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Academic literature on the topic 'QTL analysi'

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Published: 9 March 2023
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Journal articles on the topic "QTL analysi"

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Batista, Luiz Fernando Dias, Madeline E. Rivera, Aaron B. Norris, Jordan Adams, Roberta Cracco, Morgan Jackson, and Luis O. Tedeschi. "44 Effect of Quebracho (Schinopsis balansae) extract inclusion in a high roughage diet upon in vitro gas production." Journal of Animal Science 98, Supplement_2 (November 1, 2020): 53–54. http://dx.doi.org/10.1093/jas/skz397.122.

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Abstract The utilization of natural plant secondary compounds as feed additives in animal nutrition has been extensively studied because of their ability to modify digestive and metabolic functions. Condensed tannin (CT) supplementation can potentially alter ruminal fermentation, and mitigate methane (CH4) emissions. The objective of this study was to determine the effect of quebracho CT extract (QT; Schinopsis balansae) within a roughage-based diet on overall fermentability and CH4 production utilizing the in vitro gas production technique (IVGP). Twenty rumen cannulated steers (227 ± 19 kg) were randomly assigned to four dietary treatments (n=4): QT at 0, 1, 2, and 3% of DM (QT0, QT1, QT2, and QT3). A roughage-based diet containing 88% bermudagrass hay and 12% concentrate was fed daily at 2.1% of shrunk body weight. The animals were adapted to the basal diet for 24-d then introduced to predetermined treatments for 35d. Rumen inoculum was collected weekly from each steer to perform the incubations. Two hundred milligrams of air-dried base diet were incubated for 48-h with a composite rumen inoculum for each treatment over 5 wk. Kinetic analysis of cumulative 48h gas production was performed using Gasfit. Measurements of CH4 were performed via gas chromatography and digested residue was determined post-incubation. Data were analyzed using a random coefficients model. Total gas production was higher for QT0 compared to QT1 and QT3 (P = 0.001), but not different from QT2 (P = 0.554). The fractional rate of gas production was higher for QT2 compared to QT0 (P = 0.011). First and second pool gas production decreased linearly as QT inclusion increased (P = 0.042 and 0.010, respectively). There was no dietary effect in ivNDFD (P = 0.567). However, there was a linear tendency to decrease CH4 production with the addition of QT (P=0.071) likely due to changes in the microbial population.
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Barjes Alrawi, Ezzideen, Erica D. Warlick, Qing Cao, Mukta Arora, Shernan G. Holtan, Tim Krepski, Michael R. Verneris, John Wagner, Daniel J. Weisdorf, and Claudio G. Brunstein. "High Peripheral Blood Stem Cell (PBSC) CD34+ Cell Dose Increases the Risk of Chronic Gvhd after Human Leukocyte Antigen (HLA) Matched Sibling Transplantation." Blood 128, no. 22 (December 2, 2016): 5877. http://dx.doi.org/10.1182/blood.v128.22.5877.5877.

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Abstract CD34+ cell dose is a critical determinant of outcomes after allogeneic PBSC transplantation, with a CD34 dose ≥2.0 x 10e6/kg shown to positively impact hematopoietic engraftment and survival. However, it is unknown whether additional benefits are observed with even higher CD34 cell doses. Therefore, we further explored the effect of intermediate, high and very high CD34 cell doses on the incidence of engraftment, acute and chronic graft-versus-host disease (GVHD) and transplant related mortality (TRM) and on probability of survival and GVHD-Relapse-free survival (GRFS). Three hundred and five consecutive patients transplanted with GCSF-mobilized PBSC from HLA-matched sibling donors (MSD) were evaluated. Patients were ≥16 years of age, had a hematological malignancy and received a myeloablative or a nonmyeloablative conditioning regimen between 2002 and 2012. The median recipient age was 52 years (r, 19-74 years) with most being male (n=194, 63.8%) diagnosed with leukemia (72%) or lymphoma (22%), and intermediate disease risk index (DRI, n=204, 67%). The median age for the donor were 49 years (r,17-76 years). In 159 patients (52%) the donor and recipient were sex matched with 89 male patients having a female door (29%). The ABO blood type was matched in 195 patients (64%), 153(50%) received a myeloablative (MA) conditioning regimen, and 37 (12%) received a reduce intensity conditioning regimen containing ATG. The median follow up of surviving patients was 793 days (r, 14-4562 days). Patients were divided in four CD34 dose quartiles: first quartile (QT1), ≤4.8 x10e6/kg, QT2 4.8-6.0 x10e6/kg, QT3 6.0-7.5 x10e6/kg, and QT4 ≥ 7.6 x 10e6/kg. Notably, the CD3 doses were similar for all quartiles: QT1 was 3.4 x 10e8/kg (r, 0.3-10.0), QT2 was 2.7 x 10e8/kg (r, 1.1-7.6), QT3 was 2.8 x 10e8/kg (r, 0.8-7.2) and QT4 was 2.8 x 10e8/kg (r, 1.4-7.7); there was no correlation between CD34 and CD3 cell doses. Patient and donor characteristics were similar in the four groups except for shorter median follow-up (P <0.01) in QT1, more sex mismatched grafts (P <0.01) in QT3, and lower median number of cell collections (P <0.01) and more female donor: male recipient pairs (P< 0.01) in QT4. Multivariate analysis results are summarized on the table. Higher CD34+ cell dose was associated with improved platelet recovery with trends toward lower TRM and improved overall survival. Chronic GVHD however was also higher. In summary, additional studies are needed to establish a survival benefit in recipients of higher cell doses >4.8 x 10e6 CD34 cells/kg. Unless survival is positively impacted, the higher risk of chronic GVHD would argue for assigning an upper CD34 cell dose limit to reduce this risk that can significantly impair quality of life. Table Table. Disclosures No relevant conflicts of interest to declare.
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Takahashi, Hidekazu. "QTL analysis using the Windows QTL Cartographer." Breeding Research 10, no. 1 (2008): 11–14. http://dx.doi.org/10.1270/jsbbr.10.11.

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Kang, Yiwei, Miao Zhang, Yue Zhang, Weixun Wu, Pao Xue, Xiaodeng Zhan, Liyong Cao, Shihua Cheng, and Yingxin Zhang. "Genetic Mapping of Grain Shape Associated QTL Utilizing Recombinant Inbred Sister Lines in High Yielding Rice (Oryza sativa L.)." Agronomy 11, no. 4 (April 7, 2021): 705. http://dx.doi.org/10.3390/agronomy11040705.

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Grain shape is a key factor for yield and quality in rice. To investigate the genetic basis of grain shape in the high-yielding hybrid rice variety Nei2You No.6, a set of recombinant inbred sister lines (RISLs) were used to map quantitative trait loci (QTLs) determining grain length (GL), grain width (GW), and length-width ratio (LWR) in four environments. A total of 91 medium/minor-effect QTL were detected using a high-density genetic map consisting of 3203 Bin markers composed of single nucleotide polymorphisms, among which 64 QTL formed 15 clusters. Twelve of 15 clusters co-localized with QTL previously reported for grain shape/weight. Three new QTL were detected: qGL-7a, qGL-8, and qGL-11a. A QTL cluster, qLWR-12c/qGW-12, was detected across all four environments with phenotypic variation explained (PVE) ranging from 3.67% to 11.93%, which was subsequently validated in paired lines of F17 progeny and tightly linked marker assay in F10 generation. Subsequently, 17 candidate genes for qLWR-12c/qGW-12 were detected in the 431 Kb interval utilizing bulk segregant analysis (BSA). Among these, OsR498G1222170400, OsR498G1222171900, OsR498G1222185100, OsR498G1222173400, and OsR498G1222170500 were the best candidates, which lays the foundation for further cloning and will facilitate high-yield breeding in rice.
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Liu, Xiaolu, Xiangyuan Wan, Xiaodong Ma, and Jianmin Wan. "Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice using the chromosome segment substitution line population across eight environments." Genome 54, no. 1 (January 2011): 64–80. http://dx.doi.org/10.1139/g10-070.

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Quantitative trait locus (QTL) mapping and stability analysis were carried out for 16 rice ( Oryza sativa L.) quality traits across eight environments, by using a set of chromosome segment substitution lines with ‘Asominori’ as genetic background. The 16 quality traits include percentage of grain with chalkiness (PGWC), area of chalky endosperm (ACE), amylose content (AC), protein content (PC), peak viscosity, hot paste viscosity, cool paste viscosity, breakdown viscosity (BDV), setback viscosity (SBV), consistency viscosity, cooked-rice luster (LT), scent, tenderness (TD), viscosity, elasticity, and the integrated values of organleptic evaluation (IVOE). A total of 132 additive effect QTLs are detected for the 16 quality straits in the eight environments. Among these QTLs, 56 loci were detected repeatedly in at least three environments. Interestingly, several QTL clusters were observed for multiple quality traits. Especially, one QTL cluster near the G1149 marker on chromosome 8 includes nine QTLs: qPGWC-8, qACE-8, qAC-8, qPC-8a, qBDV-8a, qSBV-8b, qLT-8a, qTD-8a, and qIVOE-8a, which control PGWC, ACE, AC, PC, BDV, SBV, LT, TD, and IVOE, respectively. Moreover, this QTL cluster shows high stability and repeatability in all eight environments. In addition, one QTL cluster was located near the C2340 marker on chromosome 1 and another was detected near the XNpb67 marker on chromosome 2; each cluster contained five loci. Near the C563 marker on chromosome 3, one QTL cluster with four loci was found. Also, there were nine QTL clusters that each had two or three loci; however, their repeatability in different environments was relatively lower, and the genetic contribution rate was relatively smaller. Considering the correlations among all of the 16 quality traits with QTL cluster distributions, we can conclude that the stable and major QTL cluster on chromosome 8 is the main genetic basis for the effect of rice chalkiness, AC, PC, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice. Consequently, this QTL cluster is a novel gene resource for controlling rice high-quality traits and should be of great significance for research on formation mechanism and molecule improvement of rice quality.
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Mangin, B., P. Thoquet, and N. Grimsley. "Pleiotropic QTL Analysis." Biometrics 54, no. 1 (March 1998): 88. http://dx.doi.org/10.2307/2533998.

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Ukai, Yasuo. "Theory of QTL analysis." Breeding Research 1, no. 1 (1999): 25–31. http://dx.doi.org/10.1270/jsbbr.1.25.

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Xu, Peng, Jin Gao, Zhibin Cao, Peng W. Chee, Qi Guo, Zhenzhen Xu, Andrew H. Paterson, Xianggui Zhang, and Xinlian Shen. "Fine mapping and candidate gene analysis of qFL-chr1, a fiber length QTL in cotton." Theoretical and Applied Genetics 130, no. 6 (March 30, 2017): 1309–19. http://dx.doi.org/10.1007/s00122-017-2890-8.

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Hina, Aiman, Yongce Cao, Shiyu Song, Shuguang Li, Ripa Akter Sharmin, Mahmoud A. Elattar, Javaid Akhter Bhat, and Tuanjie Zhao. "High-Resolution Mapping in Two RIL Populations Refines Major “QTL Hotspot” Regions for Seed Size and Shape in Soybean (Glycine max L.)." International Journal of Molecular Sciences 21, no. 3 (February 4, 2020): 1040. http://dx.doi.org/10.3390/ijms21031040.

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Seed size and shape are important traits determining yield and quality in soybean. However, the genetic mechanism and genes underlying these traits remain largely unexplored. In this regard, this study used two related recombinant inbred line (RIL) populations (ZY and K3N) evaluated in multiple environments to identify main and epistatic-effect quantitative trait loci (QTLs) for six seed size and shape traits in soybean. A total of 88 and 48 QTLs were detected through composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively, and 15 QTLs were common among both methods; two of them were major (R2 > 10%) and novel QTLs (viz., qSW-1-1ZN and qSLT-20-1K3N). Additionally, 51 and 27 QTLs were identified for the first time through CIM and MCIM methods, respectively. Colocalization of QTLs occurred in four major QTL hotspots/clusters, viz., “QTL Hotspot A”, “QTL Hotspot B”, “QTL Hotspot C”, and “QTL Hotspot D” located on Chr06, Chr10, Chr13, and Chr20, respectively. Based on gene annotation, gene ontology (GO) enrichment, and RNA-Seq analysis, 23 genes within four “QTL Hotspots” were predicted as possible candidates, regulating soybean seed size and shape. Network analyses demonstrated that 15 QTLs showed significant additive x environment (AE) effects, and 16 pairs of QTLs showing epistatic effects were also detected. However, except three epistatic QTLs, viz., qSL-13-3ZY, qSL-13-4ZY, and qSW-13-4ZY, all the remaining QTLs depicted no main effects. Hence, the present study is a detailed and comprehensive investigation uncovering the genetic basis of seed size and shape in soybeans. The use of a high-density map identified new genomic regions providing valuable information and could be the primary target for further fine mapping, candidate gene identification, and marker-assisted breeding (MAB).
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UKAI, Yasuo. "Quantitative Trait and QTL Analysis." Japanese journal of crop science 68, no. 2 (1999): 179–86. http://dx.doi.org/10.1626/jcs.68.179.

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Dissertations / Theses on the topic "QTL analysi"

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MUSTAFA, MAJID HASSAN MUSTAFA. "BROWN ROT DISEASE DEVELOPMENT IN PEACH(P. PERSICA L. BATSCH): FROM FUNGAL BIOLOGY TO HIGH-THROUGHPUT ON-FIELDPHENOTYPING." Doctoral thesis, Università degli Studi di Milano, 2022. http://hdl.handle.net/2434/924066.

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Brown rot (BR) disease, caused by Monilinia spp., causes significant pre-and post-harvest losses in stone fruit production, especially in humid and warm temperatures. In this thesis, we tried to tackle the subject with three complementary approaches. First, the recent progress in BR resistance in peach fruit was reviewed. Then we highlighted best practices in phenotyping BR susceptibility/resistance procedures in field and in vitro. We concluded that the main factors contributing to disease development are Monilinia inocula availability, environmental conditions, cultivars, fruit stage and management practices. Secondly, we investigated the anti-fungal effect of some phenolics such as chlorogenic and ferulic acids and triterpenoids such as oleanolic, betulinic, and ursolic acids. Furthermore, fruit surface compound (FSC) extracts of peach fruit at two developmental stages on Monilinia fructicola and M. laxa characteristics during in vitro growth were studied. A new procedure for assaying anti-fungal activity of triterpenoids, which are notoriously difficult to assess in vitro because of their hydrophobicity, has been developed. Also, a follow-up of this study revealed that certain phenolics and triterpenoids showed modest anti-fungal activity while dramatically modulating M. fructicola gene expression. MfRGAE1 gene was overexpressed by chlorogenic and ferulic acids and MfCUT1 by betulinic acid at 4- and 7-days post-inoculation. The third objective was to investigate the genetic background responsible for disease resistance in peach by detecting Quantitative Trait Loci (QTL) and attempts to identify molecular markers for assisted selection (MAS) in peach. For this, three F2 progenies, derived from three selfied F1 selections obtained from "Contender" (C, resistant) × "Elegant Lady" (El, susceptible), were investigated for two seasons (2019 and 2021). The whole progeny was genotyped by Single-Primer Enriched Technology (SPET) and a recently developed 18K SNP array. The genome-wide QTL analysis showed intriguing areas relevant to disease resistance, mainly the QTLs on chromosomes 2 and 4, which may be candidates for future MAS applications. Several new QTLs were detected for other fruit quality traits, including maturity date, soluble solid content and fruit weight.
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Prashar, Ankush. "Arabidopsis QTL analysis using stairs and gene expression." Thesis, University of Birmingham, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.435316.

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Taenzler, Bärbel. "QTL-Analyse der Backqualität in Einkornweizen (T. m. monococcum)." [S.l. : s.n.], 2000. http://deposit.ddb.de/cgi-bin/dokserv?idn=964783304.

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Ma, Junwu. "Genome-wide QTL mapping for complex traits in pigs and focusing analysis on fatness QTL on porcine chromosome X." Toulouse 3, 2009. http://thesesups.ups-tlse.fr/584/.

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Les buts de cette thèse étaient l'acquisition de connaissances sur l'architecture génétique de caractères complexes et l'étude de la variabilité des taux de recombinaison chez le porc. La première partie de cette thèse présente une analyse sur l'ensemble du génome des locus influençant des caractères quantitatifs (QTL) au sein de croisements F2 entre des verrats de race Duroc blanc et des truies Erhulian, protocole développé en Chine à l'université d'agriculture du Jiangxi (JXAU). La population étudiée dans le cadre de cette thèse regroupe de 750 à 1030 animaux F2 mesurés sur 80 caractères concernant la composition de la carcasse (17 caractères), la qualité de la viande (58 caractères) et les caractères morphologiques des oreilles (5 caractères). Au total nous avons identifié 253 QTL pour ces caractères, dont la moitié est significatif au niveau du génome entier. Les chromosomes rassemblant le plus de QTL pour ces caractères sont les chromosomes 4, 7, 8 & X. Les niveaux de signification les plus élevés sont observés pour un (ou des) QTL affectant la longueur de carcasse, le poids de la tête et le poids des oreilles situé au sein d'un intervalle de 3 cM situé sur le chromosome 7 (Sw1856-S0066) expliquant jusqu'à 50 % de la variance phénotypique. L'allèle Duroc blanc étant l'allèle favorable pour une majorité des QTL affectant la composition de la carcasse, tandis que les allèles favorables pour la qualité de la viande présentent des origines tantôt asiatique tantôt européenne. L'INRA avait réalisé il y a près de 20 ans un programme de détection de QTL entre animaux Large White & Meishan. La localisation parallèle sur le chromosome X de QTL influençant l'engraissement et la muscularité des animaux au sein des pédigrées français et chinois nous a amené a travaillé sur la cartographie fine de ce(s) QTL qui a été développée dans la deuxième partie de cette thèse réalisée en cotutelle. Dans un premier temps afin de préciser la position du QTL située sur le chromosome X, nous avons étudié les variations de taux de recombinaison entre différentes régions du chromosome ainsi que les variations inter individuelles. .
The aims of this thesis are to gain knowledge on genetic architecture of complex traits and on fine-scale structure of recombination rate variation in pigs. The first part of this thesis presents a genome-wide scan for quantitative trait loci (QTL) in a cross between White Duroc boars and Erhualian sows that was developed at Jiangxi Agricultural University (JXAU) in China. The mapping population comprised 750-1030 F2 individuals that were evaluated for a total of 80 traits related to carcass composition (17 traits), meat quality (58 traits) and ear traits (5 traits). In total, we identified 253 QTL for these traits, of which about half reached genome-wide significance level. Numerous QTL for these traits have been found on porcine chromosomes 4, 7, 8 and X. The greatest significance levels were found for a QTL affecting carcass length, head weight and ear weight on SSC7 in an interval of 3 cM (SW1856-S0666), which explained up to 50% of the phenotypic variance. White Duroc alleles at a majority of QTL detected were favorable for carcass composition, while favorable QTL alleles for meat quality originated from both White Duroc and Erhualian. INRA performed a genome scan to reveal QTL in a Large White × Meishan cross 8 years ago. Coincidently, both INRA and JXAU mapped strong QTL for fatness and muscling traits in a similar region of the porcine chromosome X (SSCX). Thus, both sides wished to collaborate to fine map the QTL. .
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von, Delft Annette. "ProteomicQTL (pQTL):Kopplungsanalyse zur Identifizierung genetischer Modulatoren des Plasmaproteoms." Doctoral thesis, Universitätsbibliothek Leipzig, 2013. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-113003.

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Ziel der vorliegenden Arbeit war die Identifizierung genetischer Faktoren, die das Plasmaproteom regulieren. Die Untersuchungen wurden im Modellsystem einer F2-Kreuzung zweier Inzucht-Mausstämme (FVB.LDLR-/-, C57BL/6.LDLR-/-) durchgeführt, die sich in ihrer Atheroskleroseausprägung unterscheiden. Von jedem der 453 Tiere der F2-Generation wurden Plasmaproteomprofile mittels Massenspektrometrie (MALDI-TOF) generiert. Diese Spektren wurden in zwei unabhängigen Datenanalysen ausgewertet und eine Kopplungsanalyse (QTL-Analyse, quantitative trait loci) der Phänotypen mit jeweils 192 genetischen Markern in jedem der F2-Tiere durchgeführt. So wurden die Datensätze von Proteom und Genom miteinander kombiniert, um Genorte, die mit unterschiedlich regulierten Proteinen in Verbindung stehen, zu identifizieren. Dieser Ansatz ist bisher in der Literatur nicht beschrieben worden. In der vorliegenden Arbeit wird sowohl die Methodik der statistischen Auswertung als auch die weitere Analyse der generierten Daten beschrieben. Es wurden zahlreiche hochsignifikante Kopplungssignale gefunden, von denen zwei durch die Identifizierung von Proteinen verifiziert werden konnten. Es handelt sich hierbei um das Apo-A2 des HDL auf Chromosom 1 und Hämoglobin subunit alpha auf Chromosom 11. Eine Kolokalisation der gefundenen Proteine mit Loci der Atherosklerosedisposition konnte nicht identifiziert werden. Dieser Ansatz zeigt erstmals, dass eine hypothesenfreie Verbindung proteomischer und genomischer Daten möglich ist und zur Identifizierung genetisch regulierter Plasmaproteine beitragen kann.
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Zhong, Shengqiang. "Integrating QTL analysis into plant breeding practice using Bayesian statistics." [Ames, Iowa : Iowa State University], 2008.

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Guess, Adam Joseph. "QTL analysis of ray pattern in Caenorhabditis elegans recombinant inbred lines." Wright State University / OhioLINK, 2008. http://rave.ohiolink.edu/etdc/view?acc_num=wright1205197070.

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Ousova, Olga. "Analyse d'un QTL d'hypercortisolémie chez le porc : rôle de la transcortine." Bordeaux 2, 2001. http://www.theses.fr/2001BOR28867.

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Cette thèse avait pour but de préciser les facteurs génétiques responsables des différences de cortisolémie entre les races de porc Meishan et Large White. Lors d'études précédentes d'analyse de liaisons génétiques sur le croisement F2 Meishan x Large White, un QTL influençant les taux de cortisol basal et induit par un stress a été cartographié sur le chromosome 7 porcin. Par l'analyse comparative des cartes humaine, murine et porcine nous avons révélé la présence d'un gène candidat positionnel codant pour la transcortine ou CBG (corticosteroid binding globulin). En premier lieu nous avons vérifié la localisation de ce gène chez le porc. Cela a été réalisé d'abord par cartographie sur des panels d'hybrides somatiques et irradiés à l'aide d'un fragment du gène Cbg. De plus ce fragment de Cbg porcin nous a servi pour isoler un clone BAC que nous avons utilisé pour cartographier ce gène par hybridation in situ sur un étalement de chromosomes porcins. L'ensemble de ces techniques nous a permis de localiser la CBG porcine en 7q26, entre les marqueurs flanquant le QTL de cortisolémie. L'évaluation de paramètres de liaison de la transcortine pour le cortisol (fait par la technique de radioliaison en utilisant la Concanavaline A-Sepharose) a montré que les porcs de race Meishan possédaient une capacité maximale de la CBG plasmatique pour le ligand 1. 6 fois supérieure à celle des porcs de race Large White. Les mêmes mesures biochimiques sur la population de porcs F2 ont abouti à l'établissement d'une liaison génétique forte entre les taux de la CBG et la même région du chromosome 7q24-q26 où le QTL de cortisolémie a été placé. Les études moléculaires ont montré l'absence de variation de l'expression des ARNm Cbg entre les deux races porcines. Nous avons déterminé la séquence de la partie codante et promotrice du gène Cbg porcin. Les premiers résultats d'analyse d'haplotype du gène Cbg (partie promotrice, codante et 3'UTR) chez les porcs F1 et leurs parents sont discutés
This thesis was directed to precise the genetic factors underlying the variations of cortisol levels vetween pig races Large White and Meishan. Previous studies had identified on chromosome 7 a QTL associated with the levels of cortisol, basal and after a novelty stress. Comparative mapping data between human, mouse and pig genomes has suggested that transcortine or CBG (corticosteroid binding globulin) incoding gene might be a causal gene for this QTL. Firstly, using a porcine Cbg gene fragment we have mapped the porcine Cbg gene on somatic cell hybrid and radiation hybrid panels. Thereafter isolation of a BAC Cbg clone using the same DNA probe has allowed us to localise the gene Cbg on pig metaphase chromosomes by FISH. These methods together has assigned the Cbg gene to band q26 of pig chromosome 7, between the markers flanking the QTL associated with cortisol levels. Estimation of transcortin binding parameters realised using cortisol binding capacity assay after absorption on solid phase (concanacalin A-Sepharose) revealed that Meishan pigs had a maximal CBG binding capacity 1. 6 times higher than Large White pigs. Using the same biochemical measures on the F2 pig population, we showed a strong genetic linkage between CBG binding capacity and the chromosomal region 7q24-7q26 where the QTL associated with cortisol levels was localised. Molecular expression studies indicated no differences in Cbg mRNA expression in the liver of the two parental breeds. The sequence of exons and promoter region of porcine Cbg gene has been determined. The preliminary results of haplotype analysis of Cbg gene (proximal promoter, coding sequence, 3'UTR) of F1 pigs and their parents are discussed
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Cai, Jin. "Mapping QTL for fusarium head blight resistance in Chinese wheat landraces." Thesis, Kansas State University, 2012. http://hdl.handle.net/2097/13703.

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Master of Science
Department of Agronomy
Allan Fritz
Fusarium head blight (FHB) is one of the most devastative diseases in wheat. Growing resistant cultivars is one of the most effective strategies to minimize the disease damage. Huangcandou (HCD) is a Chinese wheat landrace showing a high level of resistance to FHB spread within a spike (type II). To identify quantitative traits loci (QTL) for resistance in HCD, a population of 190 recombinant inbred lines (RILs) were developed from a cross between HCD and Jagger, a susceptible hard winter wheat (HWW) released in Kansas. The population was evaluated for type II resistance at the greenhouses of Kansas State University. After initial marker screening, 261 polymorphic simple-sequence repeats (SSR) between parents were used for analysis of the RIL population. Among three QTL identified, two from HCD were mapped on the short arms of chromosomes 3B (3BS) and 3A (3AS). The QTL on the distal end of 3BS showed a major effect on type II resistance in all three experiments. This QTL coincides with a previously reported Fhb1, and explained 28.3% of phenotypic variation. The QTL on 3AS explained 9.7% of phenotypic variation for mean PSS over three experiments. The third QTL from chromosome 2D of Jagger explained 6.5% of phenotypic variation. Allelic substitution using the closest marker to each QTL revealed that substitution of Jagger alleles of two QTL on 3AS and 3BS with those from HCD significantly reduced the PSS. HCD containing both QTL on 3AS and 3BS with a large effect on type II resistance can be an alternative source of FHB resistance for improving FHB type II resistance in wheat. Besides, meta-analyses were used to estimate 95% confidence intervals (CIs) of 24 mapped QTL in five previously mapped populations derived from Chinese landraces: Wangshuibai (WSB), Haiyanzhong (HYZ), Huangfangzhu (HFZ), Baishanyuehuang (BSYH) and Huangcandou (HCD). Nineteen QTL for FHB type II resistance were projected to 10 QTL clusters. Five QTL on chromosomes 1A, 5A, 7A, and 3BS (2) were identified as confirmed QTL that have stable and consistent effects on FHB resistance and markers in these meta-QTL regions should be useful for marker-assisted breeding.
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Elisabeth, Ahlgren. "Marker generation for Fine Mapping a QTL in the chicken." Thesis, Linköpings universitet, Biologi, 2014. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-108983.

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The purpose of this study was to design and test five SNP markers in an inbred chicken cross between Red Junglefowl and domestic White Leghorn of the 8th generation. The markers lie in a region affecting the tonic immobility behaviour which differs significantly between the two species. The markers could be identified by usage of PCR and pyrosequencing. The data obtained were further used in a small scale quantitative trait locus (QTL) analysis. QTL analysis is a statistical method to link phenotypic traits to genotypic data. Four out of five markers could be genotypes and thereby, made it possible to proceed with the QTL analysis. The results showed that there is no QTL associated with the markers identified. The two flanking markers were closest to a significant difference between genotypes and it is therefore a possibility that a QTL lies close further down or up the searched region. From the line map it is indicated that there is little recombination in the marker region.
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Books on the topic "QTL analysi"

1

Hyne, Virginia. QTL analysis in segregating populations. Birmingham: University of Birmingham, 1995.

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Statistical genomics: Linkage, mapping, and QTL analysis. Boca Raton: CRC Press, 1998.

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Educational Resources Information Center (U.S.), ed. Reevaluation: QTA, a brief analysis of a critical issue in special education. [Alexandria, VA]: National Association of State Directors of Special Education, 1999.

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Educational Resources Information Center (U.S.), ed. Developmental delay: QTA, a brief analysis of a critical issue in special education. [Alexandria, VA]: Project FORUM, National Association of State Directors of Special Education, 1998.

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Educational Resources Information Center (U.S.), ed. Age of majority: QTA, a brief analysis of a critical issue in special education. [Alexandria, VA]: National Association of State Directors of Special Education, Inc., 1999.

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Educational Resources Information Center (U.S.), ed. State improvement grants: QTA, a brief analysis of a critical issue in special education. [Alexandria, VA]: National Association of State Directors of Special Education, Inc., 1999.

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Educational Resources Information Center (U.S.), ed. Statewide behavior initiatives: QTA, a brief analysis of a critical issue in special education. [Alexandria, VA]: National Association of State Directors of Special Education, Inc., 2000.

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Educational Resources Information Center (U.S.), ed. Braille instruction: QTA-a brief analysis of a critical issue in special education : quick turn around. [Alexandria, VA]: National Association of State Directors of Special Education, Inc., Project Forum, 2000.

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Educational Resources Information Center (U.S.), ed. State special education advisory panel budgets: QTA-a brief analysis of a critical issue in special education. [Alexandria, VA]: National Association of State Directors of Special Education, 2001.

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Educational Resources Information Center (U.S.), ed. Access to adult education for youth with disabilities: QTA, a brief analysis of a critical issue in special education. [Alexandria, VA]: National Association of State Directors of Special Education, Inc., 1999.

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Book chapters on the topic "QTL analysi"

1

Boopathi, N. Manikanda. "QTL Analysis." In Genetic Mapping and Marker Assisted Selection, 253–326. Singapore: Springer Singapore, 2020. http://dx.doi.org/10.1007/978-981-15-2949-8_7.

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Broman, Karl W., and Śaunak Sen. "Single-QTL analysis." In Statistics for Biology and Health, 75–133. New York, NY: Springer New York, 2009. http://dx.doi.org/10.1007/978-0-387-92125-9_4.

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Giri, Prerna, Manohar Lal Yadav, and Bhagyalaxmi Mohapatra. "QTL Linkage Analysis." In Encyclopedia of Animal Cognition and Behavior, 1–6. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-47829-6_161-1.

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Giri, Prerna, Manohar Lal Yadav, and Bhagyalaxmi Mohapatra. "QTL Linkage Analysis." In Encyclopedia of Animal Cognition and Behavior, 5821–26. Cham: Springer International Publishing, 2022. http://dx.doi.org/10.1007/978-3-319-55065-7_161.

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Tsong, Yi, and Jinglin Zhong. "Thorough QT/QTc Clinical Trials." In Modern Clinical Trial Analysis, 183–201. New York, NY: Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-4322-3_8.

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Wen, Jia, Conor Nodzak, and Xinghua Shi. "QTL Analysis Beyond eQTLs." In Methods in Molecular Biology, 201–10. New York, NY: Springer US, 2019. http://dx.doi.org/10.1007/978-1-0716-0026-9_14.

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Ye, Jian, Chunming Wang, and Genhua Yue. "Linkage Mapping and QTL Analysis." In The Jatropha Genome, 21–45. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-49653-5_2.

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Asins, Maria J., Guillermo P. Bernet, Irene Villalta, and Emilio A. Carbonell. "QTL Analysis in Plant Breeding." In Molecular Techniques in Crop Improvement, 3–21. Dordrecht: Springer Netherlands, 2009. http://dx.doi.org/10.1007/978-90-481-2967-6_1.

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Zhang, Yuan-Ming. "F2 Designs for QTL Analysis." In Methods in Molecular Biology, 17–29. Totowa, NJ: Humana Press, 2012. http://dx.doi.org/10.1007/978-1-61779-785-9_2.

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Emrich, K. "QTL Mapping in Plant Populations." In Studies in Classification, Data Analysis, and Knowledge Organization, 421–28. Berlin, Heidelberg: Springer Berlin Heidelberg, 2002. http://dx.doi.org/10.1007/978-3-642-55991-4_45.

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Conference papers on the topic "QTL analysi"

1

Palmor, Zalman J., and Dmitry Shneiderman. "Effect of Multivariable Dead Times on the Properties of the Quadruple-Tank Process." In ASME 2008 9th Biennial Conference on Engineering Systems Design and Analysis. ASMEDC, 2008. http://dx.doi.org/10.1115/esda2008-59033.

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The well known laboratory Quadruple-Tank Process (QTP) has been introduced in the laboratories of many schools around the world as it is ideally suited to illustrate concepts in multivariable control. In this paper the QTP is extended to include independent multivariable dead times (DTs) and their effects on the properties of the QTP are studied. DTs are very common in many various processes and make the control of the QTP more interesting and challenging. The addition of DTs may introduce infinite, finite or not any number of non-minimum-phase (NMP) zeros. As shown in the paper it depends on a particular combination of the multivariable DTs. The conditions for each case are stated and the location and behavior of the zeros closest to the imaginary axis due to the DTs are specified. Other properties of the QTP with DTs as the output real NMP zero directions and the decentralized integral controllability of the process are discussed too. Also, a novel laboratory QTP with DTs is described.
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Chesnokov, Yuriy. "Value of QTL analysis in precision agriculture system." In VIIth International Scientific Conference “Genetics, Physiology and Plant Breeding”. Institute of Genetics, Physiology and Plant Protection, Republic of Moldova, 2021. http://dx.doi.org/10.53040/gppb7.2021.32.

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A possible relationship between the approaches of adaptive crop production and precision agriculture to produce environmentally friendly lines and varieties with high adaptive potential and productivity is shown. In recent decades, more and more attention has been paid to technogenic and biological systems of farming, based on the ecologization and biologization of the intensification processes of adaptive crop produc-tion. Such approaches are precision agriculture (PA) system and QTL analysis. The use of these approaches allows not only to ensure a sustainable increase in productivity through the combined use of the advantages of precision agriculture and molecular genetic assessment, including the creation of new forms and varieties re-sponsive to agricultural practices of PA, but also to neutralize the negative impact of abiotic and biotic envi-ronmental factors limiting the size and quality of the crop as well as plant productivity.
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Lu, Hong, Huaijin Guan, Hui Chen, and Lu Lu. "Expression QTL and genetic regulatory network analysis of Col11a1." In 2012 5th International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2012. http://dx.doi.org/10.1109/bmei.2012.6512879.

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Bernreiter, Michael, Jan Maly, and Stefan Woltran. "Choice Logics and Their Computational Properties." In Thirtieth International Joint Conference on Artificial Intelligence {IJCAI-21}. California: International Joint Conferences on Artificial Intelligence Organization, 2021. http://dx.doi.org/10.24963/ijcai.2021/247.

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Qualitative Choice Logic (QCL) and Conjunctive Choice Logic (CCL) are formalisms for preference handling, with especially QCL being well established in the field of AI. So far, analyses of these logics need to be done on a case-by-case basis, albeit they share several common features. This calls for a more general choice logic framework, with QCL and CCL as well as some of their derivatives being particular instantiations. We provide such a framework, which allows us, on the one hand, to easily define new choice logics and, on the other hand, to examine properties of different choice logics in a uniform setting. In particular, we investigate strong equivalence, a core concept in non-classical logics for understanding formula simplification, and computational complexity. Our analysis also yields new results for QCL and CCL. For example, we show that the main reasoning task regarding preferred models is ϴ₂P-complete for QCL and CCL, while being Δ₂P-complete for a newly introduced choice logic.
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Mollah, Md Nurul Haque, and Shinto Eguchi. "Robust Composite Interval Mapping for QTL Analysis by Minimum beta-Divergence Method." In 2008 IEEE International Conference on Bioinformatics and Biomedicine. IEEE, 2008. http://dx.doi.org/10.1109/bibm.2008.43.

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Luzhansky, Edward, Fow-Sen Choa, Scott Merritt, Anthony Yu, and Michael Krainak. "Comparative Analysis of QCL MWIR and SWIR Communication with PPM Signals." In Adaptive Optics: Analysis, Methods & Systems. Washington, D.C.: OSA, 2015. http://dx.doi.org/10.1364/aoms.2015.jt5a.7.

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QIN, HONG, HONG ZHANG, and ZHAOHAI LI. "THE IMPACT OF POPULATION STRATIFICATION ON COMMONLY USED STATISTICAL PROCEDURES IN POPULATION-BASED QTL ASSOCIATION STUDIES." In Random Walk, Sequential Analysis and Related Topics - A Festschrift in Honor of Yuan-Shih Chow. WORLD SCIENTIFIC, 2006. http://dx.doi.org/10.1142/9789812772558_0021.

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Loo, Lenora W. M., Iona Cheng, Maarit Tiirikainen, Annette Lum-Jones, Ann Seifried, Lucas M. Dunklee, Steve Gallinger, Stephen N. Thibodeau, Graham Casey, and Loic Le Marchand. "Abstract 4732: Cis-expression QTL analysis of established risk variants for colorectal cancer." In Proceedings: AACR 102nd Annual Meeting 2011‐‐ Apr 2‐6, 2011; Orlando, FL. American Association for Cancer Research, 2011. http://dx.doi.org/10.1158/1538-7445.am2011-4732.

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Ostendorf, R., L. Butschek, A. Merten, A. Dreyhaupt, J. Grahmann, M. Rattunde, J. Jarvis, et al. "MOEMS EC-QCL for real-time identification of chemical compounds." In Laser Applications to Chemical, Security and Environmental Analysis. Washington, D.C.: OSA, 2016. http://dx.doi.org/10.1364/lacsea.2016.lth3e.4.

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Vallon, R., L. Bizet, B. Parvitte, G. Maisons, M. Carras, and V. Zéninari. "Detectorless Intracavity Technique with an EC-QCL for Atmospheric Gas Detection." In Laser Applications to Chemical, Security and Environmental Analysis. Washington, D.C.: OSA, 2018. http://dx.doi.org/10.1364/lacsea.2018.lm5c.5.

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Reports on the topic "QTL analysi"

1

Zamir, Dani, and Steven Tanksley. Fine Mapping and Genetic Interactions of Nearly-Isogenic Allelic Series Representing Yield and Quality QTLs Derived from Wild Tomato Species. United States Department of Agriculture, July 2002. http://dx.doi.org/10.32747/2002.7586460.bard.

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Wild germplasm represents a rich source of QTLs capable of enhancing productivity of crop plants. Using the molecular linkage map of tomato in conjunction with novel population structures, we have identified QTLs from five Lycopersicon species that improve key yield and quality associated traits of processing tomatoes. In this research we employed multi-testing sites for fine mapping analysis of the different components of the affected traits combined with genetic interaction studies. Our results demonstrate that 'exotic libraries', which comprise of marker-defined genomic regions taken from wild species and introgressed onto the background of elite crop lines, provide an important opportunity for improving of the agricultural performance of modem crop varieties. Furthermore, we showed that these genetic resources can also serve as reagents for the discovery and characterization of genes that underlie traits of agricultural value. The results set the stage for using the QTLs in marker assisted programs and for applying map-based cloning of the targeted QTL/genes. The cloning of QTLs revealed genes that control pathways for agricultural yield in tomato that may be common for other crop species.
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Wisniewski, Michael E., Samir Droby, John L. Norelli, Noa Sela, and Elena Levin. Genetic and transcriptomic analysis of postharvest decay resistance in Malus sieversii and the characterization of pathogenicity effectors in Penicillium expansum. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7600013.bard.

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Blue mold of apple caused by Penicilliumexpansumis a major postharvest disease. Selection for postharvest disease resistance in breeding programs has been ignored in favor of fruit quality traits such as size, color, taste, etc. The identification of postharvest disease resistance as a heritable trait would represent a significant accomplishment and has not been attempted in apple. Furthermore, insight into the biology of the pathogenicity of P. expansumin apple could provide new approaches to postharvest decay management. Hypothesis: Postharvest resistance of apple to P. expansumcan be mapped to specific genetic loci and significant quantitative-trait-loci (QTLs) can be identified that account for a major portion of the population variance. Susceptibility of apple fruit to P. expansumis dependent on the ability of the pathogen to produce LysM effectors that actively suppress primary and/or secondary resistance mechanisms in the fruit. Objectives: 1) Identify QTL(s) and molecular markers for blue mold resistance in GMAL4593 mapping population (‘Royal Gala’ X MalussieversiiPI613981), 2) Characterize the transcriptome of the host and pathogen (P. expansum) during the infection process 3) Determine the function of LysM genes in pathogenicity of P. expansum. Methods: A phenotypic evaluation of blue mold resistance in the GMAL4593 mapping population, conducted in several different years, will be used for QTL analysis (using MapQTL 6.0) to identify loci associated with blue mold resistance. Molecular markers will be developed for the resistance loci. Transcriptomic analysis by RNA-seq will be used to conduct a time course study of gene expression in resistant and susceptible apple GMAL4593 genotypes in response to P. expansum, as well as fungal responses to both genotypes. Candidate resistance genes identified in the transcriptomic study and or bioinformatic analysis will be positioned in the ‘Golden Delicious’ genome to identify markers that co-locate with the identified QTL(s). A functional analysis of LysM genes on pathogenicity will be conducted by eliminating or reducing the expression of individual effectors by heterologous recombination and silencing technologies. LysMeffector genes will also be expressed in a yeast expression system to study protein function. Expected Results: Identification of postharvest disease resistance QTLs and tightly-linked genetic markers. Increased knowledge of the role of effectors in blue mold pathogenic
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Paran, Ilan, and Molly Jahn. Analysis of Quantitative Traits in Pepper Using Molecular Markers. United States Department of Agriculture, January 2000. http://dx.doi.org/10.32747/2000.7570562.bard.

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Original objectives: The overall goal of the proposal was to determine the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoids content (3) Determine possible association between capsaicinoids and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoids in pepper fruit and identify candidate genes for C. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was only little known prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous simple sequence repeat (SSR) markers and the integration of several independent maps into a single resource map that consists of over 2000 markers. Unlike previous maps that consisted mostly of tomato-originated RFLP markers, the SSR-based map consists of largely pepper markers. Therefore, the SSR and integrated maps provide ample of tools for use in marker-assisted selection for diverse targets throughout the Capsicum genome. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, the most unique characteristics of pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master key for capsaicinoids accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTLs that control capsaicinoids content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTLs that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTLs controlling fruit shape, fs3.1 and fs10.1, that differentiate between elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advancement of our understanding at the genetic and molecular levels of important processes of pepper fruit development. Concomitantly to gaining biological knowledge, we were able to develop molecular tools that can be implemented for pepper improvement.
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Zhang, Hongbin, Shahal Abbo, Weidong Chen, Amir Sherman, Dani Shtienberg, and Frederick Muehlbauer. Integrative Physical and Genetic Mapping of the Chickpea Genome for Fine Mapping and Analysis of Agronomic Traits. United States Department of Agriculture, March 2010. http://dx.doi.org/10.32747/2010.7592122.bard.

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Chickpea is the third most important pulse crop in the world and ranks first in the Middle East; however, it has been subjected to only limited research in modern genomics. In the first period of this project (US-3034-98R) we constructed two large-insert BAC and BIBAC libraries, developed 325 SSR markers and mapped QTLs controlling ascochyta blight resistance (ABR) and days to first flower (DTF). Nevertheless, the utilities of these tools and results in gene discovery and marker-assisted breeding are limited due to the absence of an essential platform. The goals of this period of the project were to use the resources and tools developed in the first period of the project to develop a BAC/BIBAC physical map for chickpea and using it to identify BAC/BIBACcontigs containing agronomic genes of interest, with an emphasis on ABR and DTF, and develop DNA markers suitable for marker-assisted breeding. Toward these goals, we proposed: 1) Fingerprint ~50,000 (10x) BACs from the BAC and BIBAC libraries, assemble the clones into a genome-wide BAC/BIBAC physical map, and integrate the BAC/BIBAC map with the existing chickpea genetic maps (Zhang, USA); 2) fine-map ABR and DTFQTLs and enhance molecular tools for chickpea genetics and breeding (Shahal, Sherman and DaniShtienberg, Israel; Chen and Muehlbauer; USA); and 3) integrate the BAC/BIBAC map with the existing chickpea genetic maps (Sherman, Israel; Zhang and Chen, USA). For these objectives, a total of $460,000 was requested originally, but a total of $300,000 was awarded to the project. We first developed two new BAC and BIBAC libraries, Chickpea-CME and Chickpea- CHV. The chickpea-CMEBAC library contains 22,272 clones, with an average insert size of 130 kb and equivalent to 4.0 fold of the chickpea genome. The chickpea-CHVBIBAC library contains 38,400 clones, with an average insert size of 140 kb and equivalent to 7.5 fold of the chickpea genome. The two new libraries (11.5 x), along with the two BAC (Chickpea-CHI) and BIBAC (Chickpea-CBV) libraries (7.1 x) constructed in the first period of the project, provide libraries essential for chickpea genome physical mapping and many other genomics researches. Using these four libraries we then developed the proposed BAC/BIBAC physical map of chickpea. A total of 67,584 clones were fingerprinted, and 64,211 (~11.6 x) of the fingerprints validated and used in the physical map assembly. The physical map consists of 1,945 BAC/BIBACcontigs, with each containing an average of 39.2 clones and having an average physical length of 559 kb. The contigs collectively span ~1,088 Mb, being 1.49 fold of the 740- Mb chickpea genome. Third, we integrated the physical map with the two existing chickpea genetic maps using a total of 172 (124 + 48) SSR markers. Fourth, we identified tightly linked markers for ABR-QTL1, increased marker density at ABR-QTL2 and studied the genetic basis of resistance to pod abortion, a major problem in the east Mediterranean, caused by heat stress. Finally, we, using the integrated map, isolated the BAC/BIBACcontigs containing or closely linked to QTL4.1, QTL4.2 and QTL8 for ABR and QTL8 for DTF. The integrated BAC/BIBAC map resulted from the project will provide a powerful platform and tools essential for many aspects of advanced genomics and genetics research of this crop and related species. These includes, but are not limited to, targeted development of SNP, InDel and SSR markers, high-resolution mapping of the chickpea genome and its agronomic genes and QTLs, sequencing and decoding of all genes of the genome using the next-generation sequencing technology, and comparative genome analysis of chickpea versus other legumes. The DNA markers and BAC/BIBACcontigs containing or closely linked to ABR and DTF provide essential tools to develop SSR and SNP markers well-suited for marker-assisted breeding of the traits and clone their corresponding genes. The development of the tools and knowledge will thus promote enhanced and substantial genetic improvement of the crop and related legumes.
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Smith, Margaret, Nurit Katzir, Susan McCouch, and Yaakov Tadmor. Discovery and Transfer of Genes from Wild Zea Germplasm to Improve Grain Oil and Protein Composition of Temperate Maize. United States Department of Agriculture, 1998. http://dx.doi.org/10.32747/1998.7580683.bard.

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Project Objectives 1. Develop and amplify two interspecific populations (annual and perennial teosintes x elite maize inbred) as the basis for genetic analysis of grain quality. 2. Identify quantitative trait loci (QTLs) from teosinte that improve oil, protein, and essential amino acid composition of maize grain. 3. Develop near isogenic lines (NILs) to quantify QTL contributions to grain quality and as a resource for future breeding and gene cloning efforts. 4. Analyze the contribution of these QTLs to hybrid performance in both the US and Israel. 5. Measure the yield potential of improved grain quality hybrids. (NOTE: Yield potential could not be evaluated due to environmentally-caused failure of the breeding nursery where seed was produced for this evaluation.) Background: Maize is a significant agricultural commodity worldwide. As an open pollinated crop, variation within the species is large and, in most cases, sufficient to supply the demand for modem varieties and for new environments. In recent years there is a growing demand for maize varieties with special quality attributes. While domesticated sources of genetic variation for high oil and protein content are limited, useful alleles for these traits may remain in maize's wild relative, teosinte. We utilized advanced backcross (AB) analysis to search for QTLs contributing to oil and protein content from two teosinte accessions: Zea mays ssp. mexicana Race Chalco, an annual teosinte (referred to as Chalco), and Z diploperennis Race San Miguel, a perennial teosinte (referred to as Diplo). Major Conclusions and Achievements Two NILs targeting a Diplo introgression in bin 1.04 showed a significant increase in oil content in homozygous sib-pollinated seed when compared to sibbed seed of their counterpart non-introgressed controls. These BC4S2 NILs, referred to as D-RD29 and D-RD30, carry the Diplo allele in bin 1.04 and the introgression extends partially into bins 1.03 and 1.05. These NILs remain heterozygous in bins 4.01 and 8.02, but otherwise are homozygous for the recurrent parent (RD6502) alleles. NILs were developed also for the Chalco introgression in bin 1.04 but these do not show any improvement in oil content, suggesting that the Chalco alleles differ from the Diplo alleles in this region. Testcross Fl seed and sibbed grain from these Fl plants did not show any effect on oil content from this introgression, suggesting that it would need to be present in both parents of a maize hybrid to have an effect on oil content. Implications, both Scientific and Agricultural The Diplo region identified increases oil content by 12.5% (from 4.8% to 5.4% oil in the seed). Although this absolute difference is not large in agronomic terms, this locus could provide additive increases to oil content in combination with other maize-derived loci for high oil. To our knowledge, this is the first confirmed report of a QTL from teosinte for improved grain oil content in maize. It suggests that further research on grain quality alleles from maize wild relatives would be of both scientific and agricultural interest.
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Smith, Margaret, Nurit Katzir, Susan McCouch, and Yaakov Tadmor. Discovery and Transfer of Genes from Wild Zea Germplasm to Improve Grain Oil and Protein Composition of Temperate Maize. United States Department of Agriculture, October 2002. http://dx.doi.org/10.32747/2002.7695846.bard.

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Project Objectives 1. Develop and amplify two interspecific populations (annual and perennial teosintes x elite maize inbred) as the basis for genetic analysis of grain quality. 2. Identify quantitative trait loci (QTLs) from teosinte that improve oil, protein, and essential amino acid composition of maize grain. 3. Develop near isogenic lines (NILs) to quantify QTL contributions to grain quality and as a resource for future breeding and gene cloning efforts. 4. Analyze the contribution of these QTLs to hybrid performance in both the US and Israel. 5. Measure the yield potential of improved grain quality hybrids. (NOTE: Yield potential could not be evaluated due to environmentally-caused failure of the breeding nursery where seed was produced for this evaluation.) Background: Maize is a significant agricultural commodity worldwide. As an open pollinated crop, variation within the species is large and, in most cases, sufficient to supply the demand for modem varieties and for new environments. In recent years there is a growing demand for maize varieties with special quality attributes. While domesticated sources of genetic variation for high oil and protein content are limited, useful alleles for these traits may remain in maize's wild relative, teosinte. We utilized advanced backcross (AB) analysis to search for QTLs contributing to oil and protein content from two teosinte accessions: Zea mays ssp. mexicana Race Chalco, an annual teosinte (referred to as Chalco), and Z diploperennis Race San Miguel, a perennial teosinte (referred to as Diplo). Major Conclusions and Achievements Two NILs targeting a Diplo introgression in bin 1.04 showed a significant increase in oil content in homozygous sib-pollinated seed when compared to sibbed seed of their counterpart non-introgressed controls. These BC4S2 NILs, referred to as D-RD29 and D-RD30, carry the Diplo allele in bin 1.04 and the introgression extends partially into bins 1.03 and 1.05. These NILs remain heterozygous in bins 4.01 and 8.02, but otherwise are homozygous for the recurrent parent (RD6502) alleles. NILs were developed also for the Chalco introgression in bin 1.04 but these do not show any improvement in oil content, suggesting that the Chalco alleles differ from the Diplo alleles in this region. Testcross Fl seed and sibbed grain from these Fl plants did not show any effect on oil content from this introgression, suggesting that it would need to be present in both parents of a maize hybrid to have an effect on oil content. Implications, both Scientific and Agricultural The Diplo region identified increases oil content by 12.5% (from 4.8% to 5.4% oil in the seed). Although this absolute difference is not large in agronomic terms, this locus could provide additive increases to oil content in combination with other maize-derived loci for high oil. To our knowledge, this is the first confirmed report of a QTL from teosinte for improved grain oil content in maize. It suggests that further research on grain quality alleles from maize wild relatives would be of both scientific and agricultural interest.
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7

Levin, Ilan, John Thomas, Moshe Lapidot, Desmond McGrath, and Denis Persley. Resistance to Tomato yellow leaf curl virus (TYLCV) in tomato: molecular mapping and introgression of resistance to Australian genotypes. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7613888.bard.

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Tomato yellow leaf curl virus (TYLCV) is one of the most devastating viruses of cultivated tomatoes. Although first identified in the Mediterranean region, it is now distributed world-wide. Sequence analysis of the virus by the Australian group has shown that the virus is now present in Australia. Despite the importance of the disease and extensive research on the virus, very little is known about the resistance genes (loci) that determine host resistance and susceptibility to the virus. A symptom-less resistant line, TY-172, was developed at the Volcani Center which has shown the highest resistance level among all tested varieties. Preliminary results show that TY-172 is a good candidate to confer resistance to both TYLCV and to Tomato leaf curl virus (ToLCV) in Queensland conditions. Furthermore, Segregation analysis has previously indicated that the resistance is determined by 2-3 genes. In this proposal we aimed to substantiate that TY-172 can contribute to resistance breeding against TYLCV in Queensland, to develop DNA markers to advance such resistance breeding in both Israel and Queensland, and to exploit these markers for resistant breeding in Australian and Israeli lines. To map quantitative trait loci (QTLs) controlling TYLCVresistance in TY172, appropriate segregating populations were analyzed using 69 polymorphic DNA markers spanning the entire tomato genome. Results show that TYLCV resistance in TY172 is controlled by a previously unknown major QTL, originating from the resistant line, and four additional minor QTLs. The major QTL, termed Ty-5, maps to chromosome 4 and accounts for 39.7-to-46.6% of the variation in symptom severity among segregating plants (LOD score: 33-to-35). The minor QTLs, originated either from the resistant or susceptible parents, were mapped to chromosomes 1, 7, 9 and 11, and contributed 12% to the variation in symptom severity in addition to Ty-5. Further analysis of parental lines as well as large F₁, BC₁F₁, F₂ and BC₁F₂ populations originating from crosses carried out, in reciprocal manner, between TY172 and the susceptible processing line M-82 (LA3475) during spring-summer 2010, indicated that: (1) the minor QTLs we have previously identified are in effect not reproducible, (2)Ty-5 alone can yield highly resistant plants with practically no extra-chromosomal effects, and (3) the narrow-sense heritability estimate of resistance levels, attributed to additive factors responsive to selection, does not significantly deviate from 1. All of these results point to Ty-5 as the sole resistance locus in TY172 thus significantly increasing the likelihood of its successful molecular dissection. The DNA markers developed during the course of this study were transferred together with the TY172 genotype to Queensland. TY172 was crossed to a panel of Australian genotypes and the resulting populations were subjected to segregation analysis. Results showed that resistant locus, Ty-5, is highly reproducible in the Australian conditions as well. The Australian group was also able to make improvements to the marker assays by re-designing primer pairs to provide more robust PCR fragments. The Ty-5 locus has now been introgressed into elite Australian germplasm and selection for TYLCV resistance has begun. Cumulatively, our results show that Ty-5 can be effectively used, together with the TY172 genotype to expedite TYLCV resistance breeding and improve our understanding of the genetics that underline the response of tomato to TYLCV. Contributions to agriculture include: (1) the development of tools for more efficient resistance breeding, allowing the incorporation of resistance to local tomato varieties in Australia, Israel and elsewhere; and (2) establish a solid framework for a future attempt to clone the genes that encode such resistance. The latter will enable to decipher the resistance mechanisms that could be applied to other geminiviruses in tomato and possibly in other plant species.
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8

Paran, Ilan, and Allen Van Deynze. Regulation of pepper fruit color, chloroplasts development and their importance in fruit quality. United States Department of Agriculture, January 2014. http://dx.doi.org/10.32747/2014.7598173.bard.

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Pepper exhibits large natural variation in chlorophyll content in the immature fruit. To dissect the genetic and molecular basis of this variation, we conducted QTL mapping for chlorophyll content in a cross between light and dark green-fruited parents, PI 152225 and 1154. Two major QTLs, pc1 and pc10, that control chlorophyll content by modulation of chloroplast compartment size in a fruit-specific manner were detected in chromosomes 1 and 10, respectively. The pepper homolog of GOLDEN2- LIKE transcription factor (CaGLK2) was found as underlying pc10, similar to its effect on tomato fruit chloroplast development. A candidate gene for pc1was found as controlling chlorophyll content in pepper by the modulation of chloroplast size and number. Fine mapping of pc1 aided by bulked DNA and RNA-seq analyses enabled the identification of a zinc finger transcription factor LOL1 (LSD-One-Like 1) as a candidate gene underlying pc1. LOL1 is a positive regulator of oxidative stress- induced cell death in Arabidopsis. However, over expression of the rice ortholog resulted in an increase of chlorophyll content. Interestingly, CaAPRR2 that is linked to the QTL and was found to affect immature pepper fruit color in a previous study, did not have a significant effect on chlorophyll content in the present study. Verification of the candidate's function was done by generating CRISPR/Cas9 knockout mutants of the orthologues tomato gene, while its knockout experiment in pepper by genome editing is under progress. Phenotypic similarity as a consequence of disrupting the transcription factor in both pepper and tomato indicated its functional conservation in controlling chlorophyll content in the Solanaceae. A limited sequence diversity study indicated that null mutations in CaLOL1 and its putative interactorCaMIP1 are present in C. chinensebut not in C. annuum. Combinations of mutations in CaLOL1, CaMIP1, CaGLK2 and CaAPRR2 are required for the creation of the extreme variation in chlorophyll content in Capsicum.
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9

Weller, Joel I., Derek M. Bickhart, Micha Ron, Eyal Seroussi, George Liu, and George R. Wiggans. Determination of actual polymorphisms responsible for economic trait variation in dairy cattle. United States Department of Agriculture, January 2015. http://dx.doi.org/10.32747/2015.7600017.bard.

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The project’s general objectives were to determine specific polymorphisms at the DNA level responsible for observed quantitative trait loci (QTLs) and to estimate their effects, frequencies, and selection potential in the Holstein dairy cattle breed. The specific objectives were to (1) localize the causative polymorphisms to small chromosomal segments based on analysis of 52 U.S. Holstein bulls each with at least 100 sons with high-reliability genetic evaluations using the a posteriori granddaughter design; (2) sequence the complete genomes of at least 40 of those bulls to 20 coverage; (3) determine causative polymorphisms based on concordance between the bulls’ genotypes for specific polymorphisms and their status for a QTL; (4) validate putative quantitative trait variants by genotyping a sample of Israeli Holstein cows; and (5) perform gene expression analysis using statistical methodologies, including determination of signatures of selection, based on somatic cells of cows that are homozygous for contrasting quantitative trait variants; and (6) analyze genes with putative quantitative trait variants using data mining techniques. Current methods for genomic evaluation are based on population-wide linkage disequilibrium between markers and actual alleles that affect traits of interest. Those methods have approximately doubled the rate of genetic gain for most traits in the U.S. Holstein population. With determination of causative polymorphisms, increasing the accuracy of genomic evaluations should be possible by including those genotypes as fixed effects in the analysis models. Determination of causative polymorphisms should also yield useful information on gene function and genetic architecture of complex traits. Concordance between QTL genotype as determined by the a posteriori granddaughter design and marker genotype was determined for 30 trait-by-chromosomal segment effects that are segregating in the U.S. Holstein population; a probability of <10²⁰ was used to accept the null hypothesis that no segregating gene within the chromosomal segment was affecting the trait. Genotypes for 83 grandsires and 17,217 sons were determined by either complete sequence or imputation for 3,148,506 polymorphisms across the entire genome. Variant sites were identified from previous studies (such as the 1000 Bull Genomes Project) and from DNA sequencing of bulls unique to this project, which is one of the largest marker variant surveys conducted for the Holstein breed of cattle. Effects for stature on chromosome 11, daughter pregnancy rate on chromosome 18, and protein percentage on chromosome 20 met 3 criteria: (1) complete or nearly complete concordance, (2) nominal significance of the polymorphism effect after correction for all other polymorphisms, and (3) marker coefficient of determination >40% of total multiple-regression coefficient of determination for the 30 polymorphisms with highest concordance. The missense polymorphism Phe279Tyr in GHR at 31,909,478 base pairs on chromosome 20 was confirmed as the causative mutation for fat and protein concentration. For effect on fat percentage, 12 additional missensepolymorphisms on chromosome 14 were found that had nearly complete concordance with the suggested causative polymorphism (missense mutation Ala232Glu in DGAT1). The markers used in routine U.S. genomic evaluations were increased from 60,000 to 80,000 by adding markers for known QTLs and markers detected in BARD and other research projects. Objectives 1 and 2 were completely accomplished, and objective 3 was partially accomplished. Because no new clear-cut causative polymorphisms were discovered, objectives 4 through 6 were not completed.
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10

Hulata, Gideon, Thomas D. Kocher, Micha Ron, and Eyal Seroussi. Molecular Mechanisms of Sex Determination in Cultured Tilapias. United States Department of Agriculture, October 2010. http://dx.doi.org/10.32747/2010.7697106.bard.

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Tilapias are among the most important aquaculture commodities worldwide. Commercial production of tilapia is based on monosex culture of males. Current methods for producing all-male fingerlings, including hormone treatments and genetic manipulations, are not entirely reliable, in part because of the genetic complexity of sex determination and sexual differentiation in tilapias. The goals of this project are to map QTL and identify genes regulating sex determination in commonly cultured tilapia species, in order to provide a rational basis for designing reliable genetic approaches for producing all-male fingerlings. The original objectives for this research were: 1) to identify the gene underlying the QTL on LG1 through positional cloning and gene expression analysis; 2) to fine map the QTL on LG 3 and 23; and 3) to characterize the patterns of dominance and epistasis among QTL alleles influencing sex determination. The brain aromatase gene Cyp19b, a possible candidate for the genetic or environmental SD, was mapped to LG7 using our F2 mapping population. This region has not been identified before as affecting SD in tilapias. The QTL affecting SD on LG 1 and 23 have been fine-mapped down to 1 and 4 cM, respectively, but the key regulators for SD have not been found yet. Nevertheless, a very strong association with gender was found on LG23 for marker UNH898. Allele 276 was found almost exclusively in males, and we hypothesized that this allele is a male-associated allele (MAA). Mating of males homozygous for MAA with normal females is underway for production of all-male populations. The first progeny reaching size allowing accurate sexing had 43 males and no females. During the course of the project it became apparent that in order to achieve those objectives there is a need to develop genomic infrastructures that were lacking. Efforts have been devoted to the development of genomic resources: a database consisting of nearly 117k ESTs representing 16 tissues from tilapia were obtained; a web tool based on the RepeatMasker software was designed to assist tilapia genomics; collaboration has been established with a sequencing company to sequence the tilapia genome; steps have been taken toward constructing a microarray to enable comparative analysis of the entire transcriptome that is required in order to detect genes that are differentially expressed between genders in early developmental stages. Genomic resources developed will be invaluable for studies of cichlid physiology, evolution and development, and will hopefully lead to identification of the key regulators of SD. Thus, they will have both scientific and agricultural implications in the coming years.
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