Selective Loss of Diversity in Doubled-Haploid Lines from European Maize Landraces

Abstract

<jats:p>Maize landraces are well adapted to their local environments and present valuable sources of genetic diversity for breeding and conservation. But the maintenance of open-pollinated landraces in <jats:italic>ex-situ</jats:italic> programs is challenging, as regeneration of seed can often lead to inbreeding depression and the loss of diversity due to genetic drift. Recent reports suggest that the production of doubled-haploid (DH) lines from landraces may serve as a convenient means to preserve genetic diversity in a homozygous form that is immediately useful for modern breeding. The production of doubled-haploid (DH) lines presents an extreme case of inbreeding which results in instantaneous homozygosity genome-wide. Here, we analyzed the effect of DH production on genetic diversity, using genome-wide SNP data from hundreds of individuals of five European landraces and their related DH lines. In contrast to previous findings, we observe a dramatic loss of diversity at both the haplotype level and that of individual SNPs. We identify thousands of SNPs that exhibit allele frequency differences larger than expected under models of neutral genetic drift and document losses of shared haplotypes. We find evidence consistent with selection at functional sites that are potentially involved in the diversity differences between landrace and DH populations. Although we were unable to uncover more details about the mode of selection, we conclude that landrace DH lines may be a valuable tool for the introduction of variation into maize breeding programs but come at the cost of decreased genetic diversity.</jats:p>

Comparison between doubled haploid lines and lines obtained via the bulk method in tobacco

“…The authors stated that obtaining the DHL did not result in systematic directional selection in specific genomic regions. However, using the same genomic data, Zeitler et al (2020) obtained contradictory results; that is, there was a restriction in the variability when was used.…”

“…There are no reports in the literature on whether the constitution of DHL differs from that of lines obtained using conventional inbreeding methods. Melchinger et al (2017) evaluated DHL with single-nucleotide polymorphism (SNP) markers on corn and did not detect any restriction in its genetic variability, whereas Zeitler et al (2020) used the same genomic data to observe losses in DH variability. In some crops, such as triticale, barley, and corn, the performance of the lines obtained via DH and a conventional method, was not similar (Charmet and Branlard 1985, Bjornstad et al 1992, Ma et al 1999).…”

Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next‐generation varieties

“…It is important to note that our line panel included many old lines that have made only a limited contribution, if any, to commercial F1 hybrids or recent breeding pools. Our panel therefore certainly overestimates the genetic diversity present in the germplasm of modern breeding inbred lines (Zeitler et al ., 2020).…”

“…Furthermore, SNPs from 50 K arrays were previously identified in 27 lines (Gore et al ., 2009). These SNPs may not reflect well the total genetic diversity of landraces, as certain specific landrace haplotypes may not have been transmitted to first cycle lines due to their deleterious effect at the homozygous state (inbreeding depression) or gamete sampling (drift) (Zeitler et al ., 2020).…”

Androgenesis-Based Doubled Haploidy: Past, Present, and Future Perspectives

“…Due to the low population structure and rapid decrease of linkage disequilibrium within populations of DH lines landraces, these would be an ideal tool for association mapping. However, Zeitler et al (2020) reported that landrace DH lines may result in a decreased genetic diversity.…”