Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs

Wu, Pingxian; Yang, Qiang; Wang, Kai; Zhou, Jie; Ma, Jideng; Tang, Qianzhi; Jin, Long; Xiao, Weihang; Jiang, Anan; Jiang, Yanzhi; Zhu, Li; Li, Xuewei; Tang, Guoqing

doi:10.1016/j.ygeno.2017.09.009

Cited by 45 publications

(42 citation statements)

References 48 publications

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“…The ssGWAS model allows all the available data, including genetic markers, phenotype records and pedigree information, to be examined simultaneously in one step. Many studies have recently validated this method and effectively implemented ssGWAS in pigs (Howard et al ., ; Wu et al ., ) and other species (Silva et al ., ), achieving a greater power and more precise estimates than other models. The ssGWAS method is currently being tested in plant species by exploring the use of raw data (individual replicates) as opposed to standard approaches that use the means (across replicates), which leads to error inflation for the association analysis (unpublished data).…”

Section: Going Beyond Conventional Mappingmentioning

confidence: 99%

Salt stress under the scalpel – dissecting the genetics of salt tolerance

et al. 2019

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Summary Salt stress limits the productivity of crops grown under saline conditions, leading to substantial losses of yield in saline soils and under brackish and saline irrigation. Salt tolerant crops could alleviate these losses while both increasing irrigation opportunities and reducing agricultural demands on dwindling freshwater resources. However, despite significant efforts, progress towards this goal has been limited, largely because of the genetic complexity of salt tolerance for agronomically important yield‐related traits. Consequently, the focus is shifting to the study of traits that contribute to overall tolerance, thus breaking down salt tolerance into components that are more genetically tractable. Greater consideration of the plasticity of salt tolerance mechanisms throughout development and across environmental conditions furthers this dissection. The demand for more sophisticated and comprehensive methodologies is being met by parallel advances in high‐throughput phenotyping and sequencing technologies that are enabling the multivariate characterisation of vast germplasm resources. Alongside steady improvements in statistical genetics models, forward genetics approaches for elucidating salt tolerance mechanisms are gaining momentum. Subsequent quantitative trait locus and gene validation has also become more accessible, most recently through advanced techniques in molecular biology and genomic analysis, facilitating the translation of findings to the field. Besides fuelling the improvement of established crop species, this progress also facilitates the domestication of naturally salt tolerant orphan crops. Taken together, these advances herald a promising era of discovery for research into the genetics of salt tolerance in plants.

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Section: Going Beyond Conventional Mappingmentioning

confidence: 99%

Salt stress under the scalpel – dissecting the genetics of salt tolerance

et al. 2019

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“…Currently, whole-genome sequencing and genome-wide association studies (GWAS) are used to explore genetic variants strongly associated with production traits (Lai et al, 2016 ; Mota et al, 2017 ; Wu et al, 2018 ); however, numerous potential genes identified by GWAS have not been fully verified. To address this problem, methods which combine GWAS analysis results and MAS to screen for critical genetic variations in large livestock populations have been developed.…”

Section: Introductionmentioning

confidence: 99%

Insertion/Deletion Within the KDM6A Gene Is Significantly Associated With Litter Size in Goat

et al. 2018

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A previous whole-genome association analysis identified lysine demethylase 6A (KDM6A), which encodes a type of histone demethylase, as a candidate gene associated to goat fecundity. KDM6A gene knockout mouse disrupts gametophyte development, suggesting that it has a critical role in reproduction. In this study, goat KDM6A mRNA expression profiles were determined, insertion/deletion (indel) variants in the gene identified, indel variants effect on KDM6A gene expression assessed, and their association with first-born litter size analyzed in 2326 healthy female Shaanbei white cashmere goats. KDM6A mRNA was expressed in all tissues tested (heart, liver, spleen, lung, kidney, muscle, brain, skin and testis); the expression levels in testes at different developmental stages [1-week-old (wk), 2, 3 wk, 1-month-old (mo), 1.5 and 2 mo] indicated a potential association with the mitosis-to-meiosis transition, implying that KDM6A may have an essential role in goat fertility. Meanwhile, two novel intronic indels of 16 bp and 5 bp were identified. Statistical analysis revealed that only the 16 bp indel was associated with first-born litter size (P < 0.01), and the average first-born litter size of individuals with an insertion/insertion genotype higher than that of those with the deletion/deletion genotype (P < 0.05). There was also a significant difference in genotype distributions of the 16 bp indel between mothers of single-lamb and multi-lamb litters in the studied goat population (P = 0.001). Consistently, the 16 bp indel also had a significant effect on KDM6A gene expression. Additionally, there was no significant linkage disequilibrium (LD) between these two indel loci, consistent with the association analysis results. Together, these findings suggest that the 16 bp indel in KDM6A may be useful for marker-assisted selection (MAS) of goats.

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“…For example, genotyping-by-sequencing (GBS) on livestock has been a sufficient solution that is required for population genetic and genomic studies [15]. This method has been successfully used to identify selection signatures of important economic traits in cattle [16], pigs [17,18], chicken [19], and camels [20]. The goal of this investigation was to perform a pair-wise marker differentiation comparison in a genome-wide scan between Noire de Thibar and Queue fine de l'ouest Tunisian sheep breeds, using genotyping-by-sequencing data to reveal putative regions under strong and recent selection.…”

Section: Introductionmentioning

confidence: 99%

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds

Baazaoui

McEwan

Anderson

et al. 2019

Animals

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Simple Summary: Maintaining the flexibility of the genetic resources of native animals to face local environment constraints is still a major challenge. In Tunisia, the Noire de Thibar breed is a local sheep, typically with black coloration, known for its ability to tolerate "hypericum perforatum", which causes skin photosensitization in white colored sheep. The goal of this study was to perform a genome scan, by considering genotyping-by-sequencing (GBS) markers that were genotyped in divergent coat colored sheep (black vs. white) to identify strong, and recent, artificial selection that is involved in skin-photosensitization. Interestingly, the genomic differentiation analysis identified F ST markers within genomic regions containing key pigmentation and photosensitivity related-genes. These findings help in understanding the background of coat color genetics and its potential role in adaptation to local environment constraints.Abstract: The Tunisian Noire de Thibar sheep breed is a composite breed, recently selected to create animals that are uniformly black in order to avoid skin photosensitization after the ingestion of toxic "hypericum perforatum" weeds, which causes a major economic loss to sheep farmers. We assessed genetic differentiation and estimated marker F ST using genotyping-by-sequencing (GBS) data in black (Noire de Thibar) and related white-coated (Queue fine de l'ouest) sheep breeds to identify signals of artificial selection. The results revealed the selection signatures within candidate genes related to coat color, which are assumed to be indirectly involved in the mechanism of photosensitization in sheep. The identified genes could provide important information for molecular breeding.

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Single step genome-wide association studies based on genotyping by sequence data reveals novel loci for the litter traits of domestic pigs

Cited by 45 publications

References 48 publications

Salt stress under the scalpel – dissecting the genetics of salt tolerance

Salt stress under the scalpel – dissecting the genetics of salt tolerance

Insertion/Deletion Within the KDM6A Gene Is Significantly Associated With Litter Size in Goat

GBS Data Identify Pigmentation-Specific Genes of Potential Role in Skin-Photosensitization in Two Tunisian Sheep Breeds

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