United States, and South Korea were the top five countries in terms of publication volume in this field. Among the top 10 institutions in terms of publication volume, Chinese institutions account for 60%. Northwest A & F University held a leading position in the number of papers published and cited. Research on buckwheat shows that both domestic and international research institutions tend to collaborate more with institutions within their own countries. A comprehensive analysis of journals with a high number of publications and citations in buckwheat research indicated that studies primarily focus on its use as food and its active substances. Analysis of the authors and cited authors indicated that Wu Qi and Zhu F, among others, have high reputations and significant influence in this field. Reference analysis has determined that early research primarily focused on buckwheat as a pseudo-cereal food; mid-term research mainly concentrated on its active substances and cultivation; later research became more comprehensive, focusing on its potential in food, biotechnology, and medical health, which gradually emerged as trends and hot topics. Keyword analysis indicates that buckwheat flour, antioxidant activity, protective biological control, and buckwheat husk are current research hotspots. This study systematically summarizes the current status of research in the field, identifies research hotspots and trends, and provides a reference for future investigations into buckwheat.
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Affiliation(s)
- Yongbin Gao
- College of Agriculture, Northwest A & F University, Xianyang 712100, China; (Y.G.); (H.H.)
- Motuo County Dexing Township Agriculture and Animal Husbandry Integrated Service Center, Linzhi 860700, China; (Q.C.); (Z.S.)
| | - Hanghang Hou
- College of Agriculture, Northwest A & F University, Xianyang 712100, China; (Y.G.); (H.H.)
| | - Quzhen Cang
- Motuo County Dexing Township Agriculture and Animal Husbandry Integrated Service Center, Linzhi 860700, China; (Q.C.); (Z.S.)
| | - Zhuoma Sangdan
- Motuo County Dexing Township Agriculture and Animal Husbandry Integrated Service Center, Linzhi 860700, China; (Q.C.); (Z.S.)
| | - Guan Zhao
- Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa 851418, China;
| | - Yuhao Yuan
- College of Agriculture, Henan Agricultural University Zhengzhou, Zhengzhou 450002, China
| | - Baili Feng
- College of Agriculture, Northwest A & F University, Xianyang 712100, China; (Y.G.); (H.H.)
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Pan R, Zhu Q, Jia X, Li B, Li Z, Xiao Y, Luo S, Wang S, Shan N, Sun J, Zhou Q, Huang Y. Genome-Wide Development of InDel-SSRs and Association Analysis of Important Agronomic Traits of Taro ( Colocasia esculenta) in China. Curr Issues Mol Biol 2024; 46:13347-13363. [PMID: 39727924 PMCID: PMC11727045 DOI: 10.3390/cimb46120796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2024] [Revised: 11/04/2024] [Accepted: 11/19/2024] [Indexed: 12/28/2024] Open
Abstract
Taro (Colocasia esculenta (L.) Schott) is a tropical tuber crop whose underground corms are used as an important staple food. However, due to a lack of molecular markers, the genetic diversity, germplasm identification, and molecular breeding of taro are greatly limited. In this study, high-density InDel-SSR molecular markers covering the whole genome were developed based on the resequencing data of taro core germplasm. A total of 1,805,634 InDel-SSR loci were identified, and 219 highly polymorphic markers with an average polymorphism information content PIC value of 0.428 were screened. Furthermore, a genetic diversity analysis of 121 taro germplasm resources was conducted based on 219 markers, dividing the resources into three groups. In addition, an association analysis showed that, of the multiple InDel-SSR markers, g13.52 and g12.82 were significantly associated with leaf area and average cormel weight, respectively; the candidate genes CeARF17 (EVM0014444) and CeGA20ox (EVM0001890) were related to cormel expansion; and we excavated the candidate genes CeXXT2 (EVM0016820) and CeLOG1 (EVM0017064), which regulate leaf development. The InDel-SSRs and candidate genes identified in this study are expected to provide important support for genetically improving and breeding new varieties of taro.
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Affiliation(s)
- Rao Pan
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qianglong Zhu
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Xinbi Jia
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Bicong Li
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zihao Li
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yao Xiao
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Sha Luo
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shenglin Wang
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Nan Shan
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Jingyu Sun
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qinghong Zhou
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yingjin Huang
- Jiangxi Province Key Laboratory of Vegetable Cultivation and Utilization, Jiangxi Agricultural University, Nanchang 330045, China; (R.P.); (Q.Z.); (X.J.); (B.L.); (Z.L.); (Y.X.); (S.L.); (S.W.); (N.S.); (J.S.)
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
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Balážová Ž, Čišecká L, Gálová Z, Hromadová Z, Chňapek M, Pipan B, Meglič V. Characterization of Genetic Variability of Common and Tartary Buckwheat Genotypes Using Microsatellite Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:2147. [PMID: 39124265 PMCID: PMC11313801 DOI: 10.3390/plants13152147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Buckwheat is a highly nutritional pseudocereal with antioxidant potential. The aim of this study was to analyze the genetic variability of 21 varieties of common buckwheat (Fagopyrum esculentum Moench.) and 14 varieties of Tartary buckwheat (Fagopyrum tataricum Gaertn.) using microsatellite markers. By analyzing 21 SSR markers, an average of 11.6 alleles per locus were amplified and an average PIC value of 0.711 was determined. We determined the heterozygous status of the individuals and variability in the set using the SSR analysis on the basis of expected heterozygosity (He, 0.477), observed heterozygosity (Ho, 0.675), Shannon's index (I, 0.820), and fixation indices (FST, FIS, FIT). Based on the SSR analyses, the lower level of expected heterozygosity in the analyzed set of Tartary buckwheat genotypes was observed compared to common buckwheat. With the help of a hierarchical cluster analysis using the UPGMA algorithm, Structure analysis, and PCoA analysis for the SSR markers, we divided the buckwheat varieties in the dendrogram into two main clusters according to the species. The AMOVA analysis showed that genetic variability between the individuals prevails in the analyzed set. The SSR technique proved to be a suitable tool for the determination of intra- and inter-varietal genetic variability and for analysis of diversity.
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Affiliation(s)
- Želmíra Balážová
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Lucia Čišecká
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Zdenka Gálová
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Zuzana Hromadová
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Milan Chňapek
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva Ulica 17, SI-1000 Ljubljana, Slovenia; (B.P.); (V.M.)
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva Ulica 17, SI-1000 Ljubljana, Slovenia; (B.P.); (V.M.)
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Wang L, Zhao J, Mao Y, Liu L, Li C, Wu H, Zhao H, Wu Q. Tartary buckwheat rutin: Accumulation, metabolic pathways, regulation mechanisms, and biofortification strategies. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 208:108503. [PMID: 38484679 DOI: 10.1016/j.plaphy.2024.108503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 02/26/2024] [Accepted: 03/03/2024] [Indexed: 04/02/2024]
Abstract
Rutin is a significant flavonoid with strong antioxidant property and various therapeutic effects. It plays a crucial role in disease prevention and human health maintenance, especially in anti-inflammatory, antidiabetic, hepatoprotective and cardiovascular effects. While many plants can synthesize and accumulate rutin, tartary buckwheat is the only food crop possessing high levels of rutin. At present, the rutin content (RC) is regarded as the key index for evaluating the nutritional quality of tartary buckwheat. Consequently, rutin has become the focus for tartary buckwheat breeders and has made considerable progress. Here, we summarize research on the rutin in tartary buckwheat in the past two decades, including its accumulation, biosynthesis and breakdown pathways, and regulatory mechanisms. Furthermore, we propose several strategies to increase the RC in tartary buckwheat seeds based on current knowledge. This review aims to provide valuable references for elevating the quality of tartary buckwheat in the future.
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Affiliation(s)
- Lei Wang
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China
| | - Jiali Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China
| | - Yuanbin Mao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China
| | - Linling Liu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China
| | - Chenglei Li
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China
| | - Huala Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China
| | - Haixia Zhao
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China
| | - Qi Wu
- College of Life Science, Sichuan Agricultural University, No. 46, Xinkang Road, Ya'an, 625014, China.
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Li H, Song K, Li B, Zhang X, Wang D, Dong S, Yang L. CRISPR/Cas9 Editing Sites Identification and Multi-Elements Association Analysis in Camellia sinensis. Int J Mol Sci 2023; 24:15317. [PMID: 37894996 PMCID: PMC10607008 DOI: 10.3390/ijms242015317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/02/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
CRISPR/Cas9 is an efficient genome-editing tool, and the identification of editing sites and potential influences in the Camellia sinensis genome have not been investigated. In this study, bioinformatics methods were used to characterise the Camellia sinensis genome including editing sites, simple sequence repeats (SSRs), G-quadruplexes (GQ), gene density, and their relationships. A total of 248,134,838 potential editing sites were identified in the genome, and five PAM types, AGG, TGG, CGG, GGG, and NGG, were observed, of which 66,665,912 were found to be specific, and they were present in all structural elements of the genes. The characteristic region of high GC content, GQ density, and PAM density in contrast to low gene density and SSR density was identified in the chromosomes in the joint analysis, and it was associated with secondary metabolites and amino acid biosynthesis pathways. CRISPR/Cas9, as a technology to drive crop improvement, with the identified editing sites and effector elements, provides valuable tools for functional studies and molecular breeding in Camellia sinensis.
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Affiliation(s)
| | | | | | | | | | | | - Long Yang
- College of Plant Protection and Agricultural Big-Data Research Center, Shandong Agricultural University, Tai’an 271018, China
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Pipan B, Sinkovič L, Neji M, Janovská D, Zhou M, Meglič V. Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum. PLANTS (BASEL, SWITZERLAND) 2023; 12:3321. [PMID: 37765484 PMCID: PMC10534386 DOI: 10.3390/plants12183321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei's expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.
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Affiliation(s)
- Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Lovro Sinkovič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Mohamed Neji
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic;
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 420, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China;
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
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Xu W, Wang J, Tian C, Shi W, Wang L. Genome-Wide Development of Polymorphic Microsatellite Markers and Genetic Diversity Analysis for the Halophyte Suaeda aralocaspica (Amaranthaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091865. [PMID: 37176923 PMCID: PMC10181123 DOI: 10.3390/plants12091865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 04/14/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]
Abstract
Suaeda aralocaspica, which is an annual halophyte, grows in saline deserts in Central Asia with potential use in saline soil reclamation and salt tolerance breeding. Studying its genetic diversity is critical for effective conservation and breeding programs. In this study, we aimed to develop a set of polymorphic microsatellite markers to analyze the genetic diversity of S. aralocaspica. We identified 177,805 SSRs from the S. aralocaspica genome, with an average length of 19.49 bp, which were present at a density of 393.37 SSR/Mb. Trinucleotide repeats dominated (75.74%) different types of motifs, and the main motif was CAA/TTG (44.25%). We successfully developed 38 SSR markers that exhibited substantial polymorphism, displaying an average of 6.18 alleles with accompanying average polymorphism information content (PIC) value of 0.516. The markers were used to evaluate the genetic diversity of 52 individuals collected from three populations of S. aralocaspica in Xinjiang, China. The results showed that the genetic diversity was moderate to high, with a mean expected heterozygosity (He) of 0.614, a mean Shannon's information index (I) of 1.23, and a mean genetic differentiation index (Fst) of 0.263. The SSR markers developed in this study provide a valuable resource for future genetic studies and breeding programs of S. aralocaspica, and even other species in Suaeda.
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Affiliation(s)
- Wei Xu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Changyan Tian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Wang
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Li R, Chen Z, Zheng R, Chen Q, Deng J, Li H, Huang J, Liang C, Shi T. QTL mapping and candidate gene analysis for yield and grain weight/size in Tartary buckwheat. BMC PLANT BIOLOGY 2023; 23:58. [PMID: 36703107 PMCID: PMC9878770 DOI: 10.1186/s12870-022-04004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
BACKGROUND Grain weight/size influences not only grain yield (GY) but also nutritional and appearance quality and consumer preference in Tartary buckwheat. The identification of quantitative trait loci (QTLs)/genes for grain weight/size is an important objective of Tartary buckwheat genetic research and breeding programs. RESULTS Herein, we mapped the QTLs for GY, 1000-grain weight (TGW), grain length (GL), grain width (GW) and grain length-width ratio (L/W) in four environments using 221 recombinant inbred lines (XJ-RILs) derived from a cross of 'Xiaomiqiao × Jinqiaomai 2'. In total, 32 QTLs, including 7 for GY, 5 for TGW, 6 for GL, 11 for GW and 3 for L/W, were detected and distributed in 24 genomic regions. Two QTL clusters, qClu-1-3 and qClu-1-5, located on chromosome Ft1, were revealed to harbour 7 stable major QTLs for GY (qGY1.2), TGW (qTGW1.2), GL (qGL1.1 and qGL1.4), GW (qGW1.7 and qGW1.10) and L/W (qL/W1.2) repeatedly detected in three and above environments. A total of 59 homologues of 27 known plant grain weight/size genes were found within the physical intervals of qClu-1-3 and qClu-1-5. Six homologues, FtBRI1, FtAGB1, FtTGW6, FtMADS1, FtMKK4 and FtANT, were identified with both non-synonymous SNP/InDel variations and significantly differential expression levels between the two parents, which may play important roles in Tatary buckwheat grain weight/size control and were chosen as core candidate genes for further investigation. CONCLUSIONS Two stable major QTL clusters related to grain weight/size and six potential key candidate genes were identified by homology comparison, SNP/InDel variations and qRT‒qPCR analysis between the two parents. Our research provides valuable information for improving grain weight/size and yield in Tartary buckwheat breeding.
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Affiliation(s)
- Ruiyuan Li
- Key Laboratory of Information and Computing Science of Guizhou Province, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Zhengfeng Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Ran Zheng
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Qingfu Chen
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Jiao Deng
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Hongyou Li
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Juan Huang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Chenggang Liang
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China
| | - Taoxiong Shi
- Research Center of Buckwheat Industry Technology, Guizhou Normal University, Guiyang, 550001, Guizhou, China.
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Genome-Wide Survey and Analysis of Microsatellites in Waterlily, and Potential for Polymorphic Marker Development. Genes (Basel) 2022; 13:genes13101782. [PMID: 36292667 PMCID: PMC9601493 DOI: 10.3390/genes13101782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 09/28/2022] [Accepted: 09/28/2022] [Indexed: 11/04/2022] Open
Abstract
Waterlily (Nymphaeaceae), a diploid dicotyledon, is an ornamental aquatic plant. In 2020, the complete draft genome for the blue-petal waterlily (Nymphaea colorata) was made available in GenBank. To date, the genome-wide mining of microsatellites or simple sequence repeats (SSRs) in waterlily is still absent. In the present study, we investigated the characteristics of genome-wide microsatellites for N. colorata and developed polymorphic SSR markers across tropical and hardy waterlilies. A total of 238,816 SSRs were identified in 14 N. colorata chromosomes with an average density of 662.60 SSRs per Mb, and the largest number of SSRs were present on chromosome 1 (n = 30,426, 705.94 SSRs per Mb). The dinucleotide was the most common type, and AT-rich repeats prevail in the N. colorata genome. The SSR occurrence frequencies decreased as the number of motif repeats increased. Among 2442 protein-coding region SSRs, trinucleotides, accounting for 63.84%, were the most abundant. Gene ontology terms for signal transduction (e.g., GO: 0045859 and GO: 0019887) and the lipoic acid metabolism (ko00785,) were overrepresented in GO and KEGG enrichment analysis, respectively. In addition, 107,152 primer pairs were identified, and 13 novel polymorphism SSR markers were employed to distinguish among nine waterlily cultivars, of which Ny-5.2 and Ny-10.1 were the most informative SSR loci. This study contributes the first detailed characterization of SSRs in N. colorata genomes and delivers 13 novel polymorphism markers, which are useful for the molecular breeding strategies, genetic diversity and population structure analysis of waterlily.
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Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes. Genes (Basel) 2022; 13:genes13091518. [PMID: 36140687 PMCID: PMC9498332 DOI: 10.3390/genes13091518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/21/2022] Open
Abstract
Simple sequence repeats (SSRs) are one of the most important molecular markers, which are widespread in plants. Bamboos are important forest resources worldwide. Here, the comprehensive identification and comparative analysis of SSRs were performed in three woody and two herbaceous bamboo species. Altogether 567,175 perfect SSRs and 71,141 compound SSRs were identified from 5737.8 Mb genome sequences of five bamboo species. Di-nucleotide SSRs were the most predominant type, with an average of ~50,152.2 per species. Most SSRs were located in intergenic regions, while those located in genic regions were relatively less. Moreover, the results of annotation distribution indicated that terms with P450, peroxidase and ATP-binding cassette transporter related to lignin biosynthesis might play important roles in woody and herbaceous bamboos under the mediation of SSRs. Furthermore, the peroxidase gene family consisted of a large number of genes containing SSRs was selected for the evolutionary relationship analysis and SSR markers development. Fifteen SSR markers derived from peroxidase family genes of Phyllostachys edulis were identified as polymorphic in 34 accessions belonging to seven genera in Bambusoideae. These results provided a comprehensive insight of SSR markers into bamboo genomes, which would facilitate bamboo research related to comparative genomics, evolution and marker-assisted selection.
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