Genomic & Doubled Haploid Technologies to Efficiently Exploit Maize Exotic Germplasm and Evaluate Impact on Seed Set
North Central Regional Plant Introduction Station, Ames, Iowa
Project Number: 3625-21000-059-04
Specific Cooperative Agreement
Start Date: Aug 01, 2014
End Date: Dec 31, 2016
For exotic germplasm to be useful, it must be adaptable so it can be utilized effectively by plant breeders, contribute novel alleles, and provide one or more alleles that confer superior trait performance compared to existing alleles in elite germplasm. While possible to efficiently evaluate allelic variation at the DNA sequence level, the main challenge remains phenotypic evaluation of exotic alleles, particularly of uncharacterized loci (in contrast to genes with known function). As exotic alleles are usually evaluated within the context of other exotic alleles in the same linkage block (linkage drag) or along with other exotic chromosomes or chromosome segments, beneficial phenotypic effects of superior alleles may be masked due to negative effects of other exotic alleles on the same phenotype. This is particularly true for complex agronomic traits such as grain yield. Exotic introgression lines may be eliminated prior to trait evaluation, due to linkage disequilibrium (LD) with genes reducing seed set. Efficient procedures are needed to unlock and capture unused allelic variation for breeding; seed set will serve as an important model trait in relation to introgression of exotic germplasm.
Hypothesis: There are few favorable alleles in exotic compared to elite germplasm for quantitatively inherited agronomic traits such as grain yield, and the majority of exotic alleles have neutral or negative effects. Due to large exotic introgression segments in early generations (such as BC1), the combined effect of exotic introgressions on complex inherited traits such as grain yield is most likely negative, and rare positive exotic alleles are likely masked. In contrast, reduced seed set may be caused by a limited number of major genes. Among available GEM-BC1-DH lines, about 1/3 displayed severe fertility issues. If caused by few major genes, BC3-derived sublines from GEM-BC1-DH with normal seed set should be identified. Evaluation procedures are critical, and evaluation of introgression materials with smaller exotic chromosome segments is required to reveal favorable alleles.
Specific Objectives: (1) apply genotype-by-sequencing (GBS) data to a panel of 283 doubled haploid GEM (GEM-BC1-DH) lines to evaluate (a) the extent of allelic variation and (b) the impact of the DH process on the distribution of exotic donor segment introgression; and (2) the impact of linkage drag on evaluation of GEM lines (using BC1 versus BC3 derived GEM lines), in particular caused by genes reducing seed set.
ARS genotyped 360 GEM-BC1-DH lines using SNPs. The genomic composition of 283 GEM-BC1-DH lines is known, based on SNP data (>8000 SNPs/genotype) generated by collaborator (unpublished data). 77 lines were discarded because of heterozygosity or other reasons. From the remaining 283 lines, 78 were not included in the set of 205 lines for agronomic evaluation, because of low seed set (causing problems in seed multiplication for field trials). Those 78 lines are of interest to study the impact of linkage drag with regard to reduced seed set, comparing BC1 and BC3 derived lines. We will determine whether a higher proportion of useful lines are obtained by advancing from BC1 to BC3 prior to induction and doubling.
Those 283 BC1-derived DH lines will be evaluated for seed set in 2014. Phenotypic data related to seed set and marker data will be combined to identify chromosome segments and polymorphisms therein that affect seed set. We will produce BC1:3 sublines for all 283 GEM-BC1-DH lines for further validation in 2015, in order to capture the exotic segments present in the BC1-DH lines. Crosses to recurrent parents for BC2-F1 seed production will be completed during summer 2014. Production of BC1:3 families will be completed during winter 2014/15, and BC3 individuals expected to carry one or few exotic segments will be selfed during summer 2015. GBS and single nucleotide polymorphism (SNP) marker information will be used to relate percentage of exotic germplasm, average length of exotic segments, and extent of linkage drag with the ability to find favorable alleles. Bulked BC1:3 sub-lines will be compared with heterogeneous bulks to their respective homogeneous BC1-DH to evaluate the impact of genetic variation in finding elite exotic alleles. Due to unique exotic allele sequences, it is possible to identify BC3 genotypes with single or few exotic introgressions, and to identify recombination events within exotic segments.