11th WCGALP (2018) Summary

The premier event for researchers and professionals involved in the genetic improvement of livestock

Over 10 Gentec members attended this important conference. Gentec CEO Dr Graham Plastow chaired the fantastic session on gene editing which is a hot topic in livestock genomics in recent years. Over five days, workshops updated the genomics progress in both research and application in livestock, which significantly renewed my knowledge in genomics. The one-day field trip (sheep/deer farm) gave me a better understanding about animal breeding and production in New Zealand. The excellent conference program and social activities did wonders for my professional networking with people from academia and industry.

For me, the most attractive session was the genomics methods and tools program which spread over all five days. Powerful statistical methodology and tools have been well developed and improved in recent years, driven by the rapid increase number of phenotypes and genotypes. Single step GBLUP (SSGBLUP) is considered the most popular one in practical breeding since it can handle large pedigree, genotypes and various types of phenotypes simultaneously. SSGBLUP + APY (algorithm-proven young for easier G inversion) is widely used in the US to evaluate beef cattle and by pig-breeding companies (e.g. Topigs Norsvin and Genesus Inc.). However, SSGBLUP still needs to improve minor issues, such as the weighting of SNPs.

Another valuable session was on how to improve genomic prediction accuracy especially with whole genome sequence data, which has been a main research topic in Gentec under several projects in cattle and pigs in collaboration with our industry partners. According to a discussion with Drs Mike Goddard and Ben Hayes, they both thought that, theoretically, by adding the TOP SNPs selected from whole sequence, the accuracy of GEBV should be better or at least remain the same.

As many reports in the conference demonstrated, results from practice data are not always consistent. We faced a similar situation as described in the paper we published recently (Genomic evaluation of feed efficiency component traits in Duroc pigs using 80K, 650K and whole-genome sequence variants). We all agreed that possible solutions include increasing the number of training animals especially including the target breed, increasing the number of SNPs especially the causal ones, using Bayesian methods (e.g. BayesRC) and multi-omic data (gene expression and annotations).

Another interesting area was genomic studies in pigs. Several presentations talked about GWAS and/or genomic prediction for economically important traits in pigs we have studied widely at Gentec. Their results were quite comparable with ours. For example, important QTL were reported for the number of stillborn (SSC9) and the number of born alive (SSC2, 5, 9, 14). Many putative lethal haplotypes associated with sow fertility were detected, and the region on SSC14 was also detected in our Duroc pigs. There were also a few talks in hot-topic areas such as novel predictors or selection criteria for pig growth, pork quality and reproduction, such as hemoglobin levels and gut microbiome. We have investigated these topics in recent projects to improve resilience to disease through genomics.

Posted in Academic.