Wattles in goats are associated with the<i><scp>FMN</scp>1</i>/<i><scp>GREM</scp>1</i>region on chromosome 10

We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (F ) with pedigree-based inbreeding coefficients (F ). The linear relationship between F and F was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). F appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

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“…; Reber et al . ), 473 animals from the 10 Swiss goat breeds were genotyped for the caprine 50k Illumina BeadChip. plink v1.07 (Purcell et al .…”

Section: Methodsmentioning

confidence: 99%

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

et al. 2016

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“…The availability of the genomic sequence in goats (Dong et al, 2013) has opened up new fields of investigation to better understand and select for traits of interest in this species. The development of a high-density SNP array (Tosser-Klopp et al, 2014) and its application in genome-wide association studies has facilitated the identification of regions that control caprine traits such as polledness (Kijas et al, 2013), wattle (Reber et al, 2015), coat color (Martin et al, 2016b), supernumerary teats (Martin et al, 2016a), and milk production (Martin et al, 2017). However, very little is known about the loci controlling type traits and lactation SCS (LSCS) in this species.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association mapping for type and mammary health traits in French dairy goats identifies a pleiotropic region on chromosome 19 in the Saanen breed

Martin

Palhière

Maroteau

et al. 2018

Journal of Dairy Science

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Type traits and mammary health traits are important to dairy ruminant breeding because they influence animal health, milking ability, and longevity, as well as the economic sustainability of farms. The availability of the genomic sequence and a single nucleotide polymorphism chip in goats has opened up new fields of investigation to better understand the genes and mechanisms that underlie such complex traits and to be able to select them. Our objective was to perform a genome-wide association study in dairy goats for 11 type traits and somatic cell count (SCC) as proxies for mastitis resistance. A genome-wide association study was implemented using a daughter design composed of 1,941 Alpine and Saanen goats sired by 20 artificial insemination bucks, genotyped with the Illumina GoatSNP50 BeadChip (Illumina Inc., San Diego, CA). This association study was based on both linkage analyses and linkage disequilibrium using QTLmap software (http://dga7.jouy.inra.fr/qtlmap/) interval mapping was performed with the likelihood ratio test using linear regressions. Breeds were analyzed together and separately. The study highlighted 37 chromosome-wide significant quantitative trait loci (QTL) with linkage analyses and 222 genome-wide significant QTL for linkage disequilibrium, for type and SCC traits in dairy goats. Genomic control of those traits was mostly polygenic and breed-specific, suggesting that within-breed selection would be favored for those traits. Of note, Capra hircus autosome (CHI) 19 appeared to be highly enriched in single nucleotide polymorphisms associated with type and SCC, with 2 highly significant regions in the Saanen breed. One region (33-42 Mb) was significantly associated with SCC and includes candidate genes associated with response to intramammary infections (RARA, STAT3, STAT5A, and STAT5B). Another region of the CHI 19 (24.5-27 Mb) exhibited an adverse pleiotropic effect on milk production (milk, fat yield, and protein yield) and udder traits (udder floor position and rear udder attachment) that agreed with the negative genetic correlations that exist between those 2 groups of traits. These QTL were not found in the Alpine breed. In Alpine, the 2 most significant regions were associated with chest depth on CHI 6 (45.8-46.0 Mb) and CHI 8 (80.7-81.1 Mb). These results will be helpful for goat selection in the future and could lead to identification of causal mutations.

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“…With the availability of the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA;Tosser-Klopp et al, 2012, 2014, it is now possible to perform genome-wide scans in goats Genome-wide association study of conformation and milk yield in mixed-breed dairy goats with much greater resolution. To date, the chip has been utilized to find QTL associated with milk and type traits (Maroteau et al, 2013;Martin et al, 2017), polledness (Kijas et al, 2013), milking speed (Palhière et al, 2014), coat color (Becker et al, 2015;Martin et al, 2016a), wattles (Reber et al, 2015), and supernumerary teats (Martin et al, 2016b). In addition, due to the application of sequencing and whole-genome optical mapping, information on gene annotation for goats has become available (Dong et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Mucha

Mrode

Coffey

et al. 2018

Journal of Dairy Science

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Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [-log(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (-log(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.

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Wattles in goats are associated with theFMN1/GREM1region on chromosome 10

Cited by 23 publications

References 25 publications

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

Genetic diversity analyses reveal first insights into breed‐specific selection signatures within Swiss goat breeds

Genome-wide association mapping for type and mammary health traits in French dairy goats identifies a pleiotropic region on chromosome 19 in the Saanen breed

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

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