Varietal effects of barley carbohydrate composition on digestibility, fermentability and microbial ecophysiology in an in vitro model of the pig gastrointestinal tract.

Carbohydrate (CHO) composition can vary markedly between barley varieties. Their influence on digestibility, intestinal fermentation and microbiota in pigs was studied in vitro. Ten hulless (HLB) and 6 hulled barleys (HB) differing in B-glucan, non-starch polysaccharides (NSP), starch content, and amylose/amylopectin ratio, were hydrolyzed enzymatically and subsequently fermented for 72h. CHO fermentation kinetics were modeled; microbial composition and short-chain fatty acid (SCFA) production were analyzed. In HLB, in vitro DM digestibility was positively correlated to starch and amylopectin content and CP digestibility to amylopectin (P<0.05), whereas both were negatively correlated to insoluble NSP (P<0.05). Rate of fermentation was different (P<0.01) between barley types but not correlated to the CHO composition. However, high B-glucan contents induced faster fermentation (P<0.05, HLB; P<0.10, HB). SCFA molar ratios after fermentation of HLB were higher in propionate and branchedchain fatty acids and lower in acetate compared to HB (P<0.01). With HLB, amylose content was positively correlated to butyrate production and negatively to propionate, which was positively correlated to soluble NSP content (P<0.01). In HB, no correlation between SCFA production and the carbohydrate composition was found. TRFLP analysis revealed that Bacteroides and members of Clostridium cluster XIVa were differentially affected in HLB compared to HB as well as by the type and source of CHO. Microbial profiles were also correlated (P<0.05) to SCFA and fermentation parameters but response differed significantly between HB and HLB. The strongest correlation between CHO structure, microbial abundance and fermentation parameters was evident in HLB. Hulless barleys may offer the greatest opportunity to improve gut health in pigs

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

BACKGROUND: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). RESULTS: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. CONCLUSION: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity

Population Genomics Related to Adaptation in Elite Oat Germplasm

Six hundred thirty five oat ( L.) lines and 4561 single-nucleotide polymorphism (SNP) loci were used to evaluate population structure, linkage disequilibrium (LD), and genotype–phenotype association with heading date. The first five principal components (PCs) accounted for 25.3% of genetic variation. Neither the eigenvalues of the first 25 PCs nor the cross-validation errors from = 1 to 20 model-based analyses suggested a structured population. However, the PC and = 2 model-based analyses supported clustering of lines on spring oat vs. southern United States origin, accounting for 16% of genetic variation ( < 0.0001). Single-locus -statistic () in the highest 1% of the distribution suggested linkage groups that may be differentiated between the two population subgroups. Population structure and kinship-corrected LD of = 0.10 was observed at an average pairwise distance of 0.44 cM (0.71 and 2.64 cM within spring and southern oat, respectively). On most linkage groups LD decay was slower within southern lines than within the spring lines. A notable exception was found on linkage group Mrg28, where LD decay was substantially slower in the spring subpopulation. It is speculated that this may be caused by a heterogeneous translocation event on this chromosome. Association with heading date was most consistent across location-years on linkage groups Mrg02, Mrg12, Mrg13, and Mrg24

SNP Discovery and Chromosome Anchoring Provide the First Physically-Anchored Hexaploid Oat Map and Reveal Synteny with Model Species

A physically anchored consensus map is foundational to modern genomics research; however, construction of such a map in oat (Avena sativa L., 2n = 6x = 42) has been hindered by the size and complexity of the genome, the scarcity of robust molecular markers, and the lack of aneuploid stocks. Resources developed in this study include a modified SNP discovery method for complex genomes, a diverse set of oat SNP markers, and a novel chromosome-deficient SNP anchoring strategy. These resources were applied to build the first complete, physically-anchored consensus map of hexaploid oat. Approximately 11,000 high-confidence in silico SNPs were discovered based on nine million inter-varietal sequence reads of genomic and cDNA origin. GoldenGate genotyping of 3,072 SNP assays yielded 1,311 robust markers, of which 985 were mapped in 390 recombinant-inbred lines from six bi-parental mapping populations ranging in size from 49 to 97 progeny. The consensus map included 985 SNPs and 68 previously-published markers, resolving 21 linkage groups with a total map distance of 1,838.8 cM. Consensus linkage groups were assigned to 21 chromosomes using SNP deletion analysis of chromosome-deficient monosomic hybrid stocks. Alignments with sequenced genomes of rice and Brachypodium provide evidence for extensive conservation of genomic regions, and renewed encouragement for orthology-based genomic discovery in this important hexaploid species. These results also provide a framework for high-resolution genetic analysis in oat, and a model for marker development and map construction in other species with complex genomes and limited resources

Regions of the genome that affect agronomic performance in two-row barley

Quantitative trait locus (QTL) main effects and QTL by environment (QTL × E) interactions for seven agronomic traits (grain yield, days to heading, days to maturity, plant height, lodging severity, kernel weight, and test weight) were investigated in a two-row barley (Hordeum vulgare L.) cross, Harrington/TR306. A 127-point base map was constructed from markers (mostly RFLP) scored in 146 random double-haploid (DH) lines from the Harrington/TR306 cross. Field experiments involving the two parents and 145 random DH lines were grown in 1992 and/or 1993 at 17 locations in North America. Analysis of QTL was based on simple and composite interval mapping. Primary QTL were declared at positions where both methods gave evidence for QTL. The number of primary QTL ranged from three to six per trait, collectively explaining 34 to 52% of the genetic variance. None of these primary QTL showed major effects, but many showed effects that were consistent across environments. The addition of secondary QTL gave models that explained 39 to 80% of the genetic variance. The QTL were dispersed throughout the barley genome and some were detected in regions where QTL have been found in previous studies. Eight chromosome regions contained pleiotropic loci and/or linked clusters of loci that affected multiple traits. One region on chromosome 7 affected all traits except days to heading. This study was an intensive effort to evaluate QTL in a narrow-base population grown in a large set of environments. The results reveal the types and distributions of QTL effects manipulated by plant breeders and provide opportunities for future testing of marker-assisted selection

Panel discussion and Q&A

Genetic Approaches to Crop Adaptatio

In vitro evaluation of the fermentation characteristics in the pig intestines of hulless barleys differing in β-glucan content

Non-starch polysaccharides (NSP) in isolated form, especially β-glucans, are reported to have prebiotic effects in pigs. However, little information is available on the possible functional properties of these NSP when the latter are still present in the fibrous matrix of whole cereals. Hulless barleys (HB) are good sources of β-glucans and the content is quite variable among varieties. In order to evaluate the potential of HB as functional feeds, an in vitro experiment was carried out to study the fermentation characteristics of 6 HB varieties varying in their β-glucan contents (36-99 g/kg DM) in comparison to 3 hulled barleys and 5 oats. After a pepsin-pancreatin hydrolysis, the ingredients were incubated in a buffer solution containing minerals and pig feces as inoculum. The accumulated gas production, proportional to the amount of fiber fermented, was measured for 48 h and modeled. Short-chain fatty acid (SCFA) and ammonia concentration were measured in the fermented solutions. A cereal type effect (P < 0.05) was observed on the fermentation kinetics parameters. Rates of degradation and total gas productions were higher in HB than in oats (P < 0.05) but no difference was observed between HB varieties. On the contrary, differences were found between HB for lag time and rate of degradation. The production of SCFA was also higher with HB (6.1 mMol/g DM incubated; P < 0.05) than with hulled barleys and oats (4.9 and 2.9 mMol/g DM incubated respectively). In contrast, oats generated higher ammonia (P <0.05) production (1.4 mMol/g DM incubated, on average) than barley (1.0 mMol/g). In conclusion, HB are better fermented in vitro, produce more beneficial (SCFA) and less harmful (ammonia) metabolites and have a better potential than other cereal species to modulate gut microbiota and improve gut health