SNP Discovery and Genomic Architecture of Highly Inbred Leghorn and Fayoumi Chicken Breeds Using Whole Genome Resequencing

Advances in the use of next generation sequencing (NGS) and ability to pool individuals into groups that represent distinct livestock populations has made it possible to examine trait differences between breeds of chicken. The breeds examined are very divergent when compared on their history of laying ability and immune response. The long-term objective is to understand the genetic differences between the Leghorn and Fayoumi breeds for use in developing more productive and disease resistant chickens. Statistical testing of the sequence of the two breeds along with Gene set enrichment analysis (GSEA) to make connections between the genetic variation seen in the NGS data and the breed specific traits of egg laying and heightened immune response can be used to characterize these two breeds. Genetic terms having the highest level of differentiation between the lines appear to group into metabolic processes, with terms over-enriched for immune system process, sexual reproduction, and growth for variants examined between lines. Terms for functions within the Fayoumi and Leghorn populations aligned to immune function and reproductive function, respectively. These results are consistent with known breed phenotypes and provide a means to focus on specific DNA variations and the birds’ genetic diversity that are potentially of more commercial importance

Characterizing Haplotype Diversity in Ten US Beef Cattle Breeds

The distributions of haplotype diversity across the whole genome among 10 US beef cattle breeds were constructed. In most chromosomes for all the breeds, consistent low haplotype diversity were observed in some specific regions, 55% of which was found to match the positions of reported gene duplications. Further work is required to determine whether the low haplotype diversity is real, or a result of problems in sequencing which have limited our ability to identify informative markers in those regions. Haplotype diversity will be the subject of ongoing work to identify haplotypes that are under-represented as homozygotes, to fine-map regions with major gene effects, and to fit haplotype rather than SNP models for genomic prediction

A Limousin Specific Myostatin Allele Affects Longissimus Muscle Area and Fatty Acid Profiles in a Wagyu-Limousin F2 Population

A microsatellite-based genome scan of a Wagyu x Limousin F(2) cross population previously demonstrated QTL affecting LM area and fatty acid composition were present in regions near the centromere of BTA2. In this study, we used 70 SNP markers to examine the centromeric 24 megabases (Mb) of BTA2, including the Limousin-specific F94L myostatin allele (AB076403.1; 415C \u3e A) located at approximately 6 Mb on the draft genome sequence of BTA2. A significant effect of the F94L marker was observed (F = 60.17) for LM area, which indicated that myostatin is most likely responsible for the effect. This is consistent with previous reports that the substitution of Leu for Phe at AA 94 of myostatin (caused by the 415C \u3e A transversion) is associated with increased muscle growth. Surprisingly, several fatty acid trait QTL, which affected the amount of unsaturated fats, also mapped to or very near the myostatin marker, including the ratio of C16:1 MUFA to C16:0 saturated fat (F = 16.72), C18:1 to C18:0 (F = 18.88), and total content of MUFA (F = 17.12). In addition, QTL for extent of marbling (F = 14.73) approached significance (P = 0.05), and CLA concentration (F = 9.22) was marginally significant (P = 0.18). We also observed associations of SNP located at 16.3 Mb with KPH (F = 15.00) and for the amount of SFA (F = 12.01). These results provide insight into genetic differences between the Wagyu and Limousin breeds and may lead to a better tasting and healthier product for consumers through improved selection for lipid content of beef

Comparison of variant calling methods for whole genome sequencing data in dairy cattle

Accurate identification of SNPs from next-generation sequencing data is crucial for high-quality downstream analysis. Whole genome sequence data of 65 key ancestors of genotyped Swiss dairy populations were available for investigation (24 billion reads, 96.8% mapped to UMD31, 12x coverage). Four publically available variant calling programmes were assessed and different levels of pre-calling handling for each method were tested and compared. SNP concordance was examined with Illumina’s BovineHD Genotyping BeadChip®. Depending on variant calling software used, between 16,894,054 and 22,048,382 SNP were identified (multi-sample calling). A total of 14,644,310 SNP were identified by all four variant callers (multi-sample calling). InDel counts ranged from 1,997,791 to 2,857,754; 1,708,649 InDels were identified by all four variant callers. A minimum of pre-calling data handling resulted in the highest non-reference sensitivity and the lowest non-reference discrepancy rates