Genome‐wide association mapping and genomic prediction of Fusarium head blight resistance, heading stage and plant height in winter rye (Secale cereale)

Abstract

Rye is a multi‐purpose cereal crop grown in Central and Eastern Europe as well as in Western Canada. Fusarium head blight (FHB) is one of the diseases that have a severe negative impact on rye, but knowledge about FHB resistance at the genomic level is totally missing in rye. The objective of this study was to elucidate the genetic architecture of FHB resistance in winter rye using genome‐wide association (GWA) mapping complemented by genomic prediction (GP) in comparison with marker‐assisted selection (MAS). Additionally, plant height and heading stage were analysed. A panel of 465 S1‐inbred lines of winter rye was phenotyped in three environments (location–year combinations) for FHB resistance by inoculation with Fusarium culmorum and genotyped with a 15k SNP array. Significant genotypic variation and high heritabilities were found for FHB resistance, heading stage and plant height. FHB did not correlate with heading stage, but was moderately correlated with plant height (r = −.52, p < .001) caused by some susceptible short inbred lines. The GWA scan identified 15 QTL for FHB resistance that jointly explained 74% of the genotypic variance. In addition, we detected 11 QTL for heading stage and 8 QTL for plant height, explaining 26% and 14% of the genotypic variance, respectively. A genome‐wide prediction approach resulted in 44% higher prediction abilities than marker‐assisted selection for FHB resistance. In conclusion, genomic approaches appear promising to improve and accelerate breeding for complex traits in winter rye.

Exploiting genetic diversity in two European maize landraces for improving Gibberella ear rot resistance using genomic tools

“…Similarly to our findings, Han et al (2018) and Martin et al (2012c) reported low negative correlations between GER severity and days to silking illustrating that late materials tend to get less infected. In wheat, PHT can highly affect severity of Fusarium head blight infection (Mesterházy 1995;Gaikpa et al 2020), but this was not the case in our study with maize as judged from the non-significant correlations between PHT and GER severity (Table 2). This might be explained by the direct inoculation of the maize ears by hand while in wheat spray inoculation from above is commonly practiced.…”

Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize

“…For the other small-grain cereals, much less work has been done. Some QTL studies and GWAS were done in durum wheat due to its extreme susceptibility to FHB [ 42 , 43 , 44 , 45 ], but for triticale only a few studies [ 46 , 47 , 48 ] and for rye only one study is available [ 49 ]. In this first paper on rye, a single-locus GWAS method detected 15 QTLs among nearly 500 partially inbred lines distributed across all chromosomes except chromosome 7.…”

“…In this first paper on rye, a single-locus GWAS method detected 15 QTLs among nearly 500 partially inbred lines distributed across all chromosomes except chromosome 7. These QTLs collectively explained about 74% of the genotypic variance [ 49 ]. Similar results have been found in the other small-grain cereals.…”

“…In several recent studies, GS was compared to the traditional MAS using only QTLs with marker effects of > 5% of genotypic variation. The GP approach outperformed MAS in most cases as shown by studies in triticale, rye, and bread wheat [ 47 , 49 , 50 , 51 ].…”

Intercontinental trials reveal stable QTL for Northern corn leaf blight resistance in Europe and in Brazil

“…The main objective of this approach is to increase the frequency of the major effects within the breeding population (Bernardo 2014). In addition, this model has been proofed to increase the prediction accuracies in different crops (Gaikpa et al 2020;Galiano-Carneiro et al 2019;Herter et al 2019).…”