BACKGROUND: Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. RESULTS: Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. CONCLUSIONS: The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids.
BACKGROUND: Genetic studies in allopolyploid plants are challenging because of the presence of similar sub-genomes, which leads to multiple alleles and complex segregation ratios. In this study, we describe a novel method for establishing the exact dose and configuration of microsatellite alleles for any accession of an allopolyploid plant species. The method, named Microsatellite Allele Dose and Configuration Establishment (MADCE), can be applied to mapping populations and pedigreed (breeding) germplasm in allopolyploids. RESULTS: Two case studies are presented to demonstrate the power and robustness of the MADCE method. In the mapping case, five microsatellites were analysed. These microsatellites amplified 35 different alleles based on size. Using MADCE, we uncovered 30 highly informative segregating alleles. A conventional approach would have yielded only 19 fully informative and six partially informative alleles. Of the ten alleles that were present in all progeny (and thereby ignored or considered homozygous when using conventional approaches), six were found to segregate by dosage when analysed with MADCE. Moreover, the full allelic configuration of the mapping parents could be established, including null alleles, homozygous loci, and alleles that were present on multiple homoeologues. In the second case, 21 pedigreed cultivars were analysed using MADCE, resulting in the establishment of the full allelic configuration for all 21 cultivars and a tracing of allele flow over multiple generations. CONCLUSIONS: The procedure described in this study (MADCE) enhances the efficiency and information content of mapping studies in allopolyploids. More importantly, it is the first technique to allow the determination of the full allelic configuration in pedigreed breeding germplasm from allopolyploid plants. This enables pedigree-based marker-trait association studies the use of algorithms developed for diploid crops, and it may increase the effectiveness of LD-based association studies. The MADCE method therefore enables researchers to tackle many of the genotyping problems that arise when performing mapping, pedigree, and association studies in allopolyploids. We discuss the merits of MADCE in comparison to other marker systems in polyploids, including SNPs, and how MADCE could aid in the development of SNP markers in allopolyploids.
Authors: D J Sargent; J Clarke; D W Simpson; K R Tobutt; P Arús; A Monfort; S Vilanova; B Denoyes-Rothan; M Rousseau; K M Folta; N V Bassil; N H Battey Journal: Theor Appl Genet Date: 2006-02-28 Impact factor: 5.699
Authors: C F S Koning-Boucoiran; V W Gitonga; Z Yan; O Dolstra; C G van der Linden; J van der Schoot; G E Uenk; K Verlinden; M J M Smulders; F A Krens; C Maliepaard Journal: Theor Appl Genet Date: 2012-04-12 Impact factor: 5.699
Authors: Jahn Davik; Daniel James Sargent; May Bente Brurberg; Sigbjørn Lien; Matthew Kent; Muath Alsheikh Journal: PLoS One Date: 2015-09-23 Impact factor: 3.240
Authors: Mirjana Vukosavljev; Paul Arens; Roeland E Voorrips; Wendy Pc van 't Westende; G D Esselink; Peter M Bourke; Peter Cox; W Eric van de Weg; Richard Gf Visser; Chris Maliepaard; Marinus Jm Smulders Journal: Hortic Res Date: 2016-10-26 Impact factor: 6.793
Authors: Thijs van Dijk; Giulia Pagliarani; Anna Pikunova; Yolanda Noordijk; Hulya Yilmaz-Temel; Bert Meulenbroek; Richard G F Visser; Eric van de Weg Journal: BMC Plant Biol Date: 2014-03-01 Impact factor: 4.215
Authors: Jill M Bushakra; Kim S Lewers; Margaret E Staton; Tetyana Zhebentyayeva; Christopher A Saski Journal: BMC Plant Biol Date: 2015-10-26 Impact factor: 4.215