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.

Keywords: allelic diversity; genetic load; haploidy linkage disequilibrium; maize.

Figure 1

(A, B) Neighbor-joining tree constructed from Rogers’ distances for five European maize landraces (BU, GB, RT, SC, and SF) based on 28,133 polymorphic SNPs.

Figure 2

(A) F_ST statistic for evaluating genetic differentiation between the original landrace (S₀ generation), and the population of DH lines (D₁ generation) derived from it, averaged across all markers in a sliding window of 10 Mb width along the chromosomes for five European maize landraces (BU, GB, RT, SC, and SF). (B) Bins with significant F_ST statistics based on a permutation test (see Materials and Methods and Supplemental Notes in File S1). The heat map at the bottom, calculated based on the 28,133 SNPs analyzed, indicates the marker density within the windows (Mb⁻¹). Centromeres are indicated by gray vertical lines.

Figure 3

(A, B) LD in each generation vs. the physical distance between linked markers for five European maize landraces (BU, GB, RT, SC, and SF) calculated based on 28,133 polymorphic SNPs. The r² values for marker pairs were binned according to their physical distance, each bin corresponding to an interval of 0.05 Mb width.

Figure 4

Gene diversity (H_S) in random samples of n_DH DH lines (D₁ generation) relative to H_S in the original landrace (S₀ generation) for five European flint maize landraces (BU, GB, RT, SC, and SF) determined for 28,133 SNPs.