Is there an optimum level of diversity in utilization of genetic resources?

Abstract

Key message Capitalizing upon the genomic characteristics of long-term random mating populations, sampling from pre-selected landraces is a promising approach for broadening the genetic base of elite germplasm for quantitative traits. AbstractGenome-enabled strategies for harnessing untapped allelic variation of landraces are currently evolving. The success of such approaches depends on the choice of source material. Thus, the analysis of different strategies for sampling allelic variation from landraces and their impact on population diversity and linkage disequilibrium (LD) is required to ensure the efficient utilization of diversity. We investigated the impact of different sampling strategies on diversity parameters and LD based on high-density genotypic data of 35 European maize landraces each represented by more than 20 individuals. On average, five landraces already captured ~95% of the molecular diversity of the entire dataset. Within landraces, absence of pronounced population structure, consistency of linkage phases and moderate to low LD levels were found. When combining data of up to 10 landraces, LD decay distances decreased to a few kilobases. Genotyping 24 individuals per landrace with 5k SNPs was sufficient for obtaining representative estimates of diversity and LD levels to allow an informed pre-selection of landraces. Integrating results from European with Central and South American landraces revealed that European landraces represent a unique and diverse spectrum of allelic variation. Sampling strategies for harnessing allelic variation from landraces depend on the study objectives. If the focus lies on the improvement of elite germplasm for quantitative traits, we recommend sampling from pre-selected landraces, as it yields a wide range of diversity, allows optimal marker imputation, control for population structure and avoids the confounding effects of strong adaptive alleles.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-017-2959-4) contains supplementary material, which is available to authorized users.

Transcriptomic diversity in seedling roots of European flint maize in response to cold

“…We selected 21 doubled haploid (DH) lines from 276 genotypes of a DH population of the flint landrace 'Petkuser Ferdinand rot' [27,53] based on seed availability. This population was generated by the in vivo haploid induction method [54].…”

Selective loss of diversity in doubled-haploid lines from European maize landraces

“…The genotypes were derived from five accessions: Bugard (BU, n = 36) from France, Gelber Badischer (GB, n = 59), Schindelmeiser (SC, n = 58) and Strenzfelder (SF, n = 69) from Germany, and Rheinthaler (RT, n = 44) from Switzerland. For the landrace population samples (LR) of the same accessions, we used data of n = 137 individuals (n = 22, n = 46, n = 23, n = 23, n = 23, respectively) from Mayer et al (2017), genotyped on the 600k Affymetrix Axiom Maize Genotyping Array (Unterseer et al 2014 , Table S1). After combining the two datasets based on physical positions (AGPv2), we removed SNPs that were monomorphic across all accessions in the LR and DH.…”

“…After combining the two datasets based on physical positions (AGPv2), we removed SNPs that were monomorphic across all accessions in the LR and DH. For all further analyses, we then used updated positions (AGPv4) for the SNPs obtained from supplementary data in Mayer et al (2017). We also removed SNPs that violated Hardy-Weinberg equilibrium in all LR accessions in exact tests with mid-p adjusted p > 0.05, as well as low quality SNPs that matched the quality criteria 'off-target variant', 'CallRate-BelowThreshold' and insertion-type SNPs of the Affymetrix Axiom 600k genotyping chip (classifications followed Table S6 in Unterseer et al (2014); for details see Table S2), removing a total of 83,011 SNPs.…”

“…Conservation of germplasm exsitu provides straightforward and safe long-term access to plant breeders, but genebank accessions have to be maintained as large populations to prevent the loss of diversity due to drift (Ellstrand and Elam 1993). haploid (DH) technology as a means of conserving landrace diversity in a homozygous form that would simplify germplasm conservation and be more readily usable by plant breeders (Sood et al 2014;Gorjanc et al 2016;Melchinger et al 2017;Mayer et al 2017). The directed induction of DH lines has been developed for several crops to accelerate breeding (Smith et al 2008;Gomez-Pando et al 2009;Dunwell 2010).…”

“…We quantify the changes in genetic diversity due to DH production and investigate the role of drift and selection in creating the observed patterns. Combining published genotype and phenotype data from a number of sources Mayer et al 2017;Brauner et al 2018), we analyze and compare samples from five populations of European maize landrace accessions and their derived DH lines. In contrast to previous reports , we find that landrace genetic diversity is not fully captured by DH line libraries.…”