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Cotton (Gossypium spp.) is the world’s leading textile fiber crop, and an important source of oil and protein. Insufficient candidate gene derived-markers suitable for genetic mapping and limited information on genes that control economically important traits are the major impediments to the genetic improvement of Upland cotton (G. hirsutum L.). The objectives of this study were to develop a SNP marker discovery strategy in tetraploid cotton species, SNP characterization and marker development from fiber initiation and elongation related genes, chromosomal assignment of these genes by SNP marker-based deletion analysis or linkage mapping, and genetic and molecular analysis of mutants affecting cotton fiber development. Phylogenetic grouping and comparision to At- and Dt-genome putative ancestral diploid species of allotetraploid cotton facilitated differentiation between genome specific polymorphisms (GSPs) and marker-suitable locus-specific polymorphisms (LSPs). By employing this strategry, a total of 222 and 108 SNPs were identified and the average frequency of SNP was 2.35% and 1.30% in six EXPANSIN A genes and six MYB genes, respectively. Both gene families showed independent and incongruent evolution in the two subgenomes and a faster evolution rate in Dt-genome than that in At-genome. SNPs were concordantly mapped to different chromsomes, which confirmed their value as candidate gene marker and indicated the reliability of SNP discovery stragey. QTL mapping by two F2 populations developed from fiber mutants detected major QTL which explain 62.8-87.1% of the phenotypic variation for lint percentage or lint index in the vicinity of BNL3482-138 on chromosome 26. Single marker regression analyses indicated STV79-108, which was located to the long arm of chromosome 12 (the known location of N1 and perhaps n2 loci), also had significant association (R2 % value 15.4-30.6) with lint percentage, lint index, embryo protein percentage and micronaire. Additional QTL and significant markers associated with other seed and fiber traits were detected on different chromosomes. Inheritance analysis indicated that both genetic models N1N1n2n2 and n2n2li3lisub>3 could lead to the fiberless phenotype. The observation of fuzzless-short lint phenotype indicated fiber initiation and elongation were controlled by different mechanisms. The penetrance of Li2 gene expression was observed in this study.

Evolutionary variations during vulval development in C. elegans and its related nematode species are well analyzed. The formation of C. elegans vulva involves many complex cell-cell interactions that are mediated through well conserved EGF/EGFR/RAS, LIN12/Notch and WNT signaling pathways. These pathways specify distinct cell fates of the six epidermal vulval precursor cells (VPCs), P(3-8).p. pry-1/Axin in C. elegans is identified as a part of destruction box complex that mediates (beta)-catenin degradation and is known to negatively regulate canonical Wnt signaling pathway during its development. I focused on the genetic analysis of pry-1 I Axin function in C. briggsae, sister species to C. elegans, to study inter-species comparisons of vulva formation. Three alleles, lin(sy5353), lin(sy5411) and lin(sy5270) were genetically mapped to LG I using standard genetic and in del mapping techniques. Interestingly, a unique simultaneous Multi vulva and Vulvaless (Muv-Vul) phenotype was observed during vulva formation in Cbr-pry-1 alleles, resulting from the varying induction potentials of the VPCs along the A/P axis, compared to Cel-pry-1 animals. In order to analyze these phenotypic differences between Cel-pry-1 and Cbr-pry-1 in greater detail, I dissected vulval development in sy5353 animals. VPC competence analysis was done through cell lineages and ablations studies, while the C. briggsae vulval cell fate markers were used for cell fate specification analysis. Cell ablations revealed that P7.p and P8.p in Cbr-pry-1 animals exhibited non-competence towards anchor cell signaling. Additionally, gonad-independent inductions was observed in P(3-8).p cells and they adopted 2° cell fate specifications. Using RNAi approach, Cbr-pry-1 interactions with other vulval pathway genes were dissected and it was observed that Cbr-lin-12 is involved in VPC competence of P7.p and Cbr-pop-1 exhibited different regulatory levels during vulval development compared to C. elegans. Thus, it can be inferred that the mechanisms of vulva formation in C. briggsae has evolved through changes in the competence of VPCs. / Thesis / Master of Science (MS)

R. meliloti carrying defined deletions that remove fix114 form Fix- nodules which are devoid of intracellular bacteria. Occasionally strains which carry these deletions form pink nodules which appear effective in contrast to the normal white ineffective nodules formed by strains carrying fix114 mutations. Bacteria isolated from these pink nodules retain the original deletion and form effective pink nodules when reinoculated onto alfalfa. It is hypothesized that these isolates carry second site mutations which enable the bacteria to overcome the symbiotic block associated with the fix114 mutation. In this work, five independent isolates were examined and were shown to carry second site mutations that suppress the symbiotic ineffectiveness completely on alfalfa and incompletely on sweet clover. The five independent second site revertants can be divided into two classes based on genetic data and on their sensitivity to detergents and both classes were localized to the chromosome of the wild type Rm1021. One such second site revertant allele, sfx-1, was cloned and localized to a large 18 kb BamHI fragment. / Thesis / Master of Science (MS)

Cryptococcus neoformans is among the most common human pathogenic fungi and the leading cause of fungal meningitis. It consists of two divergent haploid serotypes A and D, as well as their hybrid serotypes AD. Hybridization between the two serotypes A and D is a widespread phenomenon in natural populations of this species. Studies have shown that serotype AD strains possess unique properties in several medically important traits: they are more virulent in animal models, more tolerant to antifungal drugs, more tolerant to UV radiation and other stresses than one or both parental serotypes. Despite the potential medical and evolutionary importance, relatively little is known about the phenotypic and genotypic consequences of the hybridization in C. neoformans. In my thesis, I present a series of studies that show: (1) recombination occurs at a very low frequency during hybridization between serotypes A and D; (2) serotypes A and D in C. neoformans have diverged from each other not only at the DNA sequence level, but also at the chromosomal structure level, both of which contributed to suppressed recombination and limited genetic introgression between the two serotypes; (3) though there is widespread hybridization, the hybrids seemed largely distinct and the genomes of the parental serotypes A and D populations are relatively unaffected by the hybrids in natural populations; and (4) the fixation of these serotype specific chromosomal rearrangements in the two serotypes, together with evidences of selective sweeps observed at both inversion junctions and genes located close to chromosomal inversions suggest that these rearranged regions (or genes surrounding these regions) were likely involved in the diversification between the two serotypes. My studies provide a genetic framework for future quantitative analyses of medically important traits of C. neoformans. / Thesis / Doctor of Philosophy (PhD)

Thesis (PhD)--Stellenbosch University, 2014. / ENGLISH ABSTRACT: This project involved the analysis of genes in Solanaceae species that have previously been shown to be involved in the phosphorylation of starch or its subsequent dephosphorylation. Both these processes are essential for normal starch mobilization. A tomato conditional mutant lacking the starch phosphorylating enzyme glucan water dikinase was analyzed. It is known that starch accumulates transiently in tomato fruit and is degraded throughout the ripening process. The study aimed to determine the effect of inhibited starch degradation on fruit development. Unfortunately no effect on starch mobilisation was found in the fruit of the mutant. Immunoblot analysis revealed expression of Glucan Water Dikinase (GWD) within the fruit of the tomato mutant indicating that the conditionality of the mutation was compromised. The second set of experiments analyzed the roles of Starch Excess4 (SEX4), Like Sex Four-1 and Like Sex Four-2 (LSF1 and LSF2) in starch degradation in potato and Nicotiana benthamiana. These enzymes have, thus far, only been studied in Arabidopsis, with the proposed role for SEX4 and LSF2 being that they are involved in dephosphorylation of the C-6 and C-3 positions of starch breakdown products. The role of LSF1 is unclear, although it is not thought to be a phosphatase. SEX4, LSF1 and LSF2 were repressed individually while the expression of SEX4 and LSF2 were also inhibited simultaneously. Using a transient repression system in N. benthamiana it was shown that all of the genes play a role in leaf starch degradation. The SEX4 and LSF2 enzymes were shown to influence the proportion of phosphate located on the starch which contained an altered ratio of C-3/C-6 phosphate. Stably transformed potato plants were produced where SEX4 and LSF2 were successfully repressed in potato leaves and tubers. Although AtLSF2 had been shown not to be essential for normal starch degradation on its own, in potato plants when LSF2 was repressed, the plants developed a starch-excess phenotype. Taken together with the N. benthamiana data this indicates that LSF2 plays a bigger role in leaf starch degradation in Solanaceae than in Arabidopsis. The ratio of C-3/C-6 phosphate was also altered in tuber starch from some of the silenced plants. Starch from SEX4 repressed potato plants contained increased amounts of glucose-6-phosphate and increased glucose-3-phosphate in the tuber when compared to the WT. An increase in the proportion of C-6 or C-3 phosphate is not surprising with SEX4 being characterized as a phosphatase specific for C-6 position and LSF2 for the C-3 position in Arabidopsis, however the combined increase in C-3 and C-6 amounts in StSEX4 silenced plants is interesting. The differences seen in the phosphate alteration in both N. benthamiana leaves and potato tubers indicates that in Solanaceae species these proteins may have a slightly altered specificity when compared with Arabidopsis, although they are undoubtedly involved in starch degradation. The effect of silencing SEX4 or LSF2 on cold-induced sweetening was also investigated, with no effect being found. This may be because of functional redundancy between the proteins and a better approach in terms of blocking cold sweetening would be to simultaneously repress SEX4 and LSF2. Overall, these enzymes seem to play similar roles in leaves of Solanum species as has been described in Arabidopsis. The starch from the engineered plants did have an altered phosphate ratio and further analysis is needed to determine if this leads to improved or additional functionality. / AFRIKAANSE OPSOMMING: Die projek omhels die ontleding van gene van die Solanaceae spesie wat voorheengetoon het dat hulle deel neem in fosforilering of defosforilering van stysel. Altwee van hierdie reaksies is belangrik vir normale stysel metabolisme. ‘n Tamatie konditionele mutant was geanaliseer waarin die stysel fosforilering ensiem glucan water dikinase nie teenwoordig was nie. Die doel van die studie was om te ondersoek watter effek het n gebrek in stysel afbraak op die rypwording en ontwokkeling vrugte. Ongelukkig was geen effek op stysel metabolism in die munant se vrugte gesien. Immunoklad analise het getoon dat GWD protein wel uitdruk word in die vrugte en dus die mutant nie heeltemal effektief was nie. Die tweede stel van experimente het in aartappels en tabak die rol van SEX4, LSF1 en LSF2 in stysel afbraak ondersoek. Hierdie ensieme was huidiglik nog net deeglik in Arabidopsis bestudeer, waar daar gewys was dat SEX4 and LSF2 in die defosforilering van stysel by die C-6 en C-3 posisie deel neem. Die rol van LSF1 is nog onbekend, maar daar word huiglik gelgo dat dit is nie ‘n fosfatase nie. SEX4, LSF1, en LSF2 was onderdruk op sy eie, waar SEX4 en LSF2 gelyktydig onderdruk was. Met behulp van n verbygaande onderdrukking in tabak, was dit getoon dat al die bogenoemde gene n gedeeltelike rol speel in die afbraak van stysel. Dit was getoon dat SEX4 and LSF2 ensiemedie verhouding van waar fosfaat op stysel gelee is beinvloed en het n verandering in die C-3/C-6 phosphaat verhouding ook gehad. Aardappels was stabiel getransformeer en daar was suksesfol plante waar SEX4 en LSF2 onderdruk was in blare en knolle geproduseer. Alhoewel daar getoon was dat AtLSF2 op sy eie nie n groot rol speel in stysel katabolisme nie was daar wel gesien dat in aardappel wanner hierdie geen afgeskakel was dat daar n stysel oorskot fenotiepe ontwikkel. As die tabak resultate saamgevat word met die aardappel wil dit voorkom asof LSF2 n groter rol binne die stysel katabolisme in Solanaceae speel as in Arabidopsis. Daar was gevind dat die verhouding van C-3/C-6 fosfaat was in die knolle verander in perty van die lyne waar geen afskakeling wel plaasgevind het. Die verhouding van C-3/C-6 fosfaat was verander in knolle stysel van sommige stilgemaak plante. Sysel van SEX4 stilgemaak plante het hoër vlakke glukose-6-fosfaat en glukose-3-fosfaat in die knolle gehad wanner dit met die WT vergelyk was. n Toename in die persentasie van C-6 fosfaat is nie verbasend nie, SEX4 word gekenmerk as die spesifieke fosfatase verantwoordelik vir die fosfaat by die C-6 posisie en LSF2 spesifiek vir die C-3 posisie in Arabidopsis. Die gekombineerde toename in beide C-6 en C-3 bedrae in StSEX4 stilgemaak plante is wel heel interesant. Verandering in beide tabak blare and aartapple knolle dui daarop dat in solanacea spesie hierdie proteiene, n effens verandering in spesifisiteit kan hê as dit met Arabidopsis vergelyk word. Daar kan wel nie getwyfel word dat hulle wel n rol speel in stysel afbraak nie. Die effect watSEX4 of LSF2 op koue-geinduseerde soetheid het is ook ondersoek maar daar was geen effek gevind nie. Dit mag wees asgevolg van die funksionele onslag tussen die twee proteien en better benadering on die koue-soetheids effek te verhoed sou wees om beide protein op die selfde stadium aft e skakel. As daar in gegeheel gekyk word lyk dit asof hierdie protein die selfde rolle het in die Solanum spesies as in Arabidopsis.Die stysel van hierdie die ontwerpte plante het ‘n veranderde fosfaat verhouding getoon en veder analise is nodig om te bepaal of dit lei tot verbeterde einskappe of bykommende funksies.

Orientador: Sandra Aidar de Queiroz / Coorientador: Roberto Carvalheiro / Banca: João Ademir de Oliveira / Banca: Patrícia Tholon / Resumo: No Brasil, são escassos os estudos referentes ao escore de condição corporal (ECC) de vacas de corte que, quando associado ao peso, têm impacto na produção de bezerros e na reprodução, pois reflete o balanço energético do corpo animal. Assim, o objetivo deste trabalho foi associar ECC com a prenhez de vacas Nelore e com o desempenho de seus produtos a desmama, bem como verificar se esta característica pode ser incluída nos critérios de seleção da raça Nelore. O ECC das vacas foi atribuído no diagnóstico de gestação ou no desmame, variando de 1 a 5. Por regressão logística, utilizando o método de seleção Stepwise, foram analisados os seguintes efeitos sobre o ECC: grupo de contemporâneos a desmama, peso e altura de garupa da vaca, ordem de parto, diagnóstico de gestação, histórico reprodutivo anterior à coleta do ECC, presença de bezerro ao pé e escores de C e P dos produtos a desmama. Na análise genética, elaborada usando-se inferência baeysiana, foram incluídos os mesmos efeitos anteriores, com peso e altura de garupa da vaca como co-variáveis, e acrescidos do efeito genético aditivo da vaca. Os resultados mostraram que vacas com ECC elevado emprenharam mais do que as de pior ECC, porém o desempenho dos seus bezerros foi inferior. Vacas multíparas foram mais pesadas e de escores mais magros (ECC 1 e 2). As correlações de Spearman entre ECC e suas fontes de variação foram, em sua maioria, de baixa magnitude. Os efeitos que mais explicaram a variação do ECC foram peso, grupo de contemporâneos e altura da garupa. A estimativa de herdabilidade do ECC foi igual a 0,22, com intervalo de credibilidade entre 0,13 e 0,31, valor de magnitude moderada, demonstrando a presença de ação gênica aditiva na determinação do ECC e que este pode ser utilizado como critério de seleção de vacas / Abstract: In Brazil few studies have been done on the body condition score (BCS) of beef cows. The knowledge of this score associated with body weight can produce an impact on calf production and cow's reproduction, because it reflects the energy balance of the animal body. The objective of this study was to associate BSC with pregnancy of cows and the performance of their calves at weaning, and to verify if this trait could be included as selection criteria. The BCS was recorded on pregnancy diagnosis or at weaning and ranged from 1 to 5. Applying logistic regression, using the Stepwise selection method, we analyzed the following effects on BSC: contemporary group at weaning, classes of weight and hip height of the cow, number of calvings, pregnancy diagnosis, reproductive history prior to collection BSC, the presence of calf and C and P score of calves at weaning. For the genetic analysis, performed using Baesyan inference, the same effects were considered, with weight and hip height as covariate, and also the genetic direct effect of the cow. The results showed that cows with higher BCS had better pregnancy rate than those with lower BSC, but the performance of their calves was worse. Multiparous cows were heavier and had leaner scores (BCS 1 and 2) than the primiparous ones. The Spearman rank correlation between BSC and their sources of variation were generally of low magnitude. Contemporary group, body weight and height of the cow were the effects that accounted for most of the variation of BSC. The heritability estimate of BCS was equal to 0.22 with credible interval ranging from 0.13 to 0.31, a moderate magnitude value that indicates the presence of additive genetic variation and that BSC can be used as selection criterion for cows / Mestre

Dentro do gênero Rhipicephalus, há o chamado complexo sanguineus formado por várias espécies presentes apenas no Velho Mundo, das quais apenas a espécie Rhipicephalus sanguineus é considerada de ocorrência no Novo Mundo. Como as espécies deste complexo apresentam grande similaridade morfológica, é possível que mais de uma espécie do complexo sanguineus esteja ocorrendo nas Américas. Um trabalho recente relatou parâmetros biológicos e genéticos significativamente diferentes entre uma população de R. sanguineus do Brasil e outra da Argentina, sugerindo que o status biosistemático de R. sanguineus na América do Sul deva ser revisto. Diante disto, e da inquestionável importância medico-veterinária de R. sanguineus na América do Sul, este projeto objetivou realizar uma análise genética de 32 populações de R. sanguineus, sendo 17 do Brasil (englobando 13 estados), 3 do Chile, 2 da Venezuela, 2 da Colômbia e 1 de cada um dos seguintes países: Argentina, Uruguai, Itália, Espanha, África do Sul, Costa Rica, Panamá, México. Uma amostra de Rhipicephalus turanicus da Espanha e uma da África do sul também foram analisadas. Para tal, carrapatos oriundos das diferentes populações foram analisados geneticamente através de seqüências dos genes mitocondriais 16S rDNA. O resultado deste trabalho permitiu inferir sobre a possibilidade da existência no mínimo de dois grupos distintos de carrapatos sob o táxon R. sanguineus na América Latina, um se aproximando dos carrapatos de origem africana e com distribuição na América tropical e subtropical e outro se aproximando das amostras européias e com distribuição temperada do sul da América do Sul / Among the genus Rhipicephalus, there is the sanguineus complex composed by many species of distribution restricted to the Old World. It has been considered that Rhipicephalus sanguineus is the only species from this complex to be present in the New World. Due to the high similarity between the sanguineus complex species, it is possible that more than one species is present in the Americas, as suggested by recent papers. The present study performed a genetic evaluation based on 16S rDNA mitochondrial gene sequences of ticks representative 26 R. sanguineus populations from South America, one from: Italy, Spain, South Africa, Costa Rica, Panama, Mexico. Additionally, Rhipicephalus turanicus ticks from South Africa and Spain were also used. The results confirm the existence of genetically distinct populations of the \"sanguineus\" complex in the Americas

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第19069号 / 人博第722号 / 新制||人||173 / 32020 / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)准教授 土屋 徹, 教授 宮下 英明, 教授 川本 卓男 / 学位規則第4条第1項該当