Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes

Background ADP-glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme catalyzing the first step in the starch biosynthesis pathway in higher plants. To date, there are no reported variants or isoforms of the AGPase enzyme in bananas (Musa spp. family Musaceae) as is the case of other plants. I...

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Autores principales:	Mahendhiran,Muhilan, Ramirez-Prado,Jorge Humberto, Escobedo-Gracia Medrano,Rosa Maria, Canto-Canché,Blondy, Tzec-Simá,Miguel, Grijalva-Arango,Rosa, James-Kay,Andrew
Lenguaje:	English
Publicado:	Pontificia Universidad Católica de Valparaíso 2014
Materias:	Haplotypes Starch metabolism enzyme Variants
Acceso en línea:	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000300006
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spelling	oai:scielo:S0717-345820140003000062014-08-18Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypesMahendhiran,MuhilanRamirez-Prado,Jorge HumbertoEscobedo-Gracia Medrano,Rosa MariaCanto-Canché,BlondyTzec-Simá,MiguelGrijalva-Arango,RosaJames-Kay,Andrew Haplotypes Starch metabolism enzyme Variants Background ADP-glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme catalyzing the first step in the starch biosynthesis pathway in higher plants. To date, there are no reported variants or isoforms of the AGPase enzyme in bananas (Musa spp. family Musaceae) as is the case of other plants. In this study, genomic DNA sequences homologous to the gene encoding one of the large subunits of the enzyme were amplified from 10 accessions of the genus Musa, including representatives of wild ancestors (AA and BB genomes), dessert bananas (AA, AAA, AB and AAB genomes), plantains (AAB genome) and cooking bananas (ABB and AAA genomes), and studied in order to find single nucleotide polymorphisms (SNP) base variations in Musa accessions. Results In the 810-base pair amplicons of the AGPase large sub-unit (LSU) gene analyzed in ten Musa accessions, a total of 36 SNPs and insertions/deletions (indels) were found. The phylogenetic analysis revealed fifteen distinct haplotypes, which were grouped into four variants. Deep examination of SNPs in the 2nd exon in the LSU of AGPase showed that at seven locations, five SNPs altered their amino acid sequence. Conclusions This work reveals the possible number of AGPase enzyme isoforms and their molecular levels in banana. Molecular markers could be designed from SNPs present in these banana accessions. This information could be useful for the development of SNP-based molecular markers for Musa germplasm, and alteration of the allosteric properties of AGPase to increase the starch content and manipulate the starch quality of banana fruits.info:eu-repo/semantics/openAccessPontificia Universidad Católica de ValparaísoElectronic Journal of Biotechnology v.17 n.3 20142014-05-01text/htmlhttp://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000300006en10.1016/j.ejbt.2014.04.004
institution	Scielo Chile
collection	Scielo Chile
language	English
topic	Haplotypes Starch metabolism enzyme Variants
spellingShingle	Haplotypes Starch metabolism enzyme Variants Mahendhiran,Muhilan Ramirez-Prado,Jorge Humberto Escobedo-Gracia Medrano,Rosa Maria Canto-Canché,Blondy Tzec-Simá,Miguel Grijalva-Arango,Rosa James-Kay,Andrew Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes
description	Background ADP-glucose pyrophosphorylase (AGPase) is a rate-limiting enzyme catalyzing the first step in the starch biosynthesis pathway in higher plants. To date, there are no reported variants or isoforms of the AGPase enzyme in bananas (Musa spp. family Musaceae) as is the case of other plants. In this study, genomic DNA sequences homologous to the gene encoding one of the large subunits of the enzyme were amplified from 10 accessions of the genus Musa, including representatives of wild ancestors (AA and BB genomes), dessert bananas (AA, AAA, AB and AAB genomes), plantains (AAB genome) and cooking bananas (ABB and AAA genomes), and studied in order to find single nucleotide polymorphisms (SNP) base variations in Musa accessions. Results In the 810-base pair amplicons of the AGPase large sub-unit (LSU) gene analyzed in ten Musa accessions, a total of 36 SNPs and insertions/deletions (indels) were found. The phylogenetic analysis revealed fifteen distinct haplotypes, which were grouped into four variants. Deep examination of SNPs in the 2nd exon in the LSU of AGPase showed that at seven locations, five SNPs altered their amino acid sequence. Conclusions This work reveals the possible number of AGPase enzyme isoforms and their molecular levels in banana. Molecular markers could be designed from SNPs present in these banana accessions. This information could be useful for the development of SNP-based molecular markers for Musa germplasm, and alteration of the allosteric properties of AGPase to increase the starch content and manipulate the starch quality of banana fruits.
author	Mahendhiran,Muhilan Ramirez-Prado,Jorge Humberto Escobedo-Gracia Medrano,Rosa Maria Canto-Canché,Blondy Tzec-Simá,Miguel Grijalva-Arango,Rosa James-Kay,Andrew
author_facet	Mahendhiran,Muhilan Ramirez-Prado,Jorge Humberto Escobedo-Gracia Medrano,Rosa Maria Canto-Canché,Blondy Tzec-Simá,Miguel Grijalva-Arango,Rosa James-Kay,Andrew
author_sort	Mahendhiran,Muhilan
title	Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes
title_short	Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes
title_full	Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes
title_fullStr	Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes
title_full_unstemmed	Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes
title_sort	single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of adp-glucose pyrophosphorylase within a representative collection of 10 musa genotypes
publisher	Pontificia Universidad Católica de Valparaíso
publishDate	2014
url	http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582014000300006
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Single nucleotide polymorphisms in partial sequences of the gene encoding the large sub-units of ADP-glucose pyrophosphorylase within a representative collection of 10 Musa genotypes

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