Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease

A novel QTL qRYM-7H for barley yellow mosaic resistance identified by GWAS and linkage analysis

Barley (Hordeum vulgare L.) is the fourth largest cereal crop in the world after rice, wheat and maize. Barley yellow mosaic disease (BYMD) is a serious threat to winter barley production. The evolution and mutation of virus strains lead to the breakdown of the resistance of the originally resistant varieties. It is therefore vital to explore new BYMD resistance genes. In this study, a natural population (334 barley varieties or lines) and a double haploid population derived from the cross between Tam407227 and Franklin were used to search for new quantitative trait loci (QTL) for BYMD resistance. Two major QTL on chromosomes 3H and 7H, respectively, were detected from the genome wide association study and validated in the DH population. Among them, The QTL on 3H (qRYM-3H/qTFRYM-3H) was confirmed to be the reported BYMD resistance gene eIF4E by haplotype analysis. And the QTL on 7H (qRYM-7H/qTFRYM-7H) is a novel QTL that has not been reported before. Another QTL on 2H was identified from the DH population. This QTL is more likely the Rmy16Hb reported previously. These three QTL showed an additive effect on improving BYMD resistance with the average disease scores from 2.45 (all sensitive alleles for these three QTL) to 0.62 (all tolerant alleles for these three QTL). The candidate genes for the novel QTL qRYM-7H/qTFRYM-7H were predicted based on transcriptome sequencing and qPCR analysis.

Genome-Wide Association Study of Host Resistance to Hessian Fly in Barley

The Hessian fly (HF), Mayetiola destructor (Diptera: Cecidomyiidae), is one of the most devastating insect pests of cereals including wheat, barley, and rye. Although wheat is the preferred host for HF, this continuously evolving pest has been emerging as a threat to barley production. However, characterization and identification of genetic resistance to HF has not been conducted in barley. In the present study, we used a genome-wide association study (GWAS) to identify barley resistance loci to HF using a geographically diverse set of 234 barley accessions. The results showed that around 90% of barley lines were highly susceptible, indicating a significant vulnerability to HF in barley, and a total of 29 accessions were resistant, serving as potential resistance resources. GWAS with a mixed linear model revealed two marker-trait associations, both on chromosome 4H. The resistance loci and associated markers will facilitate barley improvement and development for breeders. In addition, our results are fundamental for genetic studies to understand the HF resistance mechanism in barley.

Genome-wide association studies reveal stable loci for wheat grain size under different sowing dates

Background

Wheat (Tritium aestivum L.) production is critical for global food security. In recent years, due to climate change and the prolonged growing period of rice varieties, the delayed sowing of wheat has resulted in a loss of grain yield in the area of the middle and lower reaches of the Yangtze River. It is of great significance to screen for natural germplasm resources of wheat that are resistant to late sowing and to explore genetic loci that stably control grain size and yield.

Methods

A collection of 327 wheat accessions from diverse sources were subjected to genome-wide association studies using genotyping-by-sequencing. Field trials were conducted under normal, delayed, and seriously delayed sowing conditions for grain length, width, and thousand-grain weight at two sites. Additionally, the additive main effects and multiplicative interaction (AMMI) model was applied to evaluate the stability of thousand-grain weight of 327 accessions across multiple sowing dates.

Results

Four wheat germplasm resources have been screened, demonstrating higher stability of thousand-grain weight. A total of 43, 35, and 39 significant MTAs were determined across all chromosomes except for 4D under the three sowing dates, respectively. A total of 10.31% of MTAs that stably affect wheat grain size could be repeatedly identified in at least two sowing dates, with PVE ranging from 0.03% to 38.06%. Among these, six were for GL, three for GW, and one for TGW. There were three novel and stable loci (4A_598189950, 4B_307707920, 2D_622241054) located in conserved regions of the genome, which provide excellent genetic resources for pyramid breeding strategies of superior loci. Our findings offer a theoretical basis for cultivar improvement and marker-assisted selection in wheat breeding practices.

Genome-wide association studies reveal novel loci for grain size in two-rowed barley (Hordeum vulgare L.)

KEY MESSAGE

SNP-based and InDel-based GWAS on multi-environment data identified genomic regions associated with barley grain size. Barley yield and quality are greatly influenced by grain size. Improving barley grain size in breeding programs requires knowledge of genetic loci and alleles in germplasm resources. In this study, a collection of 334 worldwide two-rowed barley accessions with extensive genetic diversity was evaluated for grain size including grain length (GL), grain width (GW), and thousand-grain weight (TGW) across six independent field trials. Significant differences were observed in genotype and environments for all measured traits. SNP- and InDel-based GWAS were applied to dissect the genetic architecture of grain size with an SLAF-seq strategy. Two approaches using the FarmCPU model revealed 38 significant marker-trait associations (MTAs) with PVE ranging from 0.01% to 20.68%. Among these MTAs, five were on genomic regions where no previously reported QTL for grain size. Superior alleles of TGW-associated SNP233060 and GL-associated InDel11006 exhibited significantly higher levels of phenotype. The significant MTAs could be used in marker-assisted selection breeding.

Genome-wide association scan and transcriptome analysis reveal candidate genes for waterlogging tolerance in cultivated barley

Waterlogging is the primary abiotic factor that destabilizes the yield and quality of barley (Hordeum vulgare L.). However, the genetic basis of waterlogging tolerance remains poorly understood. In this study, we conducted a genome-wide association study (GWAS) by involving 106,131 single-nucleotide polymorphisms (SNPs) with a waterlogging score (WLS) of 250 barley accessions in two years. Out of 72 SNPs that were found to be associated with WLS, 34 were detected in at least two environments. We further performed the transcriptome analysis in root samples from TX9425 (waterlogging tolerant) and Franklin (waterlogging sensitive), resulting in the identification of 5,693 and 8,462 differentially expressed genes (DEGs) in these genotypes, respectively. The identified DEGs included various transcription factor (TF) genes, primarily including AP2/ERF, bZIP and MYB. By combining GWAS and RNA-seq, we identified 27 candidate genes associated with waterlogging, of which three TFs (HvDnaJ, HvMADS and HvERF1) were detected in multiple treatments. Moreover, by overexpressing barley HvERF1 in Arabidopsis, the transgenic lines were detected with enhanced waterlogging tolerance. Altogether, our results provide new insights into the genetic mechanisms of waterlogging, which have implications in the molecular breeding of waterlogging-tolerant barley varieties.

Evaluation of grain yield performance and its stability in various spring barley accessions under condition of different agroclimatic zones of Ukraine

Two extremely urgent problems of biological and agronomic research nowadays are ensuring an optimal balance between usage of natural resources to meet rapidly growing needs for food production and preservation of biodiversity. It is also important to extend the genetic diversity of the main crop varieties in agroecosystems. At the same time, modern varieties should be characterized by a combination of high yield and preserving yield stability under variable conditions. Solving the outlined tasks requires comprehensive research and involvement in breeding process of the genetical diversity concentrated in genebanks of the world. Barley (Hordeum vulgare L.) is one of the most important crops that satisfy the various needs of humanity. In respect to this, in 2020–2022, a multi-environment trial was conducted in three agroclimatic zones of Ukraine (Forest-Steppe, Polissia, and Northern Steppe). We studied 44 spring barley collection accessions of different ecological and geographical origin, different subspecies and groups of botanical varieties which were obtained from the National Center for Plant Genetic Resources of Ukraine. Statistical indices (Hom, Sc) and graphical models (GGE biplot, AMMI) were used to interpret the yield performance and its stability. Both individual ecological sites in different years and combinations of different sites and years of trials were characterized for productivity, discriminating power and representativeness. The environments differed quite strongly among themselves in terms of these indicators. It was established that most of the genotypes were characterized by higher adaptability to individual environmental conditions (stability in different years), compared to adaptability for all agroclimatic zones (wide adaptation). A strong cross-over genotype by environment interaction was found for most studied accessions. Nevertheless, both genotypes with very high stability in only one agroclimatic zone (Amil (UKR), Gateway (CAN)) and genotypes with a combination of high adaptability to one or two ecological niches and relatively higher wide adaptability (Stymul (UKR), Ly-1064 (UKR), Rannij (KAZ), Shedevr (UKR), and Arthur (CZE)) were identified. There were also the accessions which did not show maximum performance in the individual sites, but had relatively higher wide adaptability (Ly-1059 (UKR), Ly-1120 (UKR), Diantus (UKR), and Danielle (CZE)). In general, the naked barley genotypes were inferior to the covered ones in terms of yield potential and wide adaptability, but at the same time, some of them (CDC ExPlus (CAN), CDC Gainer (CAN), and Roseland (CAN)), accordingly to the statistical indicators, had increased stability in certain ecological sites. Among naked barley accessions relatively better wide adaptability according to the graphical analysis was found in the accession CDC McGwire (CAN), and by the statistical parameters CDC ExPlus (CAN) was better than standard. The peculiarities of yield manifestation and its variability in different spring barley genotypes in the multi-environment trial revealed in this study will contribute to the complementation and deepening of existing data in terms of the genotype by environment interaction. Our results can be used in further studies for developing spring barley variety models both with specific and wide adaptation under conditions of different agroclimatic zones of Ukraine. The disitnguished accessions of different origin and botanical affiliation are recommended for creating a new breeding material with the aim of simultaneously increasing yield potential and stability, as well as widening the genetic basis of spring barley varieties.