Pea populations derived from ten crosses were scored by coupling phase linked sequence characterized amplified region (SCAR) markers A001 and A002, and repulsion phase linked SCAR marker A004 for lodging resistance during the F2 generation. The objective of this project was to test the efficiency of implementation of these three SCAR markers in marker-assisted selection (MAS) for lodging resistance in pea breeding. Chi-square tests showed that A001 and A004 followed a two independent gene segregation model in all of the eight populations that segregated for these two markers. In the F3 field trial, the differences between mean lodging score of A001 (DNA band present) and a001 (DNA band absent) classes varied from -0.5 to -0.9 with an average of -0.6, based on a 1 to 9 lodging scale, across the eight populations surveyed. The differences between mean lodging score of a004 (DNA band absent) and A004 (DNA band present) classes varied from -0.4 to -1.1 with an average of -0.7, across the eight populations surveyed. In comparison, when the combination of two markers (A001; a004 vs. a001; A004) was used, lodging score differences varied from -0.7 to -1.5, with an average of -1.0 across the eight populations. T-test results showed that significant differences (P<0.05) in lodging score were observed between A001 and a001 classes in seven out of eight populations, and between A004 and a004 classes in six out of eight populations. Further T-tests showed that significant lodging differences were observed among the four classes of the A001 and A004 marker combination in seven out of eight populations assessed, including differences at P<0.01 level in six populations. The greater differences among marker combination classes than between individual marker classes showed that combining two markers was more effective than use of each marker alone in MAS. The marker combination explained (R2) 19-57% of lodging and 4-43% of plant height variation in the eight populations surveyed. The high temperature and potential nitrogen leaching in the summer of 2003, reduced plant growth and lodging. Under optimal growth conditions, differences in lodging between resistant and susceptible cultivars could have been greater. Five new markers generated by simple sequence repeat (SSR) primers SAD134, SAB81 and SAD141 were identified in the recombinant inbred line (RIL) population derived from MP1401 × Carneval. The markers generated from primers SAD134 and SAB81 explained 12% and 13% of lodging variation in the RILs, respectively. Primer SAD141 produced three markers which explained 19%, 11% and 25% of lodging variation in the RILs, respectively. Linkage analysis showed that none of the three markers derived from primer SAD141 were allelic. The combination of the three markers from primer SAD141 explained 28% of lodging variation. However, utilization of any of these new markers with A001 and A004 did not substantially increase the proportion of lodging variation being explained. Thus, the new markers have limited potential to improve the efficiency of MAS for lodging resistance in pea breeding.

Pea populations derived from ten crosses were scored by coupling phase linked sequence characterized amplified region (SCAR) markers A001 and A002, and repulsion phase linked SCAR marker A004 for lodging resistance during the F2 generation. The objective of this project was to test the efficiency of implementation of these three SCAR markers in marker-assisted selection (MAS) for lodging resistance in pea breeding. Chi-square tests showed that A001 and A004 followed a two independent gene segregation model in all of the eight populations that segregated for these two markers. In the F3 field trial, the differences between mean lodging score of A001 (DNA band present) and a001 (DNA band absent) classes varied from -0.5 to -0.9 with an average of -0.6, based on a 1 to 9 lodging scale, across the eight populations surveyed. The differences between mean lodging score of a004 (DNA band absent) and A004 (DNA band present) classes varied from -0.4 to -1.1 with an average of -0.7, across the eight populations surveyed. In comparison, when the combination of two markers (A001; a004 vs. a001; A004) was used, lodging score differences varied from -0.7 to -1.5, with an average of -1.0 across the eight populations. T-test results showed that significant differences (P<0.05) in lodging score were observed between A001 and a001 classes in seven out of eight populations, and between A004 and a004 classes in six out of eight populations. Further T-tests showed that significant lodging differences were observed among the four classes of the A001 and A004 marker combination in seven out of eight populations assessed, including differences at P<0.01 level in six populations. The greater differences among marker combination classes than between individual marker classes showed that combining two markers was more effective than use of each marker alone in MAS. The marker combination explained (R2) 19-57% of lodging and 4-43% of plant height variation in the eight populations surveyed. The high temperature and potential nitrogen leaching in the summer of 2003, reduced plant growth and lodging. Under optimal growth conditions, differences in lodging between resistant and susceptible cultivars could have been greater. Five new markers generated by simple sequence repeat (SSR) primers SAD134, SAB81 and SAD141 were identified in the recombinant inbred line (RIL) population derived from MP1401 × Carneval. The markers generated from primers SAD134 and SAB81 explained 12% and 13% of lodging variation in the RILs, respectively. Primer SAD141 produced three markers which explained 19%, 11% and 25% of lodging variation in the RILs, respectively. Linkage analysis showed that none of the three markers derived from primer SAD141 were allelic. The combination of the three markers from primer SAD141 explained 28% of lodging variation. However, utilization of any of these new markers with A001 and A004 did not substantially increase the proportion of lodging variation being explained. Thus, the new markers have limited potential to improve the efficiency of MAS for lodging resistance in pea breeding.

Five breeding populations were created by crossing elite U.S. sorghum parental lines (RTx430, RTx436, BTx631, BTx635, and Tx2903) with 'Sureño', a dual purpose grain mold resistant sorghum cultivar. Molecular markers associated with five previously-reported quantitative trait loci (QTL) for grain mold resistance originating in 'Sureño' were used to determine if their presence enhanced selection for grain mold resistance in these populations. The allelic status of 87 F4 lines, with respect to these QTL, was determined using both simple sequence repeats (SSR) and amplified fragment length polymorphism (AFLP) markers. All 87 F4:5 lines and their parental lines, were evaluated for grain mold resistance in replicated trials in eight diverse environments in South and Central Texas during the summer of 2002. The effects of each allele from the grain mold resistant parent 'Sureño' were determined across and within all five populations, within individual environments, and in each population x environment combination. With a few exceptions, the QTL were effective in reducing grain mold susceptibility only within the RTx430/Sureño progeny, the identical cross that was used in the original mapping study. The results indicate that while that these alleles do confer additional grain mold resistance, they are only selectable in the original mapping population. This fact limits their potential usefulness in an applied breeding program.

Five breeding populations were created by crossing elite U.S. sorghum parental lines (RTx430, RTx436, BTx631, BTx635, and Tx2903) with 'Sureño', a dual purpose grain mold resistant sorghum cultivar. Molecular markers associated with five previously-reported quantitative trait loci (QTL) for grain mold resistance originating in 'Sureño' were used to determine if their presence enhanced selection for grain mold resistance in these populations. The allelic status of 87 F4 lines, with respect to these QTL, was determined using both simple sequence repeats (SSR) and amplified fragment length polymorphism (AFLP) markers. All 87 F4:5 lines and their parental lines, were evaluated for grain mold resistance in replicated trials in eight diverse environments in South and Central Texas during the summer of 2002. The effects of each allele from the grain mold resistant parent 'Sureño' were determined across and within all five populations, within individual environments, and in each population x environment combination. With a few exceptions, the QTL were effective in reducing grain mold susceptibility only within the RTx430/Sureño progeny, the identical cross that was used in the original mapping study. The results indicate that while that these alleles do confer additional grain mold resistance, they are only selectable in the original mapping population. This fact limits their potential usefulness in an applied breeding program.

Weed control in chickpea (Cicer arietinum L.) is challenging because of poor crop competition ability and limited herbicide options. Development of chickpea varieties with resistance to different herbicide modes of action would be desirable. Resistance to imidazolinone (IMI) herbicides in chickpea has been previously identified, but the genetic inheritance and the mechanism were unknown. In many plant species, IMI resistance is caused by point mutation(s) in the acetohydroxyacid synthase (AHAS) gene resulting in an amino acid substitution. This changes the enzyme configuration at the herbicide binding site, preventing the herbicide attachment to the molecule. The main research objective was to genetically characterize chickpea resistance to imidazolinone herbicides. Two homologous AHAS genes, namely AHAS1 and AHAS2 sharing 80% similarity were identified in the chickpea genome. A point mutation in AHAS1 at cytosine 675 thymine 675 resulting in an amino acid substitution from alanine 205 to valine 205 confers the resistance to imidazolinone in chickpea. A KASP marker targeting the point mutation was developed and effectively predicted the herbicide response in the RIL population. This same population was used in molecular mapping where the major locus for herbicide resistance was mapped to chromosome 5. Segregation analysis demonstrated that the resistance is inherited as a single gene in a semi-dominant fashion. To study the synteny of AHAS across plant species, lentil (Lens culinaris) AHAS1 was sequenced. The same mutation that confers the resistance to imidazolinone in chickpea was also found in lentil. Phylogenetic analysis indicated independent clustering of AHAS1 and AHAS2 across pulse species. In vivo and in vitro AHAS enzyme activity analysis showed inhibition of AHAS activity in the susceptible genotype CDC Frontier over time and with the increasing imidazolinone concentrations. In contrast, the resistant genotype CDC Cory did not show AHAS inhibition under the same treatments. In summary, the simple genetic inheritance and the availability of KASP marker could aid in the development of chickpea varieties with resistance to imidazolinone herbicide.

Linseed oil (Linum usitatissimum L.) is valued for its food and non-food applications. Although Canada is the world’s largest linseed producer and exporter, linseed remains a minor crop in part because its yield has been stagnating over the last decade compared to other oilseeds. Narrow genetic base, absence of an efficient hybrid production system and limited genomic tools for linseed breeding are the main factors hindering yield and quality improvements. Here, we characterized the Canadian flax core collection of 407 accessions with 448 genome-wide simple sequence repeat markers and, using association mapping (AM), we demonstrated its potential for the improvement of seed quality and agronomic traits. Genetic structure analyses assigned all accessions to two major groups that were weakly differentiated (FST = 0.094). Genetic diversity was abundant in the total panel (5.32 alleles per locus) with weak familial relatedness (mean = 0.287) for most individual pairs. Linkage disequilibrium (LD) decayed relatively quickly with an average genome-wide LD of ~1 cM. AM for seven seed quality traits including oil content (OIL), palmitic acid (PAL), stearic acid (STE), oleic acid (OLE), linoleic acid (LIO), linolenic acid (LIN) and iodine value (IOD) identified nine stable candidate QTL. LIO and LIN QTL co-localized with previously identified QTL and some mapped in the vicinity of genes known to be involved in the fatty acid biosynthesis pathway. AM conducted for nine agronomic traits including yield, bolls per area (BPA), seeds per boll (SPB), thousand seed weight (TSW), start of flowering (FL5%), end of flowering (FL95%), plant height (PH), plant branching (PB) and lodging (LDG) identified twelve significant marker-trait associations for six of the traits. The associated markers explained between 0.5 to 18.5% of the phenotypic variation, with Lu526 and Lu2532 associated with TSW and Lu943 associated with flowering being the most promising for marker-assisted selection. Statistical simulation for five markers associated with TSW indicated that the favorable alleles have additive effects. None of the accessions carried the five favorable alleles but a few breeding lines had four, indicating that further improvement of TSW and yield could be achieved through marker assisted breeding

No description available.

This study conducts an ex-ante economic impact evaluation of developing low cost technologies for pyramiding useful genes from wild relatives into elite progenitors of cassava in Nigeria, Ghana and Uganda. More specifically, it estimates the change in economic surplus generated by introducing cassava varieties with tolerance to cassava mosaic disease, green mites, whiteflies, and delayed post-harvest deterioration. It compares the economic benefits of marker-assisted selection (MAS) to conventional breeding for these traits. Results indicate that varieties developed with marker-assisted breeding that incorporate all three traits are worth US$2.89 billion in Nigeria, $854 million in Ghana, and $280 million in Uganda over 20 years. If these varieties were to be developed with tolerance to CMD and Green mites alone they would be worth US$1.49 billion in Nigeria, $675 million in Ghana, and $52 million in Uganda if developed through MAS. If developed solely by conventional breeding they would be worth about US$676 million in Nigeria, $304 million in Ghana, and $18 million in Uganda. The difference is mostly due to the faster timing of release for the varieties developed with MAS and the higher probability of success. Several sensitivity analyses were conducted and benefits for MAS range from US$1.7 billion to US$4.3 billion for all three traits depending on assumptions. In all cases, the research investment is highly profitable from a societal standpoint. / Master of Science

Molecular genetic markers can be used to assess genetic diversity, assign parentage, quantify inbreeding, and demonstrate structuring of populations across a system. Striped Bass Morone saxatilis, and Walleye Sander vitreus, are widely sought gamefishes in the Commonwealth of Virginia. Striped Bass along the Atlantic Coast and within the Roanoke River drainage exhibit low genetic variation. Screening 12 microsatellite DNA markers across the range to define population genetic structure, I found that anadromous populations in the Southeast and the Chesapeake Bay were differentiated from landlocked populations in the Roanoke River basin, with an average FST of 0.066. Range-wide, Striped Bass are differentiated between the landlocked and anadromous populations, which need to be managed separately. Within stocked populations in the Roanoke River basin, there have been impacts stemming from small numbers of broodstock propagated, and inter-individual relatedness is ~20% within stocked reservoirs. Walleye across the eastern native range were screened to better understand evolutionary history and to identify native marker alleles for the upper New River population. Population genetic variation at eight microsatellite loci showed differentiated stocks in Alabama, Mississippi River, Eastern Highlands (Tennessee, New, and Ohio Rivers), and the Great Lakes drainages. All estimates of effective numbers of breeding individuals were under 25, and all populations within all watersheds had ~15-20% inter-individual relatedness, likely effects of both natural demographic processes and stocking. The extent of Eastern Highlands Walleye includes both the Ohio and Tennessee basins. Although I did not identify new marker alleles for native New River Walleye, I determined that marker-assisted selection has increased the frequencies of existing marker alleles for the native stock. Application of the results of this project will contribute to better fisheries management for both of these important species. / Master of Science / Population genetics have proven useful for defining the most appropriate units for conservational management across a variety of species. Molecular genetic markers can be used to assess genetic diversity, assign parentage, quantify inbreeding, and demonstrate structuring of populations across a system. Striped Bass Morone saxatilis and Walleye Sander vitreus are both widely sought gamefishes in the Commonwealth of Virginia. I applied population genetic approaches to recognize genetically distinct groups of populations and to recommend genetically cognizant management practices. Striped Bass across the Atlantic Coast and in the Roanoke River drainage exhibit low genetic variation. After screening variation at 12 DNA markers, I found that Striped Bass are differentiated between landlocked and migratory populations, which need to be managed separately. Within stocked populations in the Roanoke River basin, there have been impacts stemming from propagation of small numbers of broodstock, and propagation and stocking practices will need to be changed to reduce apparent inbreeding depression. Walleye populations across the eastern native range were screened to better understand evolutionary history and to seek new marker alleles for the native upper New River population. After screening genetic variation at eight DNA marker loci, I identified four evolutionarily distinct stocks of Walleye across eastern North America. Although I did not identify new marker alleles for native upper New River native Walleye, I showed that marker-assisted selection has increased the frequencies of existing marker alleles over the past twenty years. The results of this project can contribute to better fishery management strategies for both of these important gamefish species.

The overall aim of this thesis was to investigate the genetic control of beef quality in a commercial population of Aberdeen Angus-sired cattle with a view to trait improvement. The population studied included 500 Angus-cross animals, all with purebred Aberdeen Angus sires, from a selection of farms throughout Scotland. A number of carcass-related weight traits and taste panel assessed sensory traits were measured on these animals. A population of 265 Charolais cross cattle (all with purebred sires) was then used to explore the extrapolation of results across breeds. The first aim of this thesis was to investigate heritabilities for important carcass and meat quality traits and to assess the quality of a number of taste-panel derived meat quality traits by calculating three consistency statistics. Consistency statistics (parameter range 0 to 1) for the taste panel traits were moderately high, particularly for panel member consistency and reproducibility, with values ranging from 0.48 to 0.81 and 0.43 to 0.73, respectively. Estimated heritabilities were low for most of the sensory taste-panel-evaluated traits, where the maximum value was 0.16 for overall liking, but were higher for carcass traits where carcass weight heritability was 0.7. To perform these analyses it was first necessary to confirm paternity using a number of genetic markers. Therefore, a comparison of the power of both microsatellite and SNP markers for paternity exclusion was carried out to determine the more effective method. Results indicated that approximately three times as many SNP markers than microsatellite markers were required for parentage exclusion, and a panel of 15 microsatellite markers was used to assign paternity before subsequent data analysis was carried out. The remaining aims of this thesis centred on exploring genetic markers for carcass and meat quality. Firstly, the Angus animals were genotyped for the del11 myostatin mutation which was found to be segregating at a relatively low frequency (0.04) and was shown to be associated with a 17.4 kg increase in carcass weight (P < 0.05) in the heterozygous animals when compared to the homozygous wild-type animals. By analysing the haplotype associated with the mutant allele, it was determined that there have been at least two separate introductions of the mutant allele into the Aberdeen Angus breed. A number of SNPs were also tested for their effects on the carcass and meat quality traits in the Angus animals. The SNPs fell into two groups: eight that have been incorporated into commercially available tests and a further 28 from alternative candidate genes that have effects in different breeds and species. In total, 17 SNPs significantly affected at least one of the traits measured. Of these significant associations, a number have been seen previously, such as the association between calpain and tenderness (P = 0.01) and growth hormone and eye muscle area (P = 0.05), and some of which were novel, such as the association between growth hormone receptor and steak odour (P = 0.02) and corticotrophin releasing hormone and gristle distance from fat (P = 0.004). A further six SNPs, identified by resequencing of the malic enzyme 1 (ME1) and small heterodimer partner (SHP) genes, were tested for their effects on the traits measured in this thesis. Five of the SNPs, including one which caused a non-synonymous amino acid change, had a significant effect on at least one of the traits tested including fat class (P = 0.002), eye muscle area (P = 0.01), sirloin weight before maturation (P = 0.03), sirloin steak tail length (P = 0.004) and juiciness (P = 0.004) where the effect sizes were 1.79 units, 565 mm2, 0.36 kg, 17.12 mm and 0.23 taste panel units, respectively. To assess the effect of the genotyped SNPs on intramuscular fat (IMF), a simple method of visible IMF quantification in the sirloin steak was developed using digital photographs and an image analysis program. Results showed that two SNPs in the calpain gene, known to be linked with an increase in meat tenderness, were associated with an increase in visible IMF% and the del11 mutation was associated with a reduction in visible IMF%. The heritabilities, SNP association validations and novel SNP-trait associations identified in this thesis provide tools for use in breeding programs, possibly via marker assisted selection to improve meat quality traits. However, the results seem breed-specific, as most of the significant effects were not replicated in the Charolais population.