Evaluation of insertion-deletion polymorphisms with the kit Qiagen Investigator® DIPplex for forensic application in South AfricaJacobs, Gwynneth 2015 (has links)
>Magister Scientiae - MSc Insertion-deletion polymorphisms (indels) have been underutilized in forensic identification of individuals in comparison with single nucleotide polymorphisms (SNPs) and short tandem repeat (STRs) systems. The use of indels for the purpose of human identification is more advantageous than previously used methods as it combines desirable characteristics of both the SNPs and STRs i.e. low costs and simplistic typing methods as well as indels having small amplicons size, making them suitable for genotyping highly degraded DNA. Currently there is only one commercial kit available for the forensic community, the Investigator® DIPlex kit (Qiagen), which cover a total of 30 indel loci distributed over 19 autosomal chromosomes. The objective of this study was to evaluate the Qiagen Investigator® DIPplex kit for forensic application in South Africa. The kit‘s performance was evaluated by comparing different extraction methods; sensitivity, robustness and reproducibility were evaluated and forensic parameters (match probability, power of discrimination, polymorphism information content, power of exclusion and typical paternity index) were estimated based on population data generated from five South African populations (Afrikaner, Mixed Ancestry, Indian-Asian, Xhosa and Zulu). Population comparisons were performed using Fst-analysis, factorial component analysis as well as phylogenetic tree construction. DNA was extracted from buccal swabs and whole blood collected from a total of 512 individuals from the five South African population groups and genotyped using the Qiagen Investigator® DIPplex kit. Sanger DNA sequencing and sequence alignments confirmed the presence of a null allele at locus HLD97 which was present in high frequency in the Xhosa and Zulu populations. This observation was made in 14 individuals belonging to the Xhosa and Zulu populations. Null allele frequencies in all five South African populations were also estimated. Null alleles were estimated for all loci using analytical methods i.e. Charkraborty null allele estimator, Brookfield null allele estimators 1 and 2 and ML-NullFreq software program. The kit performed well in the laboratory, not requiring any additional reagents or instrumentation and successfully generating profiles with input DNA amounts as low as 0.2 ng/μL. Although well suited for forensic application, the Qiagen Investigator® DIPplex kit showed some drawbacks with regards to application on South African populations. The presence of a null allele at the HLD97 locus as well as indication of population substructure affects allele frequency estimates for the South African populations. Correction for population substructure as present within the South African populations should be considered using FST analysis and it is recommended that the HLD97 locus should be excluded from any kinship analysis performed on South African populations.
A population-based study of cervical cytology findings and human papillomavirus infection in a suburban area of ThailandPhoolcharoen, Natacha, Kantathavorn, Nuttavut, Sricharunrat, Thaniya, Saeloo, Siriporn, Krongthong, Waraphorn 2017 (has links)
Cartas al Editor
Évaluation de marqueurs génétiques du complexe Mycobacterium tuberculosis combinée à l'utilisation d'outils bioinformatiques : apport en épidémiologie et phylogénie de la tuberculose Evaluation of genetic of Mycobacterium tuberculosis combined with the use of bioinformatics tools : input for epidemiology and phylogeny of tuberculosisMillet, Julie 7 June 2011 (has links)
Ce travail de thèse intitulé «Evaluation de marqueurs génétiques du complexe Mycobacterium tuberculosis combinée à l'utilisation d'outils bioinformatiques: apport en épidémiologie et phylogénie de la tuberculose» a consisté en la sélection et l'évaluation de marqueurs minisatellites dans le cadre d'études épidémiologiques et phylogénétiques du bacille tuberculeux, Une première partie a ainsi porté sur l'épidémie de tuberculose en Guadeloupe, Martinique, et Guyane française ainsi que dans un pays continental à faible incidence de tuberculose, la Suède, Les résultats montrent les disparités existant entre les populations de patients tuberculeux des 3 départements français d'Amérique (DFA) ainsi que les similitudes génotypiques existant entre les bacilles tuberculeux. Par ailleurs le rôle majeur joué par les cas d'importation dans l'épidémie de tuberculose a été montré aussi bien dans les DFA qu'en Suède. Nous nous sommes ensuite intéressés à une utilisation optimale des minisatellites pour une meilleure discrimination de la famille génotypique émergeante « Beijing» circulant au Japon (Osaka, Kobe et Okinawa), ainsi qu'en Russie. Nous avons constaté le faible pouvoir discriminant du format classique 12-locus MIRU (Mycobacterial lnterspersed Repetitive Units) et proposons plusieurs nouvelles stratégies de typage basées plusieurs marqueurs minisatellites incluant certains locus hypervariables. Enfin, dans un troisième volet, nous avons étudié la diversité génétique des bacilles tuberculeux circulant actuellement dans la Caraïbe. laquelle semble refléter le passé historique très particulier de cette zone géographique au croisement d'une multitude de peuplements. This thesis entitled "Evaluation of genetic markers of Mycobacterium tuberculosis combined with the use of bioinformatics tools: input for epidemiology and phylogeny of tuberculosis" deals with the selection and evaluation of minisatellite markers in the context of epidemiological and phylogenetic studies of the tubercle bacillus M. tuberculosis. The first part of the present work has focused on the epidemic of tuberculosis in Guadeloupe, Martinique and French Guiana as well as in a low incidence continental country, i.e Sweden. The results show differences between populations of TB patients in the three French Departments of America and similarities between the genotypes of the circulating tubercle bacilli Moreover, results highlight the important role played by imported cases for TB epidemic the three French departments of America and Sweden. ln a second part, minisatellite markers have been evaluated for a better discrimination of strains of the emerging genotype "Beijing" circulating in Japan (Osaka, Kobe and Okinawa), and Russia. A low discriminatory power of classical format 12-locus MIRU (Mycobacterial lnterspersed Repetitive Units) was observed and new combinations of minisatellites have also been proposed including hypervariable locus. Finally, the genetic diversity of tubercle bacilli circulating in the Caribbean was investigated which currently seem to reflect historical past of this very special region at the intersection of a multitude of cultures and peoples.
Prevalência e genotipagem do papilomavírus humano em carcinomas epidermóides penianos de pacientes do Estado do Maranhão Prevalence and genotyping of human papillomavirus in squamous cell carcinomas of patients from the state of MaranhãoRAMOS, Walna Luisa Barros e 28 April 2017 (has links)
Submitted by Rosivalda Pereira (email@example.com) on 2017-09-12T19:35:08Z No. of bitstreams: 1 WalnaRamos.pdf: 1885249 bytes, checksum: a716015a5d512aaba735cf4af13d0e13 (MD5) Made available in DSpace on 2017-09-12T19:35:08Z (GMT). No. of bitstreams: 1 WalnaRamos.pdf: 1885249 bytes, checksum: a716015a5d512aaba735cf4af13d0e13 (MD5) Previous issue date: 2017-04-28 Human papillomavirus (HPV) is the etiologic agent of one of the most common sexually transmitted infections (STIs). According to the oncogenic potential, it is classified in low risk and high risk; high risk subtypes cause lesions that may progress to invasive carcinomas and has been recognized as a possible etiologic agent in penile carcinoma. Brazil has one of the highest incidences of penile cancer in the world. The general objective of this work is associate HPV infection with the histopathological profile of squamous cell carcinomas in patients from the State of Maranhão. This is a prospective analytical study of 29 samples of patients who underwent penectomy surgery at the Aldenora Bello Institute of Oncology of Maranhão. Sociodemographic data were collected through a questionnaire applied to the patients, clinical and histopathological data were collected from the medical records. Tumor samples were collected during penectomy surgeries, and the following steps were performed at the laboratory: DNA extraction and quantification, Nested PCR with PGMY and GP + primers for HPV detection, visualization of amplified products, purification of the PCR product and automated sequencing. The sequencing products were decoded through the BLAST program. Data were analyzed through the SPSS statistical program, with a 5% level of significance. It was observed that the majority of the men were over 60 years of age (69%), had stable marital union (75.9%), family income of up to one minimum wage (75.9%), were illiterate (55. 2%), lived in countryside towns (79.3%), reported using tobacco at some moment in their lives (62%). Regarding sexual habits, 62.1% reported not having performed circumcision, 41.4% had a previous STD, 72.4% had never used a condom, 48.3% had the first intercourse before age 18. The presence of HPV was detected in 69% of the cases, among the viral types, HPV 16 was the most prevalent (55.5%). Regarding to lesion, 51.7% of the cases presented more than one affected region, and the glans was affected in 93.1% of the cases. The most prevalent type of lesion was ulceration (51.7%). Among the histopathological classifications, 41.4% of the samples were classified in degree I of the Broders scale, 27.7% in stage T1 of the TNM staging and according to the Jackson classification, both stages I and II presented the same prevalence, 27.6% of samples. There was no statistically significant difference between the variables evaluated and the presence of HPV. Low education, low income and no circumcision were highly observed in the study, being possible to correlate such variables with the increase of the risk of penile cancer development. The presence of HPV in 69% of the samples and the prevalence of high risk subtypes suggest the need for more actions to prevent the spread of HPV over the population O papilomavírus humano (HPV) é o agente etiológico de umas das infecções sexualmente transmissíveis (ISTs) mais comuns. É classificado de acordo com o potencial oncogênico em baixo risco e alto risco, os subtipos de alto risco causam lesões que podem progredir para carcinomas invasivos e vem sendo reconhecido como possível agente etiológico no carcinoma peniano. O Brasil tem uma das maiores incidências de câncer de pênis do mundo. O objetivo geral deste trabalho é associar a infecção do HPV com o perfil histopatológico de carcinomas epidermóides penianos em pacientes do Estado do Maranhão. Trata-se de um estudo analítico prospectivo de 29 amostras de pacientes que foram submetidos a cirurgia de penectomia no Instituto Maranhense de Oncologia Aldenora Bello. Dados sociodemográficos foram coletados através de um questionário aplicado aos paciente, os dados clínicos e histopatológicos foram coletados dos prontuários. As amostras tumorais foram coletadas durante as cirurgias de penectomia, e em laboratório foram realizadas as etapas de: extração e quantificação do DNA, PCR Nested com os primers PGMY e GP+ para detecção do HPV, visualização dos produtos amplificados, purificação do produto da PCR e sequenciamento automatizado. Os produtos do sequenciamento foram decodificados através do programa BLAST. Os dados foram analisados através do programa estatístico SPSS, o nível de significância foi de 5%. Foi observado que a maioria dos homens estava na faixa etária acima de 60 anos (69%), apresentavam união conjugal estável (75,9%), renda familiar de até um salário mínimo (75,9%), eram analfabetos (55,2%), residiam em municípios do interior do Estado (79,3%), relataram o uso de tabaco em algum momento da vida (62%). Em relação aos hábitos sexuais, 62,1% relataram não ter realizado circuncisão, 41,4 % a ocorrência de DST prévia, 72,4% nunca fizeram uso de preservativo, 48,3% tiveram o 1º coito antes dos 18 anos. A presença de HPV foi detectada em 69% dos casos, dentre os tipos virais, o HPV 16 foi o mais prevalente (55,5%). Em relação a lesão, 51,7% dos casos apresentou mais de uma região afetada, estando a glande afetada em 93,1% dos casos. O tipo de lesão mais prevalente foi a do tipo ulceração (51,7%). Dentre as classificações histopatológicas, 41,4% das amostras foram classificadas no grau I da escala de Broders, 27,7% no estágio T1 do estadiamento TNM e na classificação de Jackson, os estágios I e II apresentam a mesma prevalência, 27,6% das amostras. Não houve diferença estatisticamente significante entre as variáveis avaliadas e a presença de HPV. A baixa escolaridade, a baixa renda e a não circuncisão foram observados no estudo com um percentual elevado, sendo possível correlacionar tais variáveis com o aumento no risco de desenvolvimento do câncer de pênis. A presença de HPV em 69% das amostras e a prevalências dos subtipos de alto risco sugerem a necessidade de mais ações de prevenção da disseminação desse vírus na população.
Almeida, Ricardo Augusto Monteiro de Barros [UNESP]
26 February 2009
Made available in DSpace on 2014-06-11T19:31:29Z (GMT). No. of bitstreams: 0 Previous issue date: 2009-02-26Bitstream added on 2014-06-13T20:41:51Z : No. of bitstreams: 1 almeida_ramb_dr_botfm.pdf: 853261 bytes, checksum: 866edf2277c1ac0e74ea9c48e8cb31a9 (MD5) Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Universidade Estadual Paulista (UNESP) Iniciativas como a “WHO/UNAIDS ‘3 by 5’ permitiram que se atingisse, no ano de 2007, a marca de 3 milhões de pessoas com acesso à terapia antiretroviral (TARV) em países de baixa e média renda. O aumento da cobertura nestes países demanda custos importantes com anti-retrovirais, porém também levanta outro problema, que é o monitoramento da terapia em localidades de poucos recursos. Há consenso no fato de que devem ser pesquisados marcadores de eficácia da TARV mais acessíveis. Considerando o comportamento da β-2 microglobulina sérica e das citocinas séricas TNF-α, IFN-γ, IL-2, IL-4 e IL-10 com relação à atividade inflamatória induzida pela replicação do HIV-1, o objetivo deste estudo foi o de verificar o comportamento destas substâncias como indicadores da presença, ou não, de falha terapêutica à HAART. Entre agosto de 2004 e novembro de 2005, 89 indivíduos infectados pelo HIV-1, atendidos pela Área de Doenças Tropicais da Faculdade de Medicina de Botucatu-UNESP, e 20 indivíduos normais, doadores de sangue do Hemocentro de Botucatu [43 mulheres e 66 homens; idade média = 39,7 anos (22 - 66 anos)] foram divididos em 4 grupos: G1- 15 indivíduos infectados pelo HIV-1, virgens de tratamento ou sem HAART há pelo menos seis meses e com contagens de linfócitos T CD4 + menores que 350 células/mm3; G2- 31 indivíduos infectados pelo HIV-1, em uso de HAART e sem falha terapêutica virológica (FT); G3- formado por 43 indivíduos infectados pelo HIV-1, em uso de HAART e com FT, e GC- formado por 20 indivíduos normais, não infectados pelo HIV-1, que serviram de controles para as citocinas séricas. Foram revisados os dados demográficos, clínicos e de HAART e realizados os exames β-2 microglobulina sérica, citocinas séricas (TNF-α, IFN-γ, IL-2, IL-4 e IL-10), genotipagem do HIV-1, carga viral plasmática (CV) e linfócitos T CD4 + e T CD8 +. Para... Initiatives such as WHO/UNAIDS ‘3 by 5’ made it possible to achieve the figure of 3 million people with access to antiretroviral therapy (ART) in middle- and low-income countries in 2007. The increase in these countries’ coverage leads to important expenditure on antiretroviral drugs; however, it also raises another problem, which is therapy monitoring in low-income locations. There is agreement on the fact that more accessible ART efficacy markers must be studied. By considering the behavior of serum β-2 microglobulin and serum cytokines TNF-α, IFN-γ, IL-2, IL-4 and IL-10 in relation to inflammatory activity induced by HIV-1 replication, the objective of this study was to assess the behavior of such substances as indicators of the presence, or not, of antiretroviral therapeutic failure (TF). From August 2004 to November 2005, 89 HIV-1-infected individuals assisted by the Tropical Diseases Sector of the Botucatu School of Medicine – UNESP and 20 normal blood donors at the Blood Transfusion Center of Botucatu [43 female and 66 male; mean age = 39.7 years (22 - 66 years)] were divided into 4 groups: G1- 15 HIV-1-infected individuals, previously untreated or without HAART for at least six months and CD4 + < 350 cells/mm3; G2- 31 HIV-1-infected individuals undergoing HAART without virological therapeutic failure (TF), G3- 43 HIV-1-infected individuals undergoing HAART with TF, and CG- 20 normal individuals who served as controls for serum cytokines. Demographic, clinical and HAART data were reviewed, and serum β-2 microglobulin, serum cytokines (TNFα, IFN-γ, IL-2, IL-4 and IL-10), HIV-1 genotyping, plasma viral load (VL) and T CD4 + and T CD8 + lymphocytes tests were performed. The Mann-Whitney test for independent samples was used for between-group comparison in the case of numeric variables, and Fisher’s exact test was applied for category variables. Statistical difference... (Complete abstract click electronic access below)
Detecção de polimorfismos do gene da proteína priônica no rebanho ovino do Estado de São Paulo: métodos e aplicabilidade à seleção para resistência ao scrapie Detection of Polymorphisms in the prion protein gene in Sheeps flock in the State of São Paulo: Methods and Applicability of Selection for Scrapie ResistanceCaio Rodrigues dos Santos 31 May 2012 (has links)
Scrapie ou paraplexia enzoótica dos ovinos é uma doença neurodegenerativa fatal que acomete ovinos e raramente caprinos. A doença é influenciada por polimorfismos nos códons 136, 154 e 171 do gene prnp que codifica a proteína priônica. Os animais podem ser susceptíveis ou resistentes, de acordo com as sequências alélicas observadas nos referidos códons. No Brasil ocorreram apenas casos de animais que foram importados, sendo o país considerado livre da doença. Neste trabalho foi realizada a genotipagem dos diferentes polimorfismos associados ao desenvolvimento do scrapie e a categorização em animais susceptíveis e resistentes. Foram sequenciadas 118 amostras provenientes de ovinos da raça Santa Inês criados em propriedades localizadas no Estado de São Paulo. Destas amostras foram identificados 6 alelos e 11 genótipos (ARQ/ARQ, ARR/ARQ, ARQ/AHQ, ARQ/VRQ, AHQ/AHQ, ARR/ARR, ARR/AHQ, VRQ/VRQ, ARQ/TRQ, TRR/TRR, TRQ/TRQ), dentre os quais o genótipo ARQ/ARQ teve ocorrência de 56,7%. Em nosso estudo foi detectada a presença da tirosina no códon 136, observação rara na medida em quenão existem relatos nacionais e relatos envolvendo a raça Santa Inês descrevendo este polimorfismo. Com os resultados obtidos, foi possível determinar a existência de grande variabilidade genética relacionada à raça Santa Inês no Estado de São Paulo, apesar da variabilidade, apenas 1,69% dos genótipos observados são extremamente resistentes ao scrapie. Estes dados demonstram que a raça nativa Santa Inês pode ser considerada potencialmente susceptível ao scrapie. Enzootic paraplexia or scrapie is a fatal neurodegenerative disease affecting mainly sheep and rarely goats. The disease is influenced by polymorphisms at codons 136, 154 and 171 of prnp gene that encodes the prion protein. The animals may be susceptible or resistant to the development of the disease according to the allelic sequences observed in these codons. In Brazil there were only cases of scrapie in imported animals, therefore the country is considered free of the disease. This study performed the genotyping of different polymorphisms associated to the development of scrapie. Then, based on these findings the animals were categorized in resistant and susceptible. A total of 118 samples were sequenced from the Santa Ines sheep raised on properties located in the State of Sao Paulo. From these samples, 6 alleles and 11 genotypes were identified (ARQ / ARQ, ARR / ARQ, ARQ / AHQ, ARQ / VRQ, AHQ / AHQ, ARR / ARR, ARR / AHQ, VRQ / VRQ, ARQ / TRQ, TRR / TRR, TRQ / TRQ), the genotype ARQ / ARQ presented a frequency of 56.7%. It was also detected the presence of tyrosine at codon 136, which may be considered a rare observation, since there is no report regarding Santa Ines breeding presenting this polymorphism. These results showed the great genetic variability in Santa Ines in Sao Paulo and only 1,69% of the genotypes observed are extremely resistant to scrapie. These data demonstrate that the Santa Ines sheep can be considered potentially susceptible to scrapie.
Recent Tuberculosis Transmission and Clustering: An Evaluation of Clinical and Molecular Epidemiological Risk Factors in Ohio, 2006-2015Alamoudi, Banan Mohammad A 2017 (has links)
No description available.
Davhana, Ndivhudzannyi Caroline
12 February 2016
MSc (Microbiology) Department of Microbiology
Agronomic, genetic and genomic approaches for predicting heterosis in sorghum [Sorghum bicolor (L.) Moench]Maulana, Frank 2016 (has links)
Doctor of Philosophy Department of Agronomy Tesfaye Tesso The approach used to identify inbred lines that can produce superior hybrids is costly and time-consuming. It requires creation of all possible crosses and evaluation of the crosses to estimate combining abilities for the desired traits. Predicting heterosis or hybrid performance in any way possible may help to reduce the number of crosses to be made and evaluated. In this study, four sets of experiments were conducted to determine whether heterosis can be predicted based on inbred line performance, genetic distance between parents and genomic prediction model. The first experiment was aimed at assessing the levels of genetic diversity, population structure and linkage disequilibrium (LD) in 279 public sorghum inbred lines, based on 66,265 SNPs generated using the genotyping-by-sequencing (GBS) platform. The inbred lines were developed at different times over the last two decades and harbor robust diversity in pedigree and agronomic characteristics. Some of the inbreds are resistant to Acetolactate synthase (ALS) and Acetyl co-enzyme-A carboxylase (ACC) inhibitor herbicides. The mean polymorphic information content (PIC) and gene diversity across the entire inbreds were 0.35 and 0.46, respectively with non-herbicide resistant inbreds harboring more diversity than the herbicide resistant ones. The population structure analysis clustered the inbred lines into three major subgroups according to pedigree and fertility-reaction with the maintainer lines (B-lines) distinctly forming a separate cluster. Analysis of molecular variance (AMOVA) revealed more variation within subgroups than among subgroups. Substantial linkage disequilibrium (LD) was detected between the markers in the population with marked variation between chromosomes. This information may facilitate the use of the inbreds in sorghum breeding programs and provide perspectives for optimizing marker density for gene mapping and marker-assisted breeding. The second experiment, based on 102 F1 hybrids developed by intercrossing closely and distantly related inbreds, was conducted to investigate the relationship of genetic distance between parents with hybrid vigor or heterosis. The F1 hybrids alongside their parents were evaluated at two environments in a randomized complete block design with three replications. The results show that correlations of genetic distance between parents with hybrid performance and heterosis were variable and dependent on the trait. Though most were statistically non-significant and not strong to be used as predictor for heterosis, the results tend to show that certain level of genetic distance between parents is needed to capture maximum heterosis and hybrid performance. The objective of the third research study was to determine whether traits measured on parents can be used to predict hybrid performance in sorghum and to assess the combining ability of selected inbreds. Forty-six parental inbred lines and 75 F1 hybrids generated from intercrossing the inbreds were evaluated in four environments in a randomized complete block design with three replications. The average performance of the parents (mid-parent) was significantly correlated with hybrid performance for thousand kernel weight, days to flowering and plant height. Significant general (GCA) and specific (SCA) combining abilities were observed for most traits, with highly significant GCA effects observed for most traits as compared to SCA indicating that additive genetic effects are more important in affecting the inheritance of the traits measured. Results show that studying parental inbred line performance could generate important information for predicting hybrid performance in sorghum. The fourth experiment was aimed at assessing the efficacy of genomic prediction of hybrid performance in sorghum. Genomic prediction was performed with five-fold cross-validation procedure on 204 F1 hybrids developed using 102 inbred lines. A total of 66,265 SNP markers generated using genotyping-by-sequencing were used in this study. Results showed that increasing training population size increased prediction accuracies for all traits with the effect being different for different traits. Also, considering additive effects alone versus additive and dominance effects in the model showed similar trend of prediction accuracy but the full model (considering both additive and dominance effects of the markers) provided better prediction at least for some of the traits. The results suggest that genomic prediction could become an effective tool for predicting the performance of untested sorghum hybrids thus adding efficiency to hybrid selection.
Rife, Trevor W.
Doctor of Philosophy Genetics Interdepartmental Program Jesse Poland The Green Revolution is credited with saving billions of lives by effectively harnessing new genetic resources and breeding strategies to create high-yielding varieties for countries lacking adequate food security. To keep the next billion people in a state of food security, plant breeders will need to rapidly incorporate novel approaches and technologies into their breeding programs. The work presented here describes new genomic and phenomic strategies and tools aimed at accelerating genetic gain in plant breeding. Plant breeders have long relied on regional testing networks to evaluate new breeding lines across many locations. These are an attractive resource for both retrospective and contemporary analysis due to the vast amount of data available. To characterize genetic progress of plant breeding programs in the Central Plains, entries from the Southern Regional Performance Nursery dating back to 1992 were evaluated in field trials. The trend for annual improvement was 1.1% yr⁻¹, matching similar reports for genetic gain. During the same time period, growth of on-farm yields stagnated. Genomic selection, a promising method to increase genetic gain, was tested using historical data from the SRPN. A temporal-based model showed that, on average, yield predictions outperformed a year-to-year phenotypic correlation. A program-based model found that the predictability of a breeding program was similar when using either data from a single program or from the entire regional collection. Modern DNA marker platforms either characterize a small number of loci or profile an entire genome. Spiked genotyping-by-sequencing (sGBS) was developed to address the need in breeding programs for both targeted loci and whole-genome selection. sGBS uses a low-cost, integrated approach that combines targeted amplicons with reduced representation genotyping-by-sequencing. This approach was validated using converted and newly-designed markers targeting known polymorphisms in the leaf rust resistance gene Lr34. Plant breeding programs generate vast quantities of data during evaluation and selection of superior genotypes. Many programs still rely on manual, error-prone methods to collect data. To make this process more robust, we have developed several open-source phenotyping apps with simple, intuitive interfaces. A contemporary Green Revolution will rely on integrating many of these innovative technologies into modern breeding programs.
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