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Liu Y, Fang X, Tang T, Wang Y, Wu Y, Luo J, Wu H, Wang Y, Zhang J, Ruan R, Zhou M, Zhang K, Yi Z. Inflorescence Transcriptome Sequencing and Development of New EST-SSR Markers in Common Buckwheat ( Fagopyrum esculentum). PLANTS (BASEL, SWITZERLAND) 2022; 11:742. [PMID: 35336623 PMCID: PMC8950064 DOI: 10.3390/plants11060742] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/05/2022] [Accepted: 03/07/2022] [Indexed: 06/14/2023]
Abstract
Common buckwheat (Fagopyrum esculentum M.) is known for its adaptability, good nutrition, and medicinal and health care value. However, genetic studies of buckwheat have been hindered by limited genomic resources and genetic markers. In this study, Illumina HiSeq 4000 high-throughput sequencing technology was used to sequence the transcriptome of green-flower common buckwheat (Gr) with coarse pedicels and white-flower Ukrainian daliqiao (UD) with fine pedicels. A total of 118,448 unigenes were obtained, with an average length of 1248 bp and an N50 of 1850 bp. A total of 39,432 differentially expressed genes (DEGs) were identified, and the DEGs of the porphyrins and chlorophyll metabolic pathway had significantly upregulated expression in Gr. Then, a total of 17,579 sequences containing SSR loci were detected, and 20,756 EST-SSR loci were found. The distribution frequency of EST-SSR in the transcriptome was 17.52%, and the average distribution density was 8.21 kb. A total of 224 pairs of primers were randomly selected for synthesis; 35 varieties of common buckwheat and 13 varieties of Tartary buckwheat were verified through these primers. The clustering results well verified the previous conclusion that common buckwheat and Tartary buckwheat had a distant genetic relationship. The EST-SSR markers identified and developed in this study will be helpful to enrich the transcriptome information and marker-assisted selection breeding of buckwheat.
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Affiliation(s)
- Yang Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Xiaomei Fang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Tian Tang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yudong Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yinhuan Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jinyu Luo
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Haotian Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Yingqian Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Jian Zhang
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Renwu Ruan
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Kaixuan Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China;
| | - Zelin Yi
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China; (Y.L.); (X.F.); (T.T.); (Y.W.); (Y.W.); (J.L.); (H.W.); (Y.W.); (J.Z.); (R.R.)
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SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum. BIOMED RESEARCH INTERNATIONAL 2022; 2022:4237913. [PMID: 35299892 PMCID: PMC8923796 DOI: 10.1155/2022/4237913] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 01/10/2022] [Accepted: 01/31/2022] [Indexed: 11/22/2022]
Abstract
To study the SSR loci information and develop molecular markers, a total of 435,858 unigenes in transcriptome of Polygonatum sibiricum were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MISA software, and SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 112,728 SSR loci were found in the transcriptome of Polygonatum sibiricum, which distributed in 435,858 unigenes with a distribution frequency of 25.86%. Mo-nucleotide and Di-nucleotide repeat were the main types, accounted for 83.83% of all SSRs. The repeat motifs of A/T and AC/GT were the predominant repeat types of Mo-nucleotide and Di-nucleotide, respectively. A total of 113,305 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. One hundred and fifty-four of the 500 randomly selected primers not only produced fragments with expected molecular size but also had high polymorphism, which could accurately separate the tested varieties. The gene function of unigenes containing SSR was mostly related to the molecular function of Polygonatum sibiricum. The SSR markers in transcriptome of Polygonatum sibiricum show rich type, strong specificity, and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. The developed markers can also provide technical methods for molecular identification of intraspecific species of Polygonatum Mill. and maker-assisted breeding of superior varieties of Polygonatum Mill.
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de Oliveira GL, de Souza AP, de Oliveira FA, Zucchi MI, de Souza LM, Moura MF. Genetic structure and molecular diversity of Brazilian grapevine germplasm: Management and use in breeding programs. PLoS One 2020; 15:e0240665. [PMID: 33057449 PMCID: PMC7561202 DOI: 10.1371/journal.pone.0240665] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/01/2020] [Indexed: 12/23/2022] Open
Abstract
The management of germplasm banks is complex, especially when many accessions are involved. Microsatellite markers are an efficient tool for assessing the genetic diversity of germplasm collections, optimizing their use in breeding programs. This study genetically characterizes a large collection of 410 grapevine accessions maintained at the Agronomic Institute of Campinas (IAC) (Brazil). The accessions were genotyped with 17 highly polymorphic microsatellite markers. Genetic data were analyzed to determine the genetic structure of the germplasm, quantify its allelic diversity, suggest the composition of a core collection, and discover cases of synonymy, duplication, and misnaming. A total of 304 alleles were obtained, and 334 unique genotypes were identified. The molecular profiles of 145 accessions were confirmed according to the literature and databases, and the molecular profiles of more than 100 genotypes were reported for the first time. The analysis of the genetic structure revealed different levels of stratification. The primary division was between accessions related to Vitis vinifera and V. labrusca, followed by their separation from wild grapevine. A core collection of 120 genotypes captured 100% of all detected alleles. The accessions selected for the core collection may be used in future phenotyping efforts, in genome association studies, and for conservation purposes. Genetic divergence among accessions has practical applications in grape breeding programs, as the choice of relatively divergent parents will maximize the frequency of progeny with superior characteristics. Together, our results can enhance the management of grapevine germplasm and guide the efficient exploitation of genetic diversity to facilitate the development of new grape cultivars for fresh fruits, wine, and rootstock.
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Affiliation(s)
| | - Anete Pereira de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP) UNICAMP, Campinas, SP, Brazil
| | - Fernanda Ancelmo de Oliveira
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Maria Imaculada Zucchi
- Laboratory of Conservation Genetics and Genomics, Agribusiness Technological Development of São Paulo (APTA), Piracicaba, SP, Brazil
| | - Lívia Moura de Souza
- Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil
| | - Mara Fernandes Moura
- Advanced Fruit Research Center, Agronomic Institute (IAC), Jundiaí, SP, Brazil
- * E-mail:
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Feng T, Jia Q, Meng X, Chen X, Wang F, Chai W, Liang Z. Evaluation of genetic diversity and construction of DNA fingerprinting in Polygonatum Mill. based on EST-SSR and SRAP molecular markers. 3 Biotech 2020; 10:322. [PMID: 32656055 DOI: 10.1007/s13205-020-02316-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 06/23/2020] [Indexed: 12/17/2022] Open
Abstract
Polygonatum sibiricum is widely consumed as a traditional Chinese herb and edible plant in China. Despite its nutritional and medical values, research on Polygonatum Mill. has been scarce, particularly as far as its genetic diversity is concerned. In this study, fourteen expressed sequence tag-derived simple sequence repeat (EST-SSR) and seven sequence-related amplified polymorphism (SRAP) markers were used to evaluate the genetic diversity in fifty Polygonatum Mill. accessions. The EST-SSRs and SRAPs produced 173 (90.58%) and 113 (93.39%) polymorphic bands, respectively. Unweighted Pair-Group Method Analysis (UPGMA) based on the combined data matrices of EST-SSRs and SRAPs divided the fifty Polygonatum Mill. accessions into fourteen groups. In addition, accessions of P. cyrtonema Hua obtained from Anhui and Zhejiang provinces were clustered according to their geographic origin. Furthermore, some accessions were gathered together based on species, such as P. kingianum Coll. et Hemsl, P. punctatum Royle ex Kunth, P. odoratum (Mill.) Druce, and P. sibiricum Red., and bootstrap analysis for clustering fully supported the grouping of the accessions. The Analysis of Molecular Variance (AMOVA) results revealed higher variation within populations (95%) rather than among populations (5%), indicating that Polygonatum Mill. has a low genetic differentiation between populations, and Principal Coordinate Analysis (PCoA) greatly supported the results of cluster analysis and AMOVA analysis. Finally, five markers which could produce abundant and stable bands were used to construct DNA fingerprinting database of Polygonatum Mill.. Our results demonstrated the utility of both EST-SSR and SRAP markers to successfully evaluate and identify Polygonatum Mill..
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Affiliation(s)
- Tinghui Feng
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Qiaojun Jia
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Xin Meng
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Xiliang Chen
- Zhejiang WSKOO Biotechnology Co.,Ltd., Wuyi, 321200 Zhejiang China
| | - Feifeng Wang
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
| | - Weiguo Chai
- Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou, 310024 Zhejiang China
| | - Zongsuo Liang
- Key Laboratory of Plant Secondary Metabolism and Regulation, College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou, 310018 Zhejiang China
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Zhu J, Guo Y, Su K, Liu Z, Ren Z, Li K, Guo X. Construction of a highly saturated Genetic Map for Vitis by Next-generation Restriction Site-associated DNA Sequencing. BMC PLANT BIOLOGY 2018; 18:347. [PMID: 30541441 PMCID: PMC6291968 DOI: 10.1186/s12870-018-1575-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/26/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND High-saturate molecular linkage maps are an important tool in studies on plant molecular biology and assisted breeding. Development of a large set of single nucleotide polymorphisms (SNPs) via next-generation sequencing (NGS)-based methods, restriction-site associated DNA sequencing (RAD-seq), and the generation of a highly saturated genetic map help improve fine mapping of quantitative trait loci (QTL). RESULTS We generated a highly saturated genetic map to identify significant traits in two elite grape cultivars and 176 F1 plants. In total, 1,426,967 high-quality restriction site-associated DNA tags were detected; 51,365, 23,683, and 70,061 markers were assessed in 19 linkage groups (LGs) for the maternal, paternal, and integrated maps, respectively. Our map was highly saturated in terms of marker density and average "Gap ≤ 5 cM" percentage. CONCLUSIONS In this study, RAD-seq of 176 F1 plants and their parents yielded 8,481,484 SNPs and 1,646,131 InDel markers, of which 65,229 and 4832, respectively, were used to construct a highly saturated genetic map for grapevine. This map is expected to facilitate genetic studies on grapevine, including an evaluation of grapevine and deciphering the genetic basis of economically and agronomically important traits. Our findings provide basic essential genetic data the grapevine genetic research community, which will lead to improvements in grapevine breeding.
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Affiliation(s)
- Junchi Zhu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
- Ministry of Education Key Laboratory of Protected Horticulture, Shenyang, 110866 People’s Republic of China
| | - Kai Su
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Zhendong Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Zhihua Ren
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Kun Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
| | - Xiuwu Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866 People’s Republic of China
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Teh SL, Fresnedo-Ramírez J, Clark MD, Gadoury DM, Sun Q, Cadle-Davidson L, Luby JJ. Genetic dissection of powdery mildew resistance in interspecific half-sib grapevine families using SNP-based maps. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2017; 37:1. [PMID: 28127252 PMCID: PMC5226326 DOI: 10.1007/s11032-016-0586-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 11/01/2016] [Indexed: 05/22/2023]
Abstract
Quantitative trait locus (QTL) identification in perennial fruit crops is impeded largely by their lengthy generation time, resulting in costly and labor-intensive maintenance of breeding programs. In a grapevine (genus Vitis) breeding program, although experimental families are typically unreplicated, the genetic backgrounds may contain similar progenitors previously selected due to their contribution of favorable alleles. In this study, we investigated the utility of joint QTL identification provided by analyzing half-sib families. The genetic control of powdery mildew was studied using two half-sib F1 families, namely GE0711/1009 (MN1264 × MN1214; N = 147) and GE1025 (MN1264 × MN1246; N = 125) with multiple species in their ancestry. Maternal genetic maps consisting of 1077 and 1641 single nucleotide polymorphism (SNP) markers, respectively, were constructed using a pseudo-testcross strategy. Ratings of field resistance to powdery mildew were obtained based on whole-plant evaluation of disease severity. This 2-year analysis uncovered two QTLs that were validated on a consensus map in these half-sib families with improved precision relative to the parental maps. Examination of haplotype combinations based on the two QTL regions identified strong association of haplotypes inherited from 'Seyval blanc', through MN1264, with powdery mildew resistance. This investigation also encompassed the use of microsatellite markers to establish a correlation between 206-bp (UDV-015b) and 357-bp (VViv67) fragment sizes with resistance-carrying haplotypes. Our work is one of the first reports in grapevine demonstrating the use of SNP-based maps and haplotypes for QTL identification and tagging of powdery mildew resistance in half-sib families.
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Affiliation(s)
- Soon Li Teh
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108 USA
| | | | - Matthew D. Clark
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108 USA
| | - David M. Gadoury
- School of Integrative Plant Science, Cornell University, New York State Agricultural Experiment Station, Geneva, NY 14456 USA
| | - Qi Sun
- BRC Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, NY 14853 USA
| | | | - James J. Luby
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN 55108 USA
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