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F2 Families (f2 + family)
Selected AbstractsA Large-scale Mutagenesis Screen to Identify Seizure-resistant ZebrafishEPILEPSIA, Issue 6 2007Scott C. Baraban Summary:,Methods: Seizures were induced with pentylenetetrazole (PTZ). Zebrafish were analyzed between 3 and 7 days postfertilization (dpf). Genome mutations were induced in founders by using N- ethyl-nitrosourea (ENU). Seizure behavior was monitored by using a high-speed camera and quantified by locomotion-tracking software. Electrographic activity was monitored by using a field-recording electrode placed in the optic tectum of agar-immobilized zebrafish. Results: Short-term PTZ exposure elicited a burst-suppression seizure pattern in 3-dpf zebrafish and more complex activity consisting of interictal- and ictal-like discharges at 7 dpf. Prolonged exposure to PTZ induced status epilepticus,like seizure activity and fatality in wild-type zebrafish larvae. With a PTZ survival assay at 6,7 dpf, we identified six zebrafish mutants in a forward-genetic screen covering nearly 2,000 F2 families. One mutant (s334) also was shown to exhibit reduced behavioral activity on short-term PTZ exposure and an inability to generate long-duration ictal-like discharge. Conclusions: Zebrafish offers a powerful tool for the identification and study of a genetic basis for seizure resistance. [source] Genome-wide linkage and QTL mapping in porcine F2 families generated from Pietrain, Meishan and Wild Boar crossesJOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 6 2003H. Geldermann Summary Three informative pig F2 families based on European Wild Boar (W), Meishan (M) and Pietrain (P) crosses have been used for genome-wide linkage and quantitative trait loci (QTL) analysis. Altogether 129 microsatellites, 56 type I loci and 46 trait definitions (specific to growth, fattening, fat deposition, muscling, meat quality, stress resistance and body conformation) were included in the study. In the linkage maps of M × P, W × P and W × M families, average spacing of markers were 18.4, 19.7 and 18.8 cM, the numbers of informative meioses were 582, 534 and 625, and the total lengths of autosomes measured were 27.3, 26.0 and 26.2 Morgan units, respectively. Maternal maps were on average 1.3 times longer than paternal maps. QTLs contributing more than 3% of F2 phenotypic variance could be identified at p < 0.05 chromosome-wide level. Differences in the numbers and positions of QTLs were observed between families. Genome-wide significant QTL effects were mapped for growth and fattening traits on eight chromosomes (1, 2, 4, 13, 14, 17, 18 and X), for fat deposition traits on seven chromosomes (1, 2, 3, 4, 6, 7 and X), for muscling traits on 11 chromosomes (1, 2, 3, 4, 6, 7, 8, 12, 14, 15 and X), for meat quality and stress resistance traits on seven chromosomes (2, 3, 6, 13, 16, 18 and X), and QTLs for body-conformation traits were detected on 14 chromosomes. Closely correlated traits showed similar QTL profiles within families. Major QTL effects for meat quality and stress resistance traits were found on SSC6 in the interval RYR1-A1BG in the W × P and M × P families, and could be attributed to segregation of the RYR1 allele T derived from Pietrain, whereas no effect in the corresponding SSC6 interval was found in family W × M, where Wild Boar and Meishan both contributed the RYR1 allele C. QTL positions were mostly similar in two of the three families for body conformation traits and for growth, fattening, fat deposition and muscling traits, especially on SSC4 (interval SW1073-NGFB). QTLs with large effects were also mapped on SSC7 in the major histocompatibility complex (MHC) (interval CYP21A2-S0102) and affected body length, weight of head and many other traits. The identification of DNA variants in genes causative for the QTLs requires further fine mapping of QTL intervals and a positional cloning. However, for these subsequent steps, the genome-wide QTL mapping in F2 families represents an essential starting point and is therefore significant for animal breeding. Zusammenfassung Drei informative F2 -Familien, die aus Kreuzungen von Europäischem Wildschwein (W), Meishan (M) und Pietrain (P) erstellt worden waren, wurden für eine genomweite Kopplungs- und QTL-Analyse benutzt. Insgesamt wurden 129 Mikrosatellitenloci, 56 Type-I-Loci und 46 Merkmalsdefinitionen (für Wachstum, Mastleistung, Fettansatz, Bemuskelung, Fleischqualität, Stressresistenz und Körperform) in die Untersuchungen einbezogen. In den Kopplungskarten der Familien M × P, W × P und W × M wurden durchschnittliche Markerabstände von 18.4, 19.7 bzw. 18.8 cM erreicht und 582, 534 bzw. 625 informative Meiosen beobachtet. Für die Gesamtlängen der Autosomen wurden in den drei Familien 27.3, 26.0 bzw. 26.2 Morgan-Einheiten gemessen. Die maternalen Kopplungskarten waren durchschnittlich 1.3-fach länger als die paternalen. QTLs, die mehr als 3% der phänotypischen Varianz in der F2 -Generation erklärten, konnten mit p < 0.05 chromosomenweitem Signifikanzniveau nachgewiesen werden. Zwischen den Familien wurden Differenzen in den Anzahlen und Positionen der QTLs beobachtet. Genomweit signifikante QTL-Effekte wurden für Wachstum und Fettansatz auf acht Chromosomen (1, 2, 4, 13, 14, 17, 18 und X) kartiert, für Fettansatz auf sieben Chromosomen (1, 2, 3, 4, 6, 7 und X), für Bemuskelung auf elf Chromosomen (1, 2, 3, 4, 6, 7, 8, 12, 14, 15 und X), für Fleischqualität/Stressresistenz auf sieben Chromosomen (2, 3, 6, 13, 16, 18 und X), und QTLs für die Körperform wurden auf 14 Chromosomen kartiert. Eng korrelierte Merkmale zeigten ähnliche QTL-Profile innerhalb Familien. Die bedeutsamsten QTL-Effekte wurden für Fleischqualitäts- und Stressresistenzmerkmale auf Chromosom 6, Intervall RYR1-A1BG, in den Familien W × P und M × P gefunden, während in diesem Chromosomenintervall in der Familie W × M, in der der RYR1 -Locus keine segregierenden Exon-Allele aufwies, kein QTL zu erkennen war. Mehrere der QTL-Positionen waren für die Körperform wie auch für Wachstum, Mastleistung, Fettansatz und Bemuskelung in zwei von drei Familien ähnlich. Dies galt besonders für Chromosom 4 (Intervall SW1073-NGFB). QTLs mit großen Effekten wurden auf Chromosom 7 im MHC (Intervall CYP21A2-S0102) kartiert; sie beeinflussten Körperlänge, Kopfgewicht, aber auch viele weitere Merkmale. Zur Identifizierung der DNA-Varianten, die einem QTL zugrunde liegen, ist eine Feinkartierung von QTLs und positionale Klonierung erforderlich. Für diese nachfolgenden Untersuchungsmethoden ist jedoch die genomweite QTL-Kartierung in F2 -Familien ein entscheidender Ausgangspunkt; sie ist deshalb bedeutungsvoll für die Tierzüchtung. [source] Linkage and QTL mapping for Sus scrofa chromosome 1JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2003P. Beeckmann Summary Linkage maps of Sus scrofa chromosome 1 (SSC1) have been produced using 10 markers in three different F2 families based on crosses of Meishan (M), Pietrain (P) and Wild Boar (W). The maps were similar for the different families and show higher paternal recombination, especially in the interval SW2130,SW803. Quantitative trait loci (QTLs) affecting body conformation, carcass composition, fat deposition and numbers of teats were identified in all three families. Major QTLs were mapped in chromosomal intervals centred at approximately 60, 120 and 170 cM. The QTLs explain up to 8.4% of phenotypic variance in the F2 generation. Pietrain QTL alleles were superior in comparison with Wild Boar and Meishan alleles for most of the trait values. Meishan alleles were associated with highest fat deposition. Additive gene effects were generally larger than dominance effects. QTL profiles on SSC1 differed between families, with the W × P family being most distinct. Zusammenfassung Kopplungskarten für Chromosom 1 (SSC1), die durch die Analyse von 10 Markern erstellt wurden, stimmten in drei untersuchten F2 -Familien (basierend auf Kreuzungen mit Meishan (M), Pietrain (P) und Wildschwein (W)) wie auch mit den bisher publizierten Karten überein. Die geschlechtsspezifischen Karten zeigten eine höhere Frequenz der Rekombinationen in der paternalen Meiose als in der maternalen, besonders im Intervall SW2130 bis SW803. Auf SSC1 konnten bedeutsame QTL-Effekte mit Wirkung auf Wachstum, Schlachtkörperzusammensetzung und Fettansatz sowie die Zitzenzahl in allen drei Familien kartiert werden, insbesondere in den Regionen um 60, 120 und 170 cM. Sie erklärten bis zu 8,4% der phänotypischen Varianz in der F2 -Generation. Pietrain-Allele zeigten positive Auswirkungen auf die meisten Fleischleistungsmerkmale. Meishan-Allele waren mit einer stärkeren Verfettung assoziiert. Es wurden Unterschiede zwischen den QTL-Profilen in den Familien beobachtet, wobei die Familie W × P besonders stark von den QTL-Profilen in den beiden anderen Familien abwich. [source] Linkage and QTL mapping for Sus scrofa chromosome 11JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2003M. Dragos-Wendrich Summary Linkage and QTL maps of Sus scrofa chromosome 11 (SSC11) have been produced based on four microsatellite markers genotyped in three F2 families from Wild Boar (W), Meishan (M) and Pietrain (P) crosses. The maps were similar across the families and in agreement with already published maps. Quantitative Trait Loci (QTLs) were identified in the W × M family and not in the M × P and W × P families. The QTLs affected live weight, loin and neck meat weight, back-fat depth and food consumption, and explained up to 4.7% of the F2 phenotypic variance. Additive and dominance effects were similar in size. The Wild Boar QTL alleles led to higher trait values in comparison with Meishan alleles. Zusammenfassung Kopplungskarten für Chromosom 11 (SSC11), die durch Analyse von vier Mikrosatelliten-Markern in drei F2 -Familien aus Kreuzungen von Wildschwein (W), Meishan (M) und Pietrain (P) erstellt wurden, zeigten eine gute Übereinstimmung zwischen den Familien sowie mit Literaturergebnissen. Quantitative Trait Loci (QTLs) waren in der Familie W × M nachzuweisen, jedoch nicht in den Familien M × P und W × P. Sie beeinflussten Lebendgewicht, Kotelettstranggewicht, Rückenspeckdicke und Futteraufnahme und erklärten bis zu 4,7% der phänotypischen Varianz in der F2 -Generation. Additiv- und Dominanzeffekte waren ähnlich groß. Wildschwein-QTL-Allele führten im Vergleich zu Meishan-Allelen zu höheren Merkmalswerten. [source] Linkage and QTL mapping for Sus scrofa chromosome 12JOURNAL OF ANIMAL BREEDING AND GENETICS, Issue 2003G. Yue Summary The SSC12 (Sus scrofa chromosome 12) linkage and QTL maps were generated using 11 markers, of which seven to 10 have been used in the three F2 families based on Wild Boar (W), Meishan (M) and Pietrain (P) crosses. Linkage maps showed identical marker order among the families, but differed in total lengths. They were in agreement with the already published maps, except for the order SWR1021,SW605. Most quantitative trait loci (QTLs) affected fat or meat content in carcass, but were also found for some other traits (heart weight, CK20 values and teat number). They explained up to 5.4% of F2 phenotypic variance. Meishan alleles had stimulating effects on fat deposition and decreasing effects on lean content and CK20 value. The QTL profiles differed between families, with QTL effects in the vicinity of the GH1 locus found solely in the M × P family. Zusammenfassung Auf der Basis von elf Markern wurden Kopplungs- und QTL-Karten für Chromosom 12 (SSC12) in drei F2 -Familien aus Kreuzungen von Wildschwein (W), Meishan (M) und Pietrain (P) erstellt. Hierbei wurden sieben bis zehn Marker pro F2 -Familie benutzt. Die Kopplungskarten zeigten eine gleichartige Anordnung der Loci für alle Familien, jedoch mit verschiedenen Kartenlängen. Sie stimmen, außer in der Anordnung SWR1021,SW605, mit bereits publizierten Karten überein. Quantitative Trait Loci (QTLs) waren hauptsächlich für Merkmale des Fett-oder Fleischanteils im Schlachtkörper festzustellen, daneben aber auch für weitere Merkmale (Herzgewicht, CK20 -Wert, Zitzenzahl). Sie erklärten bis zu 5,4% der phänotypischen Varianz in der F2 -Generation. Meishan-Allele waren assoziiert mit einer Steigerung des Fettansatzes sowie einer Reduktion der Anteile wertvoller Teilstücke und der CK20 -Werte. Die QTL-Profile unterschieden sich zwischen den Familien und ließen Assoziationen mit dem GH1 -Locus nur in der Familie M × P erkennen. [source] Cytoplasmic phylogeny and evidence of cyto-nuclear co-adaptation in Arabidopsis thalianaTHE PLANT JOURNAL, Issue 5 2010Michaël Moison Summary In recent years Arabidopsis thaliana has become a model species for genomic variability and adaptation studies. Although impressive quantities of data have been gathered on the nuclear genomic diversity of this species, little has been published regarding its cytoplasmic diversity. We analyzed the diversity of plastid (pt) and mitochondrial (mt) genomes among 95 accessions, covering most Arabidopsis geographic origins. Four intergenic regions of the pt genome were sequenced, and a total of 68 polymorphisms and 65 pt haplotypes were identified. Several strategies were developed to identify mt polymorphisms among a subset of 14 accessions. Fifteen polymorphisms were further developed as PCR-based markers and used to analyze the whole set of 95 accessions. Using statistical parsimony, we built pt and mt phylogenetic networks of haplotype groups. To root the pt network, the pt intergenic regions of two related Arabidopsis species, Arabidopsis lyrata and Arabidopsis arenosa, were also sequenced. The mt and pt phylogenies are highly congruent and could be combined into a single cytoplasmic phylogeny. To estimate whether co-adaptation between nuclear and cytoplasmic genomes exists in A. thaliana, we tested the germination capacity in challenging conditions of 27 pairs of reciprocal F2 families. We found that the cytoplasm donor had a significant effect on the germination capacity of some F2 families. [source] Sequence polymorphisms in porcine homologs of murine coat colour-related genesANIMAL GENETICS, Issue 2 2010N. Okumura Summary Herein, we report the variability among 57 porcine homologs of murine coat colour-related genes. We identified single nucleotide polymorphisms (SNPs) and insertions/deletions (InDels) within 44 expressed gene sequences by aligning eight pig complementary DNA (cDNA) samples. The sequence alignment revealed a total of 485 SNPs and 15 InDels. The polymorphisms were then validated by performing matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) with reference DNA samples obtained from 384 porcine individuals. Of the 384 individuals, three parents of the experimental F2 family were included to detect polymorphisms between them for linkage mapping. We also genotyped previously reported polymorphisms of 12 genes, and one SNP each in three genes that were detected by performing a BLAST search of the Trace database. A total of 211 SNPs and three InDels were successfully genotyped from our porcine DNA panel. We detected SNPs in 33 of the 44 genes among the parents of an experimental F2 family and then constructed a linkage map of the 33 genes for this family. The linkage assignment of each gene to the porcine chromosomes was consistent with the location of the BAC clone in the porcine genome and the corresponding gene sequence. We confirmed complete substitutions of EDNRB and MLPH in the Jinhua and Clawn miniature breeds, respectively. Furthermore, we identified polymorphic alleles exclusive to each pig group: 13 for Jinhua, two for Duroc, three for Meishan, four for the Japanese wild boar, one for the Clawn miniature pig and four for the Potbelly pig. [source] Mapping of quantitative trait loci affecting behaviour in swineANIMAL GENETICS, Issue 4 2009G. Reiner Summary Behavioural indices in vertebrates are under genetic control at least to some extent. In spite of significant behavioural problems in farm animals, information on the genetic background of behaviour is sparse. The aim of this study was to map QTL for behavioural indices in swine under healthy conditions and after infection with Sarcocystis miescheriana, as behaviour can be significantly influenced by disease. This well-described parasite model subsequently leads to acute (day 14 p.i.), subclinical (day 28 p.i.) and chronic disease (day 42 p.i.), allowing the study and comparison of the behaviour of pigs under four different states of health or disease. The study was based on a well-described Pietrain/Meishan F2 family that has recently allowed the detection of QTL for disease resistance. We have mapped six genome-wide significant and 24 chromosome-wide significant QTL for six behavioural indices in swine. Six of these QTL (i.e. 20% of total QTL) showed effects on behavioural traits of the healthy pigs (day 0). Some of them (QTL on SSC11 and 18) lost influence on behavioural activities during disease, while the effects of others (QTL on SSC5, SSC8) partly remained during the whole experiment, although with different effects on the distinct behavioural indices. The disease model has been of high relevance to detect effects of gene loci on behavioural indices. Considering the importance of segregating alleles and environmental conditions that allow the identification of the phenotype, we conclude that there are indeed QTL with interesting effects on behavioural indices in swine. [source] | |||||||||||||