Subject(s)
Solanum lycopersicum , Lycopene , Solanum lycopersicum/genetics , Fruit/genetics , Plastids/geneticsABSTRACT
Apomixis, asexual reproduction through seed, enables breeders to identify and faithfully propagate superior heterozygous genotypes by seed without the disadvantages of vegetative propagation or the expense and complexity of hybrid seed production. The availability of new tools such as genotyping by sequencing and bioinformatics pipelines for species lacking reference genomes now makes the construction of dense maps possible in apomictic species, despite complications including polyploidy, multisomic inheritance, self-incompatibility, and high levels of heterozygosity. In this study, we developed saturated linkage maps for the maternal and paternal genomes of an interspecific Brachiaria ruziziensis (R. Germ. and C. M. Evrard) × B. decumbens Stapf. F1 mapping population in order to identify markers linked to apomixis. High-resolution molecular karyotyping and comparative genomics with Setaria italica (L.) P. Beauv provided conclusive evidence for segmental allopolyploidy in B. decumbens, with strong preferential pairing of homologs across the genome and multisomic segregation relatively more common in chromosome 8. The apospory-specific genomic region (ASGR) was mapped to a region of reduced recombination on B. decumbens chromosome 5. The Pennisetum squamulatum (L.) R.Br. PsASGR-BABY BOOM-like (psASGR-BBML)-specific primer pair p779/p780 was in perfect linkage with the ASGR in the F1 mapping population and diagnostic for reproductive mode in a diversity panel of known sexual and apomict Brachiaria (Trin.) Griseb. and P. maximum Jacq. germplasm accessions and cultivars. These findings indicate that ASGR-BBML gene sequences are highly conserved across the Paniceae and add further support for the postulation of the ASGR-BBML as candidate genes for the apomictic function of parthenogenesis.
Subject(s)
Brachiaria/genetics , Chromosomes, Plant/genetics , Genetic Linkage , Parthenogenesis/genetics , Reproduction, Asexual/genetics , Apomixis/genetics , Arabidopsis Proteins/genetics , Brachiaria/growth & development , Chromosome Mapping , Genotype , Polymorphism, Single Nucleotide , Polyploidy , Seeds/genetics , Transcription Factors/geneticsABSTRACT
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
ABSTRACT
Vitiligo is a chronic stigmatizing disease, already known for millennia, which mainly affects melanocytes from epidermis basal layer, leading to the development of hypochromic and achromic patches. Its estimated prevalence is 0.5% worldwide. The involvement of genetic factors controlling susceptibility to vitiligo has been studied over the last decades, and results of previous studies present vitiligo as a complex, multifactorial and polygenic disease. In this context, a few genes, including DDR1, XBP1 and NLRP1 have been consistently and functionally associated with the disease. Notwithstanding, environmental factors that precipitate or maintain the disease are yet to be described. The pathogenesis of vitiligo has not been totally clarified until now and many theories have been proposed. Of these, the autoimmune hypothesis is now the most cited and studied among experts. Dysfunction in metabolic pathways, which could lead to production of toxic metabolites causing damage to melanocytes, has also been investigated. Melanocytes adhesion deficit in patients with vitiligo is mainly speculated by the appearance of Köebner phenomenon, recently, new genes and proteins involved in this deficit have been found.
Subject(s)
Humans , Vitiligo/genetics , Genetic Linkage/genetics , Autoimmune Diseases/genetics , Vitiligo/immunology , Vitiligo/metabolism , Genetic Predisposition to Disease , Genetic Association Studies , Melanocytes/immunologyABSTRACT
Shifts in host-plant use by phytophagous insects have played a central role in their diversification. Evolving host-use strategies will reflect a trade-off between selection pressures. The ecological niche of herbivorous insects is partitioned along several dimensions, and if populations remain in contact, recombination will break down associations between relevant loci. As such, genetic architecture can profoundly affect the coordinated divergence of traits and subsequently the ability to exploit novel habitats. The closely related species Heliconius cydno and H. melpomene differ in mimetic colour pattern, habitat and host-plant use. We investigate the selection pressures and genetic basis underlying host-use differences in these two species. Host-plant surveys reveal that H. melpomene specializes on a single species of Passiflora. This is also true for the majority of other Heliconius species in secondary growth forest at our study site, as expected under a model of interspecific competition. In contrast, H. cydno, which uses closed-forest habitats where both Heliconius and Passiflora are less common, appears not to be restricted by competition and uses a broad selection of the available Passiflora. However, other selection pressures are likely involved, and field experiments reveal that early larval survival of both butterfly species is highest on Passiflora menispermifolia, but most markedly so for H. melpomene, the specialist on that host. Finally, we demonstrate an association between host-plant acceptance and colour pattern amongst interspecific hybrids, suggesting that major loci underlying these important ecological traits are physically linked in the genome. Together, our results reveal ecological and genetic associations between shifts in habitat, host use and mimetic colour pattern that have likely facilitated both speciation and coexistence.
Subject(s)
Butterflies/genetics , Competitive Behavior/physiology , Ecosystem , Passiflora/parasitology , Pigmentation/physiology , Selection, Genetic , Animals , Butterflies/physiology , Genetic Association Studies , Larva/physiology , Panama , Species Specificity , Survival AnalysisABSTRACT
Induced systemic resistance (ISR) is a mechanism by which plants enhance defenses against any stress condition. ISR and growth promotion are enhanced when tomato (Solanum lycopersicum) is inoculated with several strains of Trichoderma ssp. This study aims to genetically map tomato candidate genes involved in ISR and growth promotion induced by the Colombian native isolate Trichoderma koningiopsis Th003. Forty-nine candidate genes previously identified on tomato plants treated with Th003 and T. hamatum T382 strains were evaluated for polymorphisms and 16 of them were integrated on the highly saturated genetic linkage map named “TOMATO EXPEN 2000”. The location of six unigenes was similar to the location of resistance gene analogs (RGAs), defense related ESTs and resistance QTLs previously reported, suggesting new possible candidates for these quantitative trait loci (QTL) regions. The candidate gene-markers may be used for future ISR or growth promotion assisted selection in tomato.
La resistencia sistémica inducida (ISR) es un mecanismo mediante el cual las plantas aumentan sus defensas frente a cualquier condición de estrés. El objetivo de este trabajo fue localizar en el mapa genético de tomate, genes candidatos involucrados en ISR y promoción de crecimiento inducidos por la cepa colombiana nativa Th003 de Trichoderma koningiopsis. Se realizó una búsqueda de polimorfismos en cuarenta y nueve genes candidatos previamente identificados en plantas de tomate inoculadas con Th003 y la cepa T382 de T. hamatum. Diez y seis de estos genes candidatos fueron integrados en el mapa genético de tomate altamente saturado, llamado “TOMATO EXPEN 2000”. La ubicación de seis unigenes fue similar a la localización de genes análogos de resistencia (RGAs), ESTs relacionados con defensa y QTLs de resistencia previamente identificados, sugiriendo posibles nuevos candidatos para estas regiones de QTLs. Los genes candidatos o marcadores pueden ser usados en futuros programas de selección asistida relacionados con ISR o promoción de crecimiento en tomate.
ABSTRACT
The genetic power of a Brazilian three-generation family with generalized aggressive periodontitis (GAgP) has been reported. The empirical logarithms of the odds (LOD) score thresholds for genetic linkage analysis of complex diseases proposed by Haines rely on confirmation from independent datasets. This study estimated the power of another large Brazilian family with GAgP for future linkage analysis. The three-generation family was seen at the Dental School of the Federal University of Bahia. Following the previously described methodology, full-mouth periodontal probing at 6 sites/tooth was performed in all 19 family members. Six out of 12 siblings were affected with GAgP. All affected family members were non-smokers and did not present diabetes or any other systemic condition or consanguinity. A parametric simulation (?=0) was performed on 100 replicates using the statistical software SLINK for linkage analysis. There was maximum expected LOD scores of 3.75 and 3.45 at penetrance rate F=0.98, and both studied phenocopy rates P=0.0 and P=0.02, respectively. The power of the study increased with the increase of the adopted penetrance rates in both studied phenocopy rates. The studied Brazilian three-generation family showed statistical power for future genetic linkage analysis of candidate genes to GAgP.
O poder genético em uma família brasileira de três gerações com periodontite agressiva generalizada (PAgG) foi reportado. Os valores dos escores logarítmicos (LOD) empíricos para análise genética de ligação de doenças complexas propostos por Haines se baseam na confirmação em conjuntos de dados independentes. O objetivo deste estudo foi de estimar o poder de uma nova grande família com PAgG para futura análise de ligação. A família de três gerações foi vista na Faculdade de Odontologia da Universidade Federal da Bahia. De acordo com metodologia previamente descrita, sondagem periodontal em 6 sítios/dente foi realizada em todos 19 membros da família. Seis de 12 irmãos apresentaram PAgG. Todos os membros afetados da família eram não fumantes, não apresentaram diabetes ou qualquer condição sistêmica ou consangüinidade. Uma simulação paramétrica (?=0) foi realizada em 100 réplicas usando software estatístico SLINK para análise de ligação. Houve escore LOD esperado máximo de 3,75 e 3,45 no valor de penetrância F=0,98 em ambas razões de fenocópia estudadas P=0,0 e P=0,02, respectivamente. O poder do estudo aumento com o aumento do grau de penetrância adotado em ambas razões fenotípicas estudadas. A família brasileira de três gerações estudada mostrou poder estatístico para futura análise de ligação genética de genes candidatos para PAgG.
Subject(s)
Adolescent , Adult , Aged , Child , Female , Humans , Male , Middle Aged , Young Adult , Aggressive Periodontitis/genetics , Genetic Predisposition to Disease , Genetic Association Studies/methods , Lod Score , Brazil , White People/genetics , Family Health , Genes, Dominant , Indians, South American/genetics , Models, Genetic , Pedigree , Penetrance , Research DesignABSTRACT
Aggressive periodontitis is a multifactorial disease with strong familial aggregation. Genetic linkage analysis is a method to localize causative or predisposing genes along the chromosome, thus helping to unravel important pathogenic pathways. Prior to applying this method, however, it is essential to estimate the power of the study design. The aim of this study was to estimate the power of a large Brazilian family with generalized aggressive periodontitis (GAgP) for future linkage analysis. A three-generation family was seen at the Dental School of the Federal University of Bahia. A full-mouth periodontal probing at 6 sites/tooth was performed in all 23 family members. Five out of 10 siblings were affected with GAgP. A parametric simulation (? = 0) was performed on 100 replicates using the statistical software SLINK for linkage analysis. The linkage LOD score criteria for complex diseases described by Haines was adopted. There was maximum expected LOD scores of 3.56 and 3.48 at penetrance rate F = 0.98, and both studied phenocopy rates p=0.0 and p=0.02, respectively. The analyzed family showed statistical power for future genetic linkage analysis of candidate genes to GAgP.
Periodontite agressiva é uma doença multifatorial que apresenta forte agregação familiar. Análise de ligação genética é um método que localiza genes que causem ou predisponham doenças ao longo do cromossomo e pode ser útil na descoberta de importantes mecanismos patogênicos. No entanto, antes de se realizar uma análise genética de ligação, é essencial estimar o poder do estudo delineado. O objetivo deste estudo foi estimar o poder de uma grande família apresentando periodontite agressiva generalizada para futura análise genética de ligação. Uma família de três gerações (23 membros) que procurou por tratamento periodontal na Faculdade de Odontologia da Universidade Federal da Bahia foi analisada. Em todos os membros familiares foi realizado um exame periodontal completo em seis sítios/dente em todas as unidades dentais presentes por um único examinador. Dos dez irmãos, cinco apresentaram a periodontite agressiva generalizada de acordo com o sistema de classificação da Academia Americana de Periodontia 1999. Uma simulação paramétrica (? = 0) foi realizada em 100 repetições com o uso do software SLINK para ligação genética. O escore logarítmico LOD descrito como critério para doenças complexas (poligênicas ou multifatoriais) por Haines foi adotado. Em nosso estudo foi encontrado um LOD esperado máximo de 3,56 e 3,48 na razão de penetrância F=0,98 nas duas razões de fenocópia estudadas p=0,0 e p =0,02, respectivamente. A família analisada mostrou ter poder estatístico suficiente para futura análise de ligação genética de genes candidatos para periodontite agressiva generalizada.
Subject(s)
Adolescent , Adult , Aged , Child , Child, Preschool , Female , Humans , Male , Middle Aged , Young Adult , Aggressive Periodontitis/genetics , Genetic Linkage , Genetic Association Studies/methods , Lod Score , Patient Selection , Family Health , Genetic Variation , Models, Genetic , Penetrance , Young AdultABSTRACT
La Diabetes Mellitus (DM) comprende un grupo heterogéneo de desordenes hiperglucémicos clasificados en subgrupos de acuerdo a su fisiopatología y etiología, entre los cuales se destacan la Diabetes Mellitus tipo1 (DM1) y la diabetes mellitus tipo 2 (DM2). La DM1 es de aparición temprana y una absoluta escasez de insulina hace que los pacientes sean insulino dependientes desde el inicio de los síntomas y la (DM2) que se manifiesta en la edad adulta y no todos los pacientes que la sufren son insulino dependientes
Diabetes mellitus (DM) comprises e heterogeneous group of hypoglycemic disorders, that are grouped according to their physiopathology and etiology; the most notorious ones are type 1 DM (DM1) and type 2 DM (DM2); DM1 is characterized by early onset and absolute lack of insulin; therefore, patients suffering from it depend on insulin since the beginning of their symptoms; in contrast, DM2 manifests during adult life and not all patients depend on insulin