A foundation for genomics: building a repository of genotypes in Rambouillet sheep

 

 

Performance Narrative:

Activities Performed

Accomplishments

Estimate the Total Percentage (%) of work Completed on the Project: 100.0% # Accomplishment/Activity Relevance to Objective
1 To establish a genomic dataset, single nucleotide polymorphisms (SNP) on 740 U.S. Rambouillet sheep (676 from the current and 64 from a previous project) were remapped to the most recent ovine reference genome (ARS-UI_Ramb_v2.0) with 32,693 common markers retained. Correctly and consistently associating SNP with the reference genome is essential for establishing a robust genomic database, and for their use to associate prospective genetic markers with performance (Objectives 1 & 3).
2 To determine the potential for genomic evaluation in U.S. Rambouillet sheep, the utility of genomic prediction was evaluated based on using SNP or haplotypes under a single-step genomic Best Linear Unbiased Prediction (GBLUP) approach. The traits considered were birth, post-weaning and yearling body weights, yearling fleece weight and fiber diameter, and number of lambs born. Given the number of animals genotyped, accurate genomic prediction is not possible with these data. However, comparing possible approaches for genomic prediction is an important precursor to applying this methodology given anticipated additional genotyping within the U.S. Rambouillet breed (Objective 1).
3 To characterize the extent of genetic diversity in U.S. Rambouillet as compared to other breeds, genomic data were analyzed in combination with 10 other populations; these data included Rambouillet from Southwestern Europe. U.S. Rambouillet data were also compared to U.S. Suffolk and Katahdin. To fully characterize the extent of genetic diversity present in U.S. Rambouillet, direct comparisons with other wool and non-wool breeds is essential (Objective 2).
4 The size of the effects of genetic markers were estimated with several statistical approaches [single-marker regression, GBLUP), and single-step GBLUP] using phenotypes or de-regressed breeding values for body weight, wool, and reproductive (number lambs born and reared) traits. The sensitivity of identifying significant genetic markers through Genome-Wide Association Studies (GWAS) is affected by the methods employed. By applying several approaches, results can be compared for consistency to discover, if present, informative SNP more reliably (Objective 3).
1 Objective 1: Build an industry resource of genotypes. DNA samples on 676 animals were genotyped using the GeneSeek Genomic Profiler (GGP) Ovine 50K array, and the resulting data edited for quality control. These data have been added to the genomic database in U.S. sheep in coordination with NSIP.

Beginning Jan. 1, 2022, a project funded through USDA-NIFA (Grant number 2022-67015-36073) will support substantially more genotyping in the Rambouillet and other U.S. breeds. When combined with the genotypes generated from this project, a sufficiently large reference population will be established in U.S. Rambouillet (> 3,000 animals both with genomic and performance information) to allow genomic prediction to be introduced to the genetic evaluation in this breed through NSIP.

2 Objective 1: Build an industry resource of genotypes. The feasibility of genomic predictions of breeding values for body weight, wool, and reproductive traits in U.S. Rambouillet sheep was investigated using SNP and haplotype information under a single-step GBLUP approach. Predictions of estimated breeding values were compared with those obtained from traditional pedigree-based evaluations. The accuracies were higher or smaller when including the genomic information, but there was little difference in bias of the predictions. More animals with both genomic and performance data are needed to test the potential of genomic prediction more fully in this breed.
3 Objective 2: Characterize the extent of genetic diversity. Genetic diversity (expected heterozygosity) of the U.S. Rambouillet was greater than that of other U.S. breeds (Katahdin, Suffolk). The U.S. Rambouillet also were less inbred than the Katahdin and Suffolk sheep considered (average F = 0.099, 0.110, and 0.132, respectively)
4 Objective 2: Characterize the extent of genetic diversity. Genetic diversity (expected heterozygosity) of the U.S. Rambouillet was among the lowest (0.402) of the 11 populations of wool breeds considered, although most like that in Southwestern European Rambouillet (0.411).

The similarity in population structures between the U.S. and Southwestern European Rambouillet is shown in Figure 1, illustrating the shared genetic diversity between these two populations. One U.S. flock drove the stratification observed within the U.S. Rambouillet population (cluster of points on the right-hand side of Figure 1).

Despite their overlapping population structures, based on the pairwise fixation index (FST), significant divergence between the U.S. and Southwestern European population was detected (FST = 0.014). The U.S. Rambouillet were also more inbred than the other fine wool breeds evaluated

5 Objective 3: Identify genetic markers associated with performance. Using single-marker regression, GBLUP and single-step GBLUP approaches, the size of SNP effects on weight, wool, and reproductive traits were evaluated. Depending on the analytical approach used, a few significant genetic markers (SNP) were identified based on chromosome-wide testing. However, each significant SNP defined only a small amount of genetic variation for a trait, with little overlap of the SNP identified across analytical approaches. No clear genetic markers for these traits were detected.
6 All objectives Two publications were prepared from the project. The first was an industry report for the American Rambouillet Sheep Breeders Association and the Finewool Breeders Consortium; it described the full results of the project, and their potential importance to Rambouillet breeders. The second publication was a journal article considering the methods investigated for genomic prediction for body weight, wool, and reproductive traits. Shortly, it will be submitted to the Journal of Animal Breeding and Genetics.