Genomic Resources and Gene/QTL Discovery in Livestock
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1 Genomic Resources and Gene/QTL Discovery in Livestock Jerry Taylor University of Missouri FAO Intl Tech Conf on Agric Biotech in Dev Count, Guadalajara, March 2 nd 2010
2 5/7/ Outline Available Genomic Tools Next generation sequencers High throughput SNP genotyping Arrays Available Populations Prospects for QTL Discovery Or why we need Genomic Selection!!
3 5/7/ Next-Gen Sequencers Rapidly Evolving MU GAIIx (v4.0 chemistry & v1.4 base calling) yields 2.8 Gb/lane New platforms with enhanced capabilities Cost/Mb is decreasing Numerous Applications RNAseq Genome resequencing De novo assembly Mutation discovery ChIPseq Small non-coding RNAs DNA methylation (esp. Pac Biosciences) Democratizing Genomics! Developing countries and small labs can be genome centers!!!
4 5/7/ MU DNA Core Service Costs Library Preparation USD Genome Sequencing Sample Preparation* (Paired-End Adapters) $225 Digital Gene Expression (DGE)- small RNA Sample Preparation $445 cdna Sample Preparation* $225 ChIP-Seq Sample Preparation* $225 mrna-seq Sample Preparation** $500 Analysis USD Raw Data Output/Flow Cell (Gb) Single Read (42 bases) $828.57/lane ($5,800/Flow Cell) 5-6Gb Single Read (84 bases) $1,414.29/lane ($9,900/Flow Cell) 11-12Gb Paired-End Read (2x42 bases) $1,657.14/lane ($11,600/Flow Cell) 11-12Gb Paired-End Read (2x84 bases) $ /lane ($15,100/Flow Cell) 22-23Gb $3000 for 1X mammalian genome sequence coverage!!!
5 RNASeq pileup over VIPR1 5/7/
6 5/7/ Public Genomic Resources Whole genome sequence on African, Asian, European cattle breeds will soon be publicly available Whole genome sequencing of 120 animals from 12 breeds Genome Coverage Average Read Length Unfiltered SNPs Library GAIIx Lanes Post Filter Reads Total Bases (2.685 Gb = 1X) (bp) and Indels Brahman (10) ,962,867 23,485,537, ,901,328 East Hanwoo Asian (15) ,458,572 35,220,941, ,662,313 Angus (3) ,918,406 67,112,512, ,797,621 AN ,024,359 23,565,486, AN ,562,373 22,621,184, AN ,331,674 20,925,841, All libraries 106 1,711,339, ,818,991,
7 5/7/ Advantages/Disadvantages Advantages Relatively inexpensive and fast Enormous information content Species independent technology Will make redundant many other forms of technology Microarrays Genotyping Disadvantages Suites of analysis tools only just becoming available Require major compute horsepower (~$40K Servers) Analysis is non-trivial requires training/experience
8 5/7/ First generation assays (~50K SNPs) available for Chicken, Pig, Sheep, Cow, Horse, Dog Under development for salmon, tilapia, catfish Second generation assays (~800K SNPs) available summer 2010 Utility: Genome-wide association mapping (GWAS) Genomic Selection High-Throughput SNP Chips Population genetics/conservation biology
9 5/7/ Advantages/Disadvantages Advantages Rapid data generation Highly accurate and complete data Work across species (30 MY evolution) Relatively inexpensive (research) Rapid research to commercialization for GS Data analysis very similar to BLUP genetic evaluation Service providers available (e.g., GeneSeek) Available in 96, 384, 1536, 3072, 50K, 800K Disadvantages Relatively expensive (commercialization) Available analysis tools (e.g., PLINK, ASREML) Contain common variants (SNP ascertained)
10 5/7/
11 5/7/ Arrays Genome-wide oligo microarrays available for chicken, cattle, sheep, pigs Availably commercially (Agilent, Illumina, Affymetrix) or through species consortia (BOM: bovineoligo.org; SPAM: pigoligoarray.org) CNV, Sequence Capture (e.g., exon, target regions), CpG arrays by custom design (e.g., Nimblegen, Agilent)
12 5/7/ Gene Expression Microarrays Advantages Relatively inexpensive ($55 per array + RNA extraction and labeling kits etc = ~$250 per sample) but require replication!!!!! Analysis tools readily available (e.g., R open source) Available for many species Disadvantages Nontrivial chemistry Non exhaustive (not all genes are queried) Probes only for one exon (alternate splicing, promoter and 3 UTR utilization missed) Not available for all species All Arrays NextGen sequencing will make most arrays redundant
13 5/7/ Available Populations The greatest limitation to all genomic technologies previous and imminent is that we do not have populations of animals with high-quality DNA, tissue samples and phenotypes... In the US The only population with adequate numbers of animals to build accurate GS prediction models is Holsteins Angus 2,700 AI bulls with EPDs Angus 3,500 steers with growth and carcass composition Angus 700 steers with feed intake Limousin 2,200 registered males and females with EPDs Angus (660), Limousin (285), Charolais (702), Hereford (1192), Simmental (521) with meat tenderness Worldwide priority is assembly of populations and phenotypes
14 5/7/ Too Many Genes for MAS!!!
15 5/7/ Use Experimental Populations to Produce EBVs for an Entire Breed Warner Bratzler Shear Force in Angus Calpastatin Calpain
16 5/7/ Genomic Selection!
17 5/7/ Genomic Selection with Reduced SNP Sets
18 The End 5/7/
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