Molecular diversity, population structure, and linkage disequilibrium in a worldwide collection of tobacco (Nicotiana tabacum L.) germplasm

BMC Genetics

Research Article

Marcello Del Corvo¹  Pietro Piffanelli¹  Alessandra Stella¹  Agostino Fricano²  Paolo Donini³  Nikolai V Ivanov³  Nicolas Bakaher³  Carlo Pozzi⁴ 

[1] Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, 26900, Lodi, Italy;Parco Tecnologico Padano, via Einstein, Loc. C.na Codazza, 26900, Lodi, Italy;Bayer CropScience, Technologiepark 38, 9052, Zwijnaarde, Belgium;Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland;Philip Morris International R&D, Philip Morris Products SA, Quai Jeanrenaud 5, 2000, Neuchâtel, Switzerland;Fondazione Edmund Mach, 38010, San Michele all'Adige, TN, Italy;

关键词: Linkage Disequilibrium;    Simple Sequence Repeat Marker;    Core Collection;    Simple Sequence Repeat Locus;    Significant Linkage Disequilibrium;   

DOI  :  10.1186/1471-2156-13-18

 received in 2011-05-13, accepted in 2012-03-21,  发布年份 2012

来源: Springer

【 摘 要 】

BackgroundThe goals of our study were to assess the phylogeny and the population structure of tobacco accessions representing a wide range of genetic diversity; identify a subset of accessions as a core collection capturing most of the existing genetic diversity; and estimate, in the tobacco core collection, the extent of linkage disequilibrium (LD) in seven genomic regions using simple sequence repeat (SSR) markers. To this end, a collection of accessions were genotyped with SSR markers. Molecular diversity was evaluated and LD was analyzed across seven regions of the genome.ResultsA genotyping database for 312 tobacco accessions was profiled with 49 SSR markers. Principal Coordinate Analysis (PCoA) and Bayesian cluster analysis revealed structuring of the tobacco population with regard to commercial classes and six main clades were identified, which correspond to "Oriental", Flue-Cured", "Burley", "Dark", "Primitive", and "Other" classes. Pairwise kinship was calculated between accessions, and an overall low level of co-ancestry was observed. A set of 89 genotypes was identified that captured the whole genetic diversity detected at the 49 loci. LD was evaluated on these genotypes, using 422 SSR markers mapping on seven linkage groups. LD was estimated as squared correlation of allele frequencies (r2). The pattern of intrachromosomal LD revealed that in tobacco LD extended up to distances as great as 75 cM with r2 > 0.05 or up to 1 cM with r2 > 0.2. The pattern of LD was clearly dependent on the population structure.ConclusionsA global population of tobacco is highly structured. Clustering highlights the accessions with the same market class. LD in tobacco extends up to 75 cM and is strongly dependent on the population structure.

【 授权许可】

Unknown   
© Fricano et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.