Multilayered regulation of developmentally programmed pre-anthesis tip degeneration of the barley inflorescence.

Leaf and floral tissue degeneration is a common feature in plants. In cereal crops such as barley (Hordeum vulgare L.), pre-anthesis tip degeneration (PTD) starts with growth arrest of the inflorescence meristem dome, which is followed basipetally by the degeneration of floral primordia and the central axis. Due to its quantitative nature and environmental sensitivity, inflorescence PTD constitutes a complex, multilayered trait affecting final grain number. This trait appears to be highly predictable and heritable under standardized growth conditions, consistent with a developmentally programmed mechanism. To elucidate the molecular underpinnings of inflorescence PTD, we combined metabolomic, transcriptomic, and genetic approaches to show that barley inflorescence PTD is accompanied by sugar depletion, amino acid degradation, and abscisic acid responses involving transcriptional regulators of senescence, defense, and light signaling. Based on transcriptome analyses, we identified GRASSY TILLERS1 (HvGT1), encoding an HD-ZIP transcription factor, as an important modulator of inflorescence PTD. A gene-edited knockout mutant of HvGT1 delayed PTD and increased differentiated apical spikelets and final spikelet number, suggesting a possible strategy to increase grain number in cereals. We propose a molecular framework that leads to barley PTD, the manipulation of which may increase yield potential in barley and other related cereals.

A molecular framework for grain number determination in barley.

Flowering plants with indeterminate inflorescences often produce more floral structures than they require. We found that floral primordia initiations in barley (Hordeum vulgare L.) are molecularly decoupled from their maturation into grains. While initiation is dominated by flowering-time genes, floral growth is specified by light signaling, chloroplast, and vascular developmental programs orchestrated by barley CCT MOTIF FAMILY 4 (HvCMF4), which is expressed in the inflorescence vasculature. Consequently, mutations in HvCMF4 increase primordia death and pollination failure, mainly through reducing rachis greening and limiting plastidial energy supply to developing heterotrophic floral tissues. We propose that HvCMF4 is a sensory factor for light that acts in connection with the vascular-localized circadian clock to coordinate floral initiation and survival. Notably, stacking beneficial alleles for both primordia number and survival provides positive implications on grain production. Our findings provide insights into the molecular underpinnings of grain number determination in cereal crops.

Genetic association of spikelet abortion with spike, grain, and shoot traits in highly-diverse six-rowed barley.

Spikelet abortion is a phenomenon where apical spikelet primordia on an immature spike abort. Regardless of the row-type, both apical and basal spikelet abortion occurs, and their extent decides the number of grain-bearing spikelets retained on the spike-thus, affecting the yield potential of barley. Reducing spikelet abortion, therefore, represents an opportunity to increase barley yields. Here, we investigated the variation for apical spikelet abortion along with 16 major spike, shoot, and grain traits in a panel of 417 six-rowed spring barleys. Our analyses showed a significantly large genotypic variation resulting in high heritability estimates for all the traits. Spikelet abortion (SA) varies from 13 to 51% depending on the genotype and its geographical origin. Among the seven spike traits, SA was negatively correlated with final spikelet number, spike length and density, while positively with awn length. This positive correlation suggests a plausible role of the rapidly growing awns during the spikelet abortion process, especially after Waddington stage 5. In addition, SA also showed a moderate positive correlation with grain length, grain area and thousand-grain weight. Our hierarchical clustering revealed distinct genetic underpinning of grain traits from the spike and shoot traits. Trait associations showed a geographical bias whereby European accessions displayed higher SA and grain and shoot trait values, whereas the trend was opposite for the Asian accessions. To study the observed phenotypic variation of SA explained by 16 other individual traits, we applied linear, quadratic, and generalized additive regression models (GAM). Our analyses of SA revealed that the GAM generally performed superior in comparison to the other models. The genetic interactions among traits suggest novel breeding targets and easy-to-phenotype "proxy-traits" for high throughput on-field selection for grain yield, especially in early generations of barley breeding programs.

Spikelet abortion in six-rowed barley is mainly influenced by final spikelet number, with potential spikelet number acting as a suppressor trait.

The potential to increase barley grain yield lies in the indeterminate nature of its inflorescence meristem, which produces spikelets, the basic reproductive unit in grasses that are linked to reproductive success. During early reproductive growth, barley spikes pass through the maximum yield potential-a stage after which no new spikelet ridges are produced. Subsequently, spikelet abortion (SA), a phenomenon in which spikelets abort during spike growth, imposes a bottleneck for increasing the grain yield potential. Here, we studied the potential of main culm spikes by counting potential spikelet number (PSN) and final spikelet number (FSN), and computed the corresponding SA (%) in a panel of 417 six-rowed spring barleys. Our phenotypic data analyses showed a significantly large within- and across-years genotypic variation with high broad-sense heritability estimates for all the investigated traits, including SA. Asian accessions displayed the lowest SA, indicating the presence of favourable alleles that may be exploited in breeding programs. A significantly negative Pearson's product-moment correlation was observed between FSN and SA. Our path analysis revealed that PSN and FSN explain 93% of the observed phenotypic variability for SA, with PSN behaving as a suppressor trait that magnifies the effect of FSN. Based on a large set of diverse barley accessions, our results provide a deeper phenotypic understanding of the quantitative genetic nature of SA, its association with traits of high agronomic importance, and a resource for further genetic analyses.

Omics for the Improvement of Abiotic, Biotic, and Agronomic Traits in Major Cereal Crops: Applications, Challenges, and Prospects.

Omics technologies, namely genomics, transcriptomics, proteomics, metabolomics, and phenomics, are becoming an integral part of virtually every commercial cereal crop breeding program, as they provide substantial dividends per unit time in both pre-breeding and breeding phases. Continuous advances in omics assure time efficiency and cost benefits to improve cereal crops. This review provides a comprehensive overview of the established omics methods in five major cereals, namely rice, sorghum, maize, barley, and bread wheat. We cover the evolution of technologies in each omics section independently and concentrate on their use to improve economically important agronomic as well as biotic and abiotic stress-related traits. Advancements in the (1) identification, mapping, and sequencing of molecular/structural variants; (2) high-density transcriptomics data to study gene expression patterns; (3) global and targeted proteome profiling to study protein structure and interaction; (4) metabolomic profiling to quantify organ-level, small-density metabolites, and their composition; and (5) high-resolution, high-throughput, image-based phenomics approaches are surveyed in this review.

Genome-Wide Association Studies and Prediction of Tan Spot (Pyrenophoratritici-repentis) Infection in European Winter Wheat via Different Marker Platforms.

Tan spot, caused by the fungus Pyrenophoratritici-repentis (Ptr), is a severe foliar disease of wheat (Triticumaestivum L.). Improving genetic resistance is a durable strategy to reduce Ptr-related losses. Here, we dissected Ptr-infection's genetic basis in 372 European wheat varieties via single sequence repeats (SSR) in addition to 35k and 90k single nucleotide polymorphism (SNP) marker platforms. In our phenotypic data analyses, Ptr infection showed a significant genotypic variance and a significant negative correlation with plant height. Genome-wide association studies revealed a highly quantitative nature of Ptr infection and identified two quantitative trait loci (QTL), viz., QTs.ipk-7A and QTs.ipk-7B, which imparted 21.23 and 5.84% of the genotypic variance, respectively. Besides, the Rht-D1 gene showed a strong allelic influence on the resistance scores. Due to the complex genetic nature of the Ptr infection, the potential of genome-wide prediction (GP) was assessed via three different genetic models on individual and combined marker platforms. The GP results indicated that the marker density and marker platforms do not considerably impact prediction accuracy (~40-42%) and that higher-order epistatic interactions may not be highly pervasive. Our results provide a further understanding of Ptr-infection's genetic nature, serve as a resource for marker-assisted breeding, and highlight the potential of genome-wide selection for improved Ptr resistance.