Estimation of parental genome contributions among doubled haploid maize lines derived from six backcross populations.
Abstract
Doubled haploid (DH) lines have increasingly been used in maize research and breeding
due to substantial progress in the in vivo haploid induction technology and the
availability of a dominant anthocyanin marker gene for haploid identification. Although
DH lines are supposed to be genetically pure, preliminary field observation indicated
some level of non-uniform plant characteristics within seed lot of some DH lines.
Molecular characterization of the DH lines and estimating their parental genome
contributions would be useful for germplasm organization and choosing pairs of DH
lines for hybrid make up or new pedigree starts. Next generation genotyping by
sequencing (GBS) provides a low cost and high marker density platform for such
purposes. The objectives of the present study were, therefore, to i) understand the genetic
purity, genetic distance and relationship among 417 maize DH lines derived from 6 BC,
populations using GBS; ii) estimate the parental genome contributions to the genome of
the DH lines derived from different genetic backgrounds; and iii) check the correlation
between parental genome contributions and grain yield under drought and optimum
environments. A total of 97190 markers that were polymorphic across the 417 DH lines
were used for the genetic purity, genetic distance, and relationship analyses. The number
of polymorphic markers per chromosome varied from 5752 on chromosome 9 to 13643
on chromosome 1, with a mean of 9719. A smaller subset of 29074 markers, ranging
from 3724 to 6665 per population, was used for estimating parental genome
contributions. About 97% of the DH lines (404 out of 417) were genetically pure, with
<2% heterogeneity (the number of markers that were not homozygous due to admixture
or contamination). Only 2 DH lines showed heterogeneity >5%, which require further
purification. Genetic distance between pairwise comparisons of the 417 DH lines ranged
from 0.055 to 0.457 and only 13 out of 86,736 pairwise comparisons (0.02%) showed a
distance <0.100, which clearly suggests the presence of large genetic differences among
the DH lines. Both populations 1 and 6 showed significantly lower (p<0.001) donor
introgression than the other four populations. Donor parent contribution was
significantly(p <0.001) higher in the CML444 genetic background than both CML395
and CML488.The average donor and recurrent parent genome contributions across the
417 DH lines was 31.7% and 64.3%, respectively. About 82% of the DH lines showed
donor genome introgression higher than the expected 25% at BC, generation, which may
be due to artificial selection during the DH process (induction, genome doubling, and
seed increase), during the development of F, or BC, seeds, or during initial agronomic
evaluation of the DH lines. Donor parent introgression up to 32% showed significant
positive correlation with grain yield under drought (r=0.312, p <0.001) and optimum (r =
0.142, P <0.050) environments. Such correlation was not observed when donor parent
introgression exceeds 32%, which may be due to simultaneous transfer of undesirable
genes flanking the genes of interest from the donor parents. As the DH-derived hybrids
were evaluated for phenotypic performance only at one managed drought screening
environment, additional data may be needed to confirm the correlations reported in this
study and also map the specific quantitative trait loci (QTL) associated with drought
tolerance and hence grain yield.