Genomic prediction and GWAS of yield, quality and disease-related traits in spring barley and winter wheat

Abstract

Genome-wide association study (GWAS) and genomic prediction (Gp) are extensively employed to accelerate genetic gain and identify QTL in plant breeding. In this study, 1,317 spring barley and 1,325 winter wheat breeding lines from a commercial breeding program were genotyped with the illumina 9 K barley or 15 K wheat SNP-chip, and phenotyped in multiple years and locations. For GWAS, in spring barley, a QTL on chr. 4H associated with powdery mildew and ramularia resistance were found. There were several SNPs on chr. 4H showing genome-wide significance with yield traits. In winter wheat, GWAS identified two SNPs on chr. 6A, and one SNP on chr. 1B, significantly associated with quality trait moisture, as well as one SNP located on chr. 5B associated with starch content in the seeds. The significant SNPs identified by multiple trait GWAS were generally the same as those found in single trait GWAS. GWAS including genotype-location information in the model identified significant SNPs in each tested location, which were not found previously when including all locations in the GWAS. for Gp, in spring barley, GP using the Bayesian Power Lasso model had higher accuracy than ridge regression BLUP in powdery mildew and yield traits, whereas the prediction accuracies were similar using Bayesian Power Lasso model and rrBLUP for yield traits in winter wheat. Both wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) are major cereal crops worldwide, ranking as the second and fourth in total grain production. The global wheat and barley production amounted to 736 and 146 million metric tons in 2016, with 21% and 41% contributed by European countries, respectiely 1. Due to their economic role worldwide, the advancement of economically important traits of wheat and barley is indispensable, in order to meet the food demands of growing human population. Recent developments in genome sequencing technologies allow plant breeders to characterize the genetic architecture of economically important cereal crops. The reference genomes are now available in both spring barley and winter wheat 2-4 , raising the possibilities for plant breeders to introduce genome-assisted selection to both crops. Several high-density SNP microarrays enabling association mapping, and increase the resolution of quantitative trait loci (QTLs) mapping using hundreds of thousands of genetic polymorphisms throughout the entire genome, are now available. For example, there are several SNP arrays with the varying number of genetic variants customized for both barley and wheat 5-9. Traditionally, the molecular-assisted breeding, using molecular biology techniques, such as gene identification and gene functional characterization, to explain the genetic mechanism of economically important traits has been used in crops. However, several studies evidenced that most traits of commercial interest in wheat and barley are highly polygenic, with many QTLs that each only account for a small proportion of total genetic variances 10,11. This severely limits the applicatio...

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

“…Although there have been several studies related to QTL mapping and genome-wide association studies (GWASs) for yield-related traits [15][16][17][18][19], only a few outcomes have been applied for wheat improvement in breeding programs [20]. High-throughput single nucleotide polymorphism (SNP) assays have been used in breeding and genotyping studies, which enable the process of association mapping to be more accurate and robust [20,21]. SNP assays developed from animal and plant transcriptomes [22] are generally more advanced, stable, capable of automatic detection, efficient, and cost-effective [23,24].…”

Fungicide strategies and resistance of Ramularia collo-cygni to demethylation and succinate dehydrogenase inhibitors in Austrian winter barley (Hordeum vulgare)

“…This can be considered as the primary strategy to reduce seedborne transmission of R. collo-cygni on barley (Havis et al 2014;Kaczmarek et al 2017). Furthermore, recently published markers associated with RLS (Tsai et al 2020) will facilitate breeding of more durable resistant barley varieties. However, intensive straw management and weed control to reduce spore distribution, crop rotation and the growth of stress-free barley plants are also important to minimize the impact of the R. collocygni population size (Stam et al 2019).…”

Quantitative trait loci (QTL) mapping of resistance to coffee berry disease (Colletotrichum kahawae Waller Bridge) in Coffea arabica L. variety Rume Sudan

“…The markers that were closely linked with the significant QTLs were statistically tested using the scores of their alleles, where the alleles with significant differences (P≤0.05) by t-test were confirmed as significant SNP markers (Xiong et al, 2019;Tsai et al, 2020).…”