Genomic BLUP with additive mutational effects

International audienc

Estimating Genomic Variance Explained per Chromosome Using Pedigree and Genomic Data in Sheep

We used a half sib data structure for a growth trait in sheep as a potentially powerful design for partitioning the genetic variance across the different chromosomes. Records for post weaning weight were used from 2455 merino sheep. The model of analysis accounted for population structure by fitting genetic group effects as well as the numerator relationship matrix (A) based on pedigree. We then fitted the matrix D representing the difference between the genomic relationship matrix (G) and A. The matrix G was based on 48,599 SNP markers across the entire genome, or on all SNPs of an individual chromosome. There was a relationship between chromosome length (L) and variance explained (Vgi), but we found significant differences in (Vgi/L) between chromosomes

Genetic tests for estimating dairy breed proportion and parentage assignment in East African crossbred cattle

Background:Smallholder dairy farming in much of the developing world is based on the use of crossbred cows that combine local adaptation traits of indigenous breeds with high milk yield potential of exotic dairy breeds. Pedigree recording is rare in such systems which means that it is impossible to make informed breeding decisions. High-density single nucleotide polymorphism (SNP) assays allow accurate estimation of breed composition and parentage assignment but are too expensive for routine application. Our aim was to determine the level of accuracy achieved with low-density SNP assays. Methods:We constructed subsets of 100 to 1500 SNPs from the 735k-SNP Illumina panel by selecting: (a) on high minor allele frequencies (MAF) in a crossbred population; (b) on large differences in allele frequency between ancestral breeds; (c) at random; or (d) with a differential evolution algorithm. These panels were tested on a dataset of 1933 crossbred dairy cattle from Kenya/Uganda and on crossbred populations from Ethiopia (N = 545) and Tanzania (N = 462). Dairy breed proportions were estimated by using the ADMIXTURE program, a regression approach, and SNP-best linear unbiased prediction, and tested against estimates obtained by ADMIXTURE based on the 735k-SNP panel. Performance for parentage assignment was based on opposing homozygotes which were used to calculate the separation value (sv) between true and false assignments. Results: Panels of SNPs based on the largest differences in allele frequency between European dairy breeds and a combined Nelore/N’Dama population gave the best predictions of dairy breed proportion (r2 = 0.962 to 0.994 for 100 to 1500 SNPs) with an average absolute bias of 0.026. Panels of SNPs based on the highest MAF in the crossbred population (Kenya/Uganda) gave the most accurate parentage assignments (sv = −1 to 15 for 100 to 1500 SNPs). Conclusions: Due to the different required properties of SNPs, panels that did well for breed composition did poorly for parentage assignment and vice versa. A combined panel of 400 SNPs was not able to assign parentages correctly, thus we recommend the use of 200 SNPs either for breed proportion prediction or parentage assignment, independently.Bill & Melinda Gates FoundationPeer Revie

Genetic architecture of resistance to virulent ovine-footrot in a case-control study of New Zealand Merino sheep

The genetic architecture of resistance and susceptibility to virulent ovine footrot was studied in a cohort of 3,208 animals from 37 informative flocks of predominant Merino (93%), and Merino Types (Poll Merino, Dohne and South African Meat Merino). Footrot was scored as a binary trait where an animal was scored as affected (1) or unaffected (0, free from footrot), after 2 known challenges. For final analysis, animals from flocks with a prevalence in the range of 30-70% were selected. Animals were genotyped with either a 50K or 15K SNP panel on the Illumina Ovine bead array resulting in combined imputed SNP genotype for 51,713 markers for all animals. The animals were of mixed ages (lambs, yearlings, hoggets and adults), sexes, and breeds. Heritability of footrot was 0.39 ± 0.04 based on a genomic relationship matrix on the underlying scale. Corresponding proportional chromosome heritabilities were in the range of 0.00 ± 0.01 (OAR12) to 0.14 ± 0.04 (OAR23) and compared against expected based on chromosome length. Two markers on OAR23 accounted for a significant component of the additive genetic variance, whilst all residual SNP markers failed to reach statistical significance, despite being located on chromosomes with disproportionate effect on the genetic variance. The polygenic nature of genetic variation in resistance to footrot is discussed