Genetic Dissection of Snow Mold Tolerance in US Pacific Northwest Winter Wheat Through Genome-Wide Association Study and Genomic Selection.

Dennis Lozada,Brian P Ward,Jayfred V Godoy,Timothy D Murray,Arron H Carter

doi:10.3389/fpls.2019.01337

Dennis Lozada, Brian P Ward + Show 3 more

Open Access

https://doi.org/10.3389/fpls.2019.01337

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Abstract

Snow mold is a yield-limiting disease of wheat in the Pacific Northwest (PNW) region of the US, where there is prolonged snow cover. The objectives of this study were to identify genomic regions associated with snow mold tolerance in a diverse panel of PNW winter wheat lines in a genome-wide association study (GWAS) and to evaluate the usefulness of genomic selection (GS) for snow mold tolerance. An association mapping panel (AMP; N = 458 lines) was planted in Mansfield and Waterville, WA in 2017 and 2018 and genotyped using the Illumina® 90K single nucleotide polymorphism (SNP) array. GWAS identified 100 significant markers across 17 chromosomes, where SNPs on chromosomes 5A and 5B coincided with major freezing tolerance and vernalization loci. Increased number of favorable alleles was related to improved snow mold tolerance. Independent predictions using the AMP as a training population (TP) to predict snow mold tolerance of breeding lines evaluated between 2015 and 2018 resulted in a mean accuracy of 0.36 across models and marker sets. Modeling nonadditive effects improved accuracy even in the absence of a close genetic relatedness between the TP and selection candidates. Selecting lines based on genomic estimated breeding values and tolerance scores resulted in a 24% increase in tolerance. The identified genomic regions associated with snow mold tolerance demonstrated the genetic complexity of this trait and the difficulty in selecting tolerant lines using markers. GS was validated and showed potential for use in PNW winter wheat for selecting on complex traits such tolerance to snow mold.

Highlights

Snow mold is a disease affecting wheat grown in the Pacific Northwest (PNW) region of the US, where plants are exposed to prolonged (>100 days) snow cover
An association mapping panel (AMP) consisting of 458 advanced soft winter wheat breeding lines adapted to the US Pacific Northwest (PNW) region was used for genome-wide association study (GWAS) and as a training population (TP) for genomic selection (GS)
The current study identified genomic regions associated with tolerance to snow mold in a diverse population of PNW winter wheat lines through a GWAS approach

Summary

Introduction

Snow mold is a disease affecting wheat grown in the Pacific Northwest (PNW) region of the US, where plants are exposed to prolonged (>100 days) snow cover This prolonged winter condition provides a favorable environment, allowing the pathogens causing the disease to grow and infect plants under the snow (Bruehl and Cunfer, 1971). Plants with pink snow mold have a whitish fungal growth (that eventually turns into a salmon color; the name pink snow mold) in their leaves, whereas leaves of plants with speckled snow mold are covered with a whitish gray fungal growth (Murray et al, 1999) Cultural practices such as seeding date, fertilizer application, and residue management can be used to manage snow mold in wheat, breeding for disease tolerance was suggested as the primary method of control for snow mold (Murray et al, 1999). The use of molecular breeding approaches to identify tolerant lines and to better understand the genetic basis of the disease is relevant for improving snow mold tolerance in current winter wheat lines

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