Towards an optimal sampling strategy for assessing genetic variation within and among white clover (Trifolium repens L.) cultivars using AFLP

Khosro Mehdi Khanlou,Erik Van Bockstaele,Leila Kheibarshekan Asl,Katrien Vandepitte

doi:10.1590/s1415-47572011000200015

Khosro Mehdi Khanlou, Erik Van Bockstaele + Show 2 more

Open Access

https://doi.org/10.1590/s1415-47572011000200015

Copy DOI

Abstract

Cost reduction in plant breeding and conservation programs depends largely on correctly defining the minimal sample size required for the trustworthy assessment of intra- and inter-cultivar genetic variation. White clover, an important pasture legume, was chosen for studying this aspect. In clonal plants, such as the aforementioned, an appropriate sampling scheme eliminates the redundant analysis of identical genotypes. The aim was to define an optimal sampling strategy, i.e., the minimum sample size and appropriate sampling scheme for white clover cultivars, by using AFLP data (283 loci) from three popular types. A grid-based sampling scheme, with an interplant distance of at least 40 cm, was sufficient to avoid any excess in replicates. Simulations revealed that the number of samples substantially influenced genetic diversity parameters. When using less than 15 per cultivar, the expected heterozygosity (He) and Shannon diversity index (I) were greatly underestimated, whereas with 20, more than 95% of total intra-cultivar genetic variation was covered. Based on AMOVA, a 20-cultivar sample was apparently sufficient to accurately quantify individual genetic structuring. The recommended sampling strategy facilitates the efficient characterization of diversity in white clover, for both conservation and exploitation.

Highlights

The characterization of genetic variation, and its partitioning within and among populations, is important for plant breeding and conservation research focused on the management of genetic resources (Herrmann et al, 2005; Nybom and Bartish, 2000)
Molecular marker techniques have come to offer an attractive alternative to such a limited scope (Kölliker et al, 2001), through facilitating the rapid estimation of genome-wide intra- and inter-cultivar genetic variation at the DNA level
Proved to be the most suitable for assessing intra-species diversity (Bonin et al, 2007). It has been successfully applied for determining genetic diversity in a multitude of legume forages including red clover (Trifolium pratense L.; Herrmann et al, 2005), alfalfa (Medicago sativa L.; Segovia-Lerma et al, 2003), bird's foot trefoil (Lotus corniculatus L.; Sardaro et al, 2008), sulla (Hedysarium coronarium L.; Marghali et al, 2005), and white clover (Trifolium repens L.; Kölliker et al, 2001)

Summary

Introduction

The characterization of genetic variation, and its partitioning within and among populations, is important for plant breeding and conservation research focused on the management of genetic resources (Herrmann et al, 2005; Nybom and Bartish, 2000). Among the variety of molecular marker techniques available, the amplified fragment length polymorphism (AFLP) technique, first described by Vos et al (1995), has proved to be the most suitable for assessing intra-species diversity (Bonin et al, 2007) It has been successfully applied for determining genetic diversity in a multitude of legume forages including red clover (Trifolium pratense L.; Herrmann et al, 2005), alfalfa (Medicago sativa L.; Segovia-Lerma et al, 2003), bird's foot trefoil (Lotus corniculatus L.; Sardaro et al, 2008), sulla (Hedysarium coronarium L.; Marghali et al, 2005), and white clover (Trifolium repens L.; Kölliker et al, 2001). The cost of using AFLP genetic markers depends greatly on the number of samples to be analyzed

Methods

Results

Conclusion