NT:Concl: siRNA strategy 'appears to hold sig potential for controlling CBSD' Ongoing: virus sequencing, graft challenge PAGXXIII
8:41pm January 13th 2015 via Hootsuite
NT: Overlapping: Mtwapa (Coastal Kenya), to test different context of viruses. 19 lines, very high resistance 18/19 <5% symptoms #PAGXXII
8:39pm January 13th 2015 via Hootsuite
NT:8 mos later with stake-derived plants (not cultured), very similar results. #PAGXXIII
8:38pm January 13th 2015 via Hootsuite
NT:11 lines had <5% any disease symptoms; correlated with high siRNA expression #PAGXXIII
8:36pm January 13th 2015 via Hootsuite
NT: Every plot surrounded by CBSD-infected plots TME204. Every plant scored for loss (1-5). Photos - wt vs transgenics #PAGXXIII
8:35pm January 13th 2015 via Hootsuite
NT: At 14w post-graft; 5/9 were CBSV and UCBSV-resistant, correlated to high expressors. April 2013 25 transgenic lines planted #PAGXXIII
8:33pm January 13th 2015 via Hootsuite
NT:Developed CBSD res TME204; after 425 transgeneic lines (2011-12), 350 screened for low-copy. 52 met low-copy, VBB-free #PAGXXIII
8:32pm January 13th 2015 via Hootsuite
.@JChrisPires Certainly - I view it as a public duty of sorts, although sometimes very difficult to look up with only a name+year! #PAGXXIII
8:28pm January 13th 2015 via Hootsuite in reply to
NT: Cassava brown streak disease (CBSD), transmitted by white flies (like CMD), leaf mottling, brown lesions on storage roots #PAGXXIII
8:27pm January 13th 2015 via Hootsuite
NT:Provided at no charge from the tech developers; a public-service project. Partners w/KALRI (Kenya), Uganda etc. #PAGXXIII
8:26pm January 13th 2015 via Hootsuite
NT:RNAi-mediated resistance; confined field trials; virology; regulatory; infrastructure and regulatory capacity; comm's #PAGXXIII
8:25pm January 13th 2015 via Hootsuite
NT:VIRCA is a product-dev project: generating preferred cassava varieties to small-holder farmers in Africa #PAGXXIII
8:24pm January 13th 2015 via Hootsuite
Nigel Taylor (Donald Danforth Plant Science MO) "The VIRCA Project" (Virus Resistant Cassava for Africa) #PAGXXIII
8:23pm January 13th 2015 via Hootsuite
MW:Q:What about CMD1? A:If anyone has the paper... can't locate that SSR marker... #PAGXXIII
8:20pm January 13th 2015 via Hootsuite
MW:First GWAS in Cassava - w/rapid progress in determining CM2 location. One new small resistance effect gene located on chr14 #PAGXXIII
8:19pm January 13th 2015 via Hootsuite
MW: 11MB region; co-locates with known SSR markers. Work suggests a third locus (CMD3) #PAGXXIII
8:17pm January 13th 2015 via Hootsuite
MW:15y, 13 locations of phenotype data (38.8K observations), scored on CMD severity. Showed GWAS, major QTL on chr8 #PAGXXIII
8:10pm January 13th 2015 via Hootsuite
MW:6128 clones genotyped & phenotyped; 40K SNPs (MAF >0.05). 2 gen of genomic selection progeny #PAGXXIII
8:07pm January 13th 2015 via Hootsuite
MW:Existing improvements are built on a narrow base (CM2) 2014 Virus Res http://t.co/yS8BLCRp4u #PAGXXIII
8:06pm January 13th 2015 via Hootsuite
MW:Part of NextGen Cassava Project http://t.co/VyXDAQPdsz Describes Cassava Mosaic Disease, progress in dev. CMD resistance #PAGXXIII
8:04pm January 13th 2015 via Hootsuite
Marnin Wolfe (Cornell Univ) "Genome-Wide Association Analyses Reveal Key Aspects of Genetic Architecture Cassava in Africa" #PAGXXIII
8:02pm January 13th 2015 via Hootsuite
RP: Want to use genome editing to target ID'd deleterious muts. Again credits the @gatesfoundation for their support. #PAGXXIII
8:01pm January 13th 2015 via Hootsuite
RP:In progress: RNA-Seq transcriptome assemblies from 6 strains to obtain annotations #PAGXXIII
7:55pm January 13th 2015 via Hootsuite
RT @KATAphone: Link to BayesR software coded by Moser. Input is PLINK! http://t.co/IBQU9xnNfj .Thank you @drhansdd !! #PAGXXIII @Farrell__JD
7:51pm January 13th 2015 via Hootsuite
RP:Obj: ID deleterious mutations, then model it. Generate Cassava hapmap, use annotations. Test against inbred NaCRRI pops #PAGXXIII
7:48pm January 13th 2015 via Hootsuite
RP: Clonally propagated - deleterious muts accumulate. A constant mutational pressure. Est 9 deleterious muts in maize/gen #PAGXXIII
7:46pm January 13th 2015 via Hootsuite
Ramu Punna (Cornell Univ) "Identifying Genetic Load By Whole Genome and Transcriptome Sequencing of Cassava Breeding" #PAGXXIII
7:43pm January 13th 2015 via Hootsuite
EM:Q:What 5 mutagens? A:EMS, MMS, but spectrum may not be wide enough. Thus the need for add'l ones #PAGXXIII
7:42pm January 13th 2015 via Hootsuite
EM: Transgenics only generated for proof-of-concept. Will do large-scale on model variety 60444. Credited @gatesfoundation #PAGXXIII
7:41pm January 13th 2015 via Hootsuite
EM: Have generated ALS kill curves. Chlorsulfuron most effective; flumetsulam and imazapyr about same. Roots most sens. #PAGXXIII
7:39pm January 13th 2015 via Hootsuite
EM:They are optimizing mutagenesis; 5 mutagens tested, 5K plantlets, 2K sent for sequencing. Showed mutant phenotypes #PAGXXIII
7:37pm January 13th 2015 via Hootsuite
EM: KeyGene lots of experience w/seed-based crops. Easy to get seed; cassava is vegetatively propagated. http://t.co/xGylGVfRIT #PAGXXIII
7:35pm January 13th 2015 via Hootsuite
EM:17 unique Nigerian farmer-preferred varieties. 3.5k SNPs via KeyGene GBS. Presented complex ALS gene family #PAGXXIII
7:32pm January 13th 2015 via Hootsuite
EM: Pilot phase, SNP genotype, char ALS gene families for mutation, develop tissue culture protocols, larger scale mut/selection #PAGXXIII
7:30pm January 13th 2015 via Hootsuite
EM:Three other efforts, supported by @gatesfoundation - ALS + glyphosate via CIBUS, also Danforth #PAGXXIII
7:29pm January 13th 2015 via Hootsuite
EM: Aim for ALS-tolerant cassava via random mut, collab between ETH and KeyGene (Netherlands) #PAGXXIII
7:28pm January 13th 2015 via Hootsuite
EM:A social problem as well - women & children perform >90% of hand-weeding. Financial return with herbicide treament >80% #PAGXXI
7:27pm January 13th 2015 via Hootsuite
EM: Weeds are a real problem - photo of a cassava farm in Nigeria. Also Cambodia. Small holders: hand-labor (200-500hr/ha) #PAGXXIII
7:26pm January 13th 2015 via Hootsuite
Emily McCallum (ETH Zürich) Development of Herbicide-Tolerant Cassava Using Random Mutagenesis #PAGXXIII
7:24pm January 13th 2015 via Hootsuite
JB:Q:Evidence of introgression into LatAm? A:Yes, going back to structure data #PAGXXIII
7:22pm January 13th 2015 via Hootsuite
JB: GBS of 288 African cassavas 'reveals cryptic identity, relatedness'. v5.1 genome at http://t.co/BpZ1PGLrgB #PAGXXIII
7:20pm January 13th 2015 via Hootsuite
JB: Tree cassava genomes best explained as M. esculenta w/ varying amts of M. glaziovii introgression #PAGXXIII
7:15pm January 13th 2015 via Hootsuite
JB: Only two cassava chloroplast haplotypes found globally (!) Wang 2014 Nature Comm ref http://t.co/oTMqcq16Ig #PAGXXIII
7:14pm January 13th 2015 via Hootsuite
JB: Cassava genetic diversity: PCA analysis from WGS clusters into 3; background G3 2014 http://t.co/NN1uz5760Z #PAGXXIII
7:12pm January 13th 2015 via Hootsuite
Jesson Bredeson (UC Berkeley CA) Genome Sequence and Genetic Diversity of Cassava and Its Wild Relatives #PAGXXIII
7:10pm January 13th 2015 via Hootsuite
DM:They hope to double insert sizes within the next few months #PAGXXIII
5:48pm January 13th 2015 via Hootsuite
DM:Looked for a single gene, found 117/960. Combined short-read with long mate-pair libraries. #PAGXXIII
5:47pm January 13th 2015 via Hootsuite
DM:'BAC Sudoku Sequencing': a row, column, pool strategy. 10 plates, 12 columns, 8 rows (total 40) #PAGXXIII
5:46pm January 13th 2015 via Hootsuite
DM: Used Blue Pippin from @sagebio and collected longer and longer inserts for human. Was able to get fragments past 100kb #PAGXXIII
5:43pm January 13th 2015 via Hootsuite
David Mead (Lucigen, WI) "100 Kb Long Span Reads and Beyond" #PAGXXIII
5:41pm January 13th 2015 via Hootsuite
