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At least 163 records · Page 9Linked to original sources
PubMed2005

SSCP-SNP in pearl millet--a new marker system for comparative genetics.

A considerable array of genomic resources are in place in pearl millet, and marker-aided selection is already in use in the public breeding programme at ICRISAT. This paper describes experiments to extend these publicly available resources to a single nucleotide polymorphism (SNP)-based marker system. A new marker system, single-strand conformational polymorphism (SSCP)-SNP, was developed using annotated rice genomic sequences to initially predict the intron-exon borders in millet expressed sequence tags (ESTs) and then to design primers that would amplify across the introns. An adequate supply of millet ESTs was available for us to identify 299 homologues of single-copy rice genes in which the intron positions could be precisely predicted. PCR primers were then designed to amplify approximately 500-bp genomic fragments containing introns. Analysis of these fragments on SSCP gels revealed considerable polymorphism. A detailed DNA sequence analysis of variation at four of the SSCP-SNP loci over a panel of eight inbred genotypes showed complex patterns of variation, with about one SNP or indel (insertion-deletion) every 59 bp in the introns, but considerably fewer in the exons. About two-thirds of the variation was derived from SNPs and one-third from indels. Most haplotypes were detected by SSCP. As a marker system, SSCP-SNP has lower development costs than simple sequence repeats (SSRs), because much of the work is in silico, and similar deployment costs and through-put potential. The rates of polymorphism were lower but useable, with a mean PIC of 0.49 relative to 0.72 for SSRs in our eight inbred genotype panel screen. The major advantage of the system is in comparative applications. Syntenic information can be used to target SSCP-SNP markers to specific chromosomal regions or, conversely, SSCP-SNP markers can be used to unravel detailed syntenic relationships in specific parts of the genome. Finally, a preliminary analysis showed that the millet SSCP-SNP primers amplified in other cereals with a success rate of about 50%. There is also considerable potential to promote SSCP-SNP to a COS (conserved orthologous set) marker system for application across species by more specifically designing primers to precisely match the model genome sequence.

Base Sequence↗
PubMed2006

Combining multistate capture-recapture data with tag recoveries to estimate demographic parameters.

Matrix population models that allow an animal to occupy more than one state over time are important tools for population and evolutionary ecologists. Definition of state can vary, including location for metapopulation models and breeding state for life history models. For populations whose members can be marked and subsequently reencountered, multistate mark-recapture models are available to estimate the survival and transition probabilities needed to construct population models. Multistate models have proved extremely useful in this context, but they often require a substantial amount of data and restrict estimation of transition probabilities to those areas or states subjected to formal sampling effort. At the same time, for many species, there are considerable tag recovery data provided by the public that could be modeled in order to increase precision and to extend inference to a greater number of areas or states. Here we present a statistical model for combining multistate capture-recapture data (e.g., from a breeding ground study) with multistate tag recovery data (e.g., from wintering grounds). We use this method to analyze data from a study of Canada Geese (Branta canadensis) in the Atlantic Flyway of North America. Our analysis produced marginal improvement in precision, due to relatively few recoveries, but we demonstrate how precision could be further improved with increases in the probability that a retrieved tag is reported.

Animal Migration↗
PubMed1998

Evidence that the mediobasal hypothalamus is the primary site of action of estradiol in inducing the preovulatory gonadotropin releasing hormone surge in the ewe.

Although a neural site of action for estradiol in inducing a LH surge via a surge of GnRH is now well established in sheep, the precise target(s) for estrogen within the brain is unknown. To address this issue, two experiments were conducted during the breeding season using an artificial model of the follicular phase. In the first experiment, bilateral 17beta-estradiol microimplants were positioned in either the medial preoptic area (MPOA) or the mediobasal hypothalamus (MBH), and LH secretion was monitored. An initial negative feedback inhibition of LH secretion was observed in ewes that had estradiol microimplants located in the MPOA (6 of 6 ewes) or caudal MBH in the vicinity of the arcuate nucleus (4 of 4). In contrast, a normal LH surge was only found in animals bearing estradiol microimplants in the MBH (5 of 10). Detailed analysis of estradiol microimplant location with respect to the estrogen receptor-alpha-immunoreactive cells of the hypothalamus revealed that 4 of the 5 ewes exhibiting a LH surge had microimplants located bilaterally within or adjacent to the area of estrogen receptor-expressing cells of the ventromedial nucleus. Two of these ewes exhibited a LH surge without showing any form of estrogen negative feedback. In the second experiment, we used the technique of hypophyseal portal blood collection to monitor GnRH secretion directly at the time of the LH surge induced by estradiol delivered either centrally or peripherally. Central estradiol implants induced the GnRH surge. The duration and mean plasma concentration of GnRH during the surge were not different between animals given peripheral or central MBH estradiol implants. Cholesterol-filled MBH microimplants did not evoke a GnRH surge. We conclude that the ventromedial nucleus is the primary site of action for estradiol in stimulating the preovulatory GnRH surge of the ewe, whereas the MPOA and possibly the caudal MBH are sites at which estrogen can act to inhibit LH secretion. These data provide evidence for the sites within the ovine hypothalamus responsible for mediating the bimodal influence of estradiol on GnRH secretion and suggest that different, and possibly independent, neuronal cell populations are responsible for the negative and positive feedback actions of estradiol.

Animals↗
PubMed1985

Carry-over effects of periparturient endocrine changes on postpartum reproductive function of Holstein heifers bred to genetically different service sires.

Effects of fetal sire on postpartum reproductive changes of the dam were studied in 21 Holstein heifers whose pregnancy had been initiated by either Angus (n = 7), Holstein (n = 7) or Brahman (n = 7) bulls. After parturition, all heifers were managed uniformly. Heifers in each service-sire-breed group were bled via jugular venipuncture thrice weekly from d 160 to 265 of pregnancy, daily thereafter until 15 d postpartum, and three times per week until d 60 postpartum. Ability of heifers to release prolactin (PRL) and luteinizing hormone (LH) was evaluated on d 10 postpartum after a simultaneous injection of thyrotropin releasing hormone (TRH; 100 micrograms) and gonadotropin releasing hormone (GnRH; 100 micrograms). Between d 5 and 60 postpartum, the reproductive tract of each heifer was examined rectally thrice weekly after collection of blood samples. Basal concentrations of LH from d 1 to 10 postpartum, as well as ability of the pituitary gland to release LH and PRL after the GnRH-TRH challenge, did not differ between service-sire-breed groups (P greater than .1). Means and profiles of progesterone concentrations during the first 60 d postpartum did not differ between service-sire-breed groups (P greater than .1). However, increases in progesterone concentrations following the GnRH-TRH challenge were synchronized more precisely in Angus (P less than .02) than in Holstein- and Brahman-service-sire groups. Daily rates of reduction in cervical and uterine horn diameters were higher (P less than .01) in Holstein- and Brahman- than in Angus-service-sire groups and were associated with higher profiles of postpartum 15-keto-13,14-dihydro-prostaglandin F2 alpha (PGFM) concentrations. Within-cow PGFM concentrations were correlated positively with cervical (r = .36) and uterine horn (r = .32) diameters. Postpartum ovarian responsiveness and uterine involution in Holstein heifers may be affected by genotypes of the conceptus they bore during pregnancy.

Animals↗
PubMed2002

Molecular research on the genetic diversity of Polish varieties and landraces of Phaseolus coccineus L. and Phaseolus vulgaris L. using the RAPD and AFLP methods.

The aim of our research was to evaluate the genetic diversity among 25 commercial varieties registered in Poland and 14 landraces of Phaseolus vulgaris var. nanus Asch. (the dwarf common bean) and Phaseolus coccineus L. (the runner bean) maintained in the National Centre of Plant Genetic Resources in Radzików. An additional goal of this study was to compare the precision and efficiency of two techniques of PCR (RAPD and AFLP), used to estimation the genetic diversity of bean. The breeding varieties of bean were registered in the period between 1950 and 2000. The landraces, collected during expeditions conducted from 1985 to 1988, mainly originated from the eastern and southern part of Poland. In the plant genetic diversity research of RAPD and AFLP markers are commonly used. Complex electrophoresis pictures of DNA fragments were taken, and revealed a considerable polymorphism. The polymorphic fragments were obtained on the basis of 6 differentiating primers using the RAPD method and 15 differentiating primers using the AFLP method. P. vulgaris and P. coccineus accessions formed distinct groups. Each of the RAPD and AFLP analyses allowed for the unique distinguishing of all accessions.

Base Sequence↗
PubMed1978

Geotropism of hornet comb construction under persistent acceleration.

Social wasps (Vespinae) are insects which build in a precise geotactical orientation. The effect of persistent acceleration on comb construction by Oriental hornet (Vespa orientalis) workers was assessed experimentally within breeding boxes of various size and shape. Groups of hornets at the building phase were subjected to a centrifugal and gravitational force with a resultant ranging between 26 degrees and 45 degrees. The comb construction within such boxes was compared to that within control boxes under ordinary gravitational pull. It was found that: a) juvenile hornets (1-2 days of age) placed in quasi-rectangular boxes built in the direction of the resultant force; b) juvenile and adult hornets (3-7 days of age) placed in spherical shaped containers also built in the direction of the resultant force; c) adult hornets who had spent their first days of life in a stationary rectangular box, apparently learned the direction of the gravitational force and "tried" to build in this direction when exposed to a centrifugal force; d) adult hornets made to spin in quasi-rectangular boxes tilted in the direction of the calculated resultant force built in the direction of the resultant. These results suggest that hornets learn the direction of the gravitational force during the first days of life and that geometrical cues within the breeding box enable them to build in the direction of the force to which they have become habituated. From the standpoint of geometric cues, only the roof of the breeding box is of critical importance.

Aging↗
PubMed2004

[Influence of FT-NIR spectrometer scanning requirements on the math model's precision].

This study is based on the agriculture product near infrared spectra database, which is a foundation database. The database has very important effects on agriculture products quality analysis and agriculture breeding. What the NIR researchers and NIR users care about is how to utilize information of the foundation database fully. To share the NIR resource, unifying the scanning term to get high quality spectra is the first step. This article uses wheat powder as sample to study the influence of different resolution, different He-Ne frequency and sample granularity on the wheat powder protein model. The results show that scanning sample by 4, 8 or 16 cm(-1) resolution has little influence on the wheat powder protein math model. The change in He-Ne frequency has influence to wavenumber accuracy, but when the change is within 1 cm(-1), the influence is indistinctive. For FT-NIR instruments with He-Ne to have better stability, we needn't often adjust the He-Ne wavenumber. Sample granularity has more distinctive influence on the NIR math models.

Chemistry, Pharmaceutical↗
PubMed2003

Breeding by design.

Breeding by Design is a concept that aims to control all allelic variation for all genes of agronomic importance. This concept can be achieved through a combination of precise genetic mapping, high-resolution chromosome haplotyping and extensive phenotyping. Thanks to marker technology, software tools and the know-how available today, this goal can now be achieved. Depending on the crop-specific generation time, controlled marker-assisted selection strategies could lead to the production of superior varieties within five to ten years.

Breeding↗
PubMed2002

Rapid and accurate determination of zygosity in transgenic animals by real-time quantitative PCR.

Successful identification of homozygous and heterozygous transgenic animals with currently available techniques demands tedious and time-consuming procedures with a high proportion of ambiguous results. Real-time PCR is a quantitative and extremely precise method with high throughput that could be applied to the analysis of large numbers of animals differing only by a factor of two in the amount of target sequences. We defined the technical conditions of real-time PCR to co-amplify a transgene and a reference gene using two fluorogenic probes and the comparative cycle threshold method. We applied these conditions to the analysis of zygosity in a line of transgenic rats. Real-time PCR allowed clear-cut identification of all transgenic animals analysed (n = 45) as homozygous or heterozygous. Southern blot analysis of these animals using an internal quantitative control and PhosphorImager quantification showed ambiguous results in six of them and was concordant with real-time PCR in the rest. Mating of homozygous and heterozygous animals, as defined by real-time PCR, showed transgene transmission to the offspring following expected Mendelian laws. Real-time PCR allows rapid, precise, non-ambiguous and high throughput identification of zygosity in transgenic animals. This technique could be helpful in the establishment of breeding programs for transgenic colonies and in experiments in which gene dosage effects could have a functional impact.

Animals↗
PubMed2005

Detection of alien chromatin introgression from Thinopyrum into wheat using S genomic DNA as a probe--a landmark approach for Thinopyrum genome research.

The introduction of alien genetic variation from the genus Thinopyrum through chromosome engineering into wheat is a valuable and proven technique for wheat improvement. A number of economically important traits have been transferred into wheat as single genes, chromosome arms or entire chromosomes. Successful transfers can be greatly assisted by the precise identification of alien chromatin in the recipient progenies. Chromosome identification and characterization are useful for genetic manipulation and transfer in wheat breeding following chromosome engineering. Genomic in situ hybridization (GISH) using an S genomic DNA probe from the diploid species Pseudoroegneria has proven to be a powerful diagnostic cytogenetic tool for monitoring the transfer of many promising agronomic traits from Thinopyrum. This specific S genomic probe not only allows the direct determination of the chromosome composition in wheat-Thinopyrum hybrids, but also can separate the Th. intermedium chromosomes into the J, J(S) and S genomes. The J(S) genome, which consists of a modified J genome chromosome distinguished by S genomic sequences of Pseudoroegneria near the centromere and telomere, carries many disease and mite resistance genes. Utilization of this S genomic probe leads to a better understanding of genomic affinities between Thinopyrum and wheat, and provides a molecular cytogenetic marker for monitoring the transfer of alien Thinopyrum agronomic traits into wheat recipient lines.

Chromatin↗
PubMed2025

Efficient CRISPR/Cas9-mediated genome editing of phytoene desaturase in Musa-AAA: a critical step for genetic improvement of east African highland bananas.

East African highland bananas (EAHBs), locally referred to as "matooke", are an important staple crop in Uganda. The EAHBs have a triploid genome (AAA) with a large phenotypic diversity in the Great Lakes region of Africa and are challenged by both abiotic and biotic factors. The EAHBs have been improved through conventional breeding and genetic engineering though facing challenges such as genetic drag of unfavorable traits and complex regulatory processes, respectively. Therefore, a more precise approach for crop improvement such as genome editing is highly recommended. In the current study, we assessed the feasibility and applicability of the CRISPR/Cas9 mediated-genome editing in EAHBs. Two sgRNAs were designed from the Nakitembe phytoene desaturase (PDS) gene and used to edit the PDS gene in Nakitembe (NKT) and NAROBan5 (M30) cultivars. A total of 47 NKT and 130 M30 events were regenerated via agrobacterium-mediated transformation of banana embryogenic cell suspensions. Up to 100% and 94.6% albinism rates were observed in Nakitembe and M30 cultivars respectively with additional albino-variegated and variegated phenotypes observed in M30 only. Carotenoid analysis revealed a significant reduction of total carotenoid content in edited events with all complete albinos showing no detectable carotenoids implying that the carotenoid biosynthetic pathway was effectively disrupted. Sequence analysis revealed that all of the edited events had frameshift mutations leading to PDS disruption. Overall, this study presents the first report of CRISPR/Cas9 genome editing in EAHBs and more interestingly on a hybrid, M30 showing high precision and efficiency. This validated genome editing system provides a robust platform for targeted EAHB improvement.

CRISPR/Cas9↗
PubMed1978

Chromosome banding studies in cattle.

A recent advance in the field of cytogenetics has been the ability to stain differentially specific areas or bands on the fixed chromosome. In terms of clinical and paraclinical work C- and G-bands have been of most value to date in allowing precise identification of chromosome homologues even in species such as cattle, where the vast majority of chromosomes are of a similar morphology. These methods have allowed at the gross level of the chromosome the precise identification of a number of Robertsonian translocations and certain aneuploids. In this study 1/29 Robertsonian translocations were found in three separate breeds. Also a 14/20 and a 6/16 Robertsonian translocation were identified as was a 61XXY sterile bull. In the future these techniques will allow the identification of as yet unidentified anomalies in cattle such as reciprocal translocations and paracentric inversions. Since many anomalies have been correlated with such clinical problems as early embryonic death, abortion, congenital anomalies and reduced reproductive efficiency in the mammalia, it is important to use cytogenetics as an additional laboratory aid in such investigations.

Aneuploidy↗
PubMed1996

A new method for rapid determination of sperm concentration in turkey semen.

The routine determination of sperm concentration not only provides a measure of semen quality but also supplies a means of delivering precise sperm numbers in modern artificial insemination (AI) programs. Methods for estimating sperm numbers in laboratory settings (e.g., hemacytometer) are not practical for use in breeding facilities. A microprocessor-controlled semen analyzer (Densimeter, Model 534-B-Mod1, Animal Reproductive Systems) is commercially available for evaluating stallion semen. We calibrated and modified the semen analyzer to determine sperm concentration in turkey semen and to provide information on the required dilution for a constant AI dose. To calibrate the semen analyzer for turkeys, six samples of pooled semen (10 toms per sample) were collected by abdominal massage. A dilution curve of undiluted and 1:0.5, 1:1, 1:1.5, 1:2, 1:3, 1:5, and 1:10 diluted semen was established using Beltsville Poultry Semen Extender. Sperm concentration in diluted samples was determined by hemacytometer counts. The hemacytometer counts were used to develop an equation for estimating sperm concentration from the semen analyzer's absorbance readings and the equation programmed into the instrument. The newly developed program on the semen analyzer was subsequently validated by comparing instrument values for sperm concentrations with concurrent hemacytometer counts, which compared well to concentrations determined by a previously calibrated photoelectric colorimeter (Klett). Correlation coefficients between the semen analyzer and hemacytometer counts and the Klett and hemacytometer counts were r = 0.996 and r = 0.992, respectively (P < 0.001). The semen analyzer method was accurate and precise and could be beneficial to commercial turkey AI programs because it is easy to use, requires limited technological skills, and provides results for determining sperm concentration and AI dose in approximately 1 min.

Animals↗
PubMed1989

Isotype switching by a microinjected mu immunoglobulin heavy chain gene in transgenic mice.

Immunization of transgenic mice carrying an immunoglobulin mu heavy chain resulted in a response dominated by expression of the transgene variable region. Unexpectedly, in a large proportion of the antibody produced by immunized mice, the transgene variable region was associated with IgG rather than IgM. This demonstrates that the transgene can undergo an isotype switch. Four transgenic founder lines all exhibited transgene isotype switching despite the likelihood of random chromosomal integration of the transgene. In addition one of the lines was analyzed by breeding studies and the transgene was found to be genetically unlinked to the immunoglobulin heavy chain (Igh) locus. These results indicate that a precise chromosomal location is not required for isotype switching and suggest the possibility that the isotype switching process can occur interchromosomally.

Animals↗
PubMed2002

Integrated physiological and agronomic modelling of N capture and use within the plant.

Today farmers have several constraints to take into account in managing their crops: (i) competitiveness: productivity must be maintained or increased whereas inputs must be decreased, (ii) the environmental consequences of cultural practices: pesticide and fertilizer use must be decreased, and (iii) product quality must be improved and nitrogen nutrition is an important factor in harvest quality. These new constraints sometimes conflict: maximum yield is often obtained with large amounts of N, increasing the risks of N leaching. The determination of rates and dates for nitrogen application must become more precise in this context. Tools are required for the forecasting of crop requirements, the diagnosis of N deficiencies during the crop cycle and breeding of new adapted varieties. Models and diagnosis indicators have been developed to meet these needs, but those relating to nitrogen are often based on empirical relationships. Moreover, the available models and indicators often fail to account for cultivar-specific responses. The improvement of agronomic tools and the breeding of new varieties adapted to new cropping systems should be based on a thorough understanding of the key metabolic processes involved, and the relative contributions of these processes to yield determination in conditions of fluctuating N supply. For both purposes, more information is required about plant and crop N economy. In this paper, the way in which N absorption and use within the plant and crop, plant responses to deficiencies and excesses of nitrogen are taken into account in major agronomic models is described first. The level of sophistication of the modules comprising these models depends on operational objectives. Secondly, the ways in which the most recent molecular plant physiology findings can, and indeed should, be integrated into models at the crop and crop cycle levels are described. The potential value of this approach for improving current agronomic models and diagnostic tools, and for breeding more efficient varieties is also discussed.

Agriculture↗
PubMed1996

The timing of thyroid-dependent programming in seasonally breeding male American tree sparrows (Spizella arborea).

There is convincing evidence that euthyroid male American tree sparrows are already programmed for seasonal reproduction and postnuptial molt by Week 4 of photostimulation. To explore more precisely when, during early photostimulation, thyroid-dependent programming of seasonal events occurs, photosensitive male tree sparrows were radiothyroidectomized or sham thyroidectomized on the first day of photostimulation (Week 0) or at Weeks 1 or 3 thereafter. Birds were monitored for testicular growth and regression over 8 or 12 weeks and then tested for photosensitivity or photorefractoriness by exposing them to constant light and exogenous L-thyroxine for 4 weeks. Molt of the primary flight feathers was scored periodically, and at the end of the experiment, hypothalami were saved for cGnRH-I (chicken gonadotropin-releasing hormone I) assay. Because (1) the thyroid is already dysfunctional by Day 4 after radiothyroidectomy, (2) thyroid-dependent photoinduced gonadal growth is programmed growth, and as demonstrated here, (3) testis length at Week 6 on long days (i.e., maximum or near-maximum testis size) is independent of the time of thyroidectomy at or after the onset of photostimulation, we conclude that male American tree sparrows were programmed for photoperiodic testicular growth during the first week of photostimulation. Based on measurements of testis length and hypothalamic cGnRH-I content, only 2 of 11 birds thyroidectomized at Week 1 were already programmed for photorefractoriness by Week 1, whereas all birds thyroidectomized at Week 3 were so programmed by Week 3. Marked differences in molt scores between photorefractory (thyroidectomized and euthyroid) and photosensitive (thyroidectomized) birds argue that postnuptial molt also was programmed roughly between Weeks 1 and 3. To explain these results, we ascribe organizational-like actions directly or indirectly to endogenous thyroid hormones and argue that the onset of photostimulation opens a window, during which time euthyroid male American tree sparrows are programmed for seasonality. A clear dissociation of photorefractoriness from photoperiodic testicular growth in birds thyroidectomized at Week 1 suggests that separate control circuits mediate these two annually periodic events.

Animals↗
PubMed2002

Genome-wide scans for QTL affecting carcass traits in Hereford x composite double backcross populations.

A genome-wide scan for chromosomal regions influencing carcass traits was conducted spanning 2.413 morgans on 29 bovine autosomes using 229 microsatellite markers. Two paternal half-sib families of backcross progenies were produced by mating Hereford x composite gene combination (CGC) bulls to both Hereford and CGC dams. Progeny of the first sire (n = 146) were born in 1996 and progeny of the second sire (n = 112) were born in 1997. Each year cattle were fed out and slaughtered serially when they were between 614 and 741 d of age. Phenotypes measured at harvest were: live weight; carcass weight; fat depth; marbling; percentage kidney, pelvic, and heart fat (KPH); and rib eye area. Dressing percentage and USDA Yield Grade were calculated from these data. The phenotypes were adjusted to age-, live weight-, and fat depth-constant endpoints using analysis of covariance. The resulting residuals were analyzed by interval mapping to detect QTL. Within family, nominal significance was established by permutation analysis. Approximate genomewide significance levels were established by applying the Bonferroni correction to the nominal probability levels. Regression and error sums of squares and degrees of freedom were pooled across families when suggestive linkage identified in one family was confirmed in the other. The results indicate promising locations for QTL affecting live weight on BTA 17 and marbling on BTA 2 that segregate in Bos taurus. Also, previously identified linkage between central markers on BTA 5 and USDA Yield Grade was confirmed in one family. Greater marker saturation in these regions coupled with refined methods for data analysis will lead to more precise determination of QTL positions.

Adipose Tissue↗
PubMed2003

The impact zone: genomics and breeding for durable disease resistance.

Durable disease resistance is a major but elusive goal of many crop improvement programs. Genomic approaches will have a significant impact on efforts to ameliorate plant diseases by increasing the definition of and access to genepools available for crop improvement. This approach will involve the detailed characterization of the many genes that confer resistance, as well as technologies for the precise manipulation and deployment of resistance genes. Genomic studies on pathogens are providing an understanding of the molecular basis of specificity and the opportunity to select targets for more durable resistance. There are, however, several biological and societal issues that will have to be resolved before the full impact of genomics on breeding for disease resistance is realized.

Breeding↗