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Research Project: National Animal Germplasm Program

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Title: Development and validation of a low-density SNP panel related to prolificacy in sheep

Author
item LACERDA, THAISA - University Of Brasilia
item Blackburn, Harvey
item YAMAGISHI, MICHEL - Embrapa
item MCMANUS, CONCEPTA - University Of Brasilia
item CAETANO, ALEXANDRE - Embrapa
item PAIVA, SAMULE - Embrapa

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 7/12/2015
Publication Date: 7/12/2015
Citation: Lacerda, T., Blackburn, H.D., Yamagishi, M., Mcmanus, C., Caetano, A., Paiva, S. 2015. Development and validation of a low-density SNP panel related to prolificacy in sheep. Meeting Abstract. ADSA-ASAS Joint Annual Meeting Orlando, FL July 12-16, 2015.

Interpretive Summary:

Technical Abstract: High-density SNP panels (e.g., 50,000 and 600,000 markers) have been used in exploratory population genetic studies with commercial and minor breeds of sheep. However, routine genetic diversity evaluations of large numbers of samples with large panels are in general cost-prohibitive for gene banks. Lower cost panels based mostly on SNPs known to be associated with production traits of interest may be a more efficient tool for genetic diversity assessment and improvement of regional gene bank collections. For this first phase of the study, we developed and validated a small SNP panel (29 SNPs) based on known prolificacy genes to test this hypothesis. SNP selection was based on known polymorphisms in major genes affecting sheep prolificacy (GDF9, BMP15 and BMPR1B), as well as new polymorphisms mined from whole genome resequencing data from GDF9 and BMP15 from the International Sheep Genome Consortium. A total of 125 animals from 15 breeds with litter size information collected by the National Animal Germplasm Program were tested. Genotyping was performed with PCR-based KASP chemistry and 27 SNPs had a call rate higher than 98%. Eight SNPs were polymorphic - three are located in introns and five in exons and three of these results in non-synonymous AA changes. No significant allele frequency differences were observed for GDF9_G4:E241K in animals originated from single or multiple parturition litters. The GDF9_G6:V332I allele was related to high prolificacy and was observed in animals that came from multiple births in five breeds with the following frequencies: Lincoln (0.416, N=8), Polypay (0.32, N=17), Navajo Churro (0.27, N=17), St Croix (0.125, N=8) and Suffolk (0.083, N=17). Allele GDF9_G7:V371M was found only in Polypay at a frequency of 0.35 which agrees with recent studies with the hyperprolific phenotype of Norwegian White Sheep. Our results suggest that the developed panel will be useful to identify possible genes/mutations associated with prolificacy in worldwide sheep breeds. Additional SNPs will be included as more information becomes available. In the next phase of this study, SNPs related to other economic important traits will be added to the panel in order to improve the characterization and management of gene banks.