Boone: RAD-Seq, tGBS, AmpliSeq - all diff. stages of workflow. Discovery for reference-free info; but known targets = AmpliSeq #PAGXXIII
9:57pm January 24th 2015 via Twitter Web Client
Boone:Q:Polyploid genomes? A:They want to probe the limits of their offering #PAGXXIII
9:56pm January 24th 2015 via Twitter Web Client
Boone:Q:QC for library prep, input DNA? A:Low input (10ng), they ask for more. Spike input low amts of +'ve control DNA #PAGXXIII
Boone:Q:Can barcodes be increased? A:We want to go well beyond that #PAGXXIII
Boone: Providing service now - turnaround from gDNA receipt only 2-3w. Future: want to use lower quality DNA as input #PAGXXIII
Boone: 96 samples, 93 EST-derived markers previously genotyped; call rate 98.6%; mean gt concordance 99.4% #PAGXXIII
Boone:Median depth of 102x, 280 amplicons/run. Visualized evenness of coverage via 40K reads/sample + CV 0.57 #PAGXXIII
9:55pm January 24th 2015 via Twitter Web Client
Boone: Test population of OR/NE barley introgression pop. Prev genotyped via RAD-Seq, others. 112 EST-derived, 208 RAD-Seq #PAGXXIII
Boone: Showed PGM + Ion Chef on a wheeled table. 'Absolutely bulletproof.' #PAGXXIII
Boone: Cost-effectiveness of AmpliSeq: many thousands of samples. Review of fast workflow, 2-4h 'outstanding turnaround' #PAGXXIII
Boone: The 300 Strong reference: a precise set of markers and effective weapon. #PAGXXIII
Boone: Variety: pygmy elephant, artichokes, salmon. Now going from RAD-Seq down to targeted SNPs. Now selectivity & speed #PAGXXIII
Boone: Floragenix is a service organization - discovery of variation, genotyping using NGS, an analytics using the cloud #PAGXXIII
Jason Boone (Floragenex) “300 Strong: Leveraging Ion AmpliSeq and Ion Torrent sequencing for targeted genotyping studies” #PAGXXIII
9:54pm January 24th 2015 via Twitter Web Client
Schnable:Q:Why Proso Millet? A:Can rotate w/wheat, very little water needed. #PAGXXIII
Schnable:Q:Polyploid analysis? A:W/many reads/site, can determine when there are paralogous loci; by %'s and sufficient depth #PAGXXIII
Schnable: 14h turnaround. Data2Bio able to turn around full tGBS projects in 6-8w. #PAGXXIII
Schnable: Accessions cluster by country - India, Chinese, Korean, US all consistent #PAGXXIII
Schnable:Of 312, ID 10.2K low missing data SNPs. tGBS discover many extremely rare alleles (even when >3 accessions) #PAGXXIII
9:53pm January 24th 2015 via Twitter Web Client
Schnable:USDA has 701 total accessions, 'many from the former USSR' still labeled that way. High phenotype diversity #PAGXXIII
Schnable: Proso Millet dev in northern China, orphan crop. No QTL study published, low-diversity sp. Rapid cycle-time #PAGXXIII
Schnable: Reference-free tGBS: done w/Maize: cp v3 against Hi-Q, percent of useful markers double #PAGXXIII
Schnable: Now ~100 plant spp with reference genomes. Many spp. are not amenable to assembly. #PAGXXIII
Schnable: For 24 founder maize assoc'n mapping panel, 1/16th of sites, discovered 19K low missing data SNPs (no imputation) #PAGXXIII
9:52pm January 24th 2015 via Twitter Web Client
Schnable: Use min of >5 reads/SNP. Errors in dels 'roughly cut in half' In unique alignments: 25% more usable data for maize #PAGXXIII
Schnable: Hi-Q involves new reagents/software. 6h spread from 6am to 9pm. Now - 4.5h continuous work. 14GBp/Proton run #PAGXXIII
Schnable: tGBS can handle polyploidy. Still digestion but ss oligo overlap; 1 or 2bp overlap. Use Proton #PAGXXIII
Schnable: Conventional GBS is 1M sites; but requires imputation. Tunable - many more reads/site (12-30 reads/site). #PAGXXIII
Schnable: Also founder of Data2Bio, tunable GBS called tGBS; able to test Hi-Q reagent in Maize. Later: Proso Millet #PAGXXIII
James Schnable (Univ NE Lincoln) “Fast turn-around genotyping w/o a ref genome, using the Ion Torrent Hi-Q Sequencing...” #PAGXXIII
9:51pm January 24th 2015 via Twitter Web Client
Flagel:Q:Behavioral against Bt corn? A:Soil-dwelling, nearly transparent so difficult to study. #PAGXXIII
Flagel:Q:Any interesting genes to LG8? A:One ABC transporter gene, but others in the gaps, still unk #PAGXXIII
Flagel:Q: Mechanism of resistance? A:Diff binding to stomach - no. Other known lepidopteran resistances - no also. #PAGXXIII
Flagel: From a non-model organism, a 'fast-track marker platform'. Just-published G3 paper http://t.co/wDksGa5vmh #PAGXXIII
Flagel: From 80 populations, assoc'd freq of allele to rel. resistance. ID 2 markers. R^2 only 0.2 - a component of resist. #PAGXXIII
Flagel: Isolating the resistance marker suspected to be recessive; data confirms a deg of dominance at about 0.1 #PAGXXIII
9:50pm January 24th 2015 via Twitter Web Client
Flagel: Looking for large genetic diff's; basically a chi-square test. 'Something big here on LG8 and nowhere else' #PAGXXIII
Flagel: 'Really slick'- combining AmpliSeq & Ion Torrent; beetle 'honeymoon suite' shown; synth soil; eggs harvested #PAGXXIII
Flagel: Pooled samples, picked 1150 for GBS; build a western corn rootworm map, F1 hybrids, F2 for 740 markers, 10 chr's #PAGXXIII
Flagel: Genome of rootworm is 2.5Bbp - they sequenced the transcriptome BMC Genet 2014 http://t.co/xjiVaePdhZ #PAGXXIII
Flagel: Resistance 'appears autosomal and nearly recessive' via F1 hybrid crossing #PAGXXIII
9:49pm January 24th 2015 via Twitter Web Client
Flagel: Heritability w/ estimated genetic contribution; about H^2 0.69 - can be mapped (+) but resistance selected for (-) #PAGXXIII
Flagel: First reported resistance '11, now IA, IL, MN, SD... appears persistent. Goal: map resistance, mode of action #PAGXXIII
Flagel: Resistant to crop rotation, several chemical pesticides. Cry3Bb1 Bt is a Monsanto toxin, intro 2003 (YieldGuard) #PAGXXIII
Flagel: Native to the US, 2009 paper: http://t.co/VNLUF2H3OQ fig illus movement. $1B USD losses/yr tough to control #PAGXXIII
Flagel: Beetle larvae look like a worm; highly fecund, tremendous damage. Roots are v. small; wind blows corn crop over #PAGXXIII
9:48pm January 24th 2015 via Twitter Web Client
Lex Flagel (Monsanto): "Genetic architecture of western corn rootworm to the Cry3Bb1 Bt protein" #PAGXXIII
Parikh: Mentions collab with GeneSeek (bovine) and IRRI (Rice), concordance >95% and >99% respectively #PAGXXIII
Parikh: From 12 to 24K targets from preloaded animal & plant genomes (bovine, maize, soybean etc.) http://t.co/iaRWOl3DpD #PAGXXIII
First up: Dr. Anup Parikh w/ AmpliSeq overview, including new AmpliSeq Any Genome http://t.co/mpsyw59nor launched at #PAGXXIII
