Application of the High Resolution Melting analysis for genetic mapping of Sequence Tagged Site markers in narrow-leafed lupin (Lupinus angustifolius L.)

• Authors: Katarzyna Kamel , Magdalena Kroc , Wojciech Święcicki
• Languages of publication: EN

Abstracts

EN

Sequence tagged site (STS) markers are valuable tools for genetic and physical mapping that can be successfully used in comparative analyses among related species. Current challenges for molecular markers genotyping in plants include the lack of fast, sensitive and inexpensive methods suitable for sequence variant detection. In contrast, high resolution melting (HRM) is a simple and high-throughput assay, which has been widely applied in sequence polymorphism identification as well as in the studies of genetic variability and genotyping. The present study is the first attempt to use the HRM analysis to genotype STS markers in narrow-leafed lupin (Lupinus angustifolius L.). The sensitivity and utility of this method was confirmed by the sequence polymorphism detection based on melting curve profiles in the parental genotypes and progeny of the narrow-leafed lupin mapping population. Application of different approaches, including amplicon size and a simulated heterozygote analysis, has allowed for successful genetic mapping of 16 new STS markers in the narrow-leafed lupin genome.

Keywords

EN

HRM; molecular markers; genotyping; narrow-leafed lupin

• Publisher: Polish Biochemical Society
• Journal: Acta Biochimica Polonica
• Year: 2015
• Volume: 62
• Issue: 3
• Pages: 533-540

Dates

published

2015

received

2015-01-22

revised

2015-05-12

accepted

2015-08-03

(unknown)

2015-08-28

Contributors

author

Katarzyna Kamel

• Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland

author

Magdalena Kroc

• Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland

author

Wojciech Święcicki

• Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland

References

• Bertioli DJ, Moretzsohn MC, Madsen LH, Sandal N, Leal-Bertioli SC, Guimarães PM, Hougaard BK, Fredslund J, Schauser L, Nielsen AM, Sato S, Tabata S, Cannon SB, Stougaard J (2009) An analysis of synteny of Arachis with Lotus and Medicago sheds new light on the structure, stability and evolution of legume genomes. BMC Genomics 10: 45-55.
• Boersma JG, Pallotta M, Li C, Buirchell BJ, Sivasithamparam K, Yang H (2005) Construction of a genetic linkage map using MFLP and identification of molecular markers linked to domestication genes in narrow-leafed lupin (Lupinus angustifolius L.). Cell Mol Biol Lett 10: 331-344.
• Croxford AE, Rogers T, Caligari PD, Wilkinson MJ (2008) High-resolution melt analysis to identify and map sequence-tagged site anchor points onto linkage maps: a white lupin (Lupinus albus) map as an exemplar. New Phytol 180: 594-607.
• De Koeyer D, Douglass K, Murphy A, Whitney S, Nolan L, Song Y, De Jong (2010) Application of high-resolution DNA melting for genotyping and variant scanning of diploid and autotetraploid potato. Mol Breed 25: 67-90.
• Distefano G, Caruso M, La Malfa S, Gentile A, Wu SB (2012) High resolution melting analysis is a more sensitive and effective alternative to gel-based platforms in analysis of SSR - an example in citrus. PLoS One 7: e44202.
• Fredslund J, Madsen LH, Hougaard BK, Nielsen AM, Bertioli D, Sandal N, Stougaard J, Schauser L. (2006) A general pipeline for the development of anchor markers for comparative genomics in plants. BMC Genomics 7: 207-216.
• Fredslund J, Schauser L, Madsen LH, Sandal N, Stougaard J (2005) PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs. Nucleic Acids Res 33: W516-W520.
• Gundry CN, Vandersteen JG, Reed GH, Pryor RJ, Chen J, Wittwer CT (2003) Amplicon melting analysis with labeled primers: a closed-tube method for differentiating homozygotes and heterozygotes. Clin Chem 49: 396-406.
• Han Y, Khu DM, Monteros MJ (2012) High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.). Mol Breed 29: 489-501.
• Hofinger BJ, Jing HC, Hammond-Kosack KE, Kanyuka K (2009) High-resolution melting analysis of cDNA-derived PCR amplicons for rapid and cost-effective identification of novel alleles in barley. Theor Appl Genet 119: 851-65.
• Hougaard BK, Madsen LH, Sandal N, de Carvalho Moretzsohn M, Fredslund J, Schauser L, Nielsen AM, Rohde T, Sato S, Tabata S, Bertioli DJ, Stougaard J (2008) Legume Anchor Markers Link Syntenic Regions Between Phaseolus vulgaris, Lotus japonicus, Medicago truncatula and Arachis. Genetics 179: 2299-2312.
• Kamphuis LG, Hane JK, Nelson MN, Gao L, Atkins CA, Singh KB (2014) Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers. Plant Biotechnol J.
• Knopkiewicz M, Gawłowska M, Święcicki W (2014) The application of high resolution melting in the analysis of simple sequence repeats and single nucleotide polymorphisms markers in a pea (Pisum sativum L.) population. Czech J Genet Plant Breed 50: 151-156.
• Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23: 1289-1291.
• Kroc M, Koczyk G, Święcicki W, Kilian A, Nelson MN (2014) New evidence of ancestral polyploidy in the Genistoid legume Lupinus angustifolius L. (narrow-leafed lupin). Theor Appl Genet 127: 1237-1249.
• Liew M, Pryor R, Palais R, Meadows C, Erali M, Lyon E, Wittwer C (2004) Genotyping of Single-Nucleotide Polymorphisms by High-Resolution Melting of Small Amplicons. Clin Chem 50: 1156-1164.
• Manly KF, Cudmore RH Jr, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12: 930-932.
• Monteros MJ, Ha BK, Boerma HR (2010) SNP assay to detect the 'Hyuuga' red-brown lesion resistance gene for Asian soybean rust. Theor Appl Genet 121: 1023-1032.
• Montgomery J, Wittwer CT, Palais R, Zhou L (2007) Simultaneous mutation scanning and genotyping by high-resolution DNA melting analysis. Nat Protoc 2: 59-66.
• Nelson MN, Phan HT, Ellwood SR, Moolhuijzen PM, Hane J, Williams A, O'Lone CE, Fosu-Nyarko J, Scobie M, Cakir M, Jones MG, Bellgard M, Ksiazkiewicz M, Wolko B, Barker SJ, Oliver RP, Cowling WA. (2006) The first gene-based map of Lupinus angustifolius L.- location of domestication genes and conserved synteny with Medicago truncatula. Theor Appl Genet 113: 225-238.
• Nelson MN, Moolhuijzen PM, Boersma JG, Chudy M, Lesniewska K, Bellgard M, Oliver RP, Swiecicki W, Wolko B, Cowling WA, Ellwood SR. (2010) Aligning a new reference genetic map of Lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus. DNA Res 17: 73-83.
• Palais RA, Liew MA, Wittwer CT (2005) Quantitative heteroduplex analysis for single nucleotide polymorphism genotyping. Anal Biochem 346: 167-175.
• Reed GH, Wittwer CT (2004) Sensitivity and specificity of single-nucleotide polymorphism scanning by high-resolution melting analysis. Clin Chem 50: 1748-1754.
• Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3 - new capabilities and interfaces. Nucleic Acids Res 40: e115.
• Voorrips R (2002) MapChart: Software for the graphical presentation of linkage maps and QTLs. J Hered 93: 77-78.
• Wu SB, Wirthensohn MG, Hunt P, Gibson JP, Sedgley M (2008) High resolution melting analysis of almond SNPs derived from ESTs. Theor Appl Genet 118: 1-14.
• Yang H, Tao Y, Zheng Z, Zhang Q, Zhou G, Sweetingham MW, Howieson JG, Li C (2013) Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L. PLoS One 8: e64799.

Identifiers

DOI

10.18388/abp.2015_977