Abstract
BackgroundConsiderations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Both are under complex genetic control: growth habit is controlled by the epistatic interactions of several genes. For inflorescence type, multiple loss-of-function alleles in one gene lead to the same phenotype. We used these two traits as models for assessing the effectiveness of AM. This research was initiated using the CAP Core germplasm array (n = 102) assembled at the start of the Barley Coordinated Agricultural Project (CAP). This array was genotyped with 4,608 SNPs and we re-sequenced genes involved in morphology, growth and development. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project. This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. Each of the larger populations was genotyped with 3,072 SNPs derived from the original set of 4,608.ResultsSignificant associations with SNPs located in the vicinity of the loci involved in growth habit and inflorescence type were found in the CAP Core. Differentiation of true and spurious associations was not possible without a priori knowledge of the candidate genes, based on re-sequencing. The re-sequencing data were used to define allele types of the determinant genes based on functional polymorphisms. In a second round of association mapping, these synthetic markers based on allele types gave the most significant associations. When the synthetic markers were used as anchor points for analysis of interactions, we detected other known-function genes and candidate loci involved in the control of growth habit and inflorescence type. We then conducted association analyses - with SNP data only - in the larger germplasm arrays. For both vernalization sensitivity and inflorescence type, the most significant associations in the larger data sets were found with SNPs coincident with the synthetic markers used in the CAP Core and with SNPs detected via interaction analysis in the CAP Core.ConclusionsSmall and highly structured collections of germplasm, such as the CAP Core, are cost-effectively phenotyped and genotyped with high-throughput markers. They are also useful for characterizing allelic diversity at loci in germplasm of interest. Our results suggest that discovery-oriented exercises in AM in such small arrays may generate a large number of false-positives. However, if haplotypes in candidate genes are available, they may be used as anchors in an analysis of interactions to identify other candidate regions harboring genes determining target traits. Using larger germplasm arrays, genome regions where the principal genes determining vernalization sensitivity and row type are located were identified.
Highlights
Considerations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates
With each of the four analyses, we found BOPA SNPs associated with growth habit located in, or closely linked to, the principal genes determining growth habit (VRN-H1, VRN-H2 and VRNH3) and inflorescence type (VRS1)
Regarding 2H, these results confirm that the extension of linkage disequilibrium (LD) in barley, even in highly structured germplasm, is sufficient to detect associations with markers in LD with a gene, such as VRS1, where different loss-of-function mutations lead to the same phenotype
Summary
Considerations in applying association mapping (AM) to plant breeding are population structure and size: not accounting for structure and/or using small populations can lead to elevated false-positive rates. The principal determinants of population structure in cultivated barley are growth habit and inflorescence type. Larger arrays of breeding germplasm were subsequently genotyped and phenotyped under the auspices of the CAP project This provided sets of 247 accessions phenotyped for growth habit and 2,473 accessions phenotyped for inflorescence type. In cultivated barley there is a high level of population structure and the major factors determining it are growth habit and inflorescence type [4,8,9,10,11]. Varieties with facultative growth habit can be either fall- or springplanted since they are not vernalization sensitive They can be as cold tolerant as winter types [14]. The photoperiod sensitivity of the facultative growth habit class varies, sensitivity to short photoperiod is advantageous from the standpoint of delaying the vegetative to reproductive transition [15] and ensuring the maximum capacity for low temperature tolerance [16]
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