Multi-trait genomic selection can increase selection accuracy for deoxynivalenol accumulation resulting from fusarium head blight in wheat.

Multi-trait genomic prediction (MTGP) can improve selection accuracy for economically valuable 'primary' traits by incorporating data on correlated secondary traits. Resistance to Fusarium head blight (FHB), a fungal disease of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.), is evaluated using four genetically correlated traits: incidence (INC), severity (SEV), Fusarium damaged kernels (FDK), and deoxynivalenol content (DON). Both FDK and DON are primary traits; DON evaluation is expensive and usually requires several months for wheat breeders to get results from service laboratories performing the evaluations. We evaluated MTGP for DON using three soft red winter wheat breeding datasets: two diversity panels from the University of Illinois (IL) and Purdue University (PU) and a dataset consisting of 2019-2020 University of Illinois breeding cohorts. For DON, relative to single-trait (ST) genomic prediction, MTGP including phenotypic data for secondary traits on both validation and training sets, resulted in 23.4 and 10.6% higher predictive abilities in IL and PU panels, respectively. The MTGP models were advantageous only when secondary traits were included in both training and validation sets. In addition, MTGP models were more accurate than ST models only when FDK was included, and once FDK was included in the model, adding additional traits hardly improved accuracy. Evaluation of MTGP models across testing cohorts indicated that MTGP could increase accuracy by more than twofold in the early stages. Overall, we show that MTGP can increase selection accuracy for resistance to DON accumulation in wheat provided FDK is evaluated on the selection candidates.

Genetic Trends in Fusarium Head Blight Resistance from 20 Years of Winter Wheat Breeding and Cooperative Testing in the Northern U.S.A.

Fusarium head blight (FHB) is a devastating disease of wheat and barley. In the U.S.A., a significant long-term investment in breeding FHB-resistant cultivars began after the 1990s. However, to this date, no study has been performed to understand and monitor the rate of genetic progress in FHB resistance as a result of this investment. Using 20 years of data (1998 to 2018) from the Northern Uniform and Preliminarily Northern Uniform winter wheat scab nurseries that consisted of 1,068 genotypes originating from nine different institutions, we studied the genetic trends in FHB resistance within the northern soft red winter wheat growing region using mixed model analyses. For the FHB resistance traits incidence, severity, Fusarium-damaged kernels, and deoxynivalenol content, the rate of genetic gain in disease resistance was estimated to be 0.30 ± 0.1, 0.60 ± 0.09, and 0.37 ± 0.11 points per year, and 0.11 ± 0.05 parts per million per year, respectively. Among the five FHB-resistance quantitative trait loci assayed for test entries from 2012 to 2018, the frequencies of favorable alleles from Fhb 2DL Wuhan1 W14, Fhb Ernie 3Bc, and Fhb 5A Ning7840 were close to zero across the years. The frequency of the favorable at Fhb1 and Fhb 5A Ernie ranged from 0.08 to 0.33 and 0.06 to 0.20, respectively, across years, and there was no trend in changes in allele frequencies over years. Overall, this study showed that substantial genetic progress has been made toward improving resistance to FHB. It is apparent that today's investment in public wheat breeding for FHB resistance is achieving results and will continue to play a vital role in reducing FHB levels in growers' fields.

Genome-Wide Association Studies for Fusarium Head Blight Resistance and Its Trade-Off With Grain Yield in Soft Red Winter Wheat.

Identification of quantitative trait loci for Fusarium head blight (FHB) resistance from different sources and pyramiding them into cultivars could provide effective protection against FHB. The objective of this study was to characterize a soft red winter wheat (SRWW) breeding population that has been subjected to intense germplasm introduction and alien introgression for FHB resistance in the past. The population was evaluated under misted FHB nurseries inoculated with Fusarium graminearum-infested corn spawn for two years. Phenotypic data included disease incidence (INC), disease severity (SEV), Fusarium damaged kernels (FDK), FHB index (FHBdx), and deoxynivalenol concentration (DON). Genome-wide association studies using 13,784 SNP markers identified 25 genomic regions at -logP ≥ 4.0 that were associated with five FHB-related traits. Of these 25, the marker trait associations that explained more than 5% phenotypic variation were localized on chromosomes 1A, 2B, 3B, 5A, 7A, 7B, and 7D, and from diverse sources including adapted SRWW lines such as Truman and Bess, and unadapted common wheat lines such as Ning7840 and Fundulea 201R. Furthermore, individuals with favorable alleles at the four loci Fhb1, Qfhb.nc-2B.1 (Q2B.1), Q7D.1, and Q7D.2 showed better FDK and DON scores (but not INC, SEV, and FHBdx) compared with other allelic combinations. Our data also showed while pyramiding multiple loci provides protection against FHB disease, it has a significant trade-off with grain yield.

Identification of regions under selection and loci controlling agronomic traits in a soft red winter wheat population.

Comprehensive information of a breeding population is a necessity to design promising crosses. This study was conducted to characterize a soft red winter wheat breeding population that was subject of intensive germplasm introductions and introgression from exotic germplasm. We used genome-wide markers and phenotypic assessment to identify signatures of selection and loci controlling agronomic traits in a soft red winter wheat population. The study of linkage disequilibrium (LD) revealed that the extent of LD and its decay varied among chromosomes with chromosomes 2B and 7D showing the most extended islands of high-LD with slow rates of decay. Four sub-populations, two with North American origin and two with Australian and Chinese origins, were identified. Genome-wide scans for selection signatures using FST and hapFLK identified 13 genomic regions under selection, of which five loci (LT, Fr-A2, Vrn-A1, Vrn-B1, Vrn3) were associated with environmental adaptation and two loci were associated with disease resistance genes (Sr36 and Fhb1). Genome-wide association studies identified major loci controlling yield and yield related traits. For days to heading and plant height, major loci with effects sizes of 2.2 days and 5 cm were identified on chromosomes 7B and 6A respectively. For test weight, number of spikes per square meter, and number of kernels per square meter, large effect loci were identified on chromosomes 1A, 4B, and 5A, respectively. However, for yield alone, no major loci were detected. A combination of selection for large effect loci for yield components and genomic selection could be a promising approach for yield improvement.