Correction: Design and Characterization of a 52K SNP Chip for Goats

Tosser‐Klopp, Gwenola; Bardou, Philippe; Bouchez, Olivier; Cabau, Cédric; Crooijmans, R.P.M.A.; Dong, Yang; Donnadieu-Tonon, Cécile; Eggen, Andre A.; Heuven, H.C.M.; Jamli, Saadiah; Jiken, Abdullah Johari; Klopp, Christophe; Lawley, Cynthia T.; McEwan, John C.; Martin, Patrice; Moréno, Carole; Mulsant, Philippe; Nabihoudine, Ibouniyamine; Pailhoux, Eric; Palhière, Isabelle; Rupp, Rachel; Sarry, Julien; Sayre, Brian; Tircazes, Aurélie; Wang, Jun; Wang, Wen; Zhang, Wenguang

doi:10.1371/journal.pone.0152632

Cited by 13 publications

(7 citation statements)

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“…This indicated that Chinese goat breeds had lower genetic variation than global goat breeds. However, we cannot rule out ascertainment bias caused by sample size and the Illumina GoatSNP50 BeadChip ( Tosser-Klopp et al, 2016 ) designed using a non-Chinese goat background. The SNP panel used in this study was developed based on the sequence data of diverse goat breeds, including Alpine, Boer, Creole, Katjang, Saanen, and Savanna goats ( Tosser-Klopp et al, 2016 ), which reduced the SNP ascertainment bias to a certain extent.…”

Section: Discussionmentioning

confidence: 99%

“…However, we cannot rule out ascertainment bias caused by sample size and the Illumina GoatSNP50 BeadChip ( Tosser-Klopp et al, 2016 ) designed using a non-Chinese goat background. The SNP panel used in this study was developed based on the sequence data of diverse goat breeds, including Alpine, Boer, Creole, Katjang, Saanen, and Savanna goats ( Tosser-Klopp et al, 2016 ), which reduced the SNP ascertainment bias to a certain extent. Focusing on Jiangxi goat breeds, the current Guangfeng population had lower values of F ROH and F HOM than the Ganxi population and previous Guangfeng population.…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Tang

Huang

et al. 2022

Front. Genet.

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Runs of homozygosity (ROH) and heterozygosity (ROHet) are windows into population demographic history and adaptive evolution. Numerous studies have shown that deleterious mutations are enriched in the ROH of humans, pigs, cattle, and chickens. However, the relationship of deleterious variants to ROH and the pattern of ROHet in goats have been largely understudied. Here, 240 Guangfeng and Ganxi goats from Jiangxi Province, China, were genotyped using the Illumina GoatSNP50 BeadChip and genome-wide ROH, ROHet, and genetic load analyses were performed in the context of 32 global goat breeds. The classes with the highest percentage of ROH and ROHet were 0.5–2 Mb and 0.5–1 Mb, respectively. The results of inbreeding coefficients (based on SNP and ROH) and ROHet measurements showed that Guangfeng goats had higher genetic variability than most Chinese goats, while Ganxi goats had a high degree of inbreeding, even exceeding that of commercial goat breeds. Next, the predicted damaging homozygotes were more enriched in long ROHs, especially in Guangfeng goats. Therefore, we suggest that information on damaging alleles should also be incorporated into the design of breeding and conservation programs. A list of genes related to fecundity, growth, and environmental adaptation were identified in the ROH hotspots of two Jiangxi goats. A sense-related ROH hotspot (chromosome 12: 50.55–50.81 Mb) was shared across global goat breeds and may have undergone selection prior to goat domestication. Furthermore, an identical ROHet hotspot (chromosome 1: 132.21–132.54 Mb) containing two genes associated with embryonic development (STAG1 and PCCB) was detected in domestic goat breeds worldwide. Tajima’s D and BetaScan2 statistics indicated that this region may be caused by long-term balancing selection. These findings not only provide guidance for the design of conservation strategies for Jiangxi goat breeds but also enrich our understanding of the adaptive evolution of goats.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Tang

Huang

et al. 2022

Front. Genet.

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“…The PCR amplification steps, PCR reaction concentrations, and PCR programs, including the sequencing technology, were carried out as described in Tarekegn et al [20]. For analysis of autosomal marker-based variation, 324 animals representing all four populations of Cameroon indigenous goats (Central Highland: n = 94; North-west Highland: n = 166; Forest goat: n = 31, and Djallonke: n = 33) were genotyped using the Caprine 50K SNP chip panel [34]. For comparison, we included genotype data from six Ethiopian indigenous goat populations (Ambo: n = 119; Afar: n = 49; Keffa: n = 51; Gumez: n = 42; Long-eared Somali: n = 48; Nubian: n = 47), representing East Africa; Egyptian Barki goat (n = 52) and Moroccan goat (n = 30), representing north Africa; one population from Iran (n = 9), and Cashmere goat (n = 108) from China.…”

Section: Methodsmentioning

confidence: 99%

“…All the four Cameroon goat populations analyzed and the 10 reference populations were genotyped using the caprine 50K SNP BeadChip array (Illumina Inc., San Diego, CA) [34]. Autosomal SNPs were filtered for call rate by sample and marker ≥ 90% and minor allele frequency (MAF) ≥ 5%.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

et al. 2019

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Indigenous goats make significant contributions to Cameroon’s national and local economy, but little effort has been devoted to identifying the populations. Here, we assessed the genetic diversity and demographic dynamics of Cameroon goat populations using mitochondrial DNA (two populations) and autosomal markers (four populations) generated with the Caprine 50K SNP chip. To infer genetic relationships at continental and global level, genotype data on six goat populations from Ethiopia and one population each from Egypt, Morocco, Iran, and China were included in the analysis. The mtDNA analysis revealed 83 haplotypes, all belonging to haplogroup A, in Cameroon goats. Four haplotypes were shared between goats found in Cameroon, Mozambique, Namibia, Zimbabwe, Kenya, and Ethiopia. Analysis of autosomal SNPs in Cameroon goats revealed the lowest H O (0.335±0.13) and H E (0.352±0.15) in the North-west Highland and Central Highland populations, respectively. Overall, the highest H O (0.401±0.12) and H E (0.422±0.12) were found for Barki and Iranian goats, respectively. Barki goats had the highest average MAF, while Central Highland Cameroon goats had the lowest. Overall, Cameroon goats demonstrated high F IS . AMOVA revealed that 13.29% of the variation was explained by genetic differences between the six population groups. Low average F ST (0.01) suggests intermixing among Cameroon goats. All measures indicated that Cameroon goats are closer to Moroccan goats than to other goat populations. PCA and STRUCTURE analyses poorly differentiated the Cameroon goats, as did genetic distance, Neighbor-Net network, and neighbor-joining tree analyses. The haplotype analysis of mtDNA showed the initial dispersion of goats to Cameroon and central Africa from north-east Africa following the Nile Delta. Whereas, the approximate Bayesian computation indicated Cameroon goats were separated from Moroccan goats after 506 generations in later times (~1518 YA), as supported by the phylogenetic net-work and admixture outputs. Overall, indigenous goats in Cameroon show weak phylogenetic structure, suggesting either extensive intermixing.

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“…In dairy cattle and sheep, this method has proved more efficient than direct imputation from lowest density to sequence [2,3]. In goats, the only genotyping tool available is a 50 k-chip (Illumina GoatSNP50 BeadChip) [4]. This means that imputation must be carried out directly from 50 k to sequence level.…”

Section: Introductionmentioning

confidence: 99%

Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats

et al. 2020

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Background: Goats were domesticated 10,500 years ago to supply humans with useful resources. Since then, specialized breeds that are adapted to their local environment have been developed and display specific genetic profiles. The VarGoats project is a 1000 genomes resequencing program designed to cover the genetic diversity of the Capra genus. In this study, our main objective was to assess the use of sequence data to detect genomic regions associated with traits of interest in French Alpine and Saanen breeds. Results: Direct imputation from the GoatSNP50 BeadChip genotypes to sequence level was investigated in these breeds using FImpute and different reference panels: within-breed, all Capra hircus sequenced individuals, European goats and French mainland goats. The best results were obtained with the French goat panel with allele and genotype concordance rates reaching 0.86 and 0.75 in the Alpine and 0.86 and 0.73 in the Saanen breed respectively. Mean correlations tended to be low in both breeds due to the high proportion of variants with low frequencies.For association analysis, imputation was performed using FImpute for 1129 French Alpine and Saanen males using within-breed and French panels on 23,338,436 filtered variants. The association results of both imputation scenarios were then compared. In Saanen goats, a large region on chromosome 19 was significantly linked to semen volume and milk yield in both scenarios. Significant variants for milk yield were annotated for 91 genes on chromosome 19 in Saanen goats. For semen volume, the annotated genes include YBOX2 which is related to azoospermia or oligospermia in other species. New signals for milk yield were detected on chromosome 2 in Alpine goats and on chromosome 5 in Saanen goats when using a multi-breed panel. Conclusion: Even with very small reference populations, an acceptable imputation quality can be achieved in French dairy goats. GWAS on imputed sequences confirmed the existence of QTLs and identified new regions of interest in dairy goats. Adding identified candidates to a genotyping array and sequencing more individuals might corroborate the involvement of identified regions while removing potential imputation errors.

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Correction: Design and Characterization of a 52K SNP Chip for Goats

Abstract: We have forgotten to thank our collaborators who provided the Creole samples. The Acknowledgements section should read:

Cited by 13 publications

References 1 publication

Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

Genome-wide diversity and demographic dynamics of Cameroon goats and their divergence from east African, north African, and Asian conspecifics

Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats

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