Significance testing and genomic inflation factor using high‐density genotypes or whole‐genome sequence data     

Sanne van den Berg  Jrmie Vandenplas  Fred A. van Eeuwijk  Marcos S. Lopes  Roel F. Veerkamp 《Zeitschrift für Tierzüchtung und Züchtungsbiologie》2019,136(6):418-429

Significance testing for genome‐wide association study (GWAS) with increasing SNP density up to whole‐genome sequence data (WGS) is not straightforward, because of strong LD between SNP and population stratification. Therefore, the objective of this study was to investigate genomic control and different significance testing procedures using data from a commercial pig breeding scheme. A GWAS was performed in GCTA with data of 4,964 Large White pigs using medium density, high density or imputed whole‐genome sequence data, fitting a genomic relationship matrix based on a leave‐one–chromosome‐out approach to account for population structure. Subsequently, genomic inflation factors were assessed on whole‐genome level and the chromosome level. To establish a significance threshold, permutation testing, Bonferroni corrections using either the total number of SNPs or the number of independent chromosome fragments, and false discovery rates (FDR) using either the Benjamini–Hochberg procedure or the Benjamini and Yekutieli procedure were evaluated. We found that genomic inflation factors did not differ between different density genotypes but do differ between chromosomes. Also, the leave‐one‐chromosome‐out approach for GWAS or using the pedigree relationships did not account appropriately for population stratification and gave strong genomic inflation. Regarding different procedures for significance testing, when the aim is to find QTL regions that are associated with a trait of interest, we recommend applying the FDR following the Benjamini and Yekutieli approach to establish a significance threshold that is adjusted for multiple testing. When the aim is to pinpoint a specific mutation, the more conservative Bonferroni correction based on the total number of SNPs is more appropriate, till an appropriate method is established to adjust for the number of independent tests.  相似文献   

Tanglehead in Southern Texas: A Native Grass with an Invasive Behavior     

David B. Wester  Fred C. Bryant  Aaron D. Tjelmeland  Joshua L. Grace  Scott L. Mitchell  John T. Edwards  Fidel Hernández  Robert K. Lyons  Megan K. Clayton  Sandra Rideout-Hanzak  Richard V. Machen  J. Alfonso Ortega-S. 《Herpetological Monographs》2018,40(2):37-44

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Breeding Strategies for Adaptation of Pearl Millet and Sorghum to Climate Variability and Change in West Africa     

B. I. G. Haussmann  H. Fred Rattunde  E. Weltzien‐Rattunde  P. S. C. Traoré  K. vom Brocke  H. K. Parzies 《Journal of Agronomy and Crop Science》2012,198(5):327-339

Semi‐arid and subhumid West Africa is characterized by high inter‐annual rainfall variability, with variable onset of the rainy season, somewhat more predictable endings, and drought or excess water occurrence at any time during the growing season. Climate change is predicted to increase this variability. This article summarizes options for plant breeders to enhance the adaptation of pearl millet (Pennisetum glaucum [L.] R. Br.) and sorghum (Sorghum bicolor [L.] Moench) to climate variability in West Africa. Developing variety types with high degrees of heterozygosity and genetic heterogeneity for adaptation traits helps achieving better individual and population buffering capacity. Traits that potentially enhance adaptive phenotypic plasticity or yield stability in variable climates include photoperiod‐sensitive flowering, plastic tillering, flooding tolerance, seedling heat tolerance and phosphorus efficiency. Farmer‐participatory dynamic gene pool management using broad‐based populations and diverse selection environments is useful to develop new diverse germplasm adapted to specific production constraints including climate variability. For sustainable productivity increase, improved cultivars should respond to farmer‐adoptable soil fertility management and water harvesting techniques. Larger‐scale, on‐farm participatory testing will enable assessments of varietal performance under evolving climatic variability, provide perspective on needs and opportunities and enhance adoption. Strengthening seed systems will be required to achieve sustainable impacts.  相似文献   

Obituary: Martin Sten Johansson 1930–2004     

Fred O. Asiegbu  Jan Stenlid 《Forest Pathology》2005,35(2):73-74

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Effects of mass inoculation on induced oleoresin response in intensively managed loblolly pine     

Klepzig KD  Robison DJ  Fowler G  Minchin PR  Hain FP  Allen HL 《Tree physiology》2005,25(6):681-688

Oleoresin flow is an important factor in the resistance of pines to attack by southern pine beetle, Dendroctonus frontalis Zimm., and its associated fungi. Abiotic factors, such as nutrient supply and water relations, have the potential to modify this plant-insect-fungus interaction; however, little is known of the effects of inoculation with beetle-associated fungi on oleoresin flow. We observed that constitutive and induced resin yield in loblolly pine, Pinus taeda L., were affected by either fungal inoculation (with the southern pine beetle-associated fungus Ophiostoma minus (Hedgcock) H. & P. Sydow) or silvicultural treatment. The effects of mass wounding (400 wounds m(-2)) and mass wounding and inoculation with O. minus were assessed by comparison with untreated (control) trees. The treatments were applied to trees in a 2 x 2 factorial combination of fertilizer and irrigation treatments. Fertilization did not significantly affect constitutive resin yield. Even as long as 105 days post-treatment, however, mass-inoculated trees produced higher induced resin yields than control or wounded-only trees, indicating a localized induced response to fungal inoculation. We noted no systemic induction of host defenses against fungal colonization. Although beetles attacking previously attacked trees face a greater resinous response from their host than beetles attacking trees that had not been previously attacked, the effect of an earlier attack may not last more than one flight season. Despite mass inoculations, O. minus did not kill the host trees, suggesting that this fungus is not a virulent plant pathogen.  相似文献   

Truffle abundance and mycophagy by northern flying squirrels in eastern Washington forests     

John F. Lehmkuhl  Laura E. Gould  Efren Czares  David R. Hosford 《Forest Ecology and Management》2004,200(1-3):49-65

Although much is known about truffle abundance and rodent mycophagy in mesic Douglas-fir forests in the Pacific Northwest, few data are available for dry interior montane forests dominated by ponderosa pine (Pinus ponderosa), Douglas-fir (Pseudotsuga menziesii), and grand fir (Abies grandis). Our objective was to quantify the relationship between the abundance and diversity of ectomycorrhizal fungal sporocarps in the soil and in the diets of northern flying squirrels (Glaucomys sabrinus) in low-elevation forests of the eastern Washington Cascades. We randomly sampled four stands each of three cover types: dry open ponderosa pine, mesic young mixed-conifer forest, and mesic mature mixed-conifer forest. We sampled the soil for hypogeous sporocarps during the spring of 1999 and 2000. We collected fecal pellets from 318 flying squirrels live-trapped during the fall of 1997–2000. We sampled 2400 m² of soil surface and found truffles in 40% of 600 plots. Total biomass collected was 609 g. Spring truffle biomass on a kg/ha basis averaged 1.72 in open pine, 3.56 in young, and 4.11 in mature forest. Twenty-two species were collected across all cover types, with all but three species belonging to the Basidiomycotina. Eleven dominant species accounted for 91–94% of truffle biomass in each cover type. Four dominant species accounted for 60–70% of spring truffle biomass: Gautieria monticola, Hysterangium coriaceum, Rhizopogon parksii, and R. vinicolor. Truffle assemblages, richness and total biomass differed among cover types: richness and biomass were highest in young and mature mixed-conifer forest, and lowest in open ponderosa pine forest. Fall squirrel diets were composed of 23 genera or groups of fungi, plus about 22% plant material. Rhizopogon was the most abundant genus in the diet, followed by plant material, then Gautieria, Leucogaster, Alpova, and Hysterangium. Diets in different cover types were similar in the composition, richness, evenness, and the ratio of fungus to plant material. Diet richness varied over the study period. Nineteen truffle genera were detected in fall fecal samples versus 12 in spring soil samples. Management of low-elevation dry forest to maintain or restore stable fire regimes might reduce truffle diversity at stand scales by simplifying stand composition and structure; but, such management might increase long-term beta and landscape truffle diversity and persistence by reducing the occurrence of high-intensity fires and stabilizing inherent fire disturbance regimes.  相似文献   

Multiple phosphorylation sites confer reproducibility of the rod's single-photon responses     

Doan T  Mendez A  Detwiler PB  Chen J  Rieke F 《Science (New York, N.Y.)》2006,313(5786):530-533

Although signals controlled by single molecules are expected to be inherently variable, rod photoreceptors generate reproducible responses to single absorbed photons. We show that this unexpected reproducibility-the consistency of amplitude and duration of rhodopsin activity-varies in a graded and systematic manner with the number but not the identity of phosphorylation sites on rhodopsin's C terminus. These results indicate that each phosphorylation site provides an independent step in rhodopsin deactivation and that collectively these steps tightly control rhodopsin's active lifetime. Other G protein cascades may exploit a similar mechanism to encode accurately the timing and number of receptor activation.  相似文献   

Histiocytic sarcoma of the spleen in flat-coated retrievers with regenerative anaemia and hypoproteinaemia     

Dobson J  Villiers E  Roulois A  Gould S  Mellor P  Hoather T  Watson P 《The Veterinary record》2006,158(24):825-829

Three flat-coated retrievers with a regenerative anaemia were examined. They were hypoproteinaemic suggesting that the anaemia might be due to blood loss, but it was not possible to identify a site of haemorrhage. All three had splenomegaly with splenic abnormalities apparent on ultrasonography. Ultimately all three animals were shown to have a histiocytic sarcoma involving the spleen and other tissues. A fourth flat-coated retriever with anaemia, hypoproteinaemia and an abdominal mass was also diagnosed with a histiocytic sarcoma of the spleen following splenectomy. It is postulated that the dogs' anaemia was due to erythrophagocytosis, either directly by neoplastic cells or by reactive macrophages.  相似文献   

Extending top-down mass spectrometry to proteins with masses greater than 200 kilodaltons     

Han X  Jin M  Breuker K  McLafferty FW 《Science (New York, N.Y.)》2006,314(5796):109-112

For characterization of sequence and posttranslational modifications, molecular and fragment ion mass data from ionizing and dissociating a protein in the mass spectrometer are far more specific than are masses of peptides from the protein's digestion. We extend the approximately 500-residue, approximately 50-kilodalton (kD) dissociation limitation of this top-down methodology by using electrospray additives, heated vaporization, and separate noncovalent and covalent bond dissociation. This process can cleave 287 interresidue bonds in the termini of a 1314-residue (144-kD) protein, specify previously unidentified disulfide bonds between 8 of 27 cysteines in a 1714-residue (200-kD) protein, and correct sequence predictions in two proteins, one with 2153 residues (229 kD).  相似文献   

Rocket launcher mechanism of collaborative actin assembly defined by single-molecule imaging     

Breitsprecher D  Jaiswal R  Bombardier JP  Gould CJ  Gelles J  Goode BL 《Science (New York, N.Y.)》2012,336(6085):1164-1168

Interacting sets of actin assembly factors work together in cells, but the underlying mechanisms have remained obscure. We used triple-color single-molecule fluorescence microscopy to image the tumor suppressor adenomatous polyposis coli (APC) and the formin mDia1 during filament assembly. Complexes consisting of APC, mDia1, and actin monomers initiated actin filament formation, overcoming inhibition by capping protein and profilin. Upon filament polymerization, the complexes separated, with mDia1 moving processively on growing barbed ends while APC remained at the site of nucleation. Thus, the two assembly factors directly interact to initiate filament assembly and then separate but retain independent associations with either end of the growing filament.  相似文献