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Ms3 dominant genetic male sterility for wheat improvement with molecular breeding

Citation

Guttieri, Mary (2020), Ms3 dominant genetic male sterility for wheat improvement with molecular breeding, Dryad, Dataset, https://doi.org/10.5061/dryad.dv41ns1tg

Abstract

Genetic dominant male sterility (DMS) has not been widely used as a breeding tool in wheat (Triticum aestivum L.), although DMS-facilitated backcross, mass selection, half-sib selection, and S1 family recurrent selection strategies have been described, and Ms2-facilitated recurrent selection has been used in China. Our objective was to revisit these strategies using the tools of molecular breeding. Development of a mechanism for seedling identification of sterile progeny was a key component of designing practical DMS-facilitated molecular breeding systems. The DMS gene Ms3 was previously localized to the centromeric region of chromosome 5A. The centromeric location is an advantage because recombination rates are very low. Once identified, a broadly informative marker would reliably predict the male-sterile phenotype. A set of 429 hybrids incorporating Ms3 were constructed, both within US hard winter wheats, and between these winter wheats and Asian spring wheats. Association of the male-sterile phenotype with those polymorphic DNA sequence tags that localized to chromosome 5A was tested using case-control association analysis. Two highly significant (logarithm of odds [LOD] > 30) single nucleotide polymorphism (SNP)–trait associations were obtained. One SNP was developed into a highly sensitive, reliable molecular marker for the Ms3-associated male-sterile. Previously described breeding strategies using DMS were updated for trait-targeted marker-assisted backcrossing and gene pyramiding, S1 recurrent selection, and early-generation genomic selection. Application of DMS to association mapping, with the particular use case of the multiparent advanced generation intercross population, is also described.

Methods

The SNPs were called by TASSEL 5.0 (Bradbury et al., 2007) using the reference sequence of the bread wheat landrace Chinese Spring (International Wheat Genome Sequencing Consortium [IWGSC] RefSeq 1.0) (Alaux et al., 2018). The 197,543 SNPs called were filtered in TASSEL to the 5666 SNPs that aligned to chromosome 5A and had minor allele frequency >0.05. Genotyping data thus subsetted were imported to JMP Genomics 9.0 (SAS Institute) using the TASSEL GBS Import Engine. Further filtering using the Subset and Reorder Genetic Data utility in JMP Genomics filtered the markers to those with <40% missing data and filtered the genotypes to those with a minimum proportion of nonmissing genotypes of 20%.

Usage Notes

Files are SAS datasets, genotype and annotation, used for association analysis.