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

                        University of Nebraska-Lincoln

Activities Performed

  # Accomplishment/Activity Relevance to Objective

 1 Single nucleotide polymorphism (SNP) data  on 740 US 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 The potential for genomic evaluation of live  weights, fleece weight, fiber diameter, and
 reproductive rate were tested. Alternative  genomic methods were evaluated including
 fitting SNP or haplotypes and using raw  phenotypes or pseudo-phenotypes (deregressed
 breeding values).

        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 US Rambouillet (Objective 1).

 3 To compare US Rambouillet genomically  with other wool-breeds, data were analyzed
 in combination with 10 other populations;  these data included Rambouillet from  Southwest Europe. US Rambouillet data  were also compared to US Suffolk and  Katahdin.

        To fully characterize the extent of genetic  diversity present in US Rambouillet, direct  comparisons with other wool and nonwool  breeds is essential (Objective 2).

 4 The size of the effects of genetic markers  was estimated with several statistical  approaches [single-marker regression,  genomic Best Linear Unbiased Prediction  (GBLUP), single-step GBLUP] using  phenotypes or de-regressed breeding  values for liveweights, yearling fleece
 weight, yearling fiber diameter, and number  of lambs born and reared.

 The sensitivity of identifying significant  genetic markers through Genome-Wide  Association Studies is affected by the  methods employed. By applying several  approaches, results can be compared for  consistency to discover informative SNP  more reliably (Objective 3).

Challenges and Developments

 # Challenge or Development Corrective Action or Project Change

 1 A post-doctoral student at the University of  Nebraska-Lincoln was recruited to assist
 with data analyses.   The student is assisting in identifying  potential genetic markers associated with  the economically important production  traits already identified using single marker  regression.

 2 Given the resources available, a limited  number of US Rambouillet sheep could be
 genotyped. This lowered the potential gains  that could be achieved in accuracy of
 genomic predictions.  Recently, USDA-NIFA has funded a  project (Grant number 2022-67015-36073)  that will allow substantial genotyping in the  Rambouillet and other US breeds.
 Increasing the size of the US Rambouillet  reference population will favorably impact  the accuracy of genomic predictions.

Outcome and Indicator Results to Date

 # Outcome/Indicator Quantifiable Results

Objective 1: to 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.
 Genomic heritabilities were estimated for  the liveweight, fleece and reproductive  traits. They ranged from 0.03 for number  of lambs born to 0.56 for yearling fiber  diameter. The validation accuracies for the  genomic predictions ranged from 0.16 for  number of lambs weaned to 0.31 for  yearling fiber diameter; these were less  than corresponding theoretical accuracies.

 Objective 2: to characterize the genetic of  genetic diversity.

 The population structure within the US  Rambouillet samples appears to be  primarily driven by samples from one flock.  Diversity (expected heterozygosity) of the  US Rambouillet was greater than that of  other US breeds (Katahdin, Suffolk), but  among the lowest (0.401) of the 11
 populations of wool breeds considered  although like that in European Rambouillet  (0.414).

 Objective 2: to characterize the genetic of  genetic diversity.

 Although the US Rambouillet was  genomically most like the European  Rambouillet, based on the pairwise fixation  index (FST), significant divergence between  these populations was detected (FST <  0.01). US Rambouillet were less inbred  than the Katahdin and Suffolk (average F  = 0.099, 0.110, and 0.132, respectively),  although with similar levels of inbreeding
 as the European Rambouillet.
 Objective 3: to identify genetic markers  associated with performance.

 Using single-marker regression, GBLUP  and single-step GBLUP, the size of SNP  effects for birth, post-weaning, and  yearling weight, yearling fleece weight and  fiber diameter, and  umber of lambs born  and reared were obtained. Depending on  the analytical approach used, a few
 significant genetic markers were identified  for these traits based on chromosomewide  testing. Further validation of these  presumptive markers is underway.

 Upcoming Activities

 1 - Investigations of the population structure in US Rambouillet sheep  continue (Objective 2).
 Their focus will include cluster analyses to  demonstrate if the US population contains significantly divergent  groups. Additional analyses of diversity to quantify runs of
 homozygosity across the genome also will be conducted.     12/31/2021

 2 -  Using the estimates of SNP effects obtained from the various  approaches for GWAS, the consistency of results will be assessed to  identify, if present, candidates for genetic markers for various  economically important traits in Rambouillet (Objective 3).      12/31/2021

 3 Project reporting will be completed, including an industry article and the  draft of at least one scientific article co-authored by the project team.        12/31/2021