When making malt, the endosperm is hydrated during steeping to make stored starch available for extraction. Differences in steep regime impact malt quality. Differences in malt quality results between the United States Department of Agriculture-Agricultural Research Service (USDA-ARS) and Montana State University (MSU) malt quality laboratories are primarily due to differences in steep regime and are reported herein. Evidence suggests that differences in steep regime in this study were primarily due to length of water immersion versus air rests, rather than other differences (e.g., temperature of steep, sorting of seed, or length of germination). The difference in steep regime caused a difference in the level of endosperm modification. To confirm this finding, three different steep regimes on seven different lines were tested and it was found that the impact on quality varied depending on the trait and in some cases on the genotype. The steep regime was found to have affected both moisture uptake and quality of hydration. Finally, the implications of these findings on malt quality analysis and breeding for malt quality are discussed.

Centromeres are dynamic chromosomal regions, and the genetic and epigenetic environment of the centromere is often regarded as oppressive to protein-coding genes. Here, we used comparative genomic and phylogenomic approaches to study the evolution of centromeres and centromere-linked genes in the genus Oryza. We report a 12.4-Mb high-quality BAC-based pericentromeric assembly for Oryza brachyantha, which diverged from cultivated rice (Oryza sativa) ∼15 million years ago. The synteny analyses reveal seven medium (>50 kb) pericentric inversions in O. sativa and 10 in O. brachyantha. Of these inversions, three resulted in centromere movement (Chr1, Chr7, and Chr9). Additionally, we identified a potential centromere-repositioning event, in which the ancestral centromere on chromosome 12 in O. brachyantha jumped ∼400 kb away, possibly mediated by a duplicated transposition event (>28 kb). More strikingly, we observed an excess of syntenic gene loss at and near the centromeric regions (P < 2.2 × 10⁻¹⁶). Most (33/47) of the missing genes moved to other genomic regions; therefore such excess could be explained by the selective loss of the copy in or near centromeric regions after gene duplication. The pattern of gene loss immediately adjacent to centromeric regions suggests centromere chromatin dynamics (e.g., spreading or microrepositioning) may drive such gene loss.

Barley (Hordeum vulgare L.) seeds are a rich source of β‐glucans that can help reduce blood serum cholesterol content in human diets. However, high levels of this polysaccharide in the seeds causes inefficiencies such as slow lautering during the brewing process due to the higher wort viscosity. Thus, depending on the end use, barley breeding programs have opposing goals with respect to β‐glucan. Discovery of new alleles for β‐glucan content in exotic barley germplasm could have significant commercial importance. We leveraged the Wild Barley Diversity Collection (WBDC; N = 314), grown at University of California‐Davis experiment station, to characterize both the variation in β‐glucan content found in this wild barley subspecies (Hordeum vulgare spp. spontaneum) and to reveal chromosomal regions associated with this trait. Grain β‐glucan content ranged from 2.56 to 11.73% in the WBDC. Within structured subpopulations, geographical coordinates as well as annual precipitation data of original collection sites showed associations with differing levels of β‐glucan content. Genome‐wide association study identified a total of 13 quantitative traits loci (QTL) spread across the seven barley chromosomes that explained most of the variation in β‐glucan content in the WBDC. Previously reported genes associated with β‐glucan content such as β‐glucan synthases and hydrolases (e.g., callose synthase) were identified within these QTL regions. Genes such as Patatin and Nudix hydrolase provide novel targets for manipulating grain β‐glucan in barley. RNA‐seq data from both developing and germinating barley seeds for the annotated genes in the QTL regions provide further corroboration for a functional role for these genes in modulating seed β‐glucan levels.

In mammals, microbial colonization of the digestive tract (GIT) occurs right after birth by several bacterial phyla. Numerous human and mouse studies have reported the importance of early gut microbial inhabitants on host health. However, few attempts have been undertaken to directly interrogate the role of early gut/rumen microbial colonization on GIT development or host health in neonatal ruminants through artificial manipulation of the rumen microbiome. Thus, the molecular changes associated with bacterial colonization are largely unknown in cattle. In this study, we dosed young calves with exogenous rumen fluid obtained from an adult donor cow, starting at birth, and repeated every other week until six weeks of age. Eight Holstein bull calves were included in this study and were separated into two groups of four: the first group was treated with rumen content freshly extracted from an adult cow, and the second group was treated with sterilized rumen content. Using whole-transcriptome RNA-sequencing, we investigated the transcriptional changes in the host liver, which is a major metabolic organ and vital to the calf’s growth performance. Additionally, the comparison of rumen epimural microbial communities between the treatment groups was performed using the rRNA reads generated by sequencing. Liver transcriptome changes were enriched with genes involved in cell signaling and protein phosphorylation. Specifically, up-regulation of SGPL1 suggests a potential increase in the metabolism of sphingolipids, an essential molecular signal for bacterial survival in digestive tracts. Notably, eight genera, belonging to four phyla, had significant increases in abundance in treated calves. Our study provides insight into host liver transcriptome changes associated with early colonization of the microbial communities in neonatal calves. Such knowledge provides a foundation for future probiotics-based research in microbial organism mediated rumen development and nutrition in ruminants.

Tocochromanols (tocols for short), commonly called Vitamin E, are lipid‐soluble plant antioxidants vital for regulating lipid peroxidation in chloroplasts and seeds. Barley ( Hordeum vulgare L.) seeds contain all eight different isoforms of tocols; however, the extent of natural variation in their composition and their underlying genetic basis is not known. Tocol levels in barley seeds were quantified in diverse H. vulgare panels comprising 297 wild lines from a diversity panel and 160 cultivated spring‐type accessions from the mini‐core panel representing the genetic diversity of the USDA barley germplasm collection. Significant differences were observed in the concentration of tocols between the two panels. To identify the genes associated with tocols, genome‐wide association analysis was conducted with single nucleotide polymorphisms (SNPs) from Illumina arrays for the mini‐core panel and genotyping‐by‐sequencing for the wild barley panel. Forty unique SNPs in the wild barley and 27 SNPs in the mini‐core panel were significantly associated with various tocols. Marker–trait associations (MTAs) were identified on chromosomes 1, 6, and 7 for key genes in the tocol biosynthesis pathway, which have also been reported in other studies. Several novel MTAs were identified on chromosomes 2, 3, 4 and 5 and were found to be in proximity to genes involved in the generation of precursor metabolites required for tocol biosynthesis. This study provides a valuable resource for barley breeding programs targeting specific isoforms of seed tocols and for investigating the physiological roles of these metabolites in seed longevity, dormancy, and germination.