Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch
Yates S, Mikaberidze A, Krattinger SG, Abrouk M, Hund A, Yu K, Studer B, Fouche S, Meile L, Pereira D, Karisto P, McDonald BA (2019) Precision phenotyping reveals novel loci for quantitative resistance to septoria tritici blotch. Plant Phenomics 2019: 3285904.
Accurate, high-throughput phenotyping for quantitative traits is a
limiting factor for progress in plant breeding. We developed an
automated image analysis to measure quantitative resistance to septoria
tritici blotch (STB), a globally important wheat disease, enabling
identification of small chromosome intervals containing plausible
candidate genes for STB resistance. 335 winter wheat cultivars were
included in a replicated field experiment that experienced natural
epidemic development by a highly diverse but fungicide-resistant
pathogen population. More than 5.4 million automatically generated
phenotypes were associated with 13,648 SNP markers to perform the GWAS.
We identified 26 chromosome intervals explaining 1.9-10.6% of the
variance associated with four independent resistance traits. Sixteen of
the intervals overlapped with known STB resistance intervals, suggesting
that our phenotyping approach can identify simultaneously (i.e., in a
single experiment) many previously defined STB resistance intervals.
Seventeen of the intervals were less than 5 Mbp in size and encoded only
173 genes, including many genes associated with disease resistance.
Five intervals contained four or fewer genes, providing high priority
targets for functional validation. Ten chromosome intervals were not
previously associated with STB resistance, perhaps representing
resistance to pathogen strains that had not been tested in earlier
experiments. The SNP markers associated with these chromosome intervals
can be used to recombine different forms of quantitative STB resistance
that are likely to be more durable than pyramids of major resistance
genes. Our experiment illustrates how high-throughput automated
phenotyping can accelerate breeding for quantitative disease resistance.