, , 2014.
, independent F3:6 nurseries evaluated each year from 2012-2015 across 8 to 10 locations in Nebraska. Mixed models incorporating spatial variations provided better fit to the grain yield data. Genotype-bysequencing, quality control and imputations provided 26,925 SNP markers. For each of the years, genomic prediction ability (PAB) was estimated by randomly marking entries as missing in steps of 10% -from 10% to 90% of dataset. Prediction ability (PAC) was also estimated by marking 100% of the entries missing in a year. Average PAB calculated using 10-fold cross validation ranged from 0.229 to 0.552, and PAC varied from 0.167 to 0.282. Further, we tracked entries from each of these four nurseries that were advanced. It was remarkably apparent that lines with "above average genomic estimate breeding value (GEBV) and observed phenotypic value (OPV)" were being retained for longer times in the breeding program. This suggests using GEBV and OPV can improve accuracy of selection decisions and recycle elite lines earlier to the crossing block, This study was funded by the Federal Ministry of Education and Research (BMBF, Germany) within the AgroClustEr Synbreed -Synergistic plant and animal breeding (grant 0315528) and by KWS SAAT SE under a PhD fellowship for
, Wolfgang Grüneberg, vol.2, issue.1
, University of São Paulo Genotyping-by-sequencing (GBS) has been applied in several species and broadly used in many genetic studies. However, there are still issues regarding genotype calling in highly heterozygous, outcrossing species. Here, GBS from 182 full-sibs of Ipomoea trifida (2n=2x=30) and their parents, M9 and M19, produced ~1.7 million tags from 516 million good, barcoded reads out of 811 million reads in total. Tags alignment rate was 74.69% when using an I, vol.38, p.959
, LGs ranged from 65 to 200 markers and from 130.88 to 269.62 cM in length, spanning 2,595.94 cM in total (average marker density = 1.53). The LGs assembled 147 (0.48% of 30,377) scaffolds from the current draft genome, representing 276 Mb (59.66% of 462 Mb); 137 scaffolds were assigned to one LG each, nine scaffolds to two LGs and one scaffold to three LGs. Although big scaffolds could be uniquely assigned to LGs, assembling may need review due to these multiple assignments. This is an interesting example on how linkage map might assist genome assembling, SNPs and Indels) were discovered and actual depths were stored in a variant call format (VCF) file using TASSEL-GBS pipeline
, After applying a k-fold validation process, the overall average imputation accuracy (concordance rate) per animal from BovineHD and BOS1 to SP was 97.75% and 98.48%, respectively. For the same scenarios, imputation accuracy per SNP, measured as a squared Pearson correlation, was also performed. BOS1 slightly outperformed BovineHD, influenced mainly by regions with reduced minor allele frequency. The SP strategy reduced the gap size in some chromosomes (i.e.: Chrs 6, 14 and 23) and did not improve uncovered regions such as in Chrs 7 and 27. LD pruning, applied to remove markers in high LD (r2 > 0.9), kept 25% more markers in the pruned BOS1 data set, compared with the pruned BovineHD set, This research investigated two high-density panels (The Affymetrix Axiom Genome-Wide BOS1 Array (648,874 SNP) and the Illumina High-Density BovineHD Bead Chip Array
, Further investigation including new analyzes, such as Copy Number Variation (CNV), is required before making decision on the HD panel genotyping strategy for Nellore cattle
, Alma Islas-Trejo, vol.4
, Since high-altitude disease is a polygenic disease and single-SNP within a positional-candidate gene explains limited variation, there is great interest in discovery functional SNP located, for example, within nodes and hubs of gene networks. Various "omics" tools such as transcriptomics combined with gene networks and systems biology assist with discovery of coding and tag SNP. Therefore, several SNP variants segregated specifically in either the LPAP or HPAP animals have been identified. Among them, 139 SNP were located in key regulator genes involved in the adaptation of the disease.These approaches helped identify splice variants corresponding to key regulator genes, -altitude (>1800m) disease is a challenging problem in beef and dairy cattle
, North Carolina State University Heritability and genetic gain of Bipolaris resistance in switchgrass
, ), a selected biomass crop, suffers from seed rot and leaf spot caused by Bipolaris oryzae (Breda de Haan) Shoemaker resulting in poor establishment and yield reduction. A sustainable approach is to improve disease resistance in switchgrass germplasm. Prior to breeding, narrow-sense heritability of leaf spot resistance based on replicated half-sib progenies in 'Kanlow' was estimated to determine genetic variability for resistance as well as an effective breeding method
, However, the heritability was not significantly different from zero, indicating either that the genetic variability of disease resistance might be low in this population and/or that improvements need to be made in the screening technique. Recurrent phenotypic selection has been completed for the first cycle in 'Cave-in-Rock' and 'Shelter' for resistance to either seed rot and leaf spot. The gain of selection for leaf spot resistance in 'Cave-in-Rock' in the first cycle was low at only 2.5% with low realized heritability at 0.03. On the other hand, seed rot resistance was significantly improved both in 'Cave-in-Rock' and 'Shelter' from 26, p.20
, Rice Research Program, 2 College of Agriculture, vol.3
, are among the major diseases affecting temperate rice worldwide, and are caused by the fungi Sclerotium oryzae (SCL) and Rhizoctonia oryzae-sativae (ROS), respectively. Resistance to these diseases is quantitatively inherited and has low heritabilities in field trials, making conventional breeding difficult. Furthermore, reports on QTL for resistance to both diseases are scarce. Thus, identification of QTL is needed for marker assisted breeding for these traits. We analyzed the association between resistance to both diseases in 643 Uruguayan rice advanced inbred lines (327 indica and 316 tropical japonica ssp.) and two sets of GBS SNPs (49.6K for indica and 28.9K for japonica). Resistance was measured in four years of field trials in Eastern Uruguay and in two (for SCL) and three (for ROS) greenhouse trials with a 0-9 scale. Phenotypic means were spatially and phenologically corrected, and weighted based on each trial heritability. Two mixed models, one with P (PCA scores) for japonica, and another with P+K (kinship) matrices for indica
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