Genome‐wide Association Mapping and Prediction of Adult Stage Septoria tritici Blotch Infection in European Winter Wheat via High‐Density Marker Arrays

Abstract

Core Ideas Elite European winter wheat varieties hold large genetic variance for resistance to Septoria tritici blotch (STB) infection. Genome‐wide association studies with high‐density marker platforms identified hitherto undetected genetic loci for STB infection. Genomic prediction suggested the effective use of genomic selection for STB resistance Septoria tritici blotch (STB) caused by the fungus Zymoseptoria tritici is a devastating foliar disease of wheat (Triticum aestivum L.) that can lead to substantial yield losses. Quantitative genetic resistance has been proposed as a durable strategy for STB control. In this study, we dissected the genetic basis of STB infection in 371 European wheat varieties based on 35k and 90k single nucleotide polymorphism marker arrays. The phenotypic data analyses suggested that large genetic variance exists for STB infection with a broad‐sense heritability of 0.78. Genome‐wide association studies (GWAS) propose the highly quantitative nature of STB infection with potential associations on chromosomes 1A, 1B, 2D, 4A, 5A, 6A, 6D, 7A, and 7B. Increased marker density in GWAS by combining markers from both arrays helped to detect additional markers explaining increased genotypic variance. Linkage disequilibrium analyses revealed genes with a possible role in disease resistance. The potential of genomic prediction (GP) assessed via two models accounting for additive effects and additive plus epistatic interactions among the loci suggested the possibility of genomic selection for improved STB resistance. Genomic prediction results also indicated that the higher‐order epistatic interactions are not abundant and that both marker platforms are equally suitable for GP of STB infection. Our results provide further understanding of the quantitative genetic nature of STB infection, serve as a resource for marker‐assisted breeding, and highlight the potential of genomic selection for improved STB resistance.

TaAPO-A1, an ortholog of riceABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite hexaploid winter wheat varieties (Triticum aestivumL.)

“…In our study, the size of the population, high-density genotyping, and the use of stringent linear mixed-effect models warranted the genetic mapping of true marker-trait-associations (MTA). As noted in another study based on a subset of varieties, the absence of distinct sub-populations in this panel suggests that the European winter wheat varieties have been bred, by and large, from a narrow genetic base and with similar goals (Muqaddasi et al 2019) which is in line with other reports based on studies using similar genetic material but different marker platforms (Kollers et al 2013; Würschum et al 2013).…”

Appraising the Genetic Architecture of Kernel Traits in Hexaploid Wheat Using GWAS

“…Recently, several studies based on 90K SNP arrays can be found which have used GWAS for kernel yield [20,64,65], for resistance against different diseases in wheat [62,66,67], and for bi-parental QTL mapping [32,[68][69][70][71]. Comparatively, GWAS-based linkage disequilibrium (LD) is a much more powerful tool to detect genetic loci in larger gene pools, with much higher resolution than traditional QTL mapping [72].…”

Genetic Analysis Using a Multi-Parent Wheat Population Identifies Novel Sources of Septoria Tritici Blotch Resistance

“…In addition, we detected 15 QTL whose positions overlapped with previously published QTL conferring resistance to STB (detailed in Figure 3 and Table S5). Of these, four QTL (QStb.teagasc-2D.1, QStb.teagasc-4B.1, QStb.teagasc-6D.2, and QStb.teagasc-7B.1) were co-located with published adult plant STB resistance QTL identified under German field conditions [76], while nine QTL co-located with QTL from a single previously published study of field STB resistance in Switzerland [74]. Notably, QStb.teagasc-7B.1 co-located with STB resistance QTL identified in both [74,76].…”

“…Of these, four QTL (QStb.teagasc-2D.1, QStb.teagasc-4B.1, QStb.teagasc-6D.2, and QStb.teagasc-7B.1) were co-located with published adult plant STB resistance QTL identified under German field conditions [76], while nine QTL co-located with QTL from a single previously published study of field STB resistance in Switzerland [74]. Notably, QStb.teagasc-7B.1 co-located with STB resistance QTL identified in both [74,76]. As these QTL appear to have been identified in more than one country, this suggests they may provide sources of durable resistance against different pathogen populations and prevailing conditions.…”

“…The QTL identified were compared with previously reported Stb genes and QTL by projecting onto the physical map in The Triticeae Toolbox (T3) database to identify the co-located genes/QTL and determine the novelty of others. For our QTL co-location study, only QTL mapping and genome-wide association scan (GWAS) studies of STB using high-throughput marker platforms were considered [60,[74][75][76][77][78][79][80][81][82][83]…”