5 pp. / Winter cereals such as barley, oats, triticale, and wheat are commonly grown as forage for the dairy industry. The purpose of this study is to generate information on yield potential of various winter cereal forage varieties. A trial testing the yield potential of eleven winter cereal forage entries including barley, oat, triticale, and wheat varieties was established at the Maricopa Ag Center on October 16, 2015. Forage yields were obtained at cuttings on December 10, February 29, and April 18. The highest yielding entry at the first cutting was Stockford barley. At the second and third cuttings, the highest yielding entry was Summit 515 wheat. Summit 515 wheat was also the highest yielding entry averaged over all cuttings. As a group, the wheat entries were higher yielding that the other winter cereals except at the first cutting where the barleys were higher yielding.

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Supplementation with graded levels of threonine to an all barley-lysine diet (0.75% total lysine) improved the daily gain, feed efficiency and carcass quality of growing-finishing pigs. An addition of 0.10% threonine produced the optimum growth response in the experimental animals. No additional improvement was obtained with higher levels of threonine or threonine plus methionine supplementation of the diet. The 0.10% level of threonine supplementation gave performance criteria which were comparable to those obtained with the barley-soybean control diet, except the former diet resulted in significantly higher backfat measurements. Threonine added at levels of 0.15% resulted in higher nitrogen retention than the other barley-lysine-threonine diets. Nitrogen retention on this diet did not differ significantly from the control diet. Barley-amino acid diets resulted in better protein ultilization than barley-soybean control diets. Feeding trials and metabolism trials indicated that methionine was not limiting in barley and that threonine was the second limiting amino acid. Growth trials with weanling rats confirmed the results obtained in the pig nutritional experiments. Rat experiments indicated that no additional beneficial effects were obtained when lysine levels were increased from 0.75% to 0.90% even when supplemented with additional threonine. Results indicated that supplementation with lysine to a total level of 0.75% and threonine at a level of 0.10% resulted in a highly balanced amino acid ratio for rats, and gave growth rates which approached those obtained on the control diet. Supplementation of the barley-lysine diet with 0.20% threonine and all other essential amino acids resulted in growth rates and nitrogen retentions which resembled the results obtained with the control diet. The replacement of the essential amino acid mixture with glycine on an equal nitrogen basis did not result in adequate nitrogen retention or growth rates. / Land and Food Systems, Faculty of / Graduate

Genetic studies were carried out on the fungal parasite Ustilago hordei (Pers.) Lagerh. and on its host, Hordeum vulgave L. (cultivated barley). In these studies of the host-parasite relationship, special emphasis was placed on the genetic investigation of the pathogenicity. The thesis is divided into four parts. Part I deals with multial1 elism of genes for virulence (v-genes) in the parasite, and demonstrated that four different levels of virulence (obtained on the barley cultivar Trebi) are controlled by alternative alleles at a single genetic locus in the parasite. This is the first demonstrated example of a series of multiple alleles determining different levels of virulence. Part II concerns the identification and characterization of v-genes in U. hordei and of resistance genes (R-genes) in H. vulgave. Three v-genes (two of them new, one of them previously known) were identified. It was shown that the previously identified gene was expressed either as a dominant or a recessive, dependingoon the conditions under which it was tested, and that the newly-identified genes were both recessive. Cultures possessing the newly-discovered v-genes were used in identifying two new R-genes in the barley host. A study of interactions involving the newly discovered v- and R-genes led to the conclusion that these interactions have their basis in gene-for-gene relationships. Part III deals with the synthesis of a complex biotype of u. hordei possessing v-genes at two genetic loci. Disease reaction obtained with this complex biotype were compared both qualitatively and quantitatively with those obtained with the simpler, parental biotypes. In tests on certain cultivars the complex biotype produced either the same or higher levels of disease reaction. Because the new biotype has ah extended host range it is considered that under certain conditions it would be comparatively more fit than either of the parental biotypes from which it was derived. Part IV of the thesis concerns the effects of nutritional deficiency on the action of v-genes. Dikaryons which were homozygous for arg, ad or met were in all cases non-pathogenic; for those which were homozygous for pdx, pathogenicity was unaffected. For dikaryons which were heterozygous for one or more nutritional deficiences, pathogenicity was either unimpaired or reduced, depending on the combination (deficiency: virulence gene: host cultivar) which was tested. It was concluded that the specificity of pathogen biotypes was not determined by the availability or non-availability of specific nutritional factors. However, the effects were not entirely non-specific, since changes in levels of virulence were shown only in certain tests. / Science, Faculty of / Botany, Department of / Graduate

Diuraphis noxia Kurdjumov (Hemiptera: Aphididae: Macrosiphini) is a major agricultural pest that causes extensive economic losses to the wheat and barley industries. Resistant cultivars were relatively successful in controlling this pest until the recent development of new D. noxia (Russian wheat aphid, RWA) biotypes. The aim was to investigate the role of the aphid endosymbiont, Buchnera aphidicola, in the RWA-host interaction. It was hypothesized that variations in the endosymbiont’s key essential amino acid biosynthetic pathway genes, their copy numbers, and/or expression levels, maybe a determining factor influence the RWA’s success in the aphid-host interaction. Aphid symbiont species content, key essential amino acid biosynthetic gene variation, plasmid copy numbers and expression levels of ten different RWA biotypes were determined, using DGGE, RT-PCR, RT-qPCR, 5’-RACE and sequencing. The RWA biotypes were shown to be monosymbiotic, with plasmid copy numbers varying between biotypes. Only a single CCC-insert in a non-coding region of the leucine plasmid differed between the biotypes. Similar variations were identified in the family Aphididae, suggesting a regulatory function for this region. The presence of this CCC-insert in a plasmid led to an increase in the leader sequence length of the leuA gene. The insert may also have a functional role through gene regulation, since it increased the expression levels of subsequent genes (leuA and leuB). An endosymbiont that upgrade the host’s diet with the required essential amino acids will be beneficial to RWAs when feeding on resistant wheat cultivars as it will enhance aphid fitness. This suggests selective pressure of resistant wheat cultivars on the aphid, i.e. the incapability to change resistant cultivar essential amino acid content, could select for individuals with beneficial endosymbionts. B. aphidicola could therefore play a role in the development of RWA biotypes. The influences that statistical normalization methods have on the final identification of differentially regulated Affymetrix probe sets in RWA-plant interactions were also investigated. The hypothesis was that a subset of the probe sets determined as differentially regulated would be consistent, regardless of the normalization and background method utilized, if all the other analyses are kept constant. This subset would be normalization-method-independent. The data of two Affymetrix RWA-plant interaction experiments were analyzed with five different normalization and background correcting methods and at three different confidence levels, with the results subjected to FDR and FWER correction algorithms. The results showed that on average a third of the regulated genes were only selected after normalization by a single method and that the total number of genes deemed regulated was highly normalization method dependent. Normalization-method-biases could also not be countered by increased confidence levels and these biases eventually determined the probe sets deemed differentially regulated, even after FDR and FWER corrections. Both these strategies actually increased normalization-method-biases and these could only be corrected by using multiple normalization methods to identify the normalization-method-biases-independent probe set subset. / Thesis (PhD)--University of Pretoria, 2011. / Genetics / unrestricted

The aim of the study was to determine the digestibility of Atriplex nummularia cv. De Kock, supplemented with three levels (15%, 30%, and 45%) of either maize or barley, using different in vitro techniques. An in vivo digestibility trial was conducted, together with a number of in vitro trials. An important development has been the introduction of biological methods (Jones&Theodorou, 2000). Three digestion techniques that simulate the digestion process are currently available to determine the nutritive value of ruminant feeds: <ol> <li>Digestion with rumen micro-organisms as in the work of Tilley&Terry (1963) or gas method (Menke et al., 1979). Digestion with faeces microorganisms (El Shaer et al., 1987), as an alternative to rumen fluid inoculum.</li> <li>Cellulase methods</li> <li> In situ incubations of samples in nylon bags in the rumen.</li></ol> The results of this study showed no significant difference (P>0.05) between the rumen- and faeces inoculum in vitro techniques, but they did differ significantly from the gas production and cellulase techniques. There was also no significant difference between the gas production and cellulase techniques. Organic matter digestibility (OMD %) of the in vitro techniques differed significantly from the in vivo OMD % values. There are several possible explanations for the difference between the in vivo and in vitro OMD %. 1. Practical mistakes could have been made. 2. The simulation of the rumen motility in vitro is often difficult and it may be that all the feed particles did not have the same exposure to the micro-organisms, as it would have in the rumen of an animal. The different rumen pools are also not fully represented in vitro. 3. The fermentation characteristics and microbial constitution of the rumen inocula differ, between the animal used for the in vivo digestibility trial and the animals used for rumen inocula collection. 4. With in vivo digestibility the time of digestion is not known, and therefore the time of rumen and gastric digestion in vitro could have been too long or too short. It was found that the in vitro faeces technique of El Shaer et al., (1987) is an easier and cheaper alternative to the classic rumen fluid in vitro technique of Tilley&Terry (1963), as modified by Engels&Van der Merwe (1967). The in vitro faeces technique uses faeces as an inoculum and therefore solves the problems associated with the use of cannulated animals. The gas production in vitro technique has certain advantages, but still has the disadvantage of needing cannulated animals for rumen inocula. The cellulase-based in vitro technique in contrast eliminates the use of cannulated animals. Although the in vitro gas production technique of Pienaar (1994) and the cellulase in vitro technique could both be used to determine the OMD % of Atriplex nummularia cv. De Kock, the values will be lower than in vivo determinations. / Dissertation (MSc(Agric))--University of Pretoria, 2009. / Animal and Wildlife Sciences / unrestricted

Pyrenophora teres f. teres is the causal agent of net form net blotch of barley. P. teres f. teres is prevalent globally across all barley growing regions and globally is the most devastating foliar disease of barley. Though economically important, the molecular mechanism whereby P. teres f. teres causes disease is poorly understood and investigations into these mechanisms have been hindered by a lack of genomic resources. To set a genomic foundation for P. teres f. teres the reference isolate 0-1 was sequenced and assembled using PacBio single molecule real-time (SMRT) sequencing and scaffolded into 12 chromosomes to provide the first finished genome of P. teres f. teres. High confidence gene models were generated for the reference genome of isolate 0-1 using a combination of pure culture and in planta RNA sequencing. An additional four P. teres f. teres isolates were sequenced and assembled to the same quality as the reference isolate 0-1 and used in a comparative genomic study. Comparisons of the five P. teres f. teres isolates showed a two-speed genome architecture with the genome being partitioned into core and accessory genomic compartments. Accessory genomic compartments clustered in sub-telomeric regions of the P. teres f. teres genome with a majority of previously identified quantitative trait loci (QTL) associated with avirulence/virulence being spanned by these accessory regions. Using these genomic resources, with a bi-parental mapping population and a natural population for QTL analysis and genome wide association study (GWAS), respectively, we identified a candidate gene for the previously mapped AvrHar. QTL analysis identified a locus extending off the end of P. teres f. teres chromosome 5 and GWAS analysis identified significant associations with a gene encoding a small secreted protein. The candidate AvrHar gene was validated using CRISPR-Cas9-RNP gene disruption in parental isolates 15A and 0-1. Disruption of AvrHar in isolate 15A did not result in a phenotypic change while disruption of the 0-1 allele resulted in a complete loss of pathogenicity. This is the first identification of an effector from P. teres f. teres validated using CRISPR-Cas9-RNP gene editing. / North Dakota Barley Council

Barley is one of the world's most important food and feed crops. It is adapted to a wide range of environments. According to Harlan and Martini (1936) barley is grown from north of the Artic Circle to the sands of the Sahara, and from the slopes of Mt. Everest to the lower delta of the Nile. Considerable progress has been made in its improvement through plant breeding. Barley is one of the best cultivated crop plants for use in genetic studies. It is a diploid plant from the family Gramineae with seven pairs of chromosomes. The cultivated species are interfertile and have a large number of readily distinguishable genetic characters. Approximately 370 characters are recognized (Nilan, 1964). Many of Barley's genes have been mapped and assigned to one of the seven chromosomes. Linkage groups in barley have been designated in a number of ways. A Roman numeral was used extensively in the earlier studies to identify each linkage group. More recently an Arabic number system has been used. This system was adopted by the Fourth Annual Barley Research Worker's Conference and will be followed in this study. The study involves 24 contrasting factors and was undertaken to determine the location of certain genes already reported in specific linkage groups and, if possible, to assign several previously unassigned genes to linkage groups. Of the 24 factor pairs studied, six have not yet been assigned to a chromosome. The inheritance and linkage associations of these unassigned genes receive major emphasis in this study.

Twenty-two barley crosses (Hordeum sp.) were studied in the F2 generation to determine the inheritance of the following contrasting characters: (N,n),(E,e),(Tr, tr), (Li,li),(Gp,gp),(K,k),(Z,z), (Gl,gl), (Gs, gs),(B,b),(Trd,trd),(O,o),(R,r),(Rb,rb), and Ge, ge). The three factors for glossyness, (gl), (gs), and (ge), were studied in relation to the other factors and each other to determine possible linkage relationships. (gl) was found to be linked with (k) and 16 percent recombination and to (z) with 13 percent recombination. (gs) appeared to be linked with (gp) in two crosses, with a third cross showing independence. No other linkage relationships were found.

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