Thesis (Ph.D.)--University of Adelaide, Dept. of Agronomy, 1980.

Thesis (Ph. D.)--Oklahoma State University, 2005. / Vita. Includes bibliographical references (p.48-52).

In this study whole-genome SNP data from 1977 animals, originating from thirteen sheep breeds in South Africa was analysed. The animals were classified into three production types: dual-purpose (Afrino, Dohne Merino, Dormer, Merino, SA Mutton Merino), meat (Black Headed Persian, Damara, Dorper, Meatmaster, White Dorper) and indigenous (Fat-tailed, Namaqua Afrikaner, Pedi). All animals were genotyped using the Illumina Ovine 50K SNP BeadChip. The aim was to investigate the genetic diversity and inbreeding levels of both indigenous and commercial sheep breeds in South Africa. The populations were first investigated individually to analyse within population diversity, whereafter they were merged in order to perform between population diversity analysis. During sample-based quality control, a total of 207 animals were removed due to low call rates. The number of SNPs remaining after marker-based quality control ranged from 32 422 to 44 778. Average observed heterozygosity values of 0.360, 0.355 and 0.340 were observed for dual-purpose, meat and indigenous populations respectively. Average linkage disequilibrium (LD) estimates were highest for dual-purpose populations at 0.277, followed by meat type populations at 0.259, and the lowest LD was observed for indigenous populations at 0.255. Dual-purpose, meat and indigenous populations showed average minor allele frequencies (MAF) of 0.393, 0.427 and 0.444 respectively. Principal component analysis (PCA) and ADMIXTURE results showed a clear differentiation between the dual-purpose populations, and the meat and indigenous populations. Average inbreeding coefficient (Fis) estimates of 0.008, -0.029 and 0.003 was observed for dual-purpose, meat and indigenous populations respectively. All populations showed a decline in effective population size (Ne) across generations. For all populations, the highest percentage of ROH was found in the shortest length category (1-3.99 Mb), and the largest number of ROH were observed on the first ten chromosomes. The average FROH estimates was highest for dual-purpose populations at 0.015, followed by the meat type and indigenous populations at 0.011 and 0.005 respectively. An unrooted phylogenetic tree based on pairwise Fst estimates showed a divergence of the dual-purpose populations from the meat and indigenous populations. Results from this study indicated lower variation within dual-purpose populations, and higher variation within indigenous populations. High population differentiation was observed between the various production types. / Dissertation (MSc Agric) (Animal Science: Animal Breeding and Genetics))--University of Pretoria, 2020. / Animal and Wildlife Sciences / MSc Agric) (Animal Science: Animal Breeding and Genetics) / Unrestricted

This study aimed to identify genomic regions of significance that are associated with body weight traits and reproduction traits in sheep by using estimated breeding values in a genome wide association study (GWAS). The following traits were investigated: body weight recorded at selection age of 14 months (BW), number of lambs born (NLB), number of lambs weaned (NLW) and total weight of lamb weaned (TWW). A total of 411 animal were genotyped using the Illumina® Ovine SNP50 BeadChip, and consisted of 152 Afrino, 129 Cradock Merino and 130 Grootfontein Merino sheep. Quality control (QC) were implemented using PLINK v1.07 where the parameters were set as 90% for individual call rate, 95% for SNP call rate, minor allele frequency of less than 2% and P <0.001 for Hardy-Weinberg equilibrium. Population parameters were calculated per dataset. The average MAF values estimated for the populations were 0.252, 0.372 and 0.372 for the Afrino, Cradock Merino and Grootfontein Merino, respectively. Inbreeding coefficients were estimated at - 0.025 (Afrino), - 0.025 (Cradock Merino) and 0.002 (Grootfontein Merino). The expected heterozygosity was 0.363 for the Afrino and 0.369 for both Merino populations. All three sheep populations had low inbreeding levels and moderate genetic variation. The population genetic substructure, ancestry proportion and genetic relatedness between the populations were investigated via principal component analysis (PCA) and admixture plots. These plots corresponded to the populations’ selection practises and breeding programs as well as to the geographical locations where the individuals were kept. The GWAS was applied to each dataset separately and per trait using the efficient mixed model association eXpedited (EMMAX) software and visualised by Manhattan plots. Nine suggestive SNPs were identified to be in possible association with the traits. Of these nine, seven SNP were identified to be in close proximity or linked to previously annotated genes. Seven genes were identified which were in association with growth and reproduction traits. The genes SIX6, C14orf13 and TRPS1 showed the most promise for body weight and growth traits. For reproduction and fertility traits the genes LIG1, CABP5, GRIK3 and HDAC9 warrants further investigation. / Dissertation (MScAgric (Animal Science))--University of Pretoria 2020. / Grootfontein Agricultural Development Institute / Animal and Wildlife Sciences / MScAgric (Animal Science) / Unrestricted

The aim of this thesis was to evaluate alternative management options for the smallholder dairy cattle production system in South Africa (SA). Specific objectives included, were to benchmark cow performance in the smallholder (SH) against their counterparts in a high-input system (H), to develop a SH herd model, and to evaluate alternative management options for the improvement of smallholder dairy herd profitability. Data on production (305-day yields of milk, fat and protein), lactation length, somatic cell count (SCC), and reproductive traits (age at first calving (AFC), and calving interval (CI) obtained from the South African National Dairy Animal Improvement scheme (NDAIS) were used in a benchmarking study. Least squares means per trait were compared between the two systems, and lactation curves for roduction traits and SCC were plotted. Results revealed that mean yields of milk, fat and protein were significantly (P<0.05) lower in the SH (4 097±165, 174±5.1 and 141±4.5 respectively) compared to the H system (6 921±141, 298±4.7, and 245±4.1, espectively). Mean lactation length was significantly (P<0.05) shorter for the SH (308±15.1) compared to the H system (346±12.8). Log-transformed SCC was significantly (P<0.05) higher in the SH (2.41±0.01) relative to the H system (2.27±0.01). Cows in H herds exhibited typical lactation curves, in contrast to flat and low-peaking curves obtained for the SH system. SH cows had significantly (P<0.05) older AFC (30±0.5) than those in the H system (27±0.5). There was no significant difference (P<0.05) in CI between the two systems. A bio-economic SH herd model was developed by adapting a previously developed model for the H system in SA. Parameters used were obtained from NDAIS, survey data, personal communications, and literature. The model integrated herd dynamics, outputs, nutrient energy requirements, management, and their associated economics. Nutrient energy requirements were estimated for maintenance, growth, reproduction, and lactation. The developed SH herd model was used to evaluate alternative herd management options, using the partial budget approach. Milk yield (MY), live weight (LW), AFC, and CI were used as indicators of cow performance. Herd management practices studied were herd size (HS), replacement rate (RR), feeding system (FS), breeding methods (natural service vs artificial insemination), and source of replacement heifers (raising vs. buying in). Improvements in profitability were attained by increasing MY or increasing herd size, using small to medium sized cows, or reducing AFC, CI or RR. Break-even points were 3 687.4 l/year, 500 kg, 29 months, 420 days and 25% for MY, LW, AFC, CI, and RR, respectively. Profitability was mostly sensitive to the prices of milk and feed. A drop in the price of milk below R4.50/l or increase in the cost of feed above R5.60/kg DM generally resulted in non-profitability. Relying on pasture only for feed was non-viable, and supplementation of pasture with concentrate was the most profitable feeding system. Feeding systems based on supplementation of pasture with concentrate, and silage were resilient to fluctuations in the price of milk, remaining profitable even when the price dropped to R4.10/l. Using artificial insemination or buying-in replacement heifers are additional management strategies that increase SH dairy farming profitability. These recommended management options should be used in combination for achieving maximum herd profitability. / Thesis (PhD (Animal Science))--University of Pretoria, 2020. / UP Postgraduate/Doctoral Research Bursary / Animal and Wildlife Sciences / PhD (Animal Science) / Unrestricted

Soybean [Glycine max (L.) Merrill] is an important source of protein and oil for both nutritional and industrial applications. Increasing seed yield and protein concentration is the main goal of many soybean breeders to meet market demands. Soybean breeders have occasionally succeeded in producing high yielding cultivars with increased protein content using conventional means despite the negative correlation that exists between these two traits. The efficiency of breeding for seed yield and protein concentration improvement in soybean could be increased using marker assisted selection (MAS) breeding strategies to select genotypes containing favorable alleles for faster cultivar development. The objective of this study was to identify quantitative trait loci (QTL) associated with seed yield, and separately, seed protein concentration and then compare phenotypic selection (PHE) and MAS approaches for seed yield and protein concentration improvement. Two hundred and eighty two F5 derived recombinant inbred lines (RILs) were developed from a cross of Essex × Williams 82 and genotyped with 1586 single nucleotide polymorphism (SNP) markers. The population was divided by days to maturity (10 days) into three tests (early, mid and late) each with 94 genotypes, with one genotype overlapping in maturity in the mid and late tests. In 2009, the three tests, parents and checks were grown in a randomized complete block design (RCBD) in: Fayetteville, AR; Harrisburg, IL and, Knoxville, TN replicated three times, and evaluated for seed yield and protein concentration. Data were combined within each test across three locations and analyzed using the MIXED procedure of SAS to determine that there were significant genotypic differences among RILs. Composite interval mapping (CIM) detected nine seed yield and ten protein concentration QTL which may be good candidates for MAS as they were environmentally stable. Selections to compare PHE, and MAS for seed yield and protein concentration provided 8 replicated field tests in four relative maturity groups grown in a RCBD replicated three times in three locations in Tennessee, in 2010. We demonstrated that both MAS and PHE may be used to select quantitative traits; however, more studies are required to optimize MAS for quantitative trait improvement. 

Wholegrains have been linked with significant health benefits such as management of cardiovascular disease, diabetes and some cancers. This study aimed to add value to the grain industry by exploring new nutraceutical targets. This was achieved using bioassay guided fractionation. Wheat extracts including wholegrain, endosperm, pericarp and aleurone from different commercial varieties were investigated for in vitro bioactivity in antioxidant, glycosidic enzyme inhibition, anti-inflammatory, anti-cancer, immune function and cholesterol lowering assays. This study found wheat to have antioxidant activity as measured by oxygen radical absorbance capacity (ORAC) assays with higher values reported for the wheat bran extracts. Amino acid trytophan was identified as the most dominant antioxidant compound in the hard wheat variety durum with a TE value of 24217 ± 3158 µmol/g compound. The unsaturated fatty acids oleic, linoleic and linolenic acids proved to be responsible for the majority of the antioxidant activity in the hard wheat bran H2 with TE values of 2424 ± 274, 5220 ± 523 and 5542 ± 102 µmol/g compound, respectively. Wheat bran and germ but not wholegrain or endosperm displayed α-glucosidase and α-amylase inhibiting properties. Through bioassay guided fractionation, phosphoglycerides, 1,2-linoleoylglycero-3-phosphate and 1-palmitoyl-2-linoleoylglycero-3-phosphate were deemed responsible for the α-glucosidase inhibition. Crude wheat extracts were not cytotoxic to a number of human cancerous cell lines. However, some specific fractions showed selective cytotoxicity to the PC3 human prostate tumour cell line. These fractions contained a number of alkylresorcinols with comparative IC50 values (µg/mL) 5-(2-oxotricosanyl)resorcinol (10.9), trans 5-(14-nonadecenyl)resorcinol (13.7), 5-heptadecylresorcinol (22.5) and trans 5-(16-heneicosyl)resorcinol (42.2) to the known anti-cancer agent Chlorambucil (58.7). In this study, wheat bran extracts have not shown any anti-inflammatory inhibition, estrogen binding inhibition, cholesterol lowering or immune function activity. Wheat bran has proved to be a highly nutritious by-product of the wheat milling industry with a number of protective health effects

Pollen grains serve a very important role in the life cycle of flowering plants, in that they are involved in the transmission of inherited characteristicsfrom generation to generation. Because of their small size the study of pollen grains has been necessarily associated with the development of the microscope. Not until the middle of the seventeenth century, when Hooke gave the world the compound microscope, was an instrument available with sufficient power to adequately reveal the shapes of pollen grains. However , two of Hooke's contemporaries, Malpighi and Grew, who used a simple microscope , are generally recognized as the co-founders of pollen grain morphology.

The purpose of this study was to examine the molecular evolution of floral developmental MADS-box genes in diploid and allotetraploid cotton (Gossypium, Malvaceae). We isolated and characterized both cDNA and genomic DNA sequences of four MADS-box genes, B-sister, APETALA3 (AP3), PISTILLATA (PI, two copies) and AGAMOUS (AG), in seven Gossypium species (2 A-genome species, 2 D-genome species, 1 C-genome species and 2 AD-genome species) as well as an outgroup species, Gossypioides kirkii. We then studied the expression patterns of each gene by reverse-transcriptase PCR (RT-PCR) in each flower part for different flower stages of G. arboreum (A-genome), G. raimondii (D-genome) and G. hirsutum (AD-genome). We found that these MADS-box genes are evolving independently at the DNA sequence level but exhibit highly variable expression patterns in allotetraploid G. hirsutum. These MADS-box genes contain highly conserved exon lengths and exon/intron structures, high nucleotide identity with homologs in Arabidopsis thaliana and Antirrhinum majus, and conserved gene phylogeny within the genus Gossypium. All the genes exhibit evidence of codon bias. The AP3 gene in Gossypium appears to be subject to positive selection, while the PI-small copy of the PI gene appears to be subject to strong functional constraints together with a very low mutation rate. Within G. hirsutum, the B-sister gene exhibits gene silencing of the A-subgenomic homoeolog and the PI-big copy of the PI gene has experienced pseudogenization by insertion of a copia-like retroelement. The AP3, PI-small and AG genes show biased expression patterns in G. hirsutum. These MADS-box genes also demonstrated developmentally regulated expression patterns in G. arboreum, G. raimondii and G. hirsutum.

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.