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Wang WW, Tan ZY, Xu YQ, Zhu AA, Li Y, Yao J, Tian R, Fang XM, Liu XY, Tian YM, Teng ZH, Zhang J, Liu DJ, Liu DX, Shang HH, Liu F, Zhang ZS. Chromosome structural variation of two cultivated tetraploid cottons and their ancestral diploid species based on a new high-density genetic map. Sci Rep 2017; 7:7640. [PMID: 28794480 PMCID: PMC5550419 DOI: 10.1038/s41598-017-08006-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 07/07/2017] [Indexed: 11/09/2022] Open
Abstract
A high-resolution genetic map is a useful tool for assaying genomic structural variation and clarifying the evolution of polyploid cotton. A total of 36956 SSRs, including 11289 released in previous studies and 25567 which were newly developed based on the genome sequences of G. arboreum and G. raimondii, were utilized to construct a new genetic map. The new high-density genetic map includes 6009 loci and spanned 3863.97 cM with an average distance of 0.64 cM between consecutive markers. Four inversions (one between Chr08 and Chr24, one between Chr09 and Chr23 and two between Chr10 and Chr20) were identified by homology analysis. Comparative genomic analysis between genetic map and two diploid cottons showed that structural variations between the A genome and At subgenome are more extensive than between D genome and Dt subgenome. A total of 17 inversions, seven simple translocations and two reciprocal translocations were identified between genetic map and G. raimondii. Good colinearity was revealed between the corresponding chromosomes of tetraploid G. hirsutum and G. barbadense genomes, but a total of 16 inversions were detected between them. These results will accelerate the process of evolution analysis of Gossipium genus.
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Affiliation(s)
- Wen-Wen Wang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Zhao-Yun Tan
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Ya-Qiong Xu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Ai-Ai Zhu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Yan Li
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Jiang Yao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Rui Tian
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Xiao-Mei Fang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Xue-Ying Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - You-Ming Tian
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Zhong-Hua Teng
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Jian Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Da-Jun Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - De-Xin Liu
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China
| | - Hai-Hong Shang
- State Key Laboratory of Cotton Biology/Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fang Liu
- State Key Laboratory of Cotton Biology/Cotton Research Institute, Chinese Academy of Agricultural Sciences, Anyang, 455000, China.
| | - Zheng-Sheng Zhang
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Southwest University, Chongqing, 400716, China.
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Chen F, Fu B, Pan Y, Zhang C, Wen H, Weng Y, Chen P, Li Y. Fine mapping identifies CsGCN5 encoding a histone acetyltransferase as putative candidate gene for tendril-less1 mutation (td-1) in cucumber. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1549-1558. [PMID: 28466109 DOI: 10.1007/s00122-017-2909-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/13/2017] [Indexed: 05/10/2023]
Abstract
Next-generation sequencing-aided map-based cloning delimited the cucumber tendril - less1 ( td - 1 ) locus into a 190.7-kb region in chromosome 6 harboring a putative, novel-function candidate gene encoding a histone acetyltransferase ( CsGCN5 ). The tendril initiated from the lateral meristem is an important and characteristic organ for the species in the Cucurbitaceae family including cucumber (Cucumis sativus L.). While the tendril has its evolutionary significance, it also poses a nuisance in cucumber cultivation under protected environments in which tendril-less cucumber has its advantages. From an EMS mutagenesis population, we identified a tendril-less mutant B007, which was controlled by a recessive gene td-1. Through next-generation sequencing-aided map-based cloning, we show CsGCN5 (Cucumis sativus GENERAL CONTROL NONDEREPRESSIBLE 5), a cucumber gene for a histone acetyltransferase as the most possible candidate for td-1. A non-synonymous SNP in the first exon of CsGCN5 resulted in an amino-acid substitution from Asp (D) in the wild type to Asn (N) in the tendril-less mutant. The candidacy of CsGCN5 was further confirmed by multiple lines of evidence in both biparental and natural cucumber populations. Non-significant expression of CsGCN5 in multiple organs was found between the wild type and the mutant. CsGCN5 exhibited strong expression in the tendril of wild-type plants suggesting its important roles in growth and development of plant tendrils. The identification and characterization of the td-1 mutant from the present study provided a useful tool in understanding the molecular mechanisms of tendril organogenesis and investigation of novel functions of the histone acetyltransferase in cucumber.
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Affiliation(s)
- Feifan Chen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Bingbing Fu
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yupeng Pan
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
| | - Chaowen Zhang
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Haifan Wen
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yiqun Weng
- Horticulture Department, University of Wisconsin, Madison, WI, 53706, USA
- USDA-ARS, Vegetable Crops Research Unit, 1575 Linden Drive, Madison, WI, 53706, USA
| | - Peng Chen
- College of Life Science, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Yuhong Li
- College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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Guo Y, Wu Y, Anderson JA, Moss JQ, Zhu L, Fu J. SSR Marker Development, Linkage Mapping, and QTL Analysis for Establishment Rate in Common Bermudagrass. THE PLANT GENOME 2017; 10. [PMID: 28464062 DOI: 10.3835/plantgenome2016.07.0074] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Common bermudagrass has been widely used as a major warm-season turf, forage, and soil stabilization grass in the southern United States. However, codominant marker development, linkage, and quantitative trait loci (QTL) mapping resources are limited in the important taxon. Accordingly, the objectives of this study were to develop simple sequence repeat (SSR) markers, construct a genetic map, and identify genomic regions associated with establishment rate. Five genomic SSR libraries were constructed, sequenced, and used in the development of 1003 validated SSR primer pairs (PPs). A linkage map was constructed using a first-generation selfed population derived from a genotype A12359 (2 = 4 = 36). A total of 249 polymorphic SSR PPs were mapped to 18 linkage groups (LGs). The total length of the map is 1094.7 cM, with an average marker interval of 4.3 cM. Ninety-eight out of 252 mapped loci (39%) were found to be distorted from the Mendelian 1:2:1 segregation ratio. Among the other 154 nondistorted loci, 88 coupling vs. 66 repulsion linkage phases were observed to confirm the allopolyploid origin of the parent. Ground coverage (GCR) phenotypic data in the establishment stage were collected in two replicated field trials. Quantitative trait loci mapping identified five genomic regions significantly related to the trait. The findings of this study provide valuable genetic tools and resources for genomic research, genetic improvement, and breeding new cultivars in the species.
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Busse F, Bartkiewicz A, Terefe-Ayana D, Niepold F, Schleusner Y, Flath K, Sommerfeldt-Impe N, Lübeck J, Strahwald J, Tacke E, Hofferbert HR, Linde M, Przetakiewicz J, Debener T. Genomic and Transcriptomic Resources for Marker Development in Synchytrium endobioticum, an Elusive but Severe Potato Pathogen. PHYTOPATHOLOGY 2017; 107:322-328. [PMID: 27827007 DOI: 10.1094/phyto-05-16-0197-r] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Synchytrium endobioticum is an obligate biotrophic fungus that causes wart diseases in potato. Like other species of the class Chytridiomycetes, it does not form mycelia and its zoospores are small, approximately 3 μm in diameter, which complicates the detection of early stages of infection. Furthermore, potato wart disease is difficult to control because belowground organs are infected and resting spores of the fungus are extremely durable. Thus, S. endobioticum is classified as a quarantine organism. More than 40 S. endobioticum pathotypes have been reported, of which pathotypes 1(D1), 2(G1), 6(O1), 8(F1), and 18(T1) are the most important in Germany. No molecular methods for the differentiation of pathotypes are available to date. In this work, we sequenced both genomic DNA and cDNA of the German pathotype 18(T1) from infected potato tissue and generated 5,422 expressed sequence tags (EST) and 423 genomic contigs. Comparative sequencing of 33 genes, single-stranded confirmation polymorphism (SSCP) analysis with polymerase chain reaction fragments of 27 additional genes, as well as the analysis of 41 simple sequence repeat (SSR) loci revealed extremely low levels of variation among five German pathotypes. From these markers, one sequence-characterized amplified region marker and five SSR markers revealed polymorphisms among the German pathotypes and an extended set of 11 additional European isolates. Pathotypes 8(F1) and 18(T1) displayed discrete polymorphisms which allow their differentiation from other pathotypes. Overall, using the information of the six markers, the 16 isolates could be differentiated into three distinct genotype groups. In addition to the presented markers, the new collection of EST from genus Synchytrium might serve in the future for molecular taxonomic studies as well as for analyses of the host-pathogen interactions in this difficult pathosystem. [Formula: see text] Copyright © 2017 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
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Affiliation(s)
- Friederike Busse
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Annette Bartkiewicz
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Diro Terefe-Ayana
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Frank Niepold
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Yvonne Schleusner
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Kerstin Flath
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Nicole Sommerfeldt-Impe
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Jens Lübeck
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Josef Strahwald
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Eckhard Tacke
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Hans-Reinhard Hofferbert
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Marcus Linde
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Jarosław Przetakiewicz
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
| | - Thomas Debener
- First, second, third, twelfth, and fourteenth authors: Institute for Plant Genetics, Leibniz Universität Hannover, Herrenhäuser Str. 2, 30419 Hannover, Germany; fourth author: Julius Kühn Institute (JKI), Institute of Epidemiology and Pathogen Diagnostics, Braunschweig, Germany; fifth, sixth, and seventh authors: JKI, Federal Research Centre for Cultivated Plants, Institute for Plant Protection of Field Crops and Grassland, Kleinmachnow, Germany; eighth and ninth authors: SaKa Pflanzenzucht GmbH & Co. KG, Windeby, Germany; tenth and eleventh authors: Böhm-Nordkartoffel Agrarproduktion GmbH & Co. OHG, Ebstorf, Germany; and thirteenth author: Plant Breeding and Acclimatization Institute-National Research Institute, Radzikow 05-870, Blonie, Poland
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Chaudhary S, Mishra BK, Vivek T, Magadum S, Yasin JK. PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple ( Ananas comosus (L.) Merrill). Hereditas 2017; 153:16. [PMID: 28096778 PMCID: PMC5226092 DOI: 10.1186/s41065-016-0019-8] [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: 08/11/2016] [Accepted: 11/02/2016] [Indexed: 11/22/2022] Open
Abstract
Background Simple Sequence Repeats or microsatellites are resourceful molecular genetic markers. There are only few reports of SSR identification and development in pineapple. Complete genome sequence of pineapple available in the public domain can be used to develop numerous novel SSRs. Therefore, an attempt was made to identify SSRs from genomic, chloroplast, mitochondrial and EST sequences of pineapple which will help in deciphering genetic makeup of its germplasm resources. Results A total of 359511 SSRs were identified in pineapple (356385 from genome sequence, 45 from chloroplast sequence, 249 in mitochondrial sequence and 2832 from EST sequences). The list of EST-SSR markers and their details are available in the database. Conclusions PineElm_SSRdb is an open source database available for non-commercial academic purpose at http://app.bioelm.com/ with a mapping tool which can develop circular maps of selected marker set. This database will be of immense use to breeders, researchers and graduates working on Ananas spp. and to others working on cross-species transferability of markers, investigating diversity, mapping and DNA fingerprinting. Electronic supplementary material The online version of this article (doi:10.1186/s41065-016-0019-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sakshi Chaudhary
- Division of Genomic Resources, ICAR- National Bureau of Plant Genomic Resources, PUSA campus, 110012 New Delhi, India
| | - Bharat Kumar Mishra
- Division of Genomic Resources, ICAR- National Bureau of Plant Genomic Resources, PUSA campus, 110012 New Delhi, India
| | - Thiruvettai Vivek
- Division of Genomic Resources, ICAR- National Bureau of Plant Genomic Resources, PUSA campus, 110012 New Delhi, India
| | - Santoshkumar Magadum
- Division of Genomic Resources, ICAR- National Bureau of Plant Genomic Resources, PUSA campus, 110012 New Delhi, India
| | - Jeshima Khan Yasin
- Division of Genomic Resources, ICAR- National Bureau of Plant Genomic Resources, PUSA campus, 110012 New Delhi, India
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Ištvánek J, Dluhošová J, Dluhoš P, Pátková L, Nedělník J, Řepková J. Gene Classification and Mining of Molecular Markers Useful in Red Clover ( Trifolium pratense) Breeding. FRONTIERS IN PLANT SCIENCE 2017; 8:367. [PMID: 28382043 PMCID: PMC5360756 DOI: 10.3389/fpls.2017.00367] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Accepted: 03/01/2017] [Indexed: 05/18/2023]
Abstract
Red clover (Trifolium pratense) is an important forage plant worldwide. This study was directed to broadening current knowledge of red clover's coding regions and enhancing its utilization in practice by specific reanalysis of previously published assembly. A total of 42,996 genes were characterized using Illumina paired-end sequencing after manual revision of Blast2GO annotation. Genes were classified into metabolic and biosynthetic pathways in response to biological processes, with 7,517 genes being assigned to specific pathways. Moreover, 17,727 enzymatic nodes in all pathways were described. We identified 6,749 potential microsatellite loci in red clover coding sequences, and we characterized 4,005 potential simple sequence repeat (SSR) markers as generating polymerase chain reaction products preferentially within 100-350 bp. Marker density of 1 SSR marker per 12.39 kbp was achieved. Aligning reads against predicted coding sequences resulted in the identification of 343,027 single nucleotide polymorphism (SNP) markers, providing marker density of one SNP marker per 144.6 bp. Altogether, 95 SSRs in coding sequences were analyzed for 50 red clover varieties and a collection of 22 highly polymorphic SSRs with pooled polymorphism information content >0.9 was generated, thus obtaining primer pairs for application to diversity studies in T. pratense. A set of 8,623 genome-wide distributed SNPs was developed and used for polymorphism evaluation in individual plants. The polymorphic information content ranged from 0 to 0.375. Temperature switch PCR was successfully used in single-marker SNP genotyping for targeted coding sequences and for heterozygosity or homozygosity confirmation in validated five loci. Predicted large sets of SSRs and SNPs throughout the genome are key to rapidly implementing genome-based breeding approaches, for identifying genes underlying key traits, and for genome-wide association studies. Detailed knowledge of genetic relationships among breeding material can also be useful for breeders in planning crosses or for plant variety protection. Single-marker assays are useful for diagnostic applications.
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Affiliation(s)
- Jan Ištvánek
- Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Jana Dluhošová
- Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | - Petr Dluhoš
- Department of Psychiatry, University Hospital Brno and Masaryk UniversityBrno, Czechia
| | - Lenka Pátková
- Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
| | | | - Jana Řepková
- Department of Experimental Biology, Faculty of Science, Masaryk UniversityBrno, Czechia
- *Correspondence: Jana Řepková
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Cattani AM, Siqueira FM, Guedes RLM, Schrank IS. Repetitive Elements in Mycoplasma hyopneumoniae Transcriptional Regulation. PLoS One 2016; 11:e0168626. [PMID: 28005945 PMCID: PMC5179023 DOI: 10.1371/journal.pone.0168626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/02/2016] [Indexed: 12/15/2022] Open
Abstract
Transcriptional regulation, a multiple-step process, is still poorly understood in the important pig pathogen Mycoplasma hyopneumoniae. Basic motifs like promoters and terminators have already been described, but no other cis-regulatory elements have been found. DNA repeat sequences have been shown to be an interesting potential source of cis-regulatory elements. In this work, a genome-wide search for tandem and palindromic repetitive elements was performed in the intergenic regions of all coding sequences from M. hyopneumoniae strain 7448. Computational analysis demonstrated the presence of 144 tandem repeats and 1,171 palindromic elements. The DNA repeat sequences were distributed within the 5' upstream regions of 86% of transcriptional units of M. hyopneumoniae strain 7448. Comparative analysis between distinct repetitive sequences found in related mycoplasma genomes demonstrated different percentages of conservation among pathogenic and nonpathogenic strains. qPCR assays revealed differential expression among genes showing variable numbers of repetitive elements. In addition, repeats found in 206 genes already described to be differentially regulated under different culture conditions of M. hyopneumoniae strain 232 showed almost 80% conservation in relation to M. hyopneumoniae strain 7448 repeats. Altogether, these findings suggest a potential regulatory role of tandem and palindromic DNA repeats in the M. hyopneumoniae transcriptional profile.
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Affiliation(s)
- Amanda Malvessi Cattani
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Franciele Maboni Siqueira
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
| | - Rafael Lucas Muniz Guedes
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Rio de Janeiro, Brazil
| | - Irene Silveira Schrank
- Centro de Biotecnologia, Programa de Pós-Graduação em Biologia Celular e Molecular, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- Centro de Biotecnologia, Departamento de Biologia Molecular e Biotecnologia, Instituto de Biociências, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Rio Grande do Sul, Brazil
- * E-mail:
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Wang Y, Lu H, Hu J. Molecular Mapping of High Resistance to Bacterial Leaf Spot in Lettuce PI 358001-1. PHYTOPATHOLOGY 2016; 106:1319-1325. [PMID: 27454703 DOI: 10.1094/phyto-09-15-0238-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Lettuce (Lactuca sativa L.) is a diploid (2n = 18) with a genome size of 2,600 Mbp, and belongs to the family Compositae. Bacterial leaf spot (BLS), caused by Xanthomonas campestris pv. vitians, is a major disease of lettuce worldwide. Leaf lettuce PI 358001-1 has been characterized as an accession highly resistant to BLS and has white seed. In order to understand inheritance of the high resistance in this germplasm line, an F3 population consisting of 163 families was developed from the cross PI 358001-1 × 'Tall Guzmaine' (a susceptible Romaine lettuce variety with black seed). The segregation ratio of reaction to disease by seedling inoculation with X. campestris pv. vitians L7 strain in the F3 families was shown to be 32:82:48 homozygous resistant/heterozygous/homozygous susceptible, fitting to 1:2:1 (n = 162, χ2 = 3.19, P = 0.20). The segregation ratio of seed color by checking F2 plants was 122:41 black/white, fitting to 3:1 (n = 163, χ2 = 0.002, P = 0.96). The results indicated that both BLS resistance and seed color were inherited as a dominant gene mode. A genetic linkage map based on 124 randomly selected F2 plants was developed to enable molecular mapping of the BLS resistance and the seed color trait. In total, 199 markers, comprising 176 amplified fragment length polymorphisms, 16 simple-sequence repeats, 5 resistant gene candidate markers, and 2 cleaved amplified polymorphic sequences (CAPS) markers were assigned to six linkage groups. The dominant resistance gene to BLS (Xcvr) was mapped on linkage group 2 and the gene locus y for seed color was identified on linkage group 5. Due to the nature of a single gene inheritance, the high-resistance gene should be readily transferred to adapted lettuce cultivars to battle against the devastating disease of lettuce.
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Affiliation(s)
- Yunwen Wang
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
| | - Huangjun Lu
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
| | - Jinguo Hu
- First and second authors: Everglades Research and Education Center, University of Florida/Institute of Food and Agricultural Sciences, Belle Glade 33430; and third author: United States Department of Agriculture-Agricultural Research Service, Western Regional Plant Introduction Station, Washington State University, Pullman 99164
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Thatikunta R, Siva Sankar A, Sreelakshmi J, Palle G, Leela C, Durga Rani CV, Gouri Shankar V, Lavanya B, Narayana Reddy P, Dudhe MY. Utilization of in silico EST-SSR markers for diversity studies in castor ( Ricinus communis L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2016; 22:535-545. [PMID: 27924126 PMCID: PMC5120032 DOI: 10.1007/s12298-016-0367-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 07/13/2016] [Accepted: 07/25/2016] [Indexed: 05/06/2023]
Abstract
Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSR-containing ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.
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Affiliation(s)
- Ramesh Thatikunta
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - A. Siva Sankar
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - J. Sreelakshmi
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - Gouthami Palle
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - C. Leela
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - Ch. V. Durga Rani
- Institute of Biotechnology, PJTSAU, Rajendranagar, Hyderabad, 500030 India
| | | | - B. Lavanya
- Department of Crop Physiology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - P. Narayana Reddy
- Department of Plant Pathology, College of Agriculture, Rajendranagar, Hyderabad, 500030 India
| | - M. Y. Dudhe
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030 India
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QTL and candidate genes associated with common bacterial blight resistance in the common bean cultivar Longyundou 5 from China. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Liu ZK, Wen JB. Transcriptomic Analysis of Eucryptorrhynchus chinensis (Coleoptera: Curculionidae) Using 454 Pyrosequencing Technology. JOURNAL OF INSECT SCIENCE (ONLINE) 2016; 16:iew067. [PMID: 27620556 PMCID: PMC5019023 DOI: 10.1093/jisesa/iew067] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2015] [Accepted: 07/04/2016] [Indexed: 06/06/2023]
Abstract
Eucryptorrhynchus chinensis Olivier (Coleoptera: Curculionidae) is one of the most important pests of Ailanthus altissima; however, so far, no studies on the genome or transcriptome of E. chinensis have been reported. Using the Roche 454 FLX Titanium platform, an RNA pool obtained from E. chinensis eggs, larva, pupae, and adults was sequenced and assembled de novo to achieve maximum diversity of sampled transcripts. We obtained 1,441,137 (∼518 Mb) raw reads with an average length of 360 bp. After trimming, 89% qualified reads were produced and assembled into 35,509 isotigs with an average length of 440 bp, N50 of 1,048 bp, and 111,643 singletons. We generated 87,894 unigenes following a cluster analysis of the isotigs and singletons, and then functionally annotated the unigenes with gene descriptions. We obtained 23,363 GO assignments, and 12,724 unigenes were assigned to KOG. Based on these annotations, 294 biochemical pathways involved in growth, reproduction, and stress or immune responses were predicted. A total of 659,026 single nucleotide variants and 6,112 simple sequence repeats were detected. Our data provide comprehensive information on the sequence and possible functions of E. chinensis transcripts.
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Affiliation(s)
- Zhen-Kai Liu
- Beijing Key Laboratory of Forest Protection, College of Forestry, Beijing Forestry University, Beijing 100083, People's Republic of China (; )
| | - Jun-Bao Wen
- Beijing Key Laboratory of Forest Protection, College of Forestry, Beijing Forestry University, Beijing 100083, People's Republic of China (; )
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Hosseinzadeh-Colagar A, Haghighatnia MJ, Amiri Z, Mohadjerani M, Tafrihi M. Microsatellite (SSR) amplification by PCR usually led to polymorphic bands: Evidence which shows replication slippage occurs in extend or nascent DNA strands. MOLECULAR BIOLOGY RESEARCH COMMUNICATIONS 2016; 5:167-174. [PMID: 28097170 PMCID: PMC5219911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Microsatellites or simple sequence repeats (SSRs) are very effective molecular markers in population genetics, genome mapping, taxonomic study and other large-scale studies. Variation in number of tandem repeats within microsatellite refers to simple sequence length polymorphism (SSLP); but there are a few studies that are showed SSRs replication slippage may be occurred during in vitro amplification which are produced 'stutter products' differing in length from the main products. The purpose of this study is introducing a reliable method to realize SSRs replication slippage. At first, three unique primers designed to amplify SSRs loci in the great gerbil (Rhombomys opimus) by PCR. Crush and soak method used to isolate interesting DNA bands from polyacrylamide gel. PCR products analyzed using by sequencing methods. Our study has been shown that Taq DNA polymerase slipped during microsatellite in vitro amplification which led to insertion or deletion of repeats in sense or antisense DNA strands. It is produced amplified fragments with various lengths in gel electrophoresis showed as 'stutter bands'. Thus, in population studies by SSRs markers recommend that replication slippage effects and stutter bands have been considered.
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Affiliation(s)
- Abasalt Hosseinzadeh-Colagar
- Address for correspondence: Department of Molecular and Cell Biology, Faculty of Basic Sciences, University of Mazandaran, Babolsar, Postal Code 47416-95447, Mazandaran, Iran ,Tel: +98 (112) 5242161, Fax: +98 (112) 5242161, E. mail: : and
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Vatanparast M, Shetty P, Chopra R, Doyle JJ, Sathyanarayana N, Egan AN. Transcriptome sequencing and marker development in winged bean (Psophocarpus tetragonolobus; Leguminosae). Sci Rep 2016; 6:29070. [PMID: 27356763 PMCID: PMC4928180 DOI: 10.1038/srep29070] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/14/2016] [Indexed: 01/08/2023] Open
Abstract
Winged bean, Psophocarpus tetragonolobus (L.) DC., is similar to soybean in yield and nutritional value but more viable in tropical conditions. Here, we strengthen genetic resources for this orphan crop by producing a de novo transcriptome assembly and annotation of two Sri Lankan accessions (denoted herein as CPP34 [PI 491423] and CPP37 [PI 639033]), developing simple sequence repeat (SSR) markers, and identifying single nucleotide polymorphisms (SNPs) between geographically separated genotypes. A combined assembly based on 804,757 reads from two accessions produced 16,115 contigs with an N50 of 889 bp, over 90% of which has significant sequence similarity to other legumes. Combining contigs with singletons produced 97,241 transcripts. We identified 12,956 SSRs, including 2,594 repeats for which primers were designed and 5,190 high-confidence SNPs between Sri Lankan and Nigerian genotypes. The transcriptomic data sets generated here provide new resources for gene discovery and marker development in this orphan crop, and will be vital for future plant breeding efforts. We also analyzed the soybean trypsin inhibitor (STI) gene family, important plant defense genes, in the context of related legumes and found evidence for radiation of the Kunitz trypsin inhibitor (KTI) gene family within winged bean.
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Affiliation(s)
- Mohammad Vatanparast
- US National Herbarium (US), Department of Botany, Smithsonian Institution-NMNH, 10th and Constitution Ave, Washington DC, 20013, USA
| | - Prateek Shetty
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Room 166, East Lansing, MI, 48824, USA
| | - Ratan Chopra
- United States Department of Agriculture, Agriculture Research Service, 3810 4th St., Lubbock, TX, 79415, USA
| | - Jeff J Doyle
- Section of Plant Breeding &Genetics, School of Integrative Plant Science, Cornell University, 412 Mann Library, Ithaca, NY, 14853, USA
| | - N Sathyanarayana
- Department of Botany, Sikkim University, 5th Mile, Tadong, Gangtok, Sikkim, 737102, India
| | - Ashley N Egan
- US National Herbarium (US), Department of Botany, Smithsonian Institution-NMNH, 10th and Constitution Ave, Washington DC, 20013, USA
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Hodel RGJ, Segovia-Salcedo MC, Landis JB, Crowl AA, Sun M, Liu X, Gitzendanner MA, Douglas NA, Germain-Aubrey CC, Chen S, Soltis DE, Soltis PS. The report of my death was an exaggeration: A review for researchers using microsatellites in the 21st century. APPLICATIONS IN PLANT SCIENCES 2016; 4:apps1600025. [PMID: 27347456 PMCID: PMC4915923 DOI: 10.3732/apps.1600025] [Citation(s) in RCA: 91] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/25/2016] [Indexed: 05/19/2023]
Abstract
Microsatellites, or simple sequence repeats (SSRs), have long played a major role in genetic studies due to their typically high polymorphism. They have diverse applications, including genome mapping, forensics, ascertaining parentage, population and conservation genetics, identification of the parentage of polyploids, and phylogeography. We compare SSRs and newer methods, such as genotyping by sequencing (GBS) and restriction site associated DNA sequencing (RAD-Seq), and offer recommendations for researchers considering which genetic markers to use. We also review the variety of techniques currently used for identifying microsatellite loci and developing primers, with a particular focus on those that make use of next-generation sequencing (NGS). Additionally, we review software for microsatellite development and report on an experiment to assess the utility of currently available software for SSR development. Finally, we discuss the future of microsatellites and make recommendations for researchers preparing to use microsatellites. We argue that microsatellites still have an important place in the genomic age as they remain effective and cost-efficient markers.
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Affiliation(s)
- Richard G. J. Hodel
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- Author for correspondence:
| | | | - Jacob B. Landis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Andrew A. Crowl
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Miao Sun
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | - Xiaoxian Liu
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
| | | | - Norman A. Douglas
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
| | | | - Shichao Chen
- College of Life Sciences and Technology, Tongji University, Shanghai 200092, China
| | - Douglas E. Soltis
- Department of Biology, University of Florida, Gainesville, Florida 32611 USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
| | - Pamela S. Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida 32611 USA
- The Genetics Institute, University of Florida, Gainesville, Florida 32611 USA
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Wang F, Wu W, Wang D, Yang W, Sun J, Liu D, Zhang A. Characterization and Genetic Analysis of a Novel Light-Dependent Lesion Mimic Mutant, lm3, Showing Adult-Plant Resistance to Powdery Mildew in Common Wheat. PLoS One 2016; 11:e0155358. [PMID: 27175509 PMCID: PMC4866716 DOI: 10.1371/journal.pone.0155358] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 04/27/2016] [Indexed: 11/18/2022] Open
Abstract
Lesion mimics (LMs) that exhibit spontaneous disease-like lesions in the absence of pathogen attack might confer enhanced plant disease resistance to a wide range of pathogens. The LM mutant, lm3 was derived from a single naturally mutated individual in the F1 population of a 3-1/Jing411 cross, backcrossed six times with 3–1 as the recurrent parent and subsequently self-pollinated twice. The leaves of young seedlings of the lm3 mutant exhibited small, discrete white lesions under natural field conditions. The lesions first appeared at the leaf tips and subsequently expanded throughout the entire leaf blade to the leaf sheath. The lesions were initiated through light intensity and day length. Histochemical staining revealed that lesion formation might reflect programmed cell death (PCD) and abnormal accumulation of reactive oxygen species (ROS). The chlorophyll content in the mutant was significantly lower than that in wildtype, and the ratio of chlorophyll a/b was increased significantly in the mutant compared with wildtype, indicating that lm3 showed impairment of the biosynthesis or degradation of chlorophyll, and that Chlorophyll b was prone to damage during lesion formation. The lm3 mutant exhibited enhanced resistance to wheat powdery mildew fungus (Blumeria graminis f. sp. tritici; Bgt) infection, which was consistent with the increased expression of seven pathogenesis-related (PR) and two wheat chemically induced (WCI) genes involved in the defense-related reaction. Genetic analysis showed that the mutation was controlled through a single partially dominant gene, which was closely linked to Xbarc203 on chromosome 3BL; this gene was delimited to a 40 Mb region between SSR3B450.37 and SSR3B492.6 using a large derived segregating population and the available Chinese Spring chromosome 3B genome sequence. Taken together, our results provide information regarding the identification of a novel wheat LM gene, which will facilitate the additional fine-mapping and cloning of the gene to understand the mechanism underlying LM initiation and disease resistance in common wheat.
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Affiliation(s)
- Fang Wang
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Wenying Wu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Dongzhi Wang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Wenlong Yang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Jiazhu Sun
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
| | - Dongcheng Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- * E-mail: (DL); (AZ)
| | - Aimin Zhang
- College of Agronomy/The Collaborative Innovation Center of Grain Crops in Henan, Henan Agricultural University, Zhengzhou, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing, China
- * E-mail: (DL); (AZ)
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Moges AD, Admassu B, Belew D, Yesuf M, Njuguna J, Kyalo M, Ghimire SR. Development of Microsatellite Markers and Analysis of Genetic Diversity and Population Structure of Colletotrichum gloeosporioides from Ethiopia. PLoS One 2016; 11:e0151257. [PMID: 26978654 PMCID: PMC4792483 DOI: 10.1371/journal.pone.0151257] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 02/25/2016] [Indexed: 01/10/2023] Open
Abstract
Twenty three polymorphic microsatellite markers were developed for citrus plant pathogenic fungus, Colletotrichum gloeosporioides, and were used to analyze genetic diversity and population structure of 163 isolates from four different geographical regions of Ethiopia. These loci produced a total of 118 alleles with an average of 5.13 alleles per microsatellite marker. The polymorphic information content values ranged from 0.104 to 0.597 with an average of 0.371. The average observed heterozygosity across all loci varied from 0.046 to 0.058. The gene diversity among the loci ranged from 0.106 to 0.664. Unweighted Neighbor-joining and population structure analysis grouped these 163 isolates into three major groups. The clusters were not according to the geographic origin of the isolates. Analysis of molecular variance showed 85% of the total variation within populations and only 5% among populations. There was low genetic differentiation in the total populations (FST = 0.049) as evidenced by high level of gene flow estimate (Nm = 4.8 per generation) among populations. The results show that Ethiopian C. gloeosporioides populations are generally characterized by a low level of genetic diversity. The newly developed microsatellite markers were useful in analyzing the genetic diversity and population structure of the C. gloeosporioides populations. Information obtained from this study could be useful as a base to design strategies for better management of leaf and fruit spot disease of citrus in Ethiopia.
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Affiliation(s)
- Asmare D. Moges
- Department of Horticulture, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, Jimma, Ethiopia
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
| | - Belayneh Admassu
- Department of Agricultural Biotechnology, Ethiopian Institute of Agricultural Research, Holetta, Ethiopia
| | - Derbew Belew
- Department of Horticulture and Plant Sciences, College of Agriculture and Veterinary Medicine, Jimma University, Jimma, Ethiopia
| | - Mohammed Yesuf
- Department of Horticulture, Ethiopian Institute of Agricultural Research, Adama, Ethiopia
| | - Joyce Njuguna
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
| | - Martina Kyalo
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
| | - Sita R. Ghimire
- Biosciences eastern and central Africa Hub, International Livestock Research Institute, Nairobi, Kenya
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Tang N, San Clemente H, Roy S, Bécard G, Zhao B, Roux C. A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy. Front Microbiol 2016; 7:233. [PMID: 26973612 PMCID: PMC4771724 DOI: 10.3389/fmicb.2016.00233] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 02/15/2016] [Indexed: 01/22/2023] Open
Abstract
Arbuscular mycorrhizal (AM) fungi are a diverse group of soil fungi (Glomeromycota) that form the most ancient mutualistic association termed AM symbiosis with a majority of land plants, improving their nutrition uptake and resistance to stresses. In contrast to their great ecological implications, the knowledge of the molecular biological mechanisms involved is still scant, partly due to the limited genomic resources available. Here, we describe the gene repertoire of a new AM fungus Gigaspora rosea (Diversisporales). Among the 86332 non-redundant virtual transcripts assembled, 15346 presented similarities with proteins in the Refseq database and 10175 were assigned with GO terms. KOG and Interpro domain annotations clearly showed an enrichment of genes involved in signal transduction in G. rosea. KEGG pathway analysis indicates that most primary metabolic processes are active in G. rosea. However, as for Rhizophagus irregularis, several metabolic genes were not found, including the fatty acid synthase (FAS) gene. This finding supports the hypothesis that AM fungi depend on the lipids produced by their hosts. Furthermore, the presence of a large number of transporters and 100s of secreted proteins, together with the reduced number of plant cell wall degrading enzymes could be interpreted as an evolutionary adaptation to its mutualistic obligate biotrophy. The detection of meiosis-related genes suggests that G. rosea might use a cryptic sexual process. Lastly, a phylogeny of basal fungi clearly shows Glomeromycota as a sister clade to Mucoromycotina, not only to the Mucorales or Mortierellales. The characterization of the gene repertoire from an AM fungal species belonging to the order of Diversisporales and its comparison with the gene sets of R. irregularis (Glomerales) and Gigaspora margarita (Diversisporales), reveal that AM fungi share several features linked to mutualistic obligate biotrophy. This work contributes to lay the foundation for forthcoming studies into the genomics of Diversisporales, and also illuminates the utility of comparing gene repertoires of species from Diversisporales and other clades of Glomeromycota to gain more insights into the genetics and evolution of this fungal group.
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Affiliation(s)
- Nianwu Tang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Hélène San Clemente
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Sébastien Roy
- AGRONUTRITION Laboratoire de BiotechnologiesToulouse, France
| | - Guillaume Bécard
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
| | - Bin Zhao
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Christophe Roux
- CNRS, Laboratoire de Recherche en Sciences Végétales, UMR, Université Paul Sabatier – Université de ToulouseCastanet Tolosan, France
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Solis J, Baisakh N, Brandt SR, Villordon A, La Bonte D. Transcriptome Profiling of Beach Morning Glory (Ipomoea imperati) under Salinity and Its Comparative Analysis with Sweetpotato. PLoS One 2016; 11:e0147398. [PMID: 26848754 PMCID: PMC4743971 DOI: 10.1371/journal.pone.0147398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 01/04/2016] [Indexed: 01/23/2023] Open
Abstract
The response and adaption to salt remains poorly understood for beach morning glory [Ipomoea imperati (Vahl) Griseb], one of a few relatives of sweetpotato, known to thrive under salty and extreme drought conditions. In order to understand the genetic mechanisms underlying salt tolerance of a Convolvulaceae member, a genome-wide transcriptome study was carried out in beach morning glory by 454 pyrosequencing. A total of 286,584 filtered reads from both salt stressed and unstressed (control) root and shoot tissues were assembled into 95,790 unigenes with an average length of 667 base pairs (bp) and N50 of 706 bp. Putative differentially expressed genes (DEGs) were identified as transcripts overrepresented under salt stressed tissues compared to the control, and were placed into metabolic pathways. Most of these DEGs were involved in stress response, membrane transport, signal transduction, transcription activity and other cellular and molecular processes. We further analyzed the gene expression of 14 candidate genes of interest for salt tolerance through quantitative reverse transcription PCR (qRT-PCR) and confirmed their differential expression under salt stress in both beach morning glory and sweetpotato. The results comparing transcripts of I. imperati against the transcriptome of other Ipomoea species, including sweetpotato are also presented in this study. In addition, 6,233 SSR markers were identified, and an in silico analysis predicted that 434 primer pairs out of 4,897 target an identifiable homologous sequence in other Ipomoea transcriptomes, including sweetpotato. The data generated in this study will help in understanding the basics of salt tolerance of beach morning glory and the SSR resources generated will be useful for comparative genomics studies and further enhance the path to the marker-assisted breeding of sweetpotato for salt tolerance.
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Affiliation(s)
- Julio Solis
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
- * E-mail: (NB); (DL)
| | - Steven R. Brandt
- Louisiana Digital Media Center, Louisiana State University, Baton Rouge, LA, United States of America
| | - Arthur Villordon
- Sweet Potato Research Station, Louisiana State University Agricultural Center, Chase, LA, United States of America
| | - Don La Bonte
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA, United States of America
- * E-mail: (NB); (DL)
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Kim HA, Shin AY, Lee MS, Lee HJ, Lee HR, Ahn J, Nahm S, Jo SH, Park JM, Kwon SY. De Novo Transcriptome Analysis of Cucumis melo L. var. makuwa. Mol Cells 2016; 39:141-8. [PMID: 26743902 PMCID: PMC4757802 DOI: 10.14348/molcells.2016.2264] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 10/30/2015] [Accepted: 11/02/2015] [Indexed: 11/27/2022] Open
Abstract
Oriental melon (Cucumis melo L. var. makuwa) is one of six subspecies of melon and is cultivated widely in East Asia, including China, Japan, and Korea. Although oriental melon is economically valuable in Asia and is genetically distinct from other subspecies, few reports of genome-scale research on oriental melon have been published. We generated 30.5 and 36.8 Gb of raw RNA sequence data from the female and male flowers, leaves, roots, and fruit of two oriental melon varieties, Korean landrace (KM) and Breeding line of NongWoo Bio Co. (NW), respectively. From the raw reads, 64,998 transcripts from KM and 100,234 transcripts from NW were de novo assembled. The assembled transcripts were used to identify molecular markers (e.g., single-nucleotide polymorphisms and simple sequence repeats), detect tissue-specific expressed genes, and construct a genetic linkage map. In total, 234 single-nucleotide polymorphisms and 25 simple sequence repeats were screened from 7,871 and 8,052 candidates, respectively, between the KM and NW varieties and used for construction of a genetic map with 94 F2 population specimens. The genetic linkage map consisted of 12 linkage groups, and 248 markers were assigned. These transcriptome and molecular marker data provide information useful for molecular breeding of oriental melon and further comparative studies of the Cucurbitaceae family.
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Affiliation(s)
- Hyun A Kim
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
| | | | | | | | | | | | - Sung-Hwan Jo
- SEEDERS, Daeduk Industry Academic Cooperation Building, Daejeon 34016,
Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350,
Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806,
Korea
- Biosystems and Bioengineering Program, University of Science and Technology, Daejeon 305-350,
Korea
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Li CY, Chiang TY, Chiang YC, Hsu HM, Ge XJ, Huang CC, Chen CT, Hung KH. Cross-Species, Amplifiable EST-SSR Markers for Amentotaxus Species Obtained by Next-Generation Sequencing. Molecules 2016; 21:67. [PMID: 26751439 PMCID: PMC6273106 DOI: 10.3390/molecules21010067] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/30/2015] [Accepted: 12/31/2015] [Indexed: 01/02/2023] Open
Abstract
Amentotaxus, a genus of Taxaceae, is an ancient lineage with six relic and endangered species. Four Amentotaxus species, namely A. argotaenia, A. formosana, A. yunnanensis, and A. poilanei, are considered a species complex because of their morphological similarities. Small populations of these species are allopatrically distributed in Asian forests. However, only a few codominant markers have been developed and applied to study population genetic structure of these endangered species. In this study, we developed and characterized polymorphic expressed sequence tag-simple sequence repeats (EST-SSRs) from the transcriptome of A. formosana. We identified 4955 putative EST-SSRs from 68,281 unigenes as potential molecular markers. Twenty-six EST-SSRs were selected for estimating polymorphism and transferability among Amentotaxus species, of which 23 EST-SSRs were polymorphic within Amentotaxus species. Among these, the number of alleles ranged from 1-4, the polymorphism information content ranged from 0.000-0.692, and the observed and expected heterozygosity were 0.000-1.000 and 0.080-0.740, respectively. Population genetic structure analyses confirmed that A. argotaenia and A. formosana were separate species and A. yunnanensis and A. poilanei were the same species. These novel EST-SSRs can facilitate further population genetic structure research of Amentotaxus species.
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Affiliation(s)
- Chiuan-Yu Li
- Taiwan Endemic Species Research Institute, Nantou 552, Taiwan.
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Tzen-Yuh Chiang
- Department of Life Sciences, National Cheng-Kung University, Tainan 701, Taiwan.
| | - Yu-Chung Chiang
- Department of Biological Sciences, National Sun Yat-sen University, Kaohsiung 804, Taiwan.
| | - Hsin-Mei Hsu
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Xue-Jun Ge
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
| | | | - Chaur-Tzuhn Chen
- Department of Forestry, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
| | - Kuo-Hsiang Hung
- Graduate Institute of Bioresources, Pingtung University of Science and Technology, Pingtung 912, Taiwan.
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Wang X, Wang L. GMATA: An Integrated Software Package for Genome-Scale SSR Mining, Marker Development and Viewing. FRONTIERS IN PLANT SCIENCE 2016; 7:1350. [PMID: 27679641 PMCID: PMC5020087 DOI: 10.3389/fpls.2016.01350] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Accepted: 08/23/2016] [Indexed: 05/19/2023]
Abstract
Simple sequence repeats (SSRs), also referred to as microsatellites, are highly variable tandem DNAs that are widely used as genetic markers. The increasing availability of whole-genome and transcript sequences provides information resources for SSR marker development. However, efficient software is required to efficiently identify and display SSR information along with other gene features at a genome scale. We developed novel software package Genome-wide Microsatellite Analyzing Tool Package (GMATA) integrating SSR mining, statistical analysis and plotting, marker design, polymorphism screening and marker transferability, and enabled simultaneously display SSR markers with other genome features. GMATA applies novel strategies for SSR analysis and primer design in large genomes, which allows GMATA to perform faster calculation and provides more accurate results than existing tools. Our package is also capable of processing DNA sequences of any size on a standard computer. GMATA is user friendly, only requires mouse clicks or types inputs on the command line, and is executable in multiple computing platforms. We demonstrated the application of GMATA in plants genomes and reveal a novel distribution pattern of SSRs in 15 grass genomes. The most abundant motifs are dimer GA/TC, the A/T monomer and the GCG/CGC trimer, rather than the rich G/C content in DNA sequence. We also revealed that SSR count is a linear to the chromosome length in fully assembled grass genomes. GMATA represents a powerful application tool that facilitates genomic sequence analyses. GAMTA is freely available at http://sourceforge.net/projects/gmata/?source=navbar.
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Affiliation(s)
- Xuewen Wang
- Germplasm Bank of Wild Species in China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- *Correspondence: Xuewen Wang
| | - Le Wang
- Key Laboratory of Forensic Genetics and Beijing Engineering Research Center of Crime Scene Evidence Examination, Institute of Forensic Science, Ministry of Public SecurityBeijing, China
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Ranade SS, Lin YC, Van de Peer Y, García-Gil MR. Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda). BMC Genet 2015; 16:149. [PMID: 26706685 PMCID: PMC4691297 DOI: 10.1186/s12863-015-0304-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/10/2015] [Indexed: 11/24/2022] Open
Abstract
Background Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1–6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (≥20) and class II (≥12 and <20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species. Results Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10−9 and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005). Conclusions Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0304-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden.
| | - Yao-Cheng Lin
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. .,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028, South Africa. .,Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium.
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden.
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De Novo Assembly and Transcriptome Characterization of Canine Retina Using High-Throughput Sequencing. GENETICS RESEARCH INTERNATIONAL 2015; 2015:638679. [PMID: 26788372 PMCID: PMC4695645 DOI: 10.1155/2015/638679] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/29/2023]
Abstract
We performed transcriptome sequencing of canine retinal tissue by 454 GS-FLX and Ion Torrent PGM platforms. RNA-Seq analysis by CLC Genomics Workbench mapped expression of 10,360 genes. Gene ontology analysis of retinal transcriptome revealed abundance of transcripts known to be involved in vision associated processes. The de novo assembly of the sequences using CAP3 generated 29,683 contigs with mean length of 560.9 and N50 of 619 bases. Further analysis of contigs predicted 3,827 full-length cDNAs and 29,481 (99%) open reading frames (ORFs). In addition, 3,782 contigs were assigned to 316 KEGG pathways which included melanogenesis, phototransduction, and retinol metabolism with 33, 15, and 11 contigs, respectively. Among the identified microsatellites, dinucleotide repeats were 68.84%, followed by trinucleotides, tetranucleotides, pentanucleotides, and hexanucleotides in proportions of 25.76, 9.40, 2.52, and 0.96%, respectively. This study will serve as a valuable resource for understanding the biology and function of canine retina.
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Abstract
BACKGROUND With the advent of high-throughput sequencing technologies large-scale identification of microsatellites became affordable and was especially directed to non-model species. By contrast, few efforts have been published toward the automatic identification of polymorphic microsatellites by exploiting sequence redundancy. Few tools for genotyping microsatellite repeats have been implemented so far that are able to manage huge amount of sequence data and handle the SAM/BAM file format. Most of them have been developed for and tested on human or model organisms with high quality reference genomes. RESULTS In this note we describe polymorphic SSR retrieval (PSR), a read counter and simple sequence repeat (SSR) length polymorphism detection tool. It is written in Perl and was developed to identify length polymorphisms in perfect microsatellites exploiting next generation sequencing (NGS) data. PSR has been developed bearing in mind plant non-model species for which de novo transcriptome assembly is generally the first sequence resource available to be used for SSR-mining. PSR is divided into two modules: the read-counting module (PSR_read_retrieval) identifies all the reads that cover the full-length of perfect microsatellites; the comparative module (PSR_poly_finder) detects both heterozygous and homozygous alleles at each microsatellite locus across all genotypes under investigation. Two threshold values to call a length polymorphism and reduce the number of false positives can be defined by the user: the minimum number of reads overlapping the repetitive stretch and the minimum read depth. The first parameter determines if the microsatellite-containing sequence must be processed or not, while the second one is decisive for the identification of minor alleles. PSR was tested on two different case studies. The first study aims at the identification of polymorphic SSRs in a set of de novo assembled transcripts defined by RNA-sequencing of two different plant genotypes. The second research activity aims to investigate sequence variations within a collection of newly sequenced chloroplast genomes. In both the cases PSR results are in agreement with those obtained by capillary gel separation. CONCLUSION PSR has been specifically developed from the need to automate the gene-based and genome-wide identification of polymorphic microsatellites from NGS data. It overcomes the limits related to the existing and time-consuming efforts based on tools developed in the pre-NGS era.
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Affiliation(s)
- Concita Cantarella
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca per l'orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy.
| | - Nunzio D'Agostino
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria - Centro di ricerca per l'orticoltura, Via Cavalleggeri 25, 84098, Pontecagnano Faiano, Italy.
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Comparative quantitative trait loci for silique length and seed weight in Brassica napus. Sci Rep 2015; 5:14407. [PMID: 26394547 PMCID: PMC4585775 DOI: 10.1038/srep14407] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 08/26/2015] [Indexed: 11/08/2022] Open
Abstract
Silique length (SL) and seed weight (SW) are important yield-associated traits in rapeseed (Brassica napus). Although many quantitative trait loci (QTL) for SL and SW have been identified in B. napus, comparative analysis for those QTL is seldom performed. In the present study, 20 and 21 QTL for SL and SW were identified in doubled haploid (DH) and DH-derived reconstructed F2 populations in rapeseed, explaining 55.1-74.3% and 24.4-62.9% of the phenotypic variation across three years, respectively. Of which, 17 QTL with partially or completely overlapped confidence interval on chromosome A09, were homologous with two overlapped QTL on chromosome C08 by aligning QTL confidence intervals with the reference genomes of Brassica crops. By high density selective genotyping of DH lines with extreme phenotypes, using a Brassica single-nucleotide polymorphism (SNP) array, the QTL on chromosome A09 was narrowed, and aligned into 1.14-Mb region from 30.84 to 31.98 Mb on chromosome R09 of B. rapa and 1.05-Mb region from 27.21 to 28.26 Mb on chromosome A09 of B. napus. The alignment of QTL with Brassica reference genomes revealed homologous QTL on A09 and C08 for SL. The narrowed QTL region provides clues for gene cloning and breeding cultivars by marker-assisted selection.
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76
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De Novo Assembly of Bitter Gourd Transcriptomes: Gene Expression and Sequence Variations in Gynoecious and Monoecious Lines. PLoS One 2015; 10:e0128331. [PMID: 26047102 PMCID: PMC4457790 DOI: 10.1371/journal.pone.0128331] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 04/26/2015] [Indexed: 11/19/2022] Open
Abstract
Bitter gourd (Momordica charantia L.) is a nutritious vegetable crop of Asian origin, used as a medicinal herb in Indian and Chinese traditional medicine. Molecular breeding in bitter gourd is in its infancy, due to limited molecular resources, particularly on functional markers for traits such as gynoecy. We performed de novo transcriptome sequencing of bitter gourd using Illumina next-generation sequencer, from root, flower buds, stem and leaf samples of gynoecious line (Gy323) and a monoecious line (DRAR1). A total of 65,540 transcripts for Gy323 and 61,490 for DRAR1 were obtained. Comparisons revealed SNP and SSR variations between these lines and, identification of gene classes. Based on available transcripts we identified 80 WRKY transcription factors, several reported in responses to biotic and abiotic stresses; 56 ARF genes which play a pivotal role in auxin-regulated gene expression and development. The data presented will be useful in both functions studies and breeding programs in bitter gourd.
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77
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Schafleitner R, Nair RM, Rathore A, Wang YW, Lin CY, Chu SH, Lin PY, Chang JC, Ebert AW. The AVRDC - The World Vegetable Center mungbean (Vigna radiata) core and mini core collections. BMC Genomics 2015; 16:344. [PMID: 25925106 PMCID: PMC4422537 DOI: 10.1186/s12864-015-1556-7] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/20/2015] [Indexed: 11/25/2022] Open
Abstract
Background Large ex situ germplasm collections generally harbor a wide range of crop diversity. AVRDC – The World Vegetable Center is holding in trust the world’s second largest mungbean (Vigna radiata) germplasm collection with more than 6,700 accessions. Screening large collections for traits of interest is laborious and expensive. To enhance the access of breeders to the diversity of the crop, mungbean core and mini core collections have been established. Results The core collection of 1,481 entries has been built by random selection of 20% of the accessions after geographical stratification and subsequent cluster analysis of eight phenotypic descriptors in the whole collection. Summary statistics, especially the low differences of means, equal variance of the traits in both the whole and core collection and the visual inspection of quantile-quantile plots comparing the variation of phenotypic traits present in both collections indicated that the core collection well represented the pattern of diversity of the whole collection. The core collection was genotyped with 20 simple sequence repeat markers and a mini core set of 289 accessions was selected, which depicted the allele and genotype diversity of the core collection. Conclusions The mungbean core and mini core collections plus their phenotypic and genotypic data are available for distribution to breeders. It is expected that these collections will enhance the access to biodiverse mungbean germplasm for breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1556-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Roland Schafleitner
- AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan.
| | - Ramakrishnan Madhavan Nair
- AVRDC - The World Vegetable Center South Asia, ICRISAT Campus, Patancheru 502 324, Hyderabad, Telangana, India.
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana, India.
| | - Yen-wei Wang
- AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan.
| | - Chen-yu Lin
- AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan.
| | - Shu-hui Chu
- AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan.
| | - Pin-yun Lin
- AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan.
| | - Jian-Cheng Chang
- AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan.
| | - Andreas W Ebert
- AVRDC - The World Vegetable Center, P.O. Box 42, Shanhua, Tainan, 74199, Taiwan.
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Zhang J, Liu W, Han H, Song L, Bai L, Gao Z, Zhang Y, Yang X, Li X, Gao A, Li L. De novo transcriptome sequencing of Agropyron cristatum to identify available gene resources for the enhancement of wheat. Genomics 2015; 106:129-36. [PMID: 25889708 DOI: 10.1016/j.ygeno.2015.04.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 04/07/2015] [Accepted: 04/08/2015] [Indexed: 01/08/2023]
Abstract
Agropyron cristatum is a wild grass of the tribe Triticeae that is widely grown in harsh environments. As a wild relative of wheat, A. cristatum carries many resistance genes that could be used to broaden the genetic diversity of wheat. Here, we report the transcriptome sequencing of the flag leaf and young spike tissues of a representative tetraploid A. cristatum. More than 90 million reads from the two tissues were assembled into 73,664 unigenes. All unigenes were functionally annotated against the KEGG, COG, and Gene Ontology databases and predicted long non-coding RNAs. Pfam prediction demonstrates that A. cristatum carries an abundance of stress resistance genes. The extent of specific genes and rare alleles make A. cristatum a vital genetic reservoir for the improvement of wheat. Altogether, the available gene resources in A. cristatum facilitate efforts to harness the genetic diversity of wild relatives to enhance wheat.
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Affiliation(s)
- Jinpeng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weihua Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiming Han
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liqiang Song
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Bai
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhihui Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinming Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuquan Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Ainong Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lihui Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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A substitution mutation in OsCCD7 cosegregates with dwarf and increased tillering phenotype in rice. J Genet 2015; 93:389-401. [PMID: 25189234 DOI: 10.1007/s12041-014-0389-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Dwarf plant height and tillering ability are two of the most important agronomic traits that determine the plant architecture, and have profound influence on grain yield in rice. To understand the molecular mechanism controlling these two traits, an EMS-induced recessive dwarf and increased tillering1 (dit1) mutant was characterized. The mutant showed proportionate reduction in each internode as compared to wild type revealing that it belonged to the category of dn-type of dwarf mutants. Besides, exogenous application of GA3 and 24-epibrassinolide, did not have any effect on the phenotype of the mutant. The gene was mapped on the long arm of chromosome 4, identified through positional candidate approach and verified by cosegregation analysis. It was found to encode carotenoid cleavage dioxygenase7 (CCD7) and identified as an allele of htd1. The mutant carried substitution of two nucleotides CC to AA in the sixth exon of the gene that resulted in substitution of serine by a stop codon in the mutant, and thus formation of a truncated protein, unlike amino acid substitution event in htd1. The new allele will facilitate further functional characterization of this gene, which may lead to unfolding of newer signalling pathways involving plant development and architecture.
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80
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Chand SK, Nanda S, Rout E, Joshi RK. Mining, characterization and validation of EST derived microsatellites from the transcriptome database of Allium sativum L. Bioinformation 2015; 11:145-50. [PMID: 25987765 PMCID: PMC4421003 DOI: 10.6026/97320630011145] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 02/28/2015] [Indexed: 12/30/2022] Open
Abstract
Expressed Sequence Tags (ESTs) with comprehensive transcript information are valuable resources for development of molecular markers as they are derived from conserved genic regions. The present study highlights the mining of EST database to deduce the class I hyper variable SSRs in A. sativum. From 21694 garlic EST sequences, 642 non-redundant SSRs were identified with an average frequency of 1 per 14.9 kb of garlic transcriptome. The most abundant SSR motifs were the mononucleotides (32.86%) followed by trinucleotides (28.50%) and dinucleotides (13.39%). Among the individual SSRs, (A/T)n accounted for the highest number (137; 21.33%) followed by (G/C)n (74; 11.52%) and (AAG)n (63;9.81%). Primers designed from a robust set of 7 AsESTSSRs resulted in the amplification of 63 polymorphic alleles in 14 accessions of garlic. The resolving power of the markers varied from 4.286 (AsSSR7) to 18.143 (AsSSR13) while the average marker index (MI) was 5.087. These EST-SSRs markers for garlic could be useful for the improvement of garlic linkage map and could be used for evaluating genetic variation and comparative genomics studies in Allium species.
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Affiliation(s)
- Subodh Kumar Chand
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Satyabrata Nanda
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Ellojita Rout
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
| | - Raj Kumar Joshi
- Functional Genomics laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India
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81
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ProGeRF: proteome and genome repeat finder utilizing a fast parallel hash function. BIOMED RESEARCH INTERNATIONAL 2015; 2015:394157. [PMID: 25811026 PMCID: PMC4355816 DOI: 10.1155/2015/394157] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 01/19/2015] [Accepted: 01/31/2015] [Indexed: 12/20/2022]
Abstract
Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population
biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and
primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity.
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82
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Kaliswamy P, Vellingiri S, Nathan B, Selvaraj S. Microsatellite analysis in the genome of Acanthaceae: An in silico approach. Pharmacogn Mag 2015; 11:152-6. [PMID: 25709226 PMCID: PMC4329617 DOI: 10.4103/0973-1296.149731] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 05/19/2014] [Accepted: 01/21/2015] [Indexed: 11/07/2022] Open
Abstract
Background: Acanthaceae is one of the advanced and specialized families with conventionally used medicinal plants. Simple sequence repeats (SSRs) play a major role as molecular markers for genome analysis and plant breeding. The microsatellites existing in the complete genome sequences would help to attain a direct role in the genome organization, recombination, gene regulation, quantitative genetic variation, and evolution of genes. Objective: The current study reports the frequency of microsatellites and appropriate markers for the Acanthaceae family genome sequences. Materials and Methods: The whole nucleotide sequences of Acanthaceae species were obtained from National Center for Biotechnology Information database and screened for the presence of SSRs. SSR Locator tool was used to predict the microsatellites and inbuilt Primer3 module was used for primer designing. Results: Totally 110 repeats from 108 sequences of Acanthaceae family plant genomes were identified, and the occurrence of dinucleotide repeats was found to be abundant in the genome sequences. The essential amino acid isoleucine was found rich in all the sequences. We also designed the SSR-based primers/markers for 59 sequences of this family that contains microsatellite repeats in their genome. Conclusion: The identified microsatellites and primers might be useful for breeding and genetic studies of plants that belong to Acanthaceae family in the future.
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Affiliation(s)
- Priyadharsini Kaliswamy
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Srividhya Vellingiri
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Bharathi Nathan
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Saravanakumar Selvaraj
- Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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83
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Schlautman B, Fajardo D, Bougie T, Wiesman E, Polashock J, Vorsa N, Steffan S, Zalapa J. Development and validation of 697 novel polymorphic genomic and EST-SSR markers in the American cranberry (Vaccinium macrocarpon Ait.). Molecules 2015; 20:2001-13. [PMID: 25633331 PMCID: PMC6272188 DOI: 10.3390/molecules20022001] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2014] [Revised: 01/13/2015] [Accepted: 01/26/2015] [Indexed: 11/16/2022] Open
Abstract
The American cranberry, Vaccinium macrocarpon Ait., is an economically important North American fruit crop that is consumed because of its unique flavor and potential health benefits. However, a lack of abundant, genome-wide molecular markers has limited the adoption of modern molecular assisted selection approaches in cranberry breeding programs. To increase the number of available markers in the species, this study identified, tested, and validated microsatellite markers from existing nuclear and transcriptome sequencing data. In total, new primers were designed, synthesized, and tested for 979 SSR loci; 697 of the markers amplified allele patterns consistent with single locus segregation in a diploid organism and were considered polymorphic. Of the 697 polymorphic loci, 507 were selected for additional genetic diversity and segregation analyses in 29 cranberry genotypes. More than 95% of the 507 loci did not display segregation distortion at the p < 0.05 level, and contained moderate to high levels of polymorphism with a polymorphic information content >0.25. This comprehensive collection of developed and validated microsatellite loci represents a substantial addition to the molecular tools available for geneticists, genomicists, and breeders in cranberry and Vaccinium.
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Affiliation(s)
- Brandon Schlautman
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Dr. Madison, WI 53706, USA.
| | - Diego Fajardo
- National Center for Genome Resources, 2935 Rodeo Park Dr. East, Sante Fe, NM 87505, USA.
| | - Tierney Bougie
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Dr. Madison, WI 53706, USA.
| | - Eric Wiesman
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA.
| | - James Polashock
- USDA-ARS, Genetic Improvement of Fruits and Vegetables Laboratory, Rutgers University Chatsworth, NJ 08019, USA.
| | - Nicholi Vorsa
- Blueberry and Cranberry Research and Extension Center, Rutgers University, Chatsworth, NJ 08019, USA.
| | - Shawn Steffan
- USDA-ARS, Vegetable Crops Research Unit, University of Wisconsin, Madison, WI 53706, USA.
| | - Juan Zalapa
- Department of Horticulture, University of Wisconsin-Madison, 1575 Linden Dr. Madison, WI 53706, USA.
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84
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Ruperao P, Edwards D. Bioinformatics: identification of markers from next-generation sequence data. Methods Mol Biol 2015; 1245:29-47. [PMID: 25373747 DOI: 10.1007/978-1-4939-1966-6_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
With the advent of sequencing technology, next-generation sequencing (NGS) technology has dramatically revolutionized plant genomics. NGS technology combined with new software tools enables the discovery, validation, and assessment of genetic markers on a large scale. Among different markers systems, simple sequence repeats (SSRs) and Single nucleotide polymorphisms (SNPs) are the markers of choice for genetics and plant breeding. SSR markers have been a choice for large-scale characterization of germplasm collections, construction of genetic maps, and QTL identification. Similarly, SNPs are the most abundant genetic variations with higher frequencies throughout the genome of plant species. This chapter discusses various tools available for genome assembly and widely focuses on SSR and SNP marker discovery.
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Affiliation(s)
- Pradeep Ruperao
- School of Agriculture and Food Sciences, University of Queensland, Brisbane, QLD, Australia
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85
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Xia EH, Yao QY, Zhang HB, Jiang JJ, Zhang LP, Gao LZ. CandiSSR: An Efficient Pipeline used for Identifying Candidate Polymorphic SSRs Based on Multiple Assembled Sequences. FRONTIERS IN PLANT SCIENCE 2015; 6:1171. [PMID: 26779212 PMCID: PMC4703815 DOI: 10.3389/fpls.2015.01171] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Accepted: 12/07/2015] [Indexed: 05/02/2023]
Abstract
Simple sequence repeats (SSRs), also known as microsatellites, are ubiquitous short tandem duplications commonly found in genomes and/or transcriptomes of diverse organisms. They represent one of the most powerful molecular markers for genetic analysis and breeding programs because of their high mutation rate and neutral evolution. However, traditionally experimental screening of the SSR polymorphic status and their subsequent applicability to genetic studies are extremely labor-intensive and time-consuming. Thankfully, the recently decreased costs of next generation sequencing and increasing availability of large genome and/or transcriptome sequences have provided an excellent opportunity and sources for large-scale mining this type of molecular markers. However, current tools are limited. Thus we here developed a new pipeline, CandiSSR, to identify candidate polymorphic SSRs (PolySSRs) based on the multiple assembled sequences. The pipeline allows users to identify putative PolySSRs not only from the transcriptome datasets but also from multiple assembled genome sequences. In addition, two confidence metrics including standard deviation and missing rate of the SSR repetitions are provided to systematically assess the feasibility of the detected PolySSRs for subsequent application to genetic characterization. Meanwhile, primer pairs for each identified PolySSR are also automatically designed and further evaluated by the global sequence similarities of the primer-binding region, ensuring the successful rate of the marker development. Screening rice genomes with CandiSSR and subsequent experimental validation showed an accuracy rate of over 90%. Besides, the application of CandiSSR has successfully identified a large number of PolySSRs in the Arabidopsis genomes and Camellia transcriptomes. CandiSSR and the PolySSR marker sources are publicly available at: http://www.plantkingdomgdb.com/CandiSSR/index.html.
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Affiliation(s)
- En-Hua Xia
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Qiu-Yang Yao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Hai-Bin Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Jian-Jun Jiang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- University of Chinese Academy of SciencesBeijing, China
| | - Li-Ping Zhang
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
| | - Li-Zhi Gao
- Plant Germplasm and Genomics Center, Germplasm Bank of Wild Species in Southwest China, Kunming Institute of Botany, Chinese Academy of SciencesKunming, China
- *Correspondence: Li-Zhi Gao,
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86
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Kim SY, Kim KH, Im CH, Ali A, Lee CY, Kong WS, Ryu JS. Identification of degenerate nuclei and development of a SCAR marker for Flammulina velutipes. PLoS One 2014; 9:e107207. [PMID: 25221949 PMCID: PMC4164608 DOI: 10.1371/journal.pone.0107207] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 08/08/2014] [Indexed: 11/18/2022] Open
Abstract
Flammulina velutipes is one of the major edible mushrooms in the world. Recently, abnormalities that have a negative impact on crop production have been reported in this mushroom. These symptoms include slow vegetative growth, a compact mycelial mat, and few or even no fruiting bodies. The morphologies and fruiting capabilities of monokaryons of wild-type and degenerate strains that arose through arthrospore formation were investigated through test crossing. Only one monokaryotic group of the degenerate strains and its hybrid strains showed abnormal phenotypes. Because the monokaryotic arthrospore has the same nucleus as the parent strain, these results indicated that only one aberrant nucleus of the two nuclei in the degenerate strain was responsible for the degeneracy. A sequence-characterized amplified region marker that is linked to the degenerate monokaryon was identified based on a polymorphic sequence that was generated using random primers. Comparative analyses revealed the presence of a degenerate-specific genomic region in a telomere, which arose via the transfer of a genomic fragment harboring a putative helicase gene. Our findings have narrowed down the potential molecular targets responsible for this phenotype for future studies and have provided a marker for the detection of degenerate strains.
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Affiliation(s)
- Sun Young Kim
- Environment-friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Kyung-Hee Kim
- Environment-friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Chak Han Im
- Environment-friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | - Asjad Ali
- Environment-friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
| | | | - Won-Sik Kong
- Mushroom Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Eumsung, Republic of Korea
| | - Jae-San Ryu
- Environment-friendly Research Division, Gyeongsangnam-do Agricultural Research and Extension Services, Jinju, Republic of Korea
- * E-mail:
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87
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Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil MDR. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC PLANT BIOLOGY 2014; 14:220. [PMID: 25143005 PMCID: PMC4160553 DOI: 10.1186/s12870-014-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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Affiliation(s)
- Sonali Sachin Ranade
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| | - Yao-Cheng Lin
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Andrea Zuccolo
- />Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy
- />Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Yves Van de Peer
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- />Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa
| | - María del Rosario García-Gil
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
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88
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Liu JJ, Hammett C. Development of novel polymorphic microsatellite markers by technology of next generation sequencing in western white pine. CONSERV GENET RESOUR 2014. [DOI: 10.1007/s12686-014-0168-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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89
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Zhou Y, Chen L, Fan X, Bian Y. De novo assembly of Auricularia polytricha transcriptome using Illumina sequencing for gene discovery and SSR marker identification. PLoS One 2014; 9:e91740. [PMID: 24626227 PMCID: PMC3953639 DOI: 10.1371/journal.pone.0091740] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/13/2014] [Indexed: 11/18/2022] Open
Abstract
Auricularia polytricha (Mont.) Sacc., a type of edible black-brown mushroom with a gelatinous and modality-specific fruiting body, is in high demand in Asia due to its nutritional and medicinal properties. Illumina Solexa sequenceing technology was used to generate very large transcript sequences from the mycelium and the mature fruiting body of A. polytricha for gene discovery and molecular marker development. De novo assembly generated 36,483 ESTs with an N50 length of 636 bp. A total of 28,108 ESTs demonstrated significant hits with known proteins in the nr database, and 94.03% of the annotated ESTs showed the greatest similarity to A. delicata, a related species of A. polytricha. Functional categorization of the Gene Ontology (GO), Clusters of Orthologous Groups (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathways revealed the conservation of genes involved in various biological processes in A. polytricha. Gene expression profile analysis indicated that a total of 2,057 ESTs were differentially expressed, including 1,020 ESTs that were up-regulated in the mycelium and 1,037 up-regulated in the fruiting body. Functional enrichment showed that the ESTs associated with biosynthesis, metabolism and assembly of proteins were more active in fruiting body development. The expression patterns of homologous transcription factors indicated that the molecular mechanisms of fruiting body formation and development were not exactly the same as for other agarics. Interestingly, an EST encoding tyrosinase was significantly up-regulated in the fruiting body, indicating that melanins accumulated during the processes of the formation of the black-brown color of the fruiting body in A. polytricha development. In addition, a total of 1,715 potential SSRs were detected in this transcriptome. The transcriptome analysis of A. polytricha provides valuable sequence resources and numerous molecular markers to facilitate further functional genomics studies and genetic researches on this fungus.
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Affiliation(s)
- Yan Zhou
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Lianfu Chen
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xiuzhi Fan
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yinbing Bian
- Institute of Applied Mycology, Huazhong Agricultural University, Wuhan, Hubei, China
- Key Laboratory of Agro-Microbial Resource Comprehensive Utilization, Ministry of Agriculture, Huazhong Agricultural University, Wuhan, Hubei, China
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90
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Tan C, Wu Y, Taliaferro CM, Bell GE, Martin DL, Smith MW. Development and characterization of genomic SSR markers in Cynodon transvaalensis Burtt-Davy. Mol Genet Genomics 2014; 289:523-31. [PMID: 24585252 DOI: 10.1007/s00438-014-0829-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 02/11/2014] [Indexed: 02/01/2023]
Abstract
Simple sequence repeat (SSR) markers are a major molecular tool for genetic and genomic research that have been extensively developed and used in major crops. However, few are available in African bermudagrass (Cynodon transvaalensis Burtt-Davy), an economically important warm-season turfgrass species. African bermudagrass is mainly used for hybridizations with common bermudagrass [C. dactylon var. dactylon (L.) Pers.] in the development of superior interspecific hybrid turfgrass cultivars. Accordingly, the major objective of this study was to develop and characterize a large set of SSR markers. Genomic DNA of C. transvaalensis '4200TN 24-2' from an Oklahoma State University (OSU) turf nursery was extracted for construction of four SSR genomic libraries enriched with [CA](n), [GA](n), [AAG](n), and [AAT](n) as core repeat motifs. A total of 3,064 clones were sequenced at the OSU core facility. The sequences were categorized into singletons and contiguous sequences to exclude redundancy. From the two sequence categories, 1,795 SSR loci were identified. After excluding duplicate SSRs by comparison with previously developed SSR markers using a nucleotide basic local alignment tool, 1,426 unique primer pairs (PPs) were designed. Out of the 1,426 designed PPs, 981 (68.8 %) amplified alleles of the expected size in the donor DNA. Polymorphisms of the SSR PPs tested in eight C. transvaalensis plants were 93 % polymorphic with 544 markers effective in all genotypes. Inheritance of the SSRs was examined in six F(1) progeny of African parents 'T577' × 'Uganda', indicating 917 markers amplified heritable alleles. The SSR markers developed in the study are the first large set of co-dominant markers in African bermudagrass and should be highly valuable for molecular and traditional breeding research.
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Affiliation(s)
- Chengcheng Tan
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
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91
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Li Y, Wen C, Weng Y. Fine mapping of the pleiotropic locus B for black spine and orange mature fruit color in cucumber identifies a 50 kb region containing a R2R3-MYB transcription factor. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:2187-96. [PMID: 23689749 DOI: 10.1007/s00122-013-2128-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2013] [Accepted: 05/08/2013] [Indexed: 05/21/2023]
Abstract
In cucumber, Cucumis sativus L., the spine and skin colors are two important fruit quality traits for variety improvement. In this study, we investigated the inheritance of spine and mature fruit skin colors in F2 and F3 populations derived from a cross between two inbred lines WI7200 (black spine and orange fruit skin colors) and WI7201 (white spine and creamy fruit skin colors). We confirmed that a single, dominant gene, B, controlled both black spine color and orange mature fruit color. Initial framework mapping with microsatellite markers located the B locus in the distal region of the short arm of cucumber chromosome 4. Fine mapping was conducted with draft genome scaffold-assisted chromosome walking and stepwise increase of mapping population sizes, which allowed for the assignment of the B locus to a 50 kb genomic DNA region with two flanking markers that were 0.06 and 0.09 cM, respectively, from the B locus in a mapping population of 2,001 F2 plants. Gene annotation of this 50 kb region identified six genes including one encoding for a R2R3-MYB transcription factor. Sequence alignment of the R2R3-MYB homologs between the two parent inbreds identified a 1 bp deletion in the third intron of this gene in WI 7201. A molecular marker based on this indel was co-segregating with the spine and fruit colors. Quantitative RT-PCR revealed higher level of expression of this R2R3-MYB gene in WI7200 than in WI7201 in both immature and mature fruits. This R2R3-MYB gene seems to be the best candidate gene for the B locus conditioning black spine and orange mature fruit colors of cultivated cucumber.
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Affiliation(s)
- Yuhong Li
- Horticulture College, Northwest A&F University, Yangling, China
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92
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Wang X, Lu P, Luo Z. GMATo: A novel tool for the identification and analysis of microsatellites in large genomes. Bioinformation 2013; 9:541-4. [PMID: 23861572 PMCID: PMC3705631 DOI: 10.6026/97320630009541] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2013] [Accepted: 01/13/2013] [Indexed: 11/23/2022] Open
Abstract
Simple Sequence Repeats (SSR), also called microsatellite, is very useful for genetic marker development and genome application.
The increasing whole sequences of more and more large genomes provide sources for SSR mining in silico. However currently
existing SSR mining tools can’t process large genomes efficiently and generate no or poor statistics. Genome-wide Microsatellite
Analyzing Tool (GMATo) is a novel tool for SSR mining and statistics at genome aspects. It is faster and more accurate than existed
tools SSR Locator and MISA. If a DNA sequence was too long, it was chunked to short segments at several Mb followed by motifs
generation and searching using Perl powerful pattern match function. Matched loci data from each chunk were then merged to
produce final SSR loci information. Only one input file is required which contains raw fasta DNA sequences and output files in
tabular format list all SSR loci information and statistical distribution at four classifications. GMATo was programmed in Java and
Perl with both graphic and command line interface, either executable alone in platform independent manner with full parameters
control. Software GMATo is a powerful tool for complete SSR characterization in genomes at any size.
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Affiliation(s)
- Xuewen Wang
- China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, NO.2 Fengyang Street, Hi-tech zone, Zhengzhou 450001, China
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93
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Blair MW, Hurtado N. EST
‐
SSR
markers from five sequenced
cDNA
libraries of common bean (
P
haseolus vulgaris
L.) comparing three bioinformatic algorithms. Mol Ecol Resour 2013; 13:688-95. [DOI: 10.1111/1755-0998.12099] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Revised: 02/05/2013] [Accepted: 02/12/2013] [Indexed: 11/30/2022]
Affiliation(s)
- Matthew W. Blair
- Departamento de Ciencias Agricolas Universidad Nacional de Colombia – sede Palmira km 12 via Chapinero Palmira Colombia
- Department of Plant Breeding and Genetics Cornell University 242 Emerson Hall Ithaca NY 14853 USA
| | - Natalia Hurtado
- Departamento de Ciencias Agricolas Universidad Nacional de Colombia – sede Palmira km 12 via Chapinero Palmira Colombia
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Du FK, Xu F, Qu H, Feng S, Tang J, Wu R. Exploiting the transcriptome of Euphrates Poplar, Populus euphratica (Salicaceae) to develop and characterize new EST-SSR markers and construct an EST-SSR database. PLoS One 2013; 8:e61337. [PMID: 23593466 PMCID: PMC3623821 DOI: 10.1371/journal.pone.0061337] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Accepted: 03/08/2013] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Microsatellite markers or Simple Sequence Repeats (SSRs) are the most popular markers in population/conservation genetics. However, the development of novel microsatellite markers has been impeded by high costs, a lack of available sequence data and technical difficulties. New species-specific microsatellite markers were required to investigate the evolutionary history of the Euphratica tree, Populus euphratica, the only tree species found in the desert regions of Western China and adjacent Central Asian countries. METHODOLOGY/PRINCIPAL FINDINGS A total of 94,090 non-redundant Expressed Sequence Tags (ESTs) from P. euphratica comprising around 63 Mb of sequence data were searched for SSRs. 4,202 SSRs were found in 3,839 ESTs, with 311 ESTs containing multiple SSRs. The most common motif types were trinucleotides (37%) and hexanucleotides (33%) repeats. We developed primer pairs for all of the identified EST-SSRs (eSSRs) and selected 673 of these pairs at random for further validation. 575 pairs (85%) gave successful amplification, of which, 464 (80.7%) were polymorphic in six to 24 individuals from natural populations across Northern China. We also tested the transferability of the polymorphic eSSRs to nine other Populus species. In addition, to facilitate the use of these new eSSR markers by other researchers, we mapped them onto Populus trichocarpa scaffolds in silico and compiled our data into a web-based database (http://202.205.131.253:8080/poplar/resources/static_page/index.html). CONCLUSIONS The large set of validated eSSRs identified in this work will have many potential applications in studies on P. euphratica and other poplar species, in fields such as population genetics, comparative genomics, linkage mapping, QTL, and marker-assisted breeding. Their use will be facilitated by their incorporation into a user-friendly web-based database.
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Affiliation(s)
- Fang K. Du
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Fang Xu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Hong Qu
- Center for Bioinformatics, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing, China
| | - Sisi Feng
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Jijun Tang
- Department of Computer Science and Engineering, University of South Carolina, Columbia, South Carolina, United States of America
| | - Rongling Wu
- Center for Computational Biology, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
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95
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96
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Moraes RCS, Vivas CV, Oliveira FA, Menezes IPP, van den Berg C, Gaiotto FA. Microsatellite markers for an endemic Atlantic Forest tree, Manilkara multifida (Sapotaceae). AOB PLANTS 2013; 5:plt006. [PMID: 23487575 PMCID: PMC3595987 DOI: 10.1093/aobpla/plt006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Accepted: 01/03/2013] [Indexed: 06/01/2023]
Abstract
Manilkara multifida is a tropical tree that is endemic to the Atlantic forests of southern Bahia, Brazil. Currently, populations of this species are restricted to fragmented landscapes that are susceptible to anthropogenic disturbances. Considering this issue, and that there is no genetic information available for this endangered species, we developed microsatellite markers for M. multifida to provide resources for future conservation genetics studies. Using an enriched genomic library, we isolated eight polymorphic microsatellite loci and optimized the amplification conditions for M. multifida. For each locus, we estimated the number of alleles, H E and H O, paternity exclusion Q, individual identity I and fixation index F, and examined the presence of null alleles. The mean number of alleles was 11.9, and the heterozygosity was high at all loci (average H E = 0.809 and H O = 0.777). The combined values for both paternity exclusion and individual identity were Q = 0.9959 and I = 5.45 × 10(-11), respectively. No evidence of null alleles was detected. The results of our analysis indicated that all eight microsatellites are promising for assessing questions involving inbreeding, gene flow, co-ancestry and mating patterns in M. multifida.
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Affiliation(s)
- Ramiris C. S. Moraes
- Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16s/n, Salobrinho, 45662-900 Ilhéus, Bahia, Brazil
| | - Caio V. Vivas
- Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16s/n, Salobrinho, 45662-900 Ilhéus, Bahia, Brazil
| | - Fernanda A. Oliveira
- Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16s/n, Salobrinho, 45662-900 Ilhéus, Bahia, Brazil
| | - Ivandilson P. P. Menezes
- Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16s/n, Salobrinho, 45662-900 Ilhéus, Bahia, Brazil
| | - Cassio van den Berg
- Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana (UEFS), Av. Transnordestina s/n, 44036-900 Feira de Santana, Bahia, Brazil
| | - Fernanda A. Gaiotto
- Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna km 16s/n, Salobrinho, 45662-900 Ilhéus, Bahia, Brazil
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97
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Wei L, Xiao M, An Z, Ma B, Mason AS, Qian W, Li J, Fu D. New insights into nested long terminal repeat retrotransposons in Brassica species. MOLECULAR PLANT 2013; 6:470-482. [PMID: 22930733 DOI: 10.1093/mp/sss081] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Long terminal repeat (LTR) retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferentially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well understood. In this study, a total of 1.52Gb of Brassica sequence containing 2020 bacterial artificial chromosomes (BACs) was scanned, and six bacterial artificial chromosome (BAC) clones with extremely nested LTR-TEs (LTR-TEs density: 7.24/kb) were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23Mya. LTR-TEs also preferably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes (3/207) could be matched to the Brassica expressed sequence tag (EST) database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.
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Affiliation(s)
- Lijuan Wei
- Chongqing Engineering Research Center for Rapeseed, College of Agronomy and Biotechnology, Southwest University, Chongqing 400716, China
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98
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Characterization and evolutionary analysis of Brassica species-diverged sequences containing simple repeat units. Genes Genomics 2013. [DOI: 10.1007/s13258-013-0076-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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99
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Liu H, Yin J, Xiao M, Gao C, Mason AS, Zhao Z, Liu Y, Li J, Fu D. Characterization and evolution of 5' and 3' untranslated regions in eukaryotes. Gene 2012; 507:106-11. [PMID: 22846368 DOI: 10.1016/j.gene.2012.07.034] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 06/26/2012] [Accepted: 07/18/2012] [Indexed: 01/21/2023]
Abstract
Untranslated regions (UTRs) in eukaryotes play a significant role in the regulation of translation and mRNA half-life, as well as interacting with specific RNA-binding proteins. However, UTRs receive less attention than more crucial elements such as genes, and the basic structural and evolutionary characteristics of UTRs of different species, and the relationship between these UTRs and the genome size and species gene number is not well understood. To address these questions, we performed a comparative analysis of 5' and 3' untranslated regions of different species by analyzing the basic characteristics of 244,976 UTRs from three eukaryote kingdoms (Plantae, Fungi, and Protista). The results showed that the UTR lengths and SSR frequencies in UTRs increased significantly with increasing species gene number while the length and G+C content in 5' UTRs and different types of repetitive sequences in 3' UTRs increased with the increase of genome size. We also found that the sequence length of 5' UTRs was significantly positively correlated with the presence of transposons and SSRs while the sequence length of 3' UTRs was significantly positively correlated with the presence of tandem repeat sequences. These results suggested that evolution of species complexity from lower organisms to higher organisms is accompanied by an increase in the regulatory complexity of UTRs, mediated by increasing UTR length, increasing G+C content of 5' UTRs, and insertion and expansion of repetitive sequences.
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Affiliation(s)
- Honglei Liu
- Engineering Research Center of South Upland Agriculture of Ministry of Education, PR China, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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Gao C, Xiao M, Ren X, Hayward A, Yin J, Wu L, Fu D, Li J. Characterization and functional annotation of nested transposable elements in eukaryotic genomes. Genomics 2012; 100:222-30. [PMID: 22800764 DOI: 10.1016/j.ygeno.2012.07.004] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2011] [Revised: 06/26/2012] [Accepted: 07/03/2012] [Indexed: 11/18/2022]
Abstract
The movement of transposable elements (TE) in eukaryotic genomes can often result in the occurrence of nested TEs (the insertion of TEs into pre-existing TEs). We performed a general TE assessment using available databases to detect nested TEs and analyze their characteristics and putative functions in eukaryote genomes. A total of 802 TEs were found to be inserted into 690 host TEs from a total number of 11,329 TEs. We reveal that repetitive sequences are associated with an increased occurrence of nested TEs and sequence biased of TE insertion. A high proportion of the genes which were associated with nested TEs are predicted to localize to organelles and participate in nucleic acid and protein binding. Many of these function in metabolic processes, and encode important enzymes for transposition and integration. Therefore, nested TEs in eukaryotic genomes may negatively influence genome expansion, and enrich the diversity of gene expression or regulation.
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Affiliation(s)
- Caihua Gao
- Engineering Research Center of South Upland Agriculture, Ministry of Education, College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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