Safeguarding Our Genetic Resources with Libraries of Doubled-Haploid Lines

Abstract

Thousands of landraces are stored in seed banks as "gold reserves" for future use in plant breeding. In many crops, their utilization is hampered because they represent heterogeneous populations of heterozygous genotypes, which harbor a high genetic load. We show, with high-density genotyping in five landraces of maize, that libraries of doubled-haploid (DH) lines capture the allelic diversity of genetic resources in an unbiased way. By comparing allelic differentiation between heterozygous plants from the original landraces and 266 derived DH lines, we find conclusive evidence that, in the DH production process, sampling of alleles is random across the entire allele frequency spectrum, and purging of landraces from their genetic load does not act on specific genomic regions. Based on overall process efficiency, we show that generating DH lines is feasible for genetic material that has never been selected for inbreeding tolerance. We conclude that libraries of DH lines will make genetic resources accessible to crop improvement by linking molecular inventories of seed banks with meaningful phenotypes.

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

“…In some cases, we found segregating SNPs in the DH lines that were monomorphic in the respective LR population, suggesting that the frequency of the minor allele in the ancestral population must have been low and was not sampled in the genotyped set of LR individuals. Comparison of our jSFS with results from Melchinger et al (2017) reveals striking differences ( Figure S5B), as these authors appear to have filtered out a substantial proportion of alleles at low frequency in one or both populations, removing much of the observed signal of allele frequency change.…”

“…We used genomic data of five European maize landraces and their derived DH lines to study the effect of instantaneous homozygosity. For the landrace derived DH lines (DH) we used data from Melchinger et al (2017) from a total of n = 266 individuals genotyped on the Illumina MaizeSNP50 BeadChip (Ganal et al 2011). 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.…”

“…Using a set of genotyped SNPs (the 50k dataset, see Methods) from Melchinger et al (2017), we compared per-site nucleotide diversity (π) in individual accessions (LR-DH pairs). We found that average π is significantly different between the LR and DH (two-sided Mann-Whitney-Wilcoxon p < 1 × 10 −6 for all comparisons).…”

“…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).…”

“…The technology permits the instantaneous development of homozygous lines within a single generation instead of six to ten generations of conventional recurrent self-pollination . While not all landraces produce DH lines with equal successt, Melchinger et al (2017) concluded that genetically stable DH line libraries of landrace accessions could be used for ex-situ conservation of maize without major loss in genetic diversity.…”