Analysis of single nucleotide polymorphism and simple sequence repeat markers for the estimates of genetic diversity by using two oilseed Brassica napus populations carrying genome contents of Brassica oleracea

Publication: Canadian Journal of Plant Science
27 January 2022

Abstract

Reliable estimates of genetic diversity among the accessions in a breeding population is important knowledge for use in breeding. Among the different types of molecular markers, single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) are largely used by breeders; however, our knowledge of the reliability of the estimates of genetic diversity based on these two types of markers in multiple populations is limited. In this study, a doubled haploid (DH) and an inbred population developed from Brassica napus × Brassica oleracea interspecific crosses were used for comparative analysis of these two types of markers. The estimates based on SNP and SSR markers showed a stronger correlation in the inbred population which was expected to carry greater genetic diversity as compared to the DH population. This inference was also evident from the analysis of different diversity groups (least, intermediate, and most similar) of these two populations for significant difference between the groups for six agronomic and seed quality traits, where this analysis failed to differentiate the diversity groups of the DH population for any of the traits. However, both marker types could differentiate the diversity groups of the inbred population for several traits. Furthermore, the six sub-populations of the inbred population could also be differentiated by both marker types. Thus, the results demonstrate the greater utility of the SSR and SNP markers in a genetically diverse population. This knowledge can be used while grouping a breeding population for diversity groups; however, caution needs to be taken while using the markers in a genetically narrow population.

Résumé

Pour mieux exploiter la diversité génétique (DG) des obtentions dans une population utilisée pour l’hybridation, il faut pouvoir l’estimer. Parmi les différentes sortes de marqueurs moléculaires, les obtenteurs recourent souvent au polymorphisme mononucélotidique (SNP) et aux microsatellites (SSR). Cependant, on ignore dans quelle mesure les estimations de la DG reposant sur ces deux types de marqueurs sont fiables dans les populations multiples. Les auteurs ont utilisé une population d’haploïdes doubles (HD) et une population autogame de croisements interspécifiques entre Brassica napus et Brassica oleracea pour comparer les deux sortes de marqueurs. Les estimations fondées sur les marqueurs SNP et SSR sont fortement corrélées dans la population autogame, qui devrait présenter une plus grande DG que la population HD. La même inférence est évidente quand on analyse les groupes de diversité (spécimens les moins, modérément et les plus semblables) des deux populations, en quête de variations significatives entre les groupes pour six paramètres agronomiques ou relatifs à la qualité de la graine. L’analyse n’a cependant pas permis d’effectuer la distinction entre les groupes de diversité dans la population HD, peu importe le caractère. Les deux types de marqueurs permettent néanmoins de différencier ces groupes pour plusieurs caractères dans la population autogame. Selon ces résultats, les marqueurs SSR et SNP sont plus utiles avec une population génétiquement diversifiée. Sachant cela, on pourrait séparer une population destinée à l’hybridation par groupes de diversité. Quand la population se compose d’éléments génétiquement très voisins, on devra cependant faire preuve de prudence lors de l’usage de ces marqueurs. [Traduit par la Rédaction]

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Information & Authors

Information

Published In

cover image Canadian Journal of Plant Science
Canadian Journal of Plant Science
Volume 102Number 3June 2022
Pages: 679 - 689
Editor: Brian Beres

History

Received: 20 September 2021
Accepted: 23 January 2022
Published online: 27 January 2022

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Key Words

  1. genetic diversity
  2. doubled haploid
  3. inbred population
  4. B. napus × B. oleracea
  5. single nucleotide polymorphism
  6. simple sequence repeat
  7. Marker efficiency

Mots-clés

  1. diversité génétique
  2. double haploïdie
  3. population autogame
  4. B. napus × B. oleracea
  5. polymorphisme mononucélotidique
  6. microsatellites
  7. efficacité des marqueurs

Authors

Affiliations

Junye Jiang
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
Berisso Kebede
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada

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