AIP in-house project milestones
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ARS 8042-31000-002-00 milestones

Project title Animal improvement program
("Improving dairy animals by increasing accuracy of genomic prediction, evaluating new traits, and redefining selection goals")
National program (NP) 101 – Food Animal Production
Objective 1 – Expand genomic data used in prediction by selecting new variants that more precisely track the true gene mutations that cause phenotypic differences
NP action plan component 2 — Understanding, improving, and effectively using animal genetic and genomic resources
NP action plan problem statements 2A — Develop bioinformatic and other required capacities for research in genomics and metagenomics
2B — Characterize functional genomic pathways and their interactions
2D — Develop and implement genetic improvement programs using genomic tools
Goal/Hypothesis SY team Months Milestones Products
Hypothesis — Addition of new variants from sequence data will improve reliability of genomic predictions compared with that from single-nucleotide polymorphism markers currently used in genotyping arrays Vacant,
CPV,
PMV
12 Obtain whole genome sequence data for 200 additional Holstein and 50 Jersey bulls New variants in U.S. dairy cattle not already discovered by global researchers
JBC 24 Routinely calculate gene content for nongenotyped cows for known Mendelian traits Peer-reviewed publication; new information for distribution to animal owners
PMV,
Vacant
36 Impute and select new variants from run 6 of the 1000 Bull Genomes Project Revised genotyping arrays with additional variants that more closely track genetic effects
JBC,
Vacant
48 Investigate potential to use edited genes or combine the best chromosomes into one animal by simulation Peer-reviewed publication(s) on simulation study results
Vacant,
PMV
60 Obtain and evaluate whole-genome sequence data for Brown Swiss, Ayrshires, Guernseys, and additional Jerseys Breed-specific variants and improved prediction reliability for all breeds
Objective 2 — Evaluate new traits that can all be predicted at birth from the same inexpensive DNA sample
NP action plan component 1 — Increasing production and production efficiencies while enhancing animal well-being across diverse food animal production systems
2 — Understanding, improving, and effectively using animal genetic and genomic resources
NP action plan problem statements 1A — Improving the efficiency of growth and nutrient utilization
1B — Improving reproductive efficiency
1C — Enhancing animal well-being and reducing stress
2A — Develop bioinformatic and other required capacities for research in genomics and metagenomics
2B — Characterize functional genomic pathways and their interactions
2D — Develop and implement genetic improvement programs using genomic tools
Goal/Hypothesis SY team Months Milestones Products
Goal — Determine if the national increase in economic progress is more valuable than the combined expenses of collecting data and computing genetic evaluations for several individual new traits PMV 12 Evaluate gestation length as new trait Genetic rankings distributed worldwide by the Council on Dairy Cattle Breeding
JBC,
Vacant
24 Incorporate recessive traits into economic indexes Genetic rankings for economic merit which account for Mendelian traits (e.g., polled) for industry use
JBC,
PMV,
Vacant
36 Estimate potential economic values and develop genetic rankings for additional new traits Peer-reviewed publication on economics and genetic rankings of new traits; industry guidance on investment in data collection
48
JBC,
PMV
60 Update net merit formula with new traits and changing prices Improved selection index for industry use
Objective 3 — Improve efficiency of genomic prediction and computation by developing faster algorithms, testing new adjustments and models, and accounting for genomic pre-selection in evaluation
NP action plan component 2 — Understanding, improving, and effectively using animal genetic and genomic resources
NP action plan problem statements 2A — Develop bioinformatic and other required capacities for research in genomics and metagenomics
2B — Characterize functional genomic pathways and their interactions
2D — Develop and implement genetic improvement programs using genomic tools
Goal/Hypothesis SY team Months Milestones Products
Hypothesis — Developing, testing, and implementing new computational methods can improve accuracy with little extra cost or provide the same or similar accuracy with reduced cost PMV,
Vacant
12 Apply new algorithms in Findmap and Findvar software to large-scale cattle sequence data New software to manage rapidly growing data efficiently
JBC,
PMV
24 Evaluate crossbred animals by combining purebred marker effects weighted by breed composition Peer-reviewed publication on genomic evaluation of crossbred cattle; new technology to transfer to Council on Dairy Cattle Breeding
JBC,
Vacant
36 Determine optimal combinations of directly measured and correlated phenotypes for novel traits Peer-reviewed publication
PMV,
Vacant
48 Develop and compare prior information for weighting different types of variants (markers vs. quantitative trait loci) Software; improved genomic evaluations
PMV,
Vacant
60 Test potential bias in trait evaluations caused by genomic preselection of mates, progeny, and herdmates Peer-reviewed publication on genomic evaluation bias caused by preselection; possible revisions in genetic evaluation software


Last Modified: 10/06/2017