Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)

Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) are increasingly used for cultivar identification, construction of genetic maps, genetic diversity assessment, association mapping and marker-assisted breeding. Although there are several highly sensitive methods for the detect...

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Autores principales: Fusari, Corina Mariana, Lia, Verónica Viviana, Puebla, Andrea Fabiana, Hopp, Horacio Esteban, Heinz, Ruth Amelia
Publicado: 2011
Materias:
CEL1
dHPLC
Heteroduplex analysis
High-throughput genotyping
SNPs
Sunflower
Animalia
Apium graveolens
Apium graveolens var. dulce
Helianthus
Helianthus annuus
Acceso en línea:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13803743_v28_n1_p73_Fusari
http://hdl.handle.net/20.500.12110/paper_13803743_v28_n1_p73_Fusari
Aporte de:
Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA) de Universidad de Buenos Aires
id paper:paper_13803743_v28_n1_p73_Fusari
record_format dspace
spelling paper:paper_13803743_v28_n1_p73_Fusari2023-06-08T16:12:16Z Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.) Fusari, Corina Mariana Lia, Verónica Viviana Puebla, Andrea Fabiana Hopp, Horacio Esteban Heinz, Ruth Amelia CEL1 dHPLC Heteroduplex analysis High-throughput genotyping SNPs Sunflower Animalia Apium graveolens Apium graveolens var. dulce Helianthus Helianthus annuus Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) are increasingly used for cultivar identification, construction of genetic maps, genetic diversity assessment, association mapping and marker-assisted breeding. Although there are several highly sensitive methods for the detection of polymorphisms, most of them are often beyond the budget of medium-throughput academic laboratories or seed companies. Heteroduplex analysis by enzymatic cleavage (CEL1CH) or denaturing high-performance liquid chromatography (dHPLC) has been successfully used to examine genetic variation in several plant and animal species. In this work, we assess and compare the performance of both methods in sunflower by genotyping SNPs from a set of 24 selected polymorphic candidate genes. The CEL1CH method allowed us to accurately detect allele differences in 10 out of 24 regions using an in-house prepared CEL1 enzyme (celery single strand endonuclease 1, Apium graveolens L.). Similarly, a total of 11 regions were successfully optimized for dHPLC analysis. As a scaling-up approach, both strategies were tested to genotype either 42 SNPs/indels in 22 sunflower accessions from the local germplasm bank or 33 SNPs/indels in 90 recombinant inbred lines (RILs) for genetic mapping purposes. Summarizing, a total of 601 genotypes were efficiently analyzed either with CEL1CH (110) or dHPCL (491). In conclusion, CEL1CH and dHPLC proved to be robust, complementary methods, allowing medium-scale laboratories to scale up the number of both SNPs and individuals to be included in genetic studies and targeted germplasm diversity characterization (EcoTILLING). © 2010 Springer Science+Business Media B.V. Fil:Fusari, C.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Lia, V.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Puebla, A.F. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Hopp, H.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Heinz, R.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. 2011 https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13803743_v28_n1_p73_Fusari http://hdl.handle.net/20.500.12110/paper_13803743_v28_n1_p73_Fusari
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-134
collection Biblioteca Digital - Facultad de Ciencias Exactas y Naturales (UBA)
topic CEL1
dHPLC
Heteroduplex analysis
High-throughput genotyping
SNPs
Sunflower
Animalia
Apium graveolens
Apium graveolens var. dulce
Helianthus
Helianthus annuus
spellingShingle CEL1
dHPLC
Heteroduplex analysis
High-throughput genotyping
SNPs
Sunflower
Animalia
Apium graveolens
Apium graveolens var. dulce
Helianthus
Helianthus annuus
Fusari, Corina Mariana
Lia, Verónica Viviana
Puebla, Andrea Fabiana
Hopp, Horacio Esteban
Heinz, Ruth Amelia
Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)
topic_facet CEL1
dHPLC
Heteroduplex analysis
High-throughput genotyping
SNPs
Sunflower
Animalia
Apium graveolens
Apium graveolens var. dulce
Helianthus
Helianthus annuus
description Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) are increasingly used for cultivar identification, construction of genetic maps, genetic diversity assessment, association mapping and marker-assisted breeding. Although there are several highly sensitive methods for the detection of polymorphisms, most of them are often beyond the budget of medium-throughput academic laboratories or seed companies. Heteroduplex analysis by enzymatic cleavage (CEL1CH) or denaturing high-performance liquid chromatography (dHPLC) has been successfully used to examine genetic variation in several plant and animal species. In this work, we assess and compare the performance of both methods in sunflower by genotyping SNPs from a set of 24 selected polymorphic candidate genes. The CEL1CH method allowed us to accurately detect allele differences in 10 out of 24 regions using an in-house prepared CEL1 enzyme (celery single strand endonuclease 1, Apium graveolens L.). Similarly, a total of 11 regions were successfully optimized for dHPLC analysis. As a scaling-up approach, both strategies were tested to genotype either 42 SNPs/indels in 22 sunflower accessions from the local germplasm bank or 33 SNPs/indels in 90 recombinant inbred lines (RILs) for genetic mapping purposes. Summarizing, a total of 601 genotypes were efficiently analyzed either with CEL1CH (110) or dHPCL (491). In conclusion, CEL1CH and dHPLC proved to be robust, complementary methods, allowing medium-scale laboratories to scale up the number of both SNPs and individuals to be included in genetic studies and targeted germplasm diversity characterization (EcoTILLING). © 2010 Springer Science+Business Media B.V.
author Fusari, Corina Mariana
Lia, Verónica Viviana
Puebla, Andrea Fabiana
Hopp, Horacio Esteban
Heinz, Ruth Amelia
author_facet Fusari, Corina Mariana
Lia, Verónica Viviana
Puebla, Andrea Fabiana
Hopp, Horacio Esteban
Heinz, Ruth Amelia
author_sort Fusari, Corina Mariana
title Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)
title_short Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)
title_full Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)
title_fullStr Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)
title_full_unstemmed Single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (Helianthus annuus L.)
title_sort single nucleotide polymorphism genotyping by heteroduplex analysis in sunflower (helianthus annuus l.)
publishDate 2011
url https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_13803743_v28_n1_p73_Fusari
http://hdl.handle.net/20.500.12110/paper_13803743_v28_n1_p73_Fusari
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