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Park H, Hyeon Heo T, Cho J, Young Choi H, Hyeon Lee D, Kyong Lee J. Evaluation and characteristic analysis of SSRs from the transcriptomic sequences of Perilla crop (Perilla frutescens L.). Gene 2024; 933:148938. [PMID: 39278375 DOI: 10.1016/j.gene.2024.148938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2024] [Revised: 08/29/2024] [Accepted: 09/09/2024] [Indexed: 09/18/2024]
Abstract
Perilla crop is a self-fertilizing annual plant, cultivated and used mainly in East Asia. Perilla frutescens var. frutescens seeds are rich in unsaturated fatty acids, which have health benefits, and Perilla frutescens var. crispa leaves are rich in anthocyanins. However, genomic analysis such as whole genome sequencing or genetic mapping has not been performed on Perilla crop. This current study confirms the abundance and diversity of 15,991 simple sequence repeats (SSRs) classified in previous studies in the Perilla genome, selects and designs 1,538 SSR primer sets, and confirms which SSR primer sets exhibit high polymorphism. Of the 15,991 SSRs classified, there were 9,910 (62%) dinucleotide repeats, 5,652 (35.3%) trinucleotide repeats, and 429 (2.7%) tetranucleotide repeats. Among these, the most identified was (CT)n with a total of 4,817. The 15,991 SSRs had 4 to 26 repeats. Four repeats were the most frequent with 11,084 (69.3%). A total of 1,538 SSR primers were selected and designed to confirm polymorphism, of which 157 showed persistent and clear polymorphism. Among these 157 SSR primer sets, 98 (62.4%) were dinucleotide repeats, 39 (24.8%) were trinucleotide repeats, and 20 (12.7%) were tetranucleotide repeats. Among 549 SSR primers that showed polymorphism, trinucleotide repeats showed persistent polymorphism at a high rate. Therefore, when developing SSR primer sets for Perilla crop in the future, it is recommended that trinucleotide repeats be selected first. These research results will be helpful in future genomic analysis and development of SSR primers in Perilla crop.
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Affiliation(s)
- Hyeon Park
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, South Korea; Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, South Korea
| | - Tae Hyeon Heo
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, South Korea; Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, South Korea
| | - Jungeun Cho
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, South Korea; Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, South Korea
| | - Hyo Young Choi
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, South Korea
| | - Da Hyeon Lee
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, South Korea
| | - Ju Kyong Lee
- Department of Applied Plant Sciences, College of Agriculture and Life Sciences, Kangwon National University, Chuncheon 24341, South Korea; Interdisciplinary Program in Smart Agriculture, Kangwon National University, Chuncheon 24341, South Korea.
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Meena RK, Kashyap P, Shamoon A, Dhyani P, Sharma H, Bhandari MS, Barthwal S, Ginwal HS. Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus. Funct Integr Genomics 2023; 23:103. [PMID: 36973584 DOI: 10.1007/s10142-023-01033-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/16/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (FST = 0.119), severe inbreeding (FIS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.
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Affiliation(s)
- Rajendra K Meena
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India.
| | - Priyanka Kashyap
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Arzoo Shamoon
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Payal Dhyani
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Hansraj Sharma
- ICFRE - Bamboo & Rattan Centre, Aizawl, 796007, Mizoram, India
- ICFRE-Rain Forest Research Institute, Jorhat, 785001, Assam, India
| | - Maneesh S Bhandari
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Santan Barthwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
| | - Harish S Ginwal
- Division of Genetics & Tree Improvement, ICFRE-Forest Research Institute, Dehradun, 248 195, Uttarakhand, India
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Construction of an Intragenic SSR-Based Linkage Map and QTL Mapping for Agronomic Traits in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chinese cabbage (Brassica rapa L. ssp. pekinensis) is one of the most widely cultivated and economically important vegetables in China. Constructing an effective genetic linkage map and mapping quantitative trait loci (QTLs) related to yield and leafy head morphology is of great importance for molecular breeding of Chinese cabbage. Using two diverse Chinese cabbage inbred lines, ZHB and G291, as parents, an F2 segregating population consisting of 240 individuals was prepared for genetic map construction and phenotype investigation in this study. The two parents are significantly different in both shape and size. Sixteen important agronomic traits of F2 individuals were investigated. A genetic map of 105 intragenic simple sequence repeat (SSR) markers distributed across 10 linkage groups (LGs) was constructed, which was 2034.1 cM in length and had an average inter-locus distance of 21.75 cM. We identified 48 QTLs for the tested important agronomic traits on the studied LGs, with LOD scores of 2.51–12.49, which explained the phenotypic variance of 3.41–26.66%. The QTLs identified in this study will facilitate further genetic analysis and marker-assisted genetic improvement of Chinese cabbage.
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Vidakovic DO, Perovic D, Semilet TV, Börner A, Khlestkina EK. The consensus rye microsatellite map with EST-SSRs transferred from wheat. Vavilovskii Zhurnal Genet Selektsii 2021; 24:459-464. [PMID: 33659829 PMCID: PMC7716552 DOI: 10.18699/vj20.48-o] [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] [Indexed: 11/19/2022] Open
Abstract
Microsatellite (SSR) markers with known precise intrachromosomal locations are widely used for mapping genes in rye and for the investigation of wheat-rye translocation lines and triticale highly demanded for mapping economically important genes and QTL-analysis. One of the sources of novel SSR markers in rye are microsatellites transferable from the wheat genome. Broadening the list of available SSRs in rye mapped to chromosomes is still needed, since some rye chromosome maps still have just a few microsatellite loci mapped. The goal of the current study was to integrate wheat EST-SSRs into the existing rye genetic maps and to construct a consensus rye microsatellite map. Four rye mapping populations (P87/P105, N6/N2, N7/N2 and N7/N6) were tested with CFE (EST-SSRs) primers. A total of 23 Xcfe loci were mapped on rye chromosomes: Xcfe023, -136 and -266 on chromosome 1R, Xcfe006, -067, -175 and -187 on 2R, Xcfe029 and -282 on 3R, Xcfe004, -100, -152, -224 and -260 on 4R, Xcfe037, -208 and -270 on 5R, Xcfe124, -159 and -277 on 6R, Xcfe010, -143 and -228 on 7R. With the exception of Xcfe159 and Xcfe224, all the Xcfe loci mapped were found in orthologous positions considering multiple evolutionary translocations in the rye genome relative to those of common wheat. The consensus map was constructed using mapping data from the four bi-parental populations. It contains a total of 123 microsatellites, 12 SNPs, 118 RFLPs and 2 isozyme loci.
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Affiliation(s)
- D O Vidakovic
- Julius Kuehn-Institute (JKI), Quedlinburg, Germany University of Novi Sad, Department of Biology and Ecology, Novi Sad, Serbia
| | - D Perovic
- Julius Kuehn-Institute (JKI), Quedlinburg, Germany
| | - T V Semilet
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
| | - A Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - E K Khlestkina
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia Novosibirsk State University, Novosibirsk, Russia
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5
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De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba. J Genet 2020. [DOI: 10.1007/s12041-020-01235-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Asadi A, Ebrahimi A, Rashidi-Monfared S, Basiri M, Akbari-Afjani J. Comprehensive functional analysis and mapping of SSR markers in the chickpea genome (Cicer arietinum L.). Comput Biol Chem 2019; 84:107169. [PMID: 31812779 DOI: 10.1016/j.compbiolchem.2019.107169] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2018] [Revised: 11/16/2019] [Accepted: 11/18/2019] [Indexed: 11/19/2022]
Abstract
Plant molecular breeding largely depends on the relationship between molecular markers and major traits. Herein, a total of 32,962 genomic simple sequence repeats (SSRs) were detected in the whole genome of chickpea with an average density of 94.93 SSRs/Mb. Chickpea chromosomes uniformity test indicated that the genomic SSRs (gSSRs) were steadily distributed across the genome. Moreover, 48,667 transcriptome sequences were analyzed and 1949 SSR-containing transcript assembly contigs (TACs) were identified. The analysis showed that di- and trinucleotide SSRs were the most frequent SSR motifs within the transcriptome sequences. Among them, AT and TTA and AG and TTC motifs within the transcriptome showed the highest frequencies among di- and trinucleotide repeat motifs, respectively. The SSRs-containing TACs were compared to the GenBank non-redundant database using BLASTX, and subsequently, gene ontology (GO) analysis was performed using QuickGO browser to reduce complexity and highlight biological processes associated with the SSRs-containing TACs. The identified SSRs-containing TACs were categorized into 35 enriched functional-related gene group. The mapping of characterized SSRs-containing TACs onto chickpea chromosomes was performed using BLASTN. The mapping result showed that, a total of 1798 SSRs-containing TACs were mapped onto the chickpea genome. Based on the functional analysis result, 249 and 242 of the mapped SSRs-containing TACs were found in the genes encoding for putative stress-related proteins and transcription factors, respectively. The results presented here can be applied to improve and speed up the chickpea breeding programs.
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Affiliation(s)
- AliAkbar Asadi
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Amin Ebrahimi
- Agronomy and Plant Breeding Department, Faculty of Agriculture, Shahrood University of Technology, Semnan, Iran
| | - Sajad Rashidi-Monfared
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran.
| | - Mohammad Basiri
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
| | - Javad Akbari-Afjani
- Agricultural Biotechnology Department, Faculty of Agriculture, Tarbiat Modares University, Tehran, Iran
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Sen S, Dehury B, Sahu J, Rathi S, Yadav RNS. Mining and comparative survey of EST-SSR markers among members of Euphorbiaceae family. Mol Biol Rep 2018; 45:453-468. [PMID: 29626317 DOI: 10.1007/s11033-018-4181-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 04/02/2018] [Indexed: 11/30/2022]
Abstract
Euphorbiaceae represents flowering plants family of tropical and sub-tropical region rich in secondary metabolites of economic importance. To understand and assess the genetic makeup among the members, this study was undertaken to characterize and compare SSR markers from publicly available ESTs and GSSs of nine selected species of the family. Mining of SSRs was performed by MISA, primer designing by Primer3, while functional annotation, gene ontology (GO) and enrichment analysis were performed by Blast2GO. A total 12,878 number of SSRs were detected from 101,701 number of EST sequences. SSR density ranged from 1 SSR/3.22 kb to 1 SSR/15.65 kb. A total of 1873 primer pairs were designed for the annotated SSR-Contigs. About 77.07% SSR-ESTs could be assigned a significant match to the protein database. 3037 unique SSR-FDM were assigned and IPR003657 (WRKY Domain) was found to be the most dominant FDM among the members. 1810 unique GO terms obtained were further subjected to enrichment analysis to obtain 513 statistically significant GO terms mapped to the SSR containing ESTs. Most frequent enriched GO terms were, GO:0003824 for molecular function, GO:0006350 for biological process and GO:0005886 for cellular component, justifying the richness of defensive secondary metabolites and phytomedicine within the family. The results from this study provides tangible insight to genetic make-up and distribution of SSRs. Functional annotation corresponded many genes of unknown functions which may be considered as novel genes or genes responsible for stress specific secondary metabolites. Further studies are required to understand stress specific genes accountable for leveraging the synthesis of secondary metabolites.
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Affiliation(s)
- Surojit Sen
- Centre for Biotechnology and Bioinformatics, Dibrugarh University, Dibrugarh, Assam, India.
| | - Budheswar Dehury
- Biomedical Informatics Centre, ICMR-Regional Medical Research Centre, Nalco Square, Chandrasekharpur, Bhubaneswar, Odisha, 751023, India
| | - Jagajjit Sahu
- Distributed Information Center, Department of Agricultural Biotechnology, Assam Agricultural University, Jorhat, Assam, 785013, India
| | - Sunayana Rathi
- Department of Biochemistry and Agricultural Chemistry, Assam Agricultural University, Jorhat, Assam, 785013, India
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Pandey S, Ansari WA, Pandey M, Singh B. Genetic diversity of cucumber estimated by morpho-physiological and EST-SSR markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:135-146. [PMID: 29398845 PMCID: PMC5787120 DOI: 10.1007/s12298-017-0489-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Revised: 10/24/2017] [Accepted: 11/21/2017] [Indexed: 05/14/2023]
Abstract
In the present study, genetic variation among 40 cucumber genotypes was analyzed by means of morpho-physiological traits and 21 EST-SSR markers. Diversity was observed for morpho-physiological characters like days to 50% female flowering (37-46.9, number of fruits/plant (1.33-5.80), average fruit weight (41-333), vine length (36-364), relative water content (58.5-92.7), electrolyte leakage (15.9-37.1), photosynthetic efficiency (0.40-0.75) and chlorophyll concentration index (11.1-28.6). The pair wise Jaccard similarity coefficient ranged from 0.00 to 0.27 for quantitative traits and 0.24 to 0.96 for EST-SSR markers indicating that the accessions represent genetically diverse populations. With twenty-one EST-SSR markers, polymorphism revealed among 40 cucumber genotypes, number of alleles varied 2-6 with an average 3.05. Polymorphism information content varied from 0.002 to 0.989 (mean = 0.308). The number of effective allele (Ne), expected heterozygosity (He) and unbiased expected heterozygosity (uHe) of these EST-SSRs were 1.079-1.753, 0.074-0.428 and 0.074-0.434, respectively. Same 21 EST-SSR markers transferability checked in four other Cucumis species: snapmelon (Cucumis melo var. momordica), muskmelon (Cucumis melo L.), pickling melon (Cucumis melo var. conomon) and wild muskmelon (Cucumis melo var. agrestis) with frequency of 61.9, 95.2, 76.2, and 76.2%, respectively. Present study provides useful information on variability, which can assist geneticists with desirable traits for cucumber germplasm utilization. Observed physiological parameters may assists in selection of genotype for abiotic stress tolerance also, EST-SSR markers may be useful for genetic studies in related species.
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Affiliation(s)
- Sudhakar Pandey
- ICAR-Indian Institute of Vegetable Research, Post Box-01, P.O.-Jakhani (Shahanshahpur), Varanasi, Uttar Pradesh 221305 India
| | - Waquar Akhter Ansari
- ICAR-Indian Institute of Vegetable Research, Post Box-01, P.O.-Jakhani (Shahanshahpur), Varanasi, Uttar Pradesh 221305 India
| | - Maneesh Pandey
- ICAR-Indian Institute of Vegetable Research, Post Box-01, P.O.-Jakhani (Shahanshahpur), Varanasi, Uttar Pradesh 221305 India
| | - Bijendra Singh
- ICAR-Indian Institute of Vegetable Research, Post Box-01, P.O.-Jakhani (Shahanshahpur), Varanasi, Uttar Pradesh 221305 India
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Pandey S, Ansari WA, Choudhary BR, Pandey M, Jena SN, Singh AK, Dubey RK, Singh B. Microsatellite analysis of genetic diversity and population structure of hermaphrodite ridge gourd ( Luffa hermaphrodita). 3 Biotech 2018; 8:17. [PMID: 29270333 PMCID: PMC5725372 DOI: 10.1007/s13205-017-1030-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Accepted: 12/04/2017] [Indexed: 11/29/2022] Open
Abstract
Out of 103 microsatellite markers used for studying the genetic diversity among local landraces of Luffa species, 56 were found polymorphic, including 38 gSSR and 18 eSSR, respectively. A total of 197 amplification products were obtained. The mean number of alleles per locus was 3.52. The PIC ranged from 0.037 to 0.986, while size of amplified product ranged from 105 to 500 bp. Cucumber-derived SSRs were amplified within L. acutangula (68%), L. aegyptiaca (61.16%), and L. hermaphrodita (60.2%), with an average of 63.12% cross-transferability. The Jaccard's coefficient ranged from 0.66 to 0.97, with an average of 0.81. High genetic variability was observed for node of 1st hermaphrodite flower (6.4-17), days to 1st hermaphrodite flower (38-52.1), days to 1st fruit harvest (43-65), number of fruit per cluster (1-5.9), fruit length (3.9-25 cm), fruit weight (18.4-175 g), number of fruit per plant (20-147.5), and yield per plant (2.2-4.7 kg). Two sub-populations were identified including 21 genotypes (sub-population I) and 06 genotypes (sub-population II), these two sub-populations showed 0.608-0.395% of the ancestral relationship to each other. This study provides information for future exploration, collection, and utilization of Luffa genotypes, as well as the polymorphic markers identified could be available for the study of landmarks in linkages, genomic structures, evolutionary ecology, and marker-assisted selection (MAS) in Luffa species.
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Affiliation(s)
- Sudhakar Pandey
- ICAR-Indian Institute of Vegetable Research, P.O.-Jakhani (Shahanshahpur), Post Box-01, Varanasi, Uttar Pradesh 221305 India
| | - W. A. Ansari
- ICAR-Indian Institute of Vegetable Research, P.O.-Jakhani (Shahanshahpur), Post Box-01, Varanasi, Uttar Pradesh 221305 India
| | - B. R. Choudhary
- ICAR-Central Institute for Arid Horticulture, Beechwal, Bikaner, Rajasthan 334006 India
| | - Maneesh Pandey
- ICAR-Indian Institute of Vegetable Research, P.O.-Jakhani (Shahanshahpur), Post Box-01, Varanasi, Uttar Pradesh 221305 India
| | - S. N. Jena
- CSIR-National Botanical Research Institute, 436, Rana Pratap Marg, Lucknow, Uttar Pradesh 226001 India
| | - A. K. Singh
- College of Agriculture and Research Station (IGKV), Korea, Chhattisgarh 497 335 India
| | - R. K. Dubey
- ICAR-Indian Institute of Vegetable Research, P.O.-Jakhani (Shahanshahpur), Post Box-01, Varanasi, Uttar Pradesh 221305 India
| | - Bijendra Singh
- ICAR-Indian Institute of Vegetable Research, P.O.-Jakhani (Shahanshahpur), Post Box-01, Varanasi, Uttar Pradesh 221305 India
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Construction of a genetic map using EST-SSR markers and QTL analysis of major agronomic characters in hexaploid sweet potato (Ipomoea batatas (L.) Lam). PLoS One 2017; 12:e0185073. [PMID: 29020092 PMCID: PMC5636084 DOI: 10.1371/journal.pone.0185073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 09/06/2017] [Indexed: 11/26/2022] Open
Abstract
The Sweet potato, Ipomoea batatas (L.) Lam, is difficult to study in genetics and genomics because it is a hexaploid. The sweet potato study not have been performed domestically or internationally. In this study was performed to construct genetic map and quantitative trait loci (QTL) analysis. A total of 245 EST-SSR markers were developed, and the map was constructed by using 210 of those markers. The total map length was 1508.1 cM, and the mean distance between markers was 7.2 cM. Fifteen characteristics were investigated for QTLs analysis. According to those, the Four QTLs were identified, and The LOD score was 3.0. Further studies need to develop molecular markers in terms of EST-SSR markers for doing to be capable of efficient breeding. The genetic map created here using EST-SSR markers will facilitate planned breeding of sweet potato cultivars with various desirable traits.
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Wang RRC, Larson SR, Jensen KB. Differential transferability of EST-SSR primers developed from the diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Thinopyrum elongatum. Genome 2017; 60:530-536. [PMID: 28235186 DOI: 10.1139/gen-2016-0157] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid species of Triticeae, Pseudoroegneria spicata (Pursh) Á. Löve (having St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (Jb = Eb = J), and Thinopyrum elongatum (Host) D.R. Dewey (Je = Ee = E), were used to produce amplicons in these three species to (i) assess relative transferability, (ii) identify polymorphic species-specific markers, and (iii) determine genome relationships among the three species. Because of the close relationship between Jb and Je genomes, EST-SSR primers derived from Th. bessarabicum and Th. elongatum had greater transferability to each other than those derived from the St-genome P. spicata. A large number of polymorphic species- and genome-specific EST-SSR amplicons were identified that will be used for construction of genetic maps of these diploid species, and tracing economically useful genes in breeding or gene transfer programs in various species of Triticeae.
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Affiliation(s)
- Richard R-C Wang
- United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA.,United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Steve R Larson
- United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA.,United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Kevin B Jensen
- United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA.,United States Department of Agriculture - Agricultural Research Services Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
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12
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Duan X, Wang K, Su S, Tian R, Li Y, Chen M. De novo transcriptome analysis and microsatellite marker development for population genetic study of a serious insect pest, Rhopalosiphum padi (L.) (Hemiptera: Aphididae). PLoS One 2017; 12:e0172513. [PMID: 28212394 PMCID: PMC5315398 DOI: 10.1371/journal.pone.0172513] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/05/2017] [Indexed: 11/21/2022] Open
Abstract
The bird cherry-oat aphid, Rhopalosiphum padi (L.), is one of the most abundant aphid pests of cereals and has a global distribution. Next-generation sequencing (NGS) is a rapid and efficient method for developing molecular markers. However, transcriptomic and genomic resources of R. padi have not been investigated. In this study, we used transcriptome information obtained by RNA-Seq to develop polymorphic microsatellites for investigating population genetics in this species. The transcriptome of R. padi was sequenced on an Illumina HiSeq 2000 platform. A total of 114.4 million raw reads with a GC content of 40.03% was generated. The raw reads were cleaned and assembled into 29,467 unigenes with an N50 length of 1,580 bp. Using several public databases, 82.47% of these unigenes were annotated. Of the annotated unigenes, 8,022 were assigned to COG pathways, 9,895 were assigned to GO pathways, and 14,586 were mapped to 257 KEGG pathways. A total of 7,936 potential microsatellites were identified in 5,564 unigenes, 60 of which were selected randomly and amplified using specific primer pairs. Fourteen loci were found to be polymorphic in the four R. padi populations. The transcriptomic data presented herein will facilitate gene discovery, gene analyses, and development of molecular markers for future studies of R. padi and other closely related aphid species.
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Affiliation(s)
- Xinle Duan
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China.,College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kang Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Sha Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Ruizheng Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Yuting Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
| | - Maohua Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, Key Laboratory of Crop Pest Integrated Pest Management on the Loess Plateau of Ministry of Agriculture College of Plant Protection, Northwest A&F University, Yangling, China
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Kim JH, Kim JH, Jo WS, Ham JG, Chung IK, Kim KM. Characterization and development of EST-SSR markers in sweet potato (Ipomoea batatas (L.) Lam). 3 Biotech 2016; 6:243. [PMID: 28330315 PMCID: PMC5234531 DOI: 10.1007/s13205-016-0565-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 11/03/2016] [Indexed: 11/29/2022] Open
Abstract
In this study, a cDNA library was constructed from the total RNA of sweet potato leaves. A total of 789 copies of the cDNA were cloned in Escherichia coli by employing the pGEM-T Easy vector. Sequencing was carried out by Solgent Co. (Korea). As many as 579 expressed sequence tag-simple sequence repeat (EST-SSR) markers were designed (73.38%) from the known cDNA nucleotide base sequences. The lengths of the developed EST-SSR markers ranged from 100 to 499 bp (average length 238 bp). Their motif sequence types were varied, with most being dinucleotides and pentanucleotides, and the most commonly found motifs were CAGAAT (29.0%) and TCT (2.8%). Based on these SSR-containing sequences, 619 pairs of high-quality SSR primers were designed using WebSat and Primer3web. The total number of primers designed was 144. Polymorphism was evident in 82 EST-SSR markers among 20 Korean sweet potato cultivars tested and in 90 EST-SSR markers in the two parents of a mapping population, Yeseumi and Annobeny. In this study, the hexaploid sweet potato (2n = 6x = 90) EST-SSR markers were developed in the absence of full-sequence data. Moreover, by acting as a molecular tag for particular traits, the EST-SSR marker can also simultaneously identify information about the corresponding gene. These EST-SSR markers will allow the molecular analysis of sweet potato to be done more efficiently. Thus, we can develop high-quality sweet potato while overcoming the challenges from climate change and other unfavorable conditions.
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Affiliation(s)
- Jin-Hee Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Jun-Hoi Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Won-Sam Jo
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Jeong-Gwan Ham
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, South Korea
| | - Il Kyung Chung
- Department of Biotechnology, Catholic University of Daegu, Gyeongsan-Si, Gyeongbuk, 38430, South Korea
| | - Kyung-Min Kim
- School of Applied Biosciences, College of Agriculture and Life Sciences, Kyungpook National University, Daegu, 41566, South Korea.
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Assessment of Functional EST-SSR Markers (Sugarcane) in Cross-Species Transferability, Genetic Diversity among Poaceae Plants, and Bulk Segregation Analysis. GENETICS RESEARCH INTERNATIONAL 2016; 2016:7052323. [PMID: 27340568 PMCID: PMC4908241 DOI: 10.1155/2016/7052323] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 04/13/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022]
Abstract
Expressed sequence tags (ESTs) are important resource for gene discovery, gene expression and its regulation, molecular marker development, and comparative genomics. We procured 10000 ESTs and analyzed 267 EST-SSRs markers through computational approach. The average density was one SSR/10.45 kb or 6.4% frequency, wherein trinucleotide repeats (66.74%) were the most abundant followed by di- (26.10%), tetra- (4.67%), penta- (1.5%), and hexanucleotide (1.2%) repeats. Functional annotations were done and after-effect newly developed 63 EST-SSRs were used for cross transferability, genetic diversity, and bulk segregation analysis (BSA). Out of 63 EST-SSRs, 42 markers were identified owing to their expansion genetics across 20 different plants which amplified 519 alleles at 180 loci with an average of 2.88 alleles/locus and the polymorphic information content (PIC) ranged from 0.51 to 0.93 with an average of 0.83. The cross transferability ranged from 25% for wheat to 97.22% for Schlerostachya, with an average of 55.86%, and genetic relationships were established based on diversification among them. Moreover, 10 EST-SSRs were recognized as important markers between bulks of pooled DNA of sugarcane cultivars through BSA. This study highlights the employability of the markers in transferability, genetic diversity in grass species, and distinguished sugarcane bulks.
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Wang Y, Quan W, Peng N, Wang C, Yang X, Liu X, Zhang H, Chen C, Ji W. Molecular cytogenetic identification of a wheat–Aegilops geniculata Roth 7Mg disomic addition line with powdery mildew resistance. MOLECULAR BREEDING 2016; 36:40. [PMID: 0 DOI: 10.1007/s11032-016-0463-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
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Farsad A, Esna-Ashari M. Genetic diversity of some Iranian sweet cherry (Prunus avium) cultivars using microsatellite markers and morphological traits. CYTOL GENET+ 2016. [DOI: 10.3103/s0095452716010059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Zhao YM, Zhou T, Li ZH, Zhao GF. Characterization of Global Transcriptome Using Illumina Paired-End Sequencing and Development of EST-SSR Markers in Two Species of Gynostemma (Cucurbitaceae). Molecules 2015; 20:21214-31. [PMID: 26633323 PMCID: PMC6332360 DOI: 10.3390/molecules201219758] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 11/05/2015] [Accepted: 11/09/2015] [Indexed: 01/16/2023] Open
Abstract
Gynostemma pentaphyllum is an important medicinal herb of the Cucurbitaceae family, but limited genomic data have hindered genetic studies. In this study, transcriptomes of two closely-related Gynostemma species, Gynostemma cardiospermum and G. pentaphyllum, were sequenced using Illumina paired-end sequencing technology. A total of 71,607 nonredundant unigenes were assembled. Of these unigenes, 60.45% (43,288) were annotated based on sequence similarity search with known proteins. A total of 11,059 unigenes were identified in the Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) database. A total of 3891 simple sequence repeats (SSRs) were detected in 3526 nonredundant unigenes, 2596 primer pairs were designed and 360 of them were randomly selected for validation. Of these, 268 primer pairs yielded clear products among six G. pentaphyllum samples. Thirty polymorphic SSR markers were used to test polymorphism and transferability in Gynostemma. Finally, 15 SSR makers that amplified in all 12 Gynostemma species were used to assess genetic diversity. Our results generated a comprehensive sequence resource for Gynostemma research.
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Affiliation(s)
- Yue-Mei Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
- College of Biopharmaceutical and Food Engineering, Shangluo University, Beixin Street, Shangluo 726000, China.
| | - Tao Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, 229 Taibai Bei Road, Xi'an 710069, China.
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Characterization and Development of EST-SSRs by Deep Transcriptome Sequencing in Chinese Cabbage (Brassica rapa L. ssp. pekinensis). Int J Genomics 2015; 2015:473028. [PMID: 26504770 PMCID: PMC4609433 DOI: 10.1155/2015/473028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/26/2015] [Indexed: 11/17/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most important markers for population analysis and have been widely used in plant genetic mapping and molecular breeding. Expressed sequence tag-SSR (EST-SSR) markers, located in the coding regions, are potentially more efficient for QTL mapping, gene targeting, and marker-assisted breeding. In this study, we investigated 51,694 nonredundant unigenes, assembled from clean reads from deep transcriptome sequencing with a Solexa/Illumina platform, for identification and development of EST-SSRs in Chinese cabbage. In total, 10,420 EST-SSRs with over 12 bp were identified and characterized, among which 2744 EST-SSRs are new and 2317 are known ones showing polymorphism with previously reported SSRs. A total of 7877 PCR primer pairs for 1561 EST-SSR loci were designed, and primer pairs for twenty-four EST-SSRs were selected for primer evaluation. In nineteen EST-SSR loci (79.2%), amplicons were successfully generated with high quality. Seventeen (89.5%) showed polymorphism in twenty-four cultivars of Chinese cabbage. The polymorphic alleles of each polymorphic locus were sequenced, and the results showed that most polymorphisms were due to variations of SSR repeat motifs. The EST-SSRs identified and characterized in this study have important implications for developing new tools for genetics and molecular breeding in Chinese cabbage.
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Turchetto C, Segatto ALA, Beduschi J, Bonatto SL, Freitas LB. Genetic differentiation and hybrid identification using microsatellite markers in closely related wild species. AOB PLANTS 2015; 7:plv084. [PMID: 26187606 PMCID: PMC4565426 DOI: 10.1093/aobpla/plv084] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 07/06/2015] [Indexed: 05/08/2023]
Abstract
Identifying the genetic basis of speciation is critical for understanding the evolutionary history of closely related wild species. Recently diverged species facilitate the study of speciation because many genetic and morphological characteristics are still shared by the organisms under study. The Petunia genus grows in South American grasslands and comprises both recently diverged wild species and commercial species. In this work, we analysed two closely related species: Petunia exserta, which has a narrow endemic range and grows exclusively in rocky shelters, and Petunia axillaris, which is widely distributed and comprises three allopatric subspecies. Petunia axillaris ssp. axillaris and P. exserta occur in sympatry, and putative hybrids between them have been identified. Here, we analysed 14 expressed sequence tag-simple sequence repeats (EST-SSRs) in 126 wild individuals and 13 putative morphological hybrids with the goals of identifying differentially encoded alleles to characterize their natural genetic diversity, establishing a genetic profile for each taxon and to verify the presence of hybridization signal. Overall, 143 alleles were identified and all taxa contained private alleles. Four major groups were identified in clustering analyses, which indicated that there are genetic distinctions among the groups. The markers evaluated here will be useful in evolutionary studies involving these species and may help categorize individuals by species, thus enabling the identification of hybrids between both their putative taxa. The individuals with intermediate morphology presented private alleles of their both putative parental species, although they showed a level of genetic mixing that was comparable with some of the individuals with typical P. exserta morphology. The EST-SSR markers scattered throughout the Petunia genome are very efficient tools for characterizing the genetic diversity in wild taxa of this genus and aid in identifying interspecific hybrids based on the presence of private alleles. These properties indicate that these markers will be helpful tools in evolutionary studies.
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Affiliation(s)
- Caroline Turchetto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PO Box 15053, Porto Alegre, Brazil
| | - Ana Lúcia A Segatto
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PO Box 15053, Porto Alegre, Brazil
| | - Júlia Beduschi
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PO Box 15053, Porto Alegre, Brazil
| | - Sandro L Bonatto
- Laboratory of Genomic and Molecular Biology, Pontifícia Universidade Católica do Rio Grande do Sul, Ipiranga 6681, 90610-001 Porto Alegre, RS, Brazil
| | - Loreta B Freitas
- Laboratory of Molecular Evolution, Department of Genetics, Universidade Federal do Rio Grande do Sul, PO Box 15053, Porto Alegre, Brazil
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Wang RRC, Larson SR, Jensen KB, Bushman BS, DeHaan LR, Wang S, Yan X. Genome evolution of intermediate wheatgrass as revealed by EST-SSR markers developed from its three progenitor diploid species. Genome 2015; 58:63-70. [DOI: 10.1139/gen-2014-0186] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey), a segmental autoallohexaploid (2n = 6x = 42), is not only an important forage crop but also a valuable gene reservoir for wheat (Triticum aestivum L.) improvement. Throughout the scientific literature, there continues to be disagreement as to the origin of the different genomes in intermediate wheatgrass. Genotypic data obtained from newly developed EST-SSR primers derived from the putative progenitor diploid species Pseudoroegneria spicata (Pursh) Á. Löve (St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (J = Jb = Eb), and Thinopyrum elongatum (Host) D. Dewey (E = Je = Ee) indicate that the V genome of Dasypyrum (Coss. & Durieu) T. Durand is not one of the three genomes in intermediate wheatgrass. Based on all available information in the literature and findings in this study, the genomic designation of intermediate wheatgrass should be changed to JvsJrSt, where Jvs and Jr represent ancestral genomes of present-day Jb of Th. bessarabicum and Je of Th. elongatum, with Jvs being more ancient. Furthermore, the information suggests that the St genome in intermediate wheatgrass is most similar to the present-day St found in diploid species of Pseudoroegneria from Eurasia.
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Affiliation(s)
- Richard R.-C. Wang
- US Department of Agriculture, Agricultural Research Services, Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Steve R. Larson
- US Department of Agriculture, Agricultural Research Services, Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Kevin B. Jensen
- US Department of Agriculture, Agricultural Research Services, Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - B. Shaun Bushman
- US Department of Agriculture, Agricultural Research Services, Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
| | - Lee R. DeHaan
- The Land Institute, 2440 E. Water Well Road, Salina, KS 67401, USA
| | - Shuwen Wang
- The Land Institute, 2440 E. Water Well Road, Salina, KS 67401, USA
| | - Xuebing Yan
- US Department of Agriculture, Agricultural Research Services, Forage and Range Research Laboratory, Logan, UT 84322-6300, USA
- College of Animal Husbandry and Veterinary Science, Henan Agricultural University, Zhengzhou, 450002, China
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Sahu J, Das Talukdar A, Devi K, Choudhury MD, Barooah M, Modi MK, Sen P. E-Microsatellite Markers for Centella asiatica (Gotu Kola) Genome: Validation and Cross-Transferability in Apiaceae Family for Plant Omics Research and Development. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2015; 19:52-65. [DOI: 10.1089/omi.2014.0113] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Jagajjit Sahu
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
- Department of Life Science and Bioinformatics, Assam University, Assam, India
| | - Anupam Das Talukdar
- Department of Life Science and Bioinformatics, Assam University, Assam, India
| | - Kamalakshi Devi
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | | | - Madhumita Barooah
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | - Mahendra Kumar Modi
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
| | - Priyabrata Sen
- Distributed Information Centre, Department of Agricultural Biotechnology, Assam Agricultural University, Assam, India
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Identification and characterization of microsatellites in expressed sequence tags and their cross transferability in different plants. Int J Genomics 2014; 2014:863948. [PMID: 25389527 PMCID: PMC4217358 DOI: 10.1155/2014/863948] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 08/31/2014] [Accepted: 09/22/2014] [Indexed: 12/20/2022] Open
Abstract
Expressed sequence tags (EST) are potential source for the development of genic microsatellite markers, gene discovery, comparative genomics, and other genomic studies. In the present study, 7630 ESTs were examined from NCBI for SSR identification and characterization. A total of 263 SSRs were identified with an average density of one SSR/4.2 kb (3.4% frequency). Analysis revealed that trinucleotide repeats (47.52%) were most abundant followed by tetranucleotide (19.77%), dinucleotide (19.01%), pentanucleotide (9.12%), and hexanucleotide repeats (4.56%). Functional annotation was done through homology search and gene ontology, and 35 EST-SSRs were selected. Primer pairs were designed for evaluation of cross transferability and polymorphism among 11 plants belonging to five different families. Total 402 alleles were generated at 155 loci with an average of 2.6 alleles/locus and the polymorphic information content (PIC) ranged from 0.15 to 0.92 with an average of 0.75. The cross transferability ranged from 34.84% to 98.06% in different plants, with an average of 67.86%. Thus, the validation study of annotated 35 EST-SSR markers which correspond to particular metabolic activity revealed polymorphism and evolutionary nature in different families of Angiospermic plants.
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Identification, cross-taxon transferability and application of full-length cDNA SSR markers in Phyllostachys pubescens. SPRINGERPLUS 2014; 3:486. [PMID: 25221740 PMCID: PMC4161718 DOI: 10.1186/2193-1801-3-486] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 08/11/2014] [Indexed: 01/17/2023]
Abstract
Current databases of Phyllostachys pubescens full-length cDNAs (FL-cDNAs) provide a rich source of sequences for the development of potential FL-cDNA simple sequence repeat (SSR) markers. We screened 10,608 P. pubescens cDNAs, discovering 1614 SSRs in 1382 SSR-containing FL-cDNAs. The SSRs were more abundant within transposable elements (TEs) than expressed sequence tags (ESTs) and genome survey sequences (GSSs), and specific dinucleotide repeats tended to associate with particular TE families: (TA)n with En/Spm and (CT)n with Mutator. A selected panel of 100 FL-cDNAs containing type I SSRs yielded 68 functional SSR markers with an average polymorphism information content (PIC) value of 0.12, among which 22 loci contained polymorphisms. These markers became less transferrable (83.1% → 69.9% → 49.3%) but more polymorphic (79.4% → 92.3% → 92.8%) with increasing phylogenetic distance (intra-genus → intra-subtribe → intra-family). Transferability and polymorphism also depended on the location of the marker, with those located in the coding region being more transferrable (69.1%) and less polymorphic (89.4%) than those in the 5'-UTR (63.4% transferable, 90.7% polymorphic) and the 3'-UTR (61.8% transferable, 91.4% polymorphic). As proof of principle, we were able to use our FL-cDNA SSR markers to identify the parental stocks in interspecific hybrids of bamboo within and beyond P. pubescens, and estimate the outcrossing rate for P. pubescens. Our research should facilitate molecular breeding in bamboo species where original genetic markers are scarce.
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Biswas MK, Xu Q, Mayer C, Deng X. Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis). PLoS One 2014; 9:e104182. [PMID: 25148383 PMCID: PMC4141690 DOI: 10.1371/journal.pone.0104182] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 07/09/2014] [Indexed: 11/18/2022] Open
Abstract
Sweet orange (Citrus sinensis) is one of the major cultivated and most-consumed citrus species. With the goal of enhancing the genomic resources in citrus, we surveyed, developed and characterized microsatellite markers in the ≈347 Mb sequence assembly of the sweet orange genome. A total of 50,846 SSRs were identified with a frequency of 146.4 SSRs/Mbp. Dinucleotide repeats are the most frequent repeat class and the highest density of SSRs was found in chromosome 4. SSRs are non-randomly distributed in the genome and most of the SSRs (62.02%) are located in the intergenic regions. We found that AT-rich SSRs are more frequent than GC-rich SSRs. A total number of 21,248 SSR primers were successfully developed, which represents 89 SSR markers per Mb of the genome. A subset of 950 developed SSR primer pairs were synthesized and tested by wet lab experiments on a set of 16 citrus accessions. In total we identified 534 (56.21%) polymorphic SSR markers that will be useful in citrus improvement. The number of amplified alleles ranges from 2 to 12 with an average of 4 alleles per marker and an average PIC value of 0.75. The newly developed sweet orange primer sequences, their in silico PCR products, exact position in the genome assembly and putative function are made publicly available. We present the largest number of SSR markers ever developed for a citrus species. Almost two thirds of the markers are transferable to 16 citrus relatives and may be used for constructing a high density linkage map. In addition, they are valuable for marker-assisted selection studies, population structure analyses and comparative genomic studies of C. sinensis with other citrus related species. Altogether, these markers provide a significant contribution to the citrus research community.
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Affiliation(s)
- Manosh Kumar Biswas
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
| | | | - Xiuxin Deng
- Key Laboratory of Horticultural Plant Biology of Ministry of Education (MOE), Huazhong Agricultural University, Wuhan, Hubei, P.R. China
- * E-mail:
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Du X, Pérez-Boada M, Fernández C, Rencoret J, del Río JC, Jiménez-Barbero J, Li J, Gutiérrez A, Martínez AT. Analysis of lignin-carbohydrate and lignin-lignin linkages after hydrolase treatment of xylan-lignin, glucomannan-lignin and glucan-lignin complexes from spruce wood. PLANTA 2014; 239:97-105. [PMID: 24085532 DOI: 10.1007/s00425-013-1957-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/05/2013] [Indexed: 05/08/2023]
Abstract
Xylan-lignin (XL), glucomannan-lignin (GML) and glucan-lignin (GL) complexes were isolated from spruce wood, hydrolyzed with xylanase or endoglucanase/β-glucosidase, and analyzed by analytical pyrolysis and 2D-NMR. The enzymatic hydrolysis removed most of the polysaccharide moieties in the complexes, and the lignin content and relative abundance of lignin-carbohydrate linkages increased. Analytical pyrolysis confirmed the action of the enzymatic hydrolysis, with strong decreases of levoglucosane and other carbohydrate-derived products. Unexpectedly it also revealed that the hydrolase treatment alters the pattern of lignin breakdown products, resulting in higher amounts of coniferyl alcohol. From the anomeric carbohydrate signals in the 2D-NMR spectra, phenyl glycoside linkages (undetectable in the original complexes) could be identified in the hydrolyzed GML complex. Lower amounts of glucuronosyl and benzyl ether linkages were also observed after the hydrolysis. From the 2D-NMR spectra of the hydrolyzed complexes, it was concluded that the lignin in GML is less condensed than in XL due to its higher content in β-O-4' ether substructures (62 % of side chains in GML vs 53 % in XL) accompanied by more coniferyl alcohol end units (16 vs 13 %). In contrast, the XL lignin has more pinoresinols (11 vs 6 %) and dibenzodioxocins (9 vs 2 %) than the GML (and both have ~13 % phenylcoumarans and 1 % spirodienones). Direct 2D-NMR analysis of the hydrolyzed GL complex was not possible due to its low solubility. However, after sample acetylation, an even less condensed lignin than in the GML complex was found (with up to 72 % β-O-4' substructures and only 1 % pinoresinols). The study provides evidence for the existence of structurally different lignins associated to hemicelluloses (xylan and glucomannan) and cellulose in spruce wood and, at the same time, offers information on some of the chemical linkages between the above polymers.
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Affiliation(s)
- Xueyu Du
- Department of Fibre and Polymer Technology, Royal Institute of Technology, KTH, Teknikringen 56-58, 10044, Stockholm, Sweden
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Asadi AA, Rashidi Monfared S. Characterization of EST-SSR markers in durum wheat EST library and functional analysis of SSR-containing EST fragments. Mol Genet Genomics 2014; 289:625-40. [PMID: 24652471 DOI: 10.1007/s00438-014-0839-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 03/01/2014] [Indexed: 11/28/2022]
Abstract
The goal of this study is to identify characterization of expressed sequence tag (EST)-simple sequence repeats (SSR) markers from EST library of durum wheat and functional analysis of SSR-containing EST sequences for application in comparative genomics and breeding. 19,141 sequences were analyzed among which 18,937 ESTs were selected. Consistent with MISA results, 313 EST-SSRs were yielded. The final EST-SSRs were compared to the GenBank non-redundant database using BLASTX and classified based on these functions. Results indicated that the perfect EST-SSRs are the most frequent. The TTG/CTG imperfect EST-SSR had gamma-gliadin putative function that can be appropriate for durum wheat. Also, the mononucleotides and trinucleotides were the most frequent. Findings suggested that the identified EST-SSRs could be categorized into 83 types. Motifs TTG in trinucleotides and TC in dinucleotides had the highest frequency. TTG is the new motif in durum wheat identified in this study. We identified new EST-SSRs with more than trinucleotide and detected motifs that have potential to code amino acids. Arginine was the most frequent amino acid. Enzymes had the highest frequency among predicted functions. EST-SSRs have been identified in this study can be used for developing ESS-SSR-based detection tool for durum wheat in future studies and will be a useful resource for molecular breeding, genetics, genomics, and environmental stress studies. Motifs coding amino acids could be used as a new source of functional markers and biological study. In addition to, designed new PCR primer pairs are new resources for to identify useful alleles in transcription factors, storage proteins, and enzymes which incorporated them again into the cultivated material.
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Affiliation(s)
- Ali Akbar Asadi
- Plant Breeding and Biotechnology Department, Agriculture College, Tarbiat Modares University, Tehran, Iran,
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Giordano A, Cogan NOI, Kaur S, Drayton M, Mouradov A, Panter S, Schrauf GE, Mason JG, Spangenberg GC. Gene discovery and molecular marker development, based on high-throughput transcript sequencing of Paspalum dilatatum Poir. PLoS One 2014; 9:e85050. [PMID: 24520314 PMCID: PMC3919698 DOI: 10.1371/journal.pone.0085050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/21/2013] [Indexed: 12/23/2022] Open
Abstract
Background Paspalum dilatatum Poir. (common name dallisgrass) is a native grass species of South America, with special relevance to dairy and red meat production. P. dilatatum exhibits higher forage quality than other C4 forage grasses and is tolerant to frost and water stress. This species is predominantly cultivated in an apomictic monoculture, with an inherent high risk that biotic and abiotic stresses could potentially devastate productivity. Therefore, advanced breeding strategies that characterise and use available genetic diversity, or assess germplasm collections effectively are required to deliver advanced cultivars for production systems. However, there are limited genomic resources available for this forage grass species. Results Transcriptome sequencing using second-generation sequencing platforms has been employed using pooled RNA from different tissues (stems, roots, leaves and inflorescences) at the final reproductive stage of P. dilatatum cultivar Primo. A total of 324,695 sequence reads were obtained, corresponding to c. 102 Mbp. The sequences were assembled, generating 20,169 contigs of a combined length of 9,336,138 nucleotides. The contigs were BLAST analysed against the fully sequenced grass species of Oryza sativa subsp. japonica, Brachypodium distachyon, the closely related Sorghum bicolor and foxtail millet (Setaria italica) genomes as well as against the UniRef 90 protein database allowing a comprehensive gene ontology analysis to be performed. The contigs generated from the transcript sequencing were also analysed for the presence of simple sequence repeats (SSRs). A total of 2,339 SSR motifs were identified within 1,989 contigs and corresponding primer pairs were designed. Empirical validation of a cohort of 96 SSRs was performed, with 34% being polymorphic between sexual and apomictic biotypes. Conclusions The development of genetic and genomic resources for P. dilatatum will contribute to gene discovery and expression studies. Association of gene function with agronomic traits will significantly enable molecular breeding and advance germplasm enhancement.
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Affiliation(s)
- Andrea Giordano
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - Noel O. I. Cogan
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
| | - Sukhjiwan Kaur
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
| | - Michelle Drayton
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
| | - Aidyn Mouradov
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
| | - Stephen Panter
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
| | - Gustavo E. Schrauf
- Facultad de Agronomia, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - John G. Mason
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
| | - German C. Spangenberg
- Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, Australia
- Molecular Plant Breeding Cooperative Research Centre, Bundoora, Victoria, Australia
- Dairy Futures Cooperative Research Centre, Bundoora, Victoria, Australia
- La Trobe University, Bundoora, Victoria, Australia
- * E-mail:
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Huang D, Zhang Y, Jin M, Li H, Song Z, Wang Y, Chen J. Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome of Aspidistra saxicola (Asparagaceae). Mol Ecol Resour 2013; 14:569-77. [PMID: 24286608 DOI: 10.1111/1755-0998.12197] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2012] [Revised: 10/28/2013] [Accepted: 10/28/2013] [Indexed: 11/29/2022]
Abstract
Recent studies utilizing transcriptome sequences generated by next-generation sequencing (NGS) technologies have demonstrated the ability to rapidly detect and characterize thousands of gene-based microsatellites from different plants. However, these simple sequence repeats (SSRs) were seldom used directly to test interspecific transferability in the populations of closely related species. Aspidistra Ker-Gawl. is a monocot genus with high species richness and diversity in flower structure, but its fresh floral materials are not easy to obtain. Until now, little is known about genetic background in the species of Aspidistra, quite apart from the fearful reduction of their natural habitats. In this study, the floral transcriptome of Aspidistra saxicola was obtained using NGS. Based on these data, a total of 5527 SSRs were identified in the unigenes. Among these SSRs, the proportions of di- and tri-nucleotide repeats were quite close (49.6% verse 46.8%), and the most tri-nucleotide repeats were AGG/CCT followed by AAG/CTT and AGC/GCT in A. saxicola, showing distinct differences with other angiosperm species. To assess genetic diversity in the species of Aspidistra, 48 SSR loci were tested in four available populations of A. elatior. The results revealed that more than a third of the loci were polymorphic. The majority of these primers could be amplified in 24 species representing the main clades of Aspidistra. The primer subsets from transcriptome data proved highly useful for detecting polymorphisms in the related species, supporting the finding that NGS is an efficient approach to molecular marker development at both intra- and interspecies levels, especially in endangered nonmodel species.
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Affiliation(s)
- Danni Huang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, School of Life Sciences, Fudan University, Shanghai 200433, China
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Todorovska E, Hadjiivanova B, Bozhanova V, Dechev D, Muhovski Y, Panchev I, Abu-Mhadi N, Peycheva V, Ivanova A. Molecular and Phenotypic Characterization of Advanced Backcross Lines Derived from Interspecific Hybridization of Durum Wheat. BIOTECHNOL BIOTEC EQ 2013. [DOI: 10.5504/bbeq.2013.0030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Barati M, Arzani A. Genetic diversity revealed by EST-SSR markers in cultivated and wild safflower. BIOCHEM SYST ECOL 2012. [DOI: 10.1016/j.bse.2012.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Sousa Azevedo AL, Costa PP, Machado JC, Machado MA, Pereira AV, José da Silva Lédo F. Cross Species Amplification of Pennisetum glaucum
Microsatellite Markers in Pennisetum purpureum
and Genetic Diversity of Napier Grass Accessions. CROP SCIENCE 2012; 52:1776-1785. [PMID: 0 DOI: 10.2135/cropsci2011.09.0480] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Affiliation(s)
- Ana Luisa Sousa Azevedo
- Embrapa Dairy Cattle Research Center; Eugênio do Nascimento 610 Juiz de Fora MG 36038-330 Brazil
| | - Pricila Palla Costa
- Embrapa Dairy Cattle Research Center; Eugênio do Nascimento 610 Juiz de Fora MG 36038-330 Brazil
| | - Juarez Campolina Machado
- Embrapa Dairy Cattle Research Center; Eugênio do Nascimento 610 Juiz de Fora MG 36038-330 Brazil
| | - Marco Antonio Machado
- Embrapa Dairy Cattle Research Center; Eugênio do Nascimento 610 Juiz de Fora MG 36038-330 Brazil
| | - Antônio Vander Pereira
- Embrapa Dairy Cattle Research Center; Eugênio do Nascimento 610 Juiz de Fora MG 36038-330 Brazil
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Xu H, Yin D, Li L, Wang Q, Li X, Yang X, Liu W, An D. Development and application of EST-based markers specific for chromosome arms of rye (Secale cereale L.). Cytogenet Genome Res 2012; 136:220-8. [PMID: 22354334 DOI: 10.1159/000336478] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/21/2011] [Indexed: 11/19/2022] Open
Abstract
To develop a set of molecular markers specific for the chromosome arms of rye, a total of 1,098 and 93 primer pairs derived from the expressed sequence tag (EST) sequences distributed on all 21 wheat chromosomes and 7 rye chromosomes, respectively, were initially screened on common wheat 'Chinese Spring' and rye cultivar 'Imperial'. Four hundred and fourteen EST-based markers were specific for the rye genome. Seven disomic chromosome addition lines, 10 telosomic addition lines and 1 translocation line of 'Chinese Spring-Imperial' were confirmed by genomic in situ hybridization and fluorescencein situ hybridization, and used to screen the rye-specific markers. Thirty-one of the 414 markers produced stable specific amplicons in 'Imperial', as well as individual addition lines and were assigned to 13 chromosome arms of rye except for 6RS. Six rye cultivars, wheat cultivar 'Xiaoyan 6' and accessions of 4 wheat relatives were then used to test the specificity of the 31 EST-based markers. To confirm the specificity, 4 wheat-rye derivatives of 'Xiaoyan 6 × German White', with chromosomes 1RS, 2R and 4R, were amplified by some of the EST-based markers. The results indicated that they can effectively be used to detect corresponding rye chromosomes or chromosome arms introgressed into a wheat background, and hence to accelerate the utilization of rye genes in wheat breeding.
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Affiliation(s)
- H Xu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, China
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Dobrovolskaya O, Boeuf C, Salse J, Pont C, Sourdille P, Bernard M, Salina E. Microsatellite mapping of Ae. speltoides and map-based comparative analysis of the S, G, and B genomes of Triticeae species. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1145-1157. [PMID: 21792632 DOI: 10.1007/s00122-011-1655-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2008] [Accepted: 07/09/2011] [Indexed: 05/31/2023]
Abstract
The first microsatellite linkage map of Ae. speltoides Tausch (2n = 2x = 14, SS), which is a wild species with a genome closely related to the B and G genomes of polyploid wheats, was developed based on two F(2) mapping populations using microsatellite (SSR) markers from Ae. speltoides, wheat genomic SSRs (g-SSRs) and EST-derived SSRs. A total of 144 different microsatellite loci were mapped in the Ae. speltoides genome. The transferability of the SSRs markers between the related S, B, and G genomes allowed possible integration of new markers into the T. timopheevii G genome chromosomal maps and map-based comparisons. Thirty-one new microsatellite loci assigned to the genetic framework of the T. timopheevii G genome maps were composed of wheat g-SSR (genomic SSR) markers. Most of the used Ae. speltoides SSRs were mapped onto chromosomes of the G genome supporting a close relationship between the G and S genomes. Comparative microsatellite mapping of the S, B, and G genomes demonstrated colinearity between the chromosomes within homoeologous groups, except for intergenomic T6A(t)S.1G, T4AL.5AL.7BS translocations. A translocation between chromosomes 2 and 6 that is present in the T. aestivum B genome was found in neither Ae. speltoides nor in T. timopheevii. Although the marker order was generally conserved among the B, S, and G genomes, the total length of the Ae. speltoides chromosomal maps and the genetic distances between homoeologous loci located in the proximal regions of the S genome chromosomes were reduced compared with the B, and G genome chromosomes.
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Affiliation(s)
- O Dobrovolskaya
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentieva Ave. 10, Novosibirsk, 630090, Russia.
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Wang Z, Li J, Luo Z, Huang L, Chen X, Fang B, Li Y, Chen J, Zhang X. Characterization and development of EST-derived SSR markers in cultivated sweetpotato (Ipomoea batatas). BMC PLANT BIOLOGY 2011; 11:139. [PMID: 22011271 PMCID: PMC3206431 DOI: 10.1186/1471-2229-11-139] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 10/20/2011] [Indexed: 05/04/2023]
Abstract
BACKGROUND Currently there exists a limited availability of genetic marker resources in sweetpotato (Ipomoea batatas), which is hindering genetic research in this species. It is necessary to develop more molecular markers for potential use in sweetpotato genetic research. With the newly developed next generation sequencing technology, large amount of transcribed sequences of sweetpotato have been generated and are available for identifying SSR markers by data mining. RESULTS In this study, we investigated 181,615 ESTs for the identification and development of SSR markers. In total, 8,294 SSRs were identified from 7,163 SSR-containing unique ESTs. On an average, one SSR was found per 7.1 kb of EST sequence with tri-nucleotide motifs (42.9%) being the most abundant followed by di- (41.2%), tetra- (9.2%), penta- (3.7%) and hexa-nucleotide (3.1%) repeat types. The top five motifs included AG/CT (26.9%), AAG/CTT (13.5%), AT/TA (10.6%), CCG/CGG (5.8%) and AAT/ATT (4.5%). After removing possible duplicate of published EST-SSRs of sweetpotato, a total of non-repeat 7,958 SSR motifs were identified. Based on these SSR-containing sequences, 1,060 pairs of high-quality SSR primers were designed and used for validation of the amplification and assessment of the polymorphism between two parents of one mapping population (E Shu 3 Hao and Guang 2k-30) and eight accessions of cultivated sweetpotatoes. The results showed that 816 primer pairs could yield reproducible and strong amplification products, of which 195 (23.9%) and 342 (41.9%) primer pairs exhibited polymorphism between E Shu 3 Hao and Guang 2k-30 and among the 8 cultivated sweetpotatoes, respectively. CONCLUSION This study gives an insight into the frequency, type and distribution of sweetpotato EST-SSRs and demonstrates successful development of EST-SSR markers in cultivated sweetpotato. These EST-SSR markers could enrich the current resource of molecular markers for the sweetpotato community and would be useful for qualitative and quantitative trait mapping, marker-assisted selection, evolution and genetic diversity studies in cultivated sweetpotato and related Ipomoea species.
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Affiliation(s)
- Zhangying Wang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jun Li
- College of Life Science, China West Normal University, Nanchong, 637002 China
| | - Zhongxia Luo
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Lifei Huang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xinliang Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Boping Fang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Yujun Li
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Jingyi Chen
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
| | - Xiongjian Zhang
- Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640 China
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Paux E, Sourdille P, Mackay I, Feuillet C. Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 2011; 30:1071-88. [PMID: 21989506 DOI: 10.1016/j.biotechadv.2011.09.015] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 08/24/2011] [Accepted: 09/25/2011] [Indexed: 01/04/2023]
Abstract
In the past two decades, the wheat community has made remarkable progress in developing molecular resources for breeding. A wide variety of molecular tools has been established to accelerate genetic and physical mapping for facilitating the efficient identification of molecular markers linked to genes and QTL of agronomic interest. Already, wheat breeders are benefiting from a wide range of techniques to follow the introgression of the most favorable alleles in elite material and develop improved varieties. Breeders soon will be able to take advantage of new technological developments based on Next Generation Sequencing. In this paper, we review the molecular toolbox available to wheat scientists and breeders for performing fundamental genomic studies and breeding. Special emphasis is given on the production and detection of single nucleotide polymorphisms (SNPs) that should enable a step change in saturating the wheat genome for more efficient genetic studies and for the development of new selection methods. The perspectives offered by the access to an ordered full genome sequence for further marker development and enhanced precision breeding is also discussed. Finally, we discuss the advantages and limitations of marker-assisted selection for supporting wheat improvement.
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Affiliation(s)
- Etienne Paux
- INRA-UBP 1095, Genetics Diversity and Ecophysiology of Cereals, 234 Avenue du Brézet, Clermont-Ferrand, France
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Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 2011. [PMID: 21929789 DOI: 10.1186/1471‐2164‐12‐451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development. RESULTS Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value < 10-5). Of these annotated unigenes, 10,805 and 27,588 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 22,003 (25.52%) unigenes were mapped onto 119 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Furthermore, 44,750 unigenes showed homology to 15,460 Arabidopsis genes based on BLASTx analysis against The Arabidopsis Information Resource (TAIR, Version 10) and revealed relatively high gene coverage. In total, 7,702 unigenes were converted into SSR markers (EST-SSR). Dinucleotide SSRs were the dominant repeat motif (67.07%, 5,166), followed by trinucleotide (24.89%, 1,917), tetranucleotide (4.31%, 332), hexanucleotide (2.62%, 202), and pentanucleotide (1.10%, 85) SSRs. AG/CT (46.29%) was the dominant repeat motif, followed by AC/GT (16.07%), AT/AT (10.53%), AAG/CTT (6.23%), and AGG/CCT (3.39%). Fifty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions. CONCLUSIONS This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.
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Affiliation(s)
- Wenliang Wei
- Key Laboratory of Oil Crops Biology of the Ministry of Agriculture, Sesame Germplasm and Genetic Breeding Laboratory, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062, China
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Wei W, Qi X, Wang L, Zhang Y, Hua W, Li D, Lv H, Zhang X. Characterization of the sesame (Sesamum indicum L.) global transcriptome using Illumina paired-end sequencing and development of EST-SSR markers. BMC Genomics 2011; 12:451. [PMID: 21929789 PMCID: PMC3184296 DOI: 10.1186/1471-2164-12-451] [Citation(s) in RCA: 297] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 09/19/2011] [Indexed: 11/23/2022] Open
Abstract
Background Sesame is an important oil crop, but limited transcriptomic and genomic data are currently available. This information is essential to clarify the fatty acid and lignan biosynthesis molecular mechanism. In addition, a shortage of sesame molecular markers limits the efficiency and accuracy of genetic breeding. High-throughput transcriptomic sequencing is essential to generate a large transcriptome sequence dataset for gene discovery and molecular marker development. Results Sesame transcriptomes from five tissues were sequenced using Illumina paired-end sequencing technology. The cleaned raw reads were assembled into a total of 86,222 unigenes with an average length of 629 bp. Of the unigenes, 46,584 (54.03%) had significant similarity with proteins in the NCBI nonredundant protein database and Swiss-Prot database (E-value < 10-5). Of these annotated unigenes, 10,805 and 27,588 unigenes were assigned to gene ontology categories and clusters of orthologous groups, respectively. In total, 22,003 (25.52%) unigenes were mapped onto 119 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Furthermore, 44,750 unigenes showed homology to 15,460 Arabidopsis genes based on BLASTx analysis against The Arabidopsis Information Resource (TAIR, Version 10) and revealed relatively high gene coverage. In total, 7,702 unigenes were converted into SSR markers (EST-SSR). Dinucleotide SSRs were the dominant repeat motif (67.07%, 5,166), followed by trinucleotide (24.89%, 1,917), tetranucleotide (4.31%, 332), hexanucleotide (2.62%, 202), and pentanucleotide (1.10%, 85) SSRs. AG/CT (46.29%) was the dominant repeat motif, followed by AC/GT (16.07%), AT/AT (10.53%), AAG/CTT (6.23%), and AGG/CCT (3.39%). Fifty EST-SSRs were randomly selected to validate amplification and to determine the degree of polymorphism in the genomic DNA pools. Forty primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 24 sesame accessions. Conclusions This study demonstrates that Illumina paired-end sequencing is a fast and cost-effective approach to gene discovery and molecular marker development in non-model organisms. Our results provide a comprehensive sequence resource for sesame research.
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Affiliation(s)
- Wenliang Wei
- Key Laboratory of Oil Crops Biology of the Ministry of Agriculture, Sesame Germplasm and Genetic Breeding Laboratory, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences (OCRI-CAAS), Wuhan, 430062, China
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Wöhrmann T, Weising K. In silico mining for simple sequence repeat loci in a pineapple expressed sequence tag database and cross-species amplification of EST-SSR markers across Bromeliaceae. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:635-647. [PMID: 21625993 DOI: 10.1007/s00122-011-1613-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2011] [Accepted: 04/30/2011] [Indexed: 05/30/2023]
Abstract
A collection of 5,659 expressed sequence tags (ESTs) from pineapple [Ananas comosus (L.) Merr.] was screened for simple sequence repeats (EST-SSRs) with motif lengths between 1 and 6 bp. Lower thresholds of 15, 7 and 5 repeat units were used to define microsatellites of the mono-, di-, and tri- to hexanucleotide repeat type, respectively. Based on these criteria, 696 SSRs were identified among 3,389 EST unigenes, together representing 2,840 kb. This corresponds to an average density of one SSR every 4.1 kb of non-redundant EST sequences. Dinucleotide repeats were most abundant (38.4% of all SSRs) followed by trinucleotide repeats (38.1%). Flanking primer pairs were designed for 537 EST-SSR loci, and 49 of these were screened for their functionality in 12 accessions of A. comosus, 14 accessions of 5 additional Ananas species and 1 species of Pseudananas. Distinct PCR products of the expected size range were obtained with 36 primer pairs. Eighteen loci analyzed in more detail were all polymorphic in pineapple, and primer pairs flanking these loci also generated PCR products from a wide range of genera and species from six subfamilies of the Bromeliaceae. The potential to reveal polymorphism in a heterologous target species was demonstrated in Deuterocohnia brevifolia (subfamily Pitcairnioideae).
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Affiliation(s)
- Tina Wöhrmann
- Plant Molecular Systematics, Institute of Biology, Department of Sciences, University of Kassel, Heinrich-Plett-Str. 40, 34132 Kassel, Germany
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Bandopadhyay R, Rustgi S, Chaudhuri RK, Khurana P, Khurana JP, Tyagi AK, Balyan HS, Houben A, Gupta PK. Use of methylation filtration and C(0)t fractionation for analysis of genome composition and comparative genomics in bread wheat. J Genet Genomics 2011; 38:315-25. [PMID: 21777856 DOI: 10.1016/j.jgg.2011.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2010] [Revised: 06/08/2011] [Accepted: 06/13/2011] [Indexed: 11/16/2022]
Abstract
We investigated the compositional and structural differences in sequences derived from different fractions of wheat genomic DNA obtained using methylation filtration and C(0)t fractionation. Comparative analysis of these sequences revealed large compositional and structural variations in terms of GC content, different structural elements including repeat sequences (e.g., transposable elements and simple sequence repeats), protein coding genes, and non-coding RNA genes. A correlation between methylation status [determined on the basis of selective inclusion/exclusion in methylation-filtered (MF) library] of different repeat elements and expression level was observed. The expression levels were determined by comparing MF sequences with expressed sequence tags (ESTs) available in the public domain. Only a limited overlap among MF, high C(0)t (HC), and ESTs was observed, suggesting that these sequences may largely either represent the low-copy non-transcribed sequences or include genes with low expression levels. Thus, these results indicated a need to study MF and HC sequences along with ESTs to fully appreciate complexity of wheat gene space.
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Affiliation(s)
- Rajib Bandopadhyay
- Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut, India
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Bushman BS, Larson SR, Tuna M, West MS, Hernandez AG, Vullaganti D, Gong G, Robins JG, Jensen KB, Thimmapuram J. Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:119-129. [PMID: 21465186 DOI: 10.1007/s00122-011-1571-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 03/11/2011] [Indexed: 05/30/2023]
Abstract
Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.
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Affiliation(s)
- B Shaun Bushman
- USDA-ARS Forage and Range Research Lab, 695 N 1100 E, Logan, UT 84322-6300, USA.
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Zhang L, Yang G, Liu P, Hong D, Li S, He Q. Genetic and correlation analysis of silique-traits in Brassica napus L. by quantitative trait locus mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 122:263-70. [PMID: 20830464 DOI: 10.1007/s00122-010-1441-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2010] [Accepted: 08/25/2010] [Indexed: 05/08/2023]
Abstract
Rapeseed yield is directly and indirectly influenced by the silique-traits, such as silique length (SL), seeds per silique (SS), seed weight (SW), because the silique is an organ which produced yield and a major photosynthesis organ as well. In this study, a linkage map comprising 150 simple sequence repeat and 195 amplified fragment length polymorphism markers covering 1,759.6 cM was constructed in a doubled haploid population from a cross between two genotypes of 'HZ396' and 'Y106'. In field experiments across three seasons and two locations in China 140 doubled haploid lines and their corresponding parents were evaluated for silique-traits. In total, 26 quantitative trait loci (QTL) were detected, of which 15 were clustered and integrated into 5 pleiotropic unique QTL by meta-analysis. These unique QTL, which in a certain sense reflected the significant positive correlation between SS and SL and the significant negative correlation between SW and SS by the genomic location and effects of QTL detected, were mapped on linkage groups N7, N8 and N13. A trait-by-trait meta-analysis revealed 5, 2 and 3 consensus QTL for SL, SS and SW, respectively. Epistatic effects varied according to the specific traits performed. All the epistatic interactions showed significant additive by additive effects while no significant epistasis by environment effect was identified. These findings provided a better understanding of the genetic factors controlling silique-traits and gained insights into the gene networks affecting silique-traits at QTL level in rapeseed.
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Affiliation(s)
- Liwu Zhang
- National Key Lab of Crop Genetic Improvement, National Center of Rapeseed Improvement in Wuhan, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
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Castillo A, Dorado G, Feuillet C, Sourdille P, Hernandez P. Genetic structure and ecogeographical adaptation in wild barley (Hordeum chilense Roemer et Schultes) as revealed by microsatellite markers. BMC PLANT BIOLOGY 2010; 10:266. [PMID: 21118494 PMCID: PMC3014967 DOI: 10.1186/1471-2229-10-266] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2010] [Accepted: 11/30/2010] [Indexed: 05/18/2023]
Abstract
BACKGROUND Multi-allelic microsatellite markers have become the markers of choice for the determination of genetic structure in plants. Synteny across cereals has allowed the cross-species and cross-genera transferability of SSR markers, which constitute a valuable and cost-effective tool for the genetic analysis and marker-assisted introgression of wild related species. Hordeum chilense is one of the wild relatives with a high potential for cereal breeding, due to its high crossability (both interspecies and intergenera) and polymorphism for adaptation traits. In order to analyze the genetic structure and ecogeographical adaptation of this wild species, it is necessary to increase the number of polymorphic markers currently available for the species. In this work, the possibility of using syntenic wheat SSRs as a new source of markers for this purpose has been explored. RESULTS From the 98 wheat EST-SSR markers tested for transferability and polymorphism in the wild barley genome, 53 primer pairs (54.0%) gave cross-species transferability and 20 primer pairs (20.4%) showed polymorphism. The latter were used for further analysis in the H. chilense germplasm. The H. chilense-Triticum aestivum addition lines were used to test the chromosomal location of the new polymorphic microsatellite markers. The genetic structure and diversity was investigated in a collection of 94 H. chilense accessions, using a set of 49 SSR markers distributed across the seven chromosomes. Microsatellite markers showed a total of 351 alleles over all loci. The number of alleles per locus ranged from two to 27, with a mean of 7.2 alleles per locus and a mean Polymorphic Information Content (PIC) of 0.5. CONCLUSIONS According to the results, the germplasm can be divided into two groups, with morphological and ecophysiological characteristics being key determinants of the population structure. Geographic and ecological structuring was also revealed in the analyzed germplasm. A significant correlation between geographical and genetic distance was detected in the Central Chilean region for the first time in the species. In addition, significant ecological influence in genetic distance has been detected for one of the population structure groups (group II) in the Central Chilean region. Finally, the association of the SSR markers with ecogeographical variables was investigated and one marker was found significantly associated with precipitation. These findings have a potential application in cereal breeding.
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Affiliation(s)
- Almudena Castillo
- Instituto de Agricultura Sostenible (IAS, CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
| | - Gabriel Dorado
- Dep. Bioquímica y Biología Molecular, Campus Rabanales, C6-1-E17, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Catherine Feuillet
- INRA UBP UMR 1095, Genetics, Diversity & Ecophysiology of Cereals, Clermont Ferrand, France
| | - Pierre Sourdille
- INRA UBP UMR 1095, Genetics, Diversity & Ecophysiology of Cereals, Clermont Ferrand, France
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible (IAS, CSIC), Alameda del Obispo s/n, 14080 Córdoba, Spain
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Hao CY, Perretant MR, Choulet F, Wang LF, Paux E, Sourdille P, Zhang XY, Feuillet C, Balfourier F. Genetic diversity and linkage disequilibrium studies on a 3.1-Mb genomic region of chromosome 3B in European and Asian bread wheat (Triticum aestivum L.) populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:1209-1225. [PMID: 20559816 DOI: 10.1007/s00122-010-1382-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2009] [Accepted: 06/03/2010] [Indexed: 05/29/2023]
Abstract
Genetic diversity and linkage disequilibrium (LD) were investigated in 376 Asian and European accessions of bread wheat (Triticum aestivum L.). After a first and rapid screening about diversity and genetic structure at the whole genome scale using 70 simple sequence repeats (SSRs), we focused on a sequenced contig (ctg954) of 3.1 Mb located on the short arm of chromosome 3B of cv. Chinese Spring, using 32 SSRs and 10 single nucleotide polymorphisms. This contig is part of a multiple fungal resistance region. Mean polymorphism information content value on the 32 SSRs was slightly higher in the Asian genepool (0.396) than that for the European (0.329) pool. Compared with results at the whole genome scale, data from this 3.1-Mb region indicated similar trends in genetic diversity indices between both genepools. Population structure and molecular variance analyses demonstrated significant genetic differentiation and geographical subdivision in both groups of accessions. Concerning LD at the contig level, the European population had a significantly higher mean r(2) value (0.23) than the Asian population (0.18), indicating a stronger LD in the European material. With a mean of 1 marker every 74 kb, the resolution reached here allowed to perform a detailed comparative analysis of the LD and genetic diversity along the complete 3.1-Mb region in both genepools. A sliding-window approach revealed some interesting regions of the contig where LD is increasing when genetic diversity is decreasing. This study provides an in-depth understanding of molecular population genetics in European and Asian wheat gene pools, and prospects for association mapping of important sources of fungal disease resistance.
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Affiliation(s)
- C Y Hao
- INRA UMR 1095, Genetics Diversity and Ecophysiology of Cereals, Clermont-Ferrand, France
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Oliver RE, Obert DE, Hu G, Bonman JM, O'Leary-Jepsen E, Jackson EW. Development of oat-based markers from barley and wheat microsatellites. Genome 2010; 53:458-71. [PMID: 20555435 DOI: 10.1139/g10-021] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Although microsatellites are an efficient and reliable genetic marker system, availability is limited in cultivated oat (Avena sativa L.). Previous research has suggested that microsatellites from related species may be adapted to oat. This study investigated the stability of existing oat microsatellites, sequenced polymorphic oat amplicons derived from wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) primers, and redesigned primers to develop oat-based markers. We evaluated 161 published oat microsatellites and identified 9 with polymorphism between mapping parents Ogle1040 and TAM O-301 (OT). We also studied 30 wheat, 1 Aegilops tauschii Coss., and 9 barley primers with reported oat polymorphism. Sixteen primers (1 A. tauschii, 10 wheat, 5 barley) amplified random oat sequences and were used to generate 28 new oat STS markers. Eight primers, 4 each from wheat and barley, amplified oat repetitive motifs, generating 10 new oat SSRs. Four additional SSRs were developed from characterization of thaumatin-like pathogenesis-related protein sequences formerly utilized as the Rast1-4 oat marker. These new markers, along with 9 existing oat SSRs and 6 previously identified disease resistance loci, were mapped in the OT population, joining 3 pairs of linkage groups. Map locations of multiallelic SSRs and disease-resistance QTL interactions suggested possible homoeologous relationships among the oat chromosomes.
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Affiliation(s)
- R E Oliver
- USDA-ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, ID 83210, USA
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Wen M, Wang H, Xia Z, Zou M, Lu C, Wang W. Developmenrt of EST-SSR and genomic-SSR markers to assess genetic diversity in Jatropha Curcas L. BMC Res Notes 2010; 3:42. [PMID: 20181259 PMCID: PMC2844395 DOI: 10.1186/1756-0500-3-42] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2010] [Accepted: 02/24/2010] [Indexed: 11/23/2022] Open
Abstract
Background Jatropha curcas L. has attracted a great deal of attention worldwide, regarding its potential as a new biodiesel crop. However, the understanding of this crop remains very limited and little genomic research has been done. We used simple sequence repeat (SSR) markers that could be transferred from Manihot esculenta (cassava) to analyze the genetic relationships among 45 accessions of J. curcas from our germplasm collection. Results In total, 187 out of 419 expressed sequence tag (EST)-SSR and 54 out of 182 genomic (G)-SSR markers from cassava were polymorphic among the J. curcas accessions. The EST-SSR markers comprised 26.20% dinucleotide repeats, 57.75% trinucleotide repeats, 7.49% tetranucleotide repeats, and 8.56% pentanucleotide repeats, whereas the majority of the G-SSR markers were dinucleotide repeats (62.96%). The 187 EST-SSRs resided in genes that are involved mainly in biological and metabolic processes. Thirty-six EST-SSRs and 20 G-SSRs were chosen to analyze the genetic diversity among 45 J. curcas accessions. A total of 183 polymorphic alleles were detected. On the basis of the distribution of these polymorphic alleles, the 45 accessions were classified into six groups, in which the genotype showed a correlation with geographic origin. The estimated mean genetic diversity index was 0.5572, which suggests that our J. curcas germplasm collection has a high level of genetic diversity. This should facilitate subsequent studies on genetic mapping and molecular breeding. Conclusion We identified 241 novel EST-SSR and G-SSR markers in J. curcas, which should be useful for genetic mapping and quantitative trait loci analysis of important agronomic traits. By using these markers, we found that the intergroup gene diversity of J. curcas was greater than the intragroup diversity, and that the domestication of the species probably occurred partly in America and partly in Hainan, China.
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Affiliation(s)
- Mingfu Wen
- Institute of Tropical Biosciences & Biotechnology, Chinese Academy of Tropical Agricultural Science, 571101, Haikou, Hainan, PR China.
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Zeng S, Xiao G, Guo J, Fei Z, Xu Y, Roe BA, Wang Y. Development of a EST dataset and characterization of EST-SSRs in a traditional Chinese medicinal plant, Epimedium sagittatum (Sieb. Et Zucc.) Maxim. BMC Genomics 2010; 11:94. [PMID: 20141623 PMCID: PMC2829513 DOI: 10.1186/1471-2164-11-94] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2009] [Accepted: 02/08/2010] [Indexed: 11/30/2022] Open
Abstract
Background Epimedium sagittatum (Sieb. Et Zucc.) Maxim, a traditional Chinese medicinal plant species, has been used extensively as genuine medicinal materials. Certain Epimedium species are endangered due to commercial overexploition, while sustainable application studies, conservation genetics, systematics, and marker-assisted selection (MAS) of Epimedium is less-studied due to the lack of molecular markers. Here, we report a set of expressed sequence tags (ESTs) and simple sequence repeats (SSRs) identified in these ESTs for E. sagittatum. Results cDNAs of E. sagittatum are sequenced using 454 GS-FLX pyrosequencing technology. The raw reads are cleaned and assembled into a total of 76,459 consensus sequences comprising of 17,231 contigs and 59,228 singlets. About 38.5% (29,466) of the consensus sequences significantly match to the non-redundant protein database (E-value < 1e-10), 22,295 of which are further annotated using Gene Ontology (GO) terms. A total of 2,810 EST-SSRs is identified from the Epimedium EST dataset. Trinucleotide SSR is the dominant repeat type (55.2%) followed by dinucleotide (30.4%), tetranuleotide (7.3%), hexanucleotide (4.9%), and pentanucleotide (2.2%) SSR. The dominant repeat motif is AAG/CTT (23.6%) followed by AG/CT (19.3%), ACC/GGT (11.1%), AT/AT (7.5%), and AAC/GTT (5.9%). Thirty-two SSR-ESTs are randomly selected and primer pairs are synthesized for testing the transferability across 52 Epimedium species. Eighteen primer pairs (85.7%) could be successfully transferred to Epimedium species and sixteen of those show high genetic diversity with 0.35 of observed heterozygosity (Ho) and 0.65 of expected heterozygosity (He) and high number of alleles per locus (11.9). Conclusion A large EST dataset with a total of 76,459 consensus sequences is generated, aiming to provide sequence information for deciphering secondary metabolism, especially for flavonoid pathway in Epimedium. A total of 2,810 EST-SSRs is identified from EST dataset and ~1580 EST-SSR markers are transferable. E. sagittatum EST-SSR transferability to the major Epimedium germplasm is up to 85.7%. Therefore, this EST dataset and EST-SSRs will be a powerful resource for further studies such as taxonomy, molecular breeding, genetics, genomics, and secondary metabolism in Epimedium species.
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Affiliation(s)
- Shaohua Zeng
- Key Laboratory of Pant Germplasm Enhancement and Speciality Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei 430074, China
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Dobrovolskaya OB, Sourdille P, Bernard M, Salina EA. Chromosome synteny of the a genome of two evolutionary wheat lines. RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409110118] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Horvath A, Didier A, Koenig J, Exbrayat F, Charmet G, Balfourier F. Analysis of diversity and linkage disequilibrium along chromosome 3B of bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1523-37. [PMID: 19756470 DOI: 10.1007/s00122-009-1153-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Accepted: 08/30/2009] [Indexed: 05/21/2023]
Abstract
A highly polymorphic core collection of bread wheat and a more narrow-based breeding material, gathered from pedigrees of seven modern cultivars, was analysed in order to compare genetic diversity indices and linkage disequilibrium (LD) patterns along the chromosome 3B with microsatellite (SSR) and Diversity Arrays Technology markers. Five ancestral gene pools could be identified within the core collection, indicating a strong geographical structure (Northwest Europe, Southeast Europe, CIMMYT-ICARDA group, Asia, Nepal). The breeding material showed a temporal structure, corresponding to different periods of breeding programmes [old varieties (from old landraces to 1919), semi-modern varieties (1920-1959), modern varieties (1960-2006)]. Basic statistics showed a higher genetic diversity in the core collection than in the breeding material, indicating a stronger selection pressure in this latter material. More generally, the chromosome 3B had a lower diversity than the whole B-genome. LD was weak in all studied materials. Amongst geographical groups, the CIMMYT-ICARDA pool presented the longest ranged LD in contrast to Asian accessions. In the breeding material, LD increased from old cultivars to modern varieties. Genitors of seven modern cultivars were found to be different; most marker pairs in significant LD were observed amongst genitors of Alexandre and Koreli varieties, indicating an important inbreeding effect. At low genetic distances (0-5 cM), the breeding material had higher LD than the core collection, but globally the two materials had similar values in all classes. Marker pairs in significant LD are generally observed around the centromere in both arms and at distal position on the short arm of the chromosome 3B.
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Affiliation(s)
- Aniko Horvath
- INRA, UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
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Mullan DJ, Mirzaghaderi G, Walker E, Colmer TD, Francki MG. Development of wheat-Lophopyrum elongatum recombinant lines for enhanced sodium 'exclusion' during salinity stress. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1313-23. [PMID: 19727655 DOI: 10.1007/s00122-009-1136-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Accepted: 08/12/2009] [Indexed: 05/09/2023]
Abstract
Lophopyrum elongatum (tall wheatgrass), a wild relative of wheat, can be used as a source of novel genes for improving salt tolerance of bread wheat. Sodium 'exclusion' is a major physiological mechanism for salt tolerance in a wheat-tall wheatgrass amphiploid, and a large proportion ( approximately 50%) for reduced Na(+) accumulation in the Xag leaf, as compared to wheat, was earlier shown to be contributed by genetic effects from substitution of chromosome 3E from tall wheatgrass for wheat chromosomes 3A and 3D. Homoeologous recombination between 3E and wheat chromosomes 3A and 3D was induced using the ph1b mutant, and putative recombinants were identified as having SSR markers specific for tall wheatgrass loci. As many as 14 recombinants with smaller segments of tall wheatgrass chromatin were identified and low-resolution breakpoint analysis was achieved using wheat SSR loci. Seven recombinants were identified to have leaf Na+ concentrations similar to those in 3E(3A) or 3E(3D) substitution lines, when grown in 200 mM NaCl in nutrient solution. Phenotypic analysis identified recombinants with introgressions at the distal end on the long arm of homoeologous group 3 chromosomes being responsible for Na(+) 'exclusion'. A total of 55 wheat SSR markers mapped to the long arm of homoeologous group 3 markers by genetic and deletion bin mapping were used for high resolution of wheat-tall wheatgrass chromosomal breakpoints in selected recombinants. Molecular marker analysis and genomic in situ hybridisation confirmed the 524-568 recombinant line as containing the smallest introgression of tall wheatgrass chromatin on the distal end of the long arm of wheat chromosome 3A and identified this line as suitable for developing wheat germplasm with Na(+) 'exclusion'.
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Affiliation(s)
- Daniel J Mullan
- State Agricultural Biotechnology Centre, Murdoch University, Murdoch 6150, Australia
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Dobrovolskaya O, Martinek P, Voylokov AV, Korzun V, Röder MS, Börner A. Microsatellite mapping of genes that determine supernumerary spikelets in wheat (T. aestivum) and rye (S. cereale). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:867-74. [PMID: 19568730 DOI: 10.1007/s00122-009-1095-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2009] [Accepted: 06/13/2009] [Indexed: 05/19/2023]
Abstract
The wheat and rye spike normally bears one spikelet per rachis node, and the appearance of supernumerary spikelets is rare. The loci responsible for the 'multirow spike' or MRS trait in wheat, and the 'monstrosum spike' trait in rye were mapped by genotyping F(2) populations with microsatellite markers. Both MRS and the 'monstrosum' trait are under the control of a recessive allele at a single locus. The Mrs1 locus is located on chromosome 2DS, co-segregating with the microsatellite locus Xwmc453. The placement of flanking microsatellite loci into chromosome deletion bin 2DS-5 (FL 0.47-1.0) delimited the physical location of Mrs1 to the distal half of chromosome arm 2DS, within the gene rich region 2S0.8. The Mo1 locus maps about 10 cM from the centromere on chromosome arm 2RS. The similar effect on phenotype of mo1 and mrs1, together with their presence in regions of conserved synteny, suggest that they may well be members of an orthologous set of Triticeae genes governing spike branching. The practical importance of the MRS spike is that it produces more spikelets per spike, and thereby enhances the sink capacity of wheat, which is believed to limit the yield potential of the crop.
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Affiliation(s)
- Oxana Dobrovolskaya
- Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Gatersleben, Germany.
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