Integration of two or more genomic maps provides a higher density of markers and greater genome coverage than can be obtained with the resources available for a single mapping study. Map integration is important in any species for which an annotated complete genome sequence is not available. For organisms currently being sequenced, a pre-sequence integrated map is essential to provide the "backbone" for assembly of the sequence. Map integration also facilitates the identification and resolution of discrepancies among different maps; mapping of QTLs, ESTs, and BACs; and positioning of candidate genes. However, the inconsistencies in markers and populations used in individual mapping studies limit our ability to fully integrate the available data. By concentrating on marker orders rather than marker distances, one can join together published map data to include a majority of markers with the best estimate of their order in the genome. In this study, a comprehensive reference map was constructed from 28 published cotton AD genome maps. The output reference map contains 7,424 markers and represents over 93% of the combined mapping information from the 28 individual AD genome genetic maps. This study applied the use of bioinformatics and computational biology in cotton genome mapping integration. The output will be stored and displayed through CottonDB (http://www.cottondb.org), a public cotton genome database.

Integration of two or more genomic maps provides a higher density of markers and greater genome coverage than can be obtained with the resources available for a single mapping study. Map integration is important in any species for which an annotated complete genome sequence is not available. For organisms currently being sequenced, a pre-sequence integrated map is essential to provide the "backbone" for assembly of the sequence. Map integration also facilitates the identification and resolution of discrepancies among different maps; mapping of QTLs, ESTs, and BACs; and positioning of candidate genes. However, the inconsistencies in markers and populations used in individual mapping studies limit our ability to fully integrate the available data. By concentrating on marker orders rather than marker distances, one can join together published map data to include a majority of markers with the best estimate of their order in the genome. In this study, a comprehensive reference map was constructed from 28 published cotton AD genome maps. The output reference map contains 7,424 markers and represents over 93% of the combined mapping information from the 28 individual AD genome genetic maps. This study applied the use of bioinformatics and computational biology in cotton genome mapping integration. The output will be stored and displayed through CottonDB (http://www.cottondb.org), a public cotton genome database.

In order to get full understanding of how evolution proceeds in natural settings it is necessary to reveal the genetic basis of the phenotypic traits that play a role for individual fitness in different environments. There are a few possible approaches, most of which stem from traditional mapping efforts in domestic animals and other model species. Here we set the stage for gene mapping in natural populations of birds by producing a large number of anchor markers of broad utility for avian genetical research and use these markers to generate a genetic map of the collared flycatcher (Ficedula albicollis). The map reveals a very high degree of synteny and gene order conservation between bird species separated by as much as 100 million years. This is encouraging for later stages of mapping procedures in natural populations since this means that there is a possibility to use the information from already characterized avian genomes to track candidate genes for detailed analysis in non-model species. One interesting aspect of the low degree of rearrangements occurring in the avian genomes is that this could play a role in the low rate of hybridization barriers formed in birds compared to for instance mammals. An analysis of Z-linked gene markers reveals relatively long-range linkage disequilibrium (LD) in collared flycatchers compared to other outbred species but still, LD seems to decay within < 50 kb indicating that > 20.000 markers would be needed to cover the genome in an association scan. A detailed scan of 74 Z-linked genes evenly distributed along the chromosome in both the collared flycatcher and the pied flycatcher (Ficedula hypoleuca) indicates that there are regions that evolve under directional selection, regions that might harbor loci of importance for adaptive divergence and/or hybrid inviability.

Tambaqui (Colossoma macropomum) is the largest native Characiform species from the Amazon and Orinoco river basins of South America. Tambaqui farming is growing rapidly in Brazil, its production reached 139.209 tons in 2014, what corresponds to 57.7% of increase compared with 2013. However, few genetic studies of tambaqui are currently available. The tambaqui genetic studies for cultured and wild populations need a holistic approach for a rational action facing ecological and market challenges in aquaculture. Approaches based on genetic studies have provided important tools to understand population dynamics, local adaptation, and gene function to improve selection strategies to be applied in breeding programs. The next-generation sequencing (NGS) allowed a great advance in genomic and transcriptomic approaches, especially related to non-model species. The genotype-by-sequencing (GBS) is one of this approaches based on genome complexity reduction using restriction enzymes (REs). This thesis presents the application of these approaches to provide advances in the genetic background for tambaqui studies. The GBS approach provided a high-density SNPs panel that allowed us to develop the first linkage map, and association studies with environmental variables, local adaptation, and lack of intermuscular bones, both using tambaqui as a model. This work can give us many theoretical references to be applied in genetic breeding programs for tambaqui, allowing a better understanding of genetic processes related to traits of interest in aquaculture. / O tambaqui (Colossoma macropomum) é a maior espécie nativa de Characiforme da América do Sul e é encontrado nas bacias do rio Amazonas e Orinoco. O cultivo do tambaqui está crescendo rapidamente no Brasil, sua produção atingiu 139.209 toneladas em 2014, o que corresponde a 57,7% de aumento em relação a 2013. No entanto, poucos estudos genéticos realizados com o tambaqui estão disponíveis atualmente. Estudos genéticos em tambaqui, tanto em populações cultivadas quanto em populações selvagens, necessitam de uma abordagem holística para uma ação racional frente aos desafios ecológicos e mercadológicos na aquicultura. Abordagens baseadas em estudos genéticos têm fornecido ferramentas importantes para se entender a dinâmica populacional, adaptação local e função gênica visando melhorar as estratégias de seleção a serem aplicadas em programas de melhoramento genético. O sequenciamento de nova geração (NGS) permitiu um grande avanço nas abordagens genômicas e transcriptômicas, especialmente relacionadas a espécies não-modelo. A genotipagem por sequenciamento (GBS) é uma dessas abordagens que utilizam enzimas de restrição (REs) para reduzir a complexidade do genoma. Esta tese apresenta a aplicação desta abordagem objetivando proporcionar avanços significativos nos estudos genéticos de base para tambaqui. A técnica de GBS forneceu um painel de SNPs de alta densidade que nos permitiu desenvolver o primeiro mapa de ligação e estudos de associação com variáveis ambientais, adaptação local e ausência de ossos intermusculares no tambaqui. Este trabalho pode nos dar muitas referências teóricas a serem aplicadas em programas de melhoramento genético do tambaqui, permitindo uma melhor compreensão dos processos genéticos relacionados a traços de interesse na aquicultura.

Abstract Drought is the most common abiotic stress limiting chickpea production in the world. Ninety percent of the worlds chickpea is produced in areas relying upon conserved, receding soil moisture, therefore, crop productivity is largely dependent on efficient utilization of available soil moisture. Because of the variability in drought pattern from year to year, trait based selection could have an advantage over selection on the basis of grain yield alone. Trait based breeding, however, requires trait dissection into components. Successful marker identification would facilitate integration of MAS procedures in breeding programs enabling the pyramiding of favourable alleles.<p> The genetic map produced in this study was based on a population of recombinant inbred lines of a cross of ILC 588 x ILC 3279 containing 52 SSR markers spanned 335 cM of the chickpea genome at an average density of 6.4 cM. A total of 13 genomic regions were shown to be associated with drought tolerance traits. Some of these genomic regions showed pleiotropic effect on multiple traits. This was also supported by the analysis of phenotypic data where these traits were found to be correlated. For example, early flowering and maturity had a strong association with high grain yield. High grain yield was also associated with better portioning ability between biomass and grain yield, i.e. harvest index. Drought tolerance score (DTS) was associated with various important traits including biomass, early flowering, early maturity.<p> This study also concluded that chickpea genotypes differed in terms of root length, root length density, root weight density and root length to weight ratio at every 20 cm soil layer up to 100 cm depth in response to water deficits. Consideration of an efficient root system vs. a larger root system is also important, since in this research, large root systems were offset by low harvest index, presumably due to the lack of assimilate available for grain growth. A restricted root system is important in environments like Western Canada, where crop growth termination is usually required prior to fall frost. This study also reported significant associations of stomatal conductance (gs) with each of HI, grain yield under drought, drought susceptibility index and drought tolerance score (DTS). Stomatal conductance can also be used to assess plant stress due to drought. Values of gs less than 250 mmol m-2s-1 during flowering indicated drought stress under greenhouse conditions. A higher degree of plant stress due to drought was shown by increased stomatal closure at midday (gs <150 mmol m-2s-1). The study of 157 RILs under natural drought stress during 2005-07 revealed that the 17 RILs which had high grain yield under drought (Group A), also tended to have higher gs than the 42 RILs that had lower grain yield (Group B). Group A had mean gs values of 390 mmol m-2s-1 during the week before flowering, while Group B had mean gs value of 330 mmol m-2s-1. Stomatal conductance increased at flowering and then sharply decreased later in the reproductive period, particularly in Group B. These findings were also supported by canopy temperature differential measurements as Group A was also able to maintain lower canopy temperature than Group B, indicating the ability of these plants to maintain adequate transpiration and a cooler canopy under drought stress. This research indicated that gs and canopy temperature can be used to assess chickpea drought stress and to screen drought tolerant genotypes. This study identified a QTL on LG7 for gs, QTLs on LG1, LG3 and LG6 associated with canopy temperature differential, as well as QTLs associated with grain yield under drought, HI, DTS, days to flower, days to maturity, reproductive period and plant height. These QTLs identified for traits related to higher chickpea productivity under drought stress could have important implications for accelerating the process of pyramiding of favourable genes into adapted genotypes and on future marker-assisted breeding for drought prone areas.

Abstract Drought is the most common abiotic stress limiting chickpea production in the world. Ninety percent of the worlds chickpea is produced in areas relying upon conserved, receding soil moisture, therefore, crop productivity is largely dependent on efficient utilization of available soil moisture. Because of the variability in drought pattern from year to year, trait based selection could have an advantage over selection on the basis of grain yield alone. Trait based breeding, however, requires trait dissection into components. Successful marker identification would facilitate integration of MAS procedures in breeding programs enabling the pyramiding of favourable alleles.<p> The genetic map produced in this study was based on a population of recombinant inbred lines of a cross of ILC 588 x ILC 3279 containing 52 SSR markers spanned 335 cM of the chickpea genome at an average density of 6.4 cM. A total of 13 genomic regions were shown to be associated with drought tolerance traits. Some of these genomic regions showed pleiotropic effect on multiple traits. This was also supported by the analysis of phenotypic data where these traits were found to be correlated. For example, early flowering and maturity had a strong association with high grain yield. High grain yield was also associated with better portioning ability between biomass and grain yield, i.e. harvest index. Drought tolerance score (DTS) was associated with various important traits including biomass, early flowering, early maturity.<p> This study also concluded that chickpea genotypes differed in terms of root length, root length density, root weight density and root length to weight ratio at every 20 cm soil layer up to 100 cm depth in response to water deficits. Consideration of an efficient root system vs. a larger root system is also important, since in this research, large root systems were offset by low harvest index, presumably due to the lack of assimilate available for grain growth. A restricted root system is important in environments like Western Canada, where crop growth termination is usually required prior to fall frost. This study also reported significant associations of stomatal conductance (gs) with each of HI, grain yield under drought, drought susceptibility index and drought tolerance score (DTS). Stomatal conductance can also be used to assess plant stress due to drought. Values of gs less than 250 mmol m-2s-1 during flowering indicated drought stress under greenhouse conditions. A higher degree of plant stress due to drought was shown by increased stomatal closure at midday (gs <150 mmol m-2s-1). The study of 157 RILs under natural drought stress during 2005-07 revealed that the 17 RILs which had high grain yield under drought (Group A), also tended to have higher gs than the 42 RILs that had lower grain yield (Group B). Group A had mean gs values of 390 mmol m-2s-1 during the week before flowering, while Group B had mean gs value of 330 mmol m-2s-1. Stomatal conductance increased at flowering and then sharply decreased later in the reproductive period, particularly in Group B. These findings were also supported by canopy temperature differential measurements as Group A was also able to maintain lower canopy temperature than Group B, indicating the ability of these plants to maintain adequate transpiration and a cooler canopy under drought stress. This research indicated that gs and canopy temperature can be used to assess chickpea drought stress and to screen drought tolerant genotypes. This study identified a QTL on LG7 for gs, QTLs on LG1, LG3 and LG6 associated with canopy temperature differential, as well as QTLs associated with grain yield under drought, HI, DTS, days to flower, days to maturity, reproductive period and plant height. These QTLs identified for traits related to higher chickpea productivity under drought stress could have important implications for accelerating the process of pyramiding of favourable genes into adapted genotypes and on future marker-assisted breeding for drought prone areas.

Hypervariable, nuclear-encoded microsatellites were used to (i) estimate genetic effective size (Ne) of red drum spawning over a two-week period in nine brood tanks at a TPWD hatchery; (ii) estimate heritability of early-larval growth and of growth rate and cold tolerance of juveniles; and (iii) test Mendelian segregation and independent assortment of 31 nuclear-encoded microsatellites. Assuming all tanks contributed equally to an offspring population, the maximum (expected) and observed Ne over the nine brood tanks was 43.2 and 27.0, respectively. The estimate of Ne based on observed variation in family size was 19.4. Simulations indicated that over a limited time period the simplest approach to maximizing Ne for a release population would be to utilize equal numbers of progeny from each brood tank. A family (genetic) effect was found to contribute significantly to the variance in early larval growth, juvenile growth rate, and cold tolerance. Estimates of narrow-sense heritability for these three traits were 0.07 +- 0.03, 0.52 +- 0.21 and 0.20 +- 0.10 (two growth intervals measured), and 0.30 +- 0.11, respectively, under the genetic models employed. The relatively low estimate of heritability for early larval growth suggests that genetic improvement for this trait likely would be slow. The heritability estimates for juvenile growth rate and cold tolerance, alternatively, suggest that genetic selection for these traits could be effective. Segregation at all 31 microsatellites fit Mendelian expectations for autosomal loci; a null allele was inferred at two of the microsatellites. Results from pairwise tests of independent assortment demonstrated that 20 of the 31 microsatellites could be placed into seven linkage groups. Additional linkage groups inferred from a prior study increased the number of inferred linkage groups in red drum to nine, with a range of two - five (avg. = 2.78) microsatellites in each linkage group. The remaining 11 microsatellites tested in this study assorted independently from all other microsatellites, suggesting the possibility of 11 additional linkage groups.

In order to combine previous observations from different sources on sex determination, and to identify sex chromosomes including the major sex determination locus in Nile tilapia, physical and genetic maps based on sex-linked markers and genes (such as sex-linked AFLPs, microsatellites, ovarian aromatase and DMO genes) were integrated and anchored. An accurate physical map using FISH techniques on mitotic cells was developed based on a previous map and 23 tilapia BAC clones previously assigned to linkage groups (LGs) 1, 3, 6, 7, 10 and 12; and on meiotic cells, 2 BAC clones containing the SLAM OniY227 and the dmrt4 gene were mapped. The six linkage groups were then assigned to different chromosomes, but surprisingly, the putative sex LG1 was located to a small submetacentric chromosome and not to the larger subtelocentric chromosome 1, where LG3 was assigned instead. The other LGs were assigned to different chromosomes and oriented with respect to the centromeres. A detailed comparison of the physical distribution of markers on chromosome 1 with respect to LG3 revealed a suppression in recombination in the subtelomeric region of the q arm between the marker GM354 (0 cM) and clcn5 (29 cM) and an abrupt increment of recombination between clcn5 (29 cM) and GM128 (77 cM) close to the centromere (Flpter=0.2). The unpairing region (20% of the total length) observed on the larger bivalents of XY fish during early pachytene in meiotic cells has been confirmed by DAPI staining and FISH to be at the terminal part of the q arm, opposite to the centromere. Comparison with six other tilapia species (2n=44) revealed a well conserved karyological distribution of the suspected LGs associated with sex determination (1 and 3). Besides, in O. karongae (2n=38) it was shown by SATA and UNH995/UNH104 marker hybridisation that LG1 has been re-arranged into the subtelomeric chromosome 2 as a result of a telomere-telomere fusion. A pool of 15 tilapia BAC clones previously localised on chromosome 1 and containing sex-linked AFLPs, dmrt1, dmrt4 and several SINEs were screened for new microsatellites; BACs were digested with SAU3AI and TC, GT, ATCT and CTGT probes radio-labelled with 32P. The high abundance of repetitive sequences in the BACs used led to only one useful polymorphic and co-dominant marker being obtained, associated to a BAC clone containing a copy of the dmrt1 gene on chromosome 1 (Flpter=0.85). Four linkage maps were constructed from an XY male, XY neofemale, XX neomale and XX female, mapping 4 and 8 markers on LG1 and LG3 (including the dmrt1 associated microsatellite) respectively. A specific sex-determination locus was identified on LG1 clearly linked with UNH995. However there appeared to be different allelic strengths for this sex determination locus, as shown by different sex ratios associated with different UNH995 genotypes. Additionally, one of the two XX fish mapped, showed the location of the recessive black blotching trait on LG3 (chromosome 1) between the markers GM128 and GM526, close to the centromere (Flpter=0.14). The results presented suggest a nascent Y chromosome in early stage of differentiation in Nile tilapia and with a functional master gene on LG1 close to the marker UNH995 (Flpter=0.67) located on the q arm of a small submetacentric chromosome. The potential influences of the autosomal LG3 (chromosome 1) in sex differentiation are also discussed.

Doctor of Philosophy / Department of Plant Pathology / Robert L. Bowden / John F. Leslie / Gibberella zeae is an ascomycete filamentous fungus and the major cause of Fusarium head blight, also called scab, in small grains. This dissertation contains three related studies of G. zeae. In the first, the genetic map was aligned with the first assembly of the genomic sequence released by The Broad Institute (Cambridge, MA). Approximately 99% of the sequence was anchored to the genetic map, indicating the high quality of the sequence assembly and validity of the genetic map. The alignments grouped the linkage groups and supercontigs into four sets, which is consistent with the hypothesis that there are four chromosomes in this fungus. In the second, the sex pheromone precursor genes (ppg1 and ppg2) and the pheromone receptor genes (pre1 and pre2) were identified and characterized. Deletion of ppg1 or pre2 ([Delta]ppg1 or [Delta]pre2 strains) reduced the number of perithecia produced by self-fertilization, but did not completely block perithecial formation. The proportion of crosses resulting from outcrossing increased when the [Delta]ppg1 strains were used as the female in crosses with male strains containing an intact ppg1 gene. [Delta]ppg2 and [Delta]pre1 mutants had no discernable effect on morphological phenotype or self-fertilization. Thus, one of the pheromone/receptor pairs (ppg1/pre2) found in many Ascomycetes has a role in, but is not essential for, selfing or outcrossing in G. zeae, whereas the other pheromone/receptor pair (ppg2/pre1) no longer has a detectable function in sexual reproduction. In the third study, spore germination of G. zeae was tested in the presence of α- factor-like pheromone peptides of G. zeae or N. crassa. The pheromone peptide of N. crassa more efficiently inhibited spore germination than did the peptide from G. zeae. Arginine and lysine residues were the most important determinants in blocking spore germination. In conclusion, this research has validated the genetic map and the genomic assembly of G. zeae, characterized sex pheromone functions and characterized pheromone peptide ability to inhibit spore germination. The pheromone peptides of G. zeae and N. crassa may be useful as control agents for G. zeae and pheromone peptide efficacy might be further enhanced by judicious substitutions for some of the amino acids.

Notre étude a porté sur le contrôle génétique des comportements sociaux ou de peur et leur relation avec les caractères de production au sein d’un croisement entre deux lignées de cailles sélectionnées de façon divergente sur la motivation sociale. Les résultats alertent sur un possible effet délétère de la sélection pour une plus forte productivité sur la sociabilité et la réactivité émotionnelle des animaux. Dans le même temps, ils indiquent des synergies possibles entre une plus forte motivation sociale et la précocité de la ponte, ou une plus faible réactivité émotionnelle et une production d’œufs plus importante. L’étude a permis la construction de la première carte génétique de moyenne densité à l’aide de marqueurs SNP chez la caille. Les analyses de liaison ont révélé un total de 45 QTLs dont 23 pour les caractères comportementaux et 22 pour ceux de production. Ce sont pour les critères de motivation sociale que les QTLs sont les plus nombreux (15). Certaines régions contrôlent à la fois la réactivité émotionnelle et le poids ou la sociabilité et l’âge au premier œuf. Plusieurs gènes candidats en lien avec la sociabilité ont été suggérés. / Our study focused on the genetic control of social and fear behaviors and their relationships with production traits in a second generation crossing between two lines of quail divergently selected for their social reinstatement behavior. The results warn us about a possible deleterious effect of the selection for higher productivity on the animal’s sociability and emotional reactivity. At the same time, they also indicate possible synergies between a stronger social motivation and a precocious laying onset, or a lower emotional reactivity toward a novel object and a higher egg production. The study allowed us to construct the first genetic map of medium density using SNP markers in the quail. Linkage analyses reveal a total of 45 QTLs with 23 linked to behavioral traits and 22 to the production traits. Most of the behavioral QTLs were linked to the social motivation (15). Also, some regions control both emotional reactivity and weight or sociability and the age at first egg. At this stage of the study, several candidate genes related to sociability were suggested.