Projects (incomplete list)

Joint analysis of phenotypic, pedigree and genomic data

We focused on single-step genomic evaluation. It is BLUP, where the numerator relationship matrix A is replaced by matrix H that combines pedigree and genomic relationships; a lead paper by Aguilar et al. (2010) was chosen as 2013 most cited paper in Genetics and Breeding. The end result of single-step is dramatic simplification of evaluation procedures combined with superior accuracy, ability to use any model and speed similar to that of BLUP. Single-step is already applied for routine evaluation by major genetics companies across species.

 

Last problem in ssGBLUP was difficulty in inversion of G with a large number of genotyped animals; over 1 million Holsteins are genotyped. We came with a surprising algorithm called APY that makes getting the inverse child-play for millions of animals simple, with a higher accuracy than a regular inverse (that BTW does not exist). Read papers by myself et al., Fragomeni et al. Masuda et al. on this exciting discovery. Results of APY put a new thinking on limits of genetic selection and on GWAS, with potential for many exciting papers. Also see a new editorial for JABG.

 

Efficient yet simple animal-breeding programming in Fortran 90
Use of object-oriented and matrix operations in  Fortran 90/95/2000  can lead to programs that are almost as simple as in a matrix language but much more efficient. Read a paper titled: Complex models, larger data, simpler computing? This project has resulted in a large number of application programs. Why not C/C++/Java? We focus on algorithms That can be programmed in any language. For numerical computations, Fortran seems to be the most efficient yet reasonably simple.

Climate change and heat stress in dairy cattle and pigs
Whenever there is a heat stress, for example in Southeastern USA, some animals perform satisfactorily but some perform poorly. We developed a methodology to study genetics of heat tolerance using easily available weather records. This project has been described briefly in a UGA extension letter. Our studies indicate that continued selection for performance in moderate climates makes cow less heat tolerant for production and particularly reproduction. Analyzes of US national data for Holsteins indicated negative trends for heat tolerance. Models from dairy are adopted in pigs for growth and for fertility.

Better modeling of competitive/associative effects

Total production of animals in a pen, like pigs or chicken, depends not only on individual performance but on dynamics of interactions among the animals. Selection of animals for individual performance may have produced aggressive animals that do not function well in groups, causing reduced growth, injuries and even deaths. Current models based on original work in trees seem to produce ambivalent results. We are trying to find better models based on behavior of specific species.


These and other projects can benefit from your collaboration. If you are looking for a graduate school or a place for a sabbatical, please consider the University of Georgia.

last updated  February 15,2015