Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat Triticum aestivum L. as examplesReport as inadecuate




Development of genome-specific primers for homoeologous genes in allopolyploid species: the waxy and starch synthase II genes in allohexaploid wheat Triticum aestivum L. as examples - Download this document for free, or read online. Document in PDF available to download.

BMC Research Notes

, 3:140

First Online: 24 May 2010Received: 12 May 2010Accepted: 24 May 2010DOI: 10.1186-1756-0500-3-140

Cite this article as: Huang, XQ. & Brûlé-Babel, A. BMC Res Notes 2010 3: 140. doi:10.1186-1756-0500-3-140

Abstract

BackgroundIn allopolypoid crops, homoeologous genes in different genomes exhibit a very high sequence similarity, especially in the coding regions of genes. This makes it difficult to design genome-specific primers to amplify individual genes from different genomes. Development of genome-specific primers for agronomically important genes in allopolypoid crops is very important and useful not only for the study of sequence diversity and association mapping of genes in natural populations, but also for the development of gene-based functional markers for marker-assisted breeding. Here we report on a useful approach for the development of genome-specific primers in allohexaploid wheat.

FindingsIn the present study, three genome-specific primer sets for the waxy Wx genes and four genome-specific primer sets for the starch synthase II SSII genes were developed mainly from single nucleotide polymorphisms SNPs and-or insertions or deletions Indels in introns and intron-exon junctions. The size of a single PCR product ranged from 750 bp to 1657 bp. The total length of amplified PCR products by these genome-specific primer sets accounted for 72.6%-87.0% of the Wx genes and 59.5%-61.6% of the SSII genes. Five genome-specific primer sets for the Wx genes one for Wx-7A, three for Wx-4A and one for Wx-7D could distinguish the wild type wheat and partial waxy wheat lines. These genome-specific primer sets for the Wx and SSII genes produced amplifications in hexaploid wheat, cultivated durum wheat, and Aegilops tauschii accessions, but failed to generate amplification in the majority of wild diploid and tetraploid accessions.

ConclusionsFor the first time, we report on the development of genome-specific primers from three homoeologous Wx and SSII genes covering the majority of the genes in allohexaploid wheat. These genome-specific primers are being used for the study of sequence diversity and association mapping of the three homoeologous Wx and SSII genes in natural populations of both hexaploid wheat and cultivated tetraploid wheat. The strategies used in this paper can be used to develop genome-specific primers for homoeologous genes in any allopolypoid species. They may be also suitable for i the development of gene-specific primers for duplicated paralogous genes in any diploid species, and ii the development of allele-specific primers at the same gene locus.

AbbreviationsAGPADP-glucose pyrophosphorylase

BACbacterial artificial chromosome

CSChinese Spring

dNTPdeoxyribonucleotide triphosphate

GBSSgranule-bound starch synthase

Indelinsertion or deletion

LMW-GSlow molecular weight glutenin subunit

NTnulli-tetrasomic

PCRpolymerase chain reaction

SBEstarch branching enzymes

SGPstarch granule protein

SNPsingle nucleotide polymorphism

SSstarch synthases

TBEtris borate EDTA

Tmmelting temperature

WxWaxy.

Electronic supplementary materialThe online version of this article doi:10.1186-1756-0500-3-140 contains supplementary material, which is available to authorized users.

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Author: Xiu-Qiang Huang - Anita Brûlé-Babel

Source: https://link.springer.com/







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