Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat

Guan, Shengyu; Li, Weining; Jin, Hai; Zhang, Lu; Liu, Guoshi

doi:10.3390/genes14051122

Cited by 4 publications

(2 citation statements)

References 38 publications

(38 reference statements)

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“…To further expand research in this direction for dairy goats, work is being undertaken to develop a new panel of liquid SNP chips at a lower cost, making them more accessible for both scientific research and future practical breeding. This panel contains 54,188 SNPs based on genotyping technology using targeted sequencing (GBTS) [43].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Milk Composition in Karachai Goats

Selionova,

Trukhachev,

Aibazov

et al. 2024

Animals

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This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (±0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number—only 1 SNP—for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study of Milk Composition in Karachai Goats

Selionova,

Trukhachev,

Aibazov

et al. 2024

Animals

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“…This technology combined the advantages of the bead chips and the NGS with features including low cost, high accuracy, and flexible design. GBTS has been widely applied in species such as maize [19], wheat [20], chicken [21,22], pigs [23], sheep [24], and goats [25] but is rarely reported in cattle.…”

Section: Introductionmentioning

confidence: 99%

Developing a liquid capture chip to accelerate the genetic progress of cattle

Chen,

Guo,

et al. 2024

Animal Research and One Health

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Large‐scale genotyping at a low cost is crucial for molecular breeding of livestock. In this study, the Cattle110K capture chip was developed, based on the genotyping by target sequencing system. The chip panel included 112,180 single necleotide polymorphisms (SNPs), from potential functional regions screened by genome‐wide associated study, BayesB, expression quantitative trait loci‐mapping, ATAC‐seq, and reported functional markers. All the SNPs on the panel were distributed evenly on the cattle genome, with more than 99% of the markers having a minor allele frequency greater than 0.05. Assessment results indicated that a total of 1.2 M high‐quality SNPs were identified in the 110 K regions, averaging approximately 10 SNPs per target sequence. The genotype consistency for the repetitive samples using the Cattle110K liquid chip was 99.21% while the concordance between the Illumina BovineHD BeadChip and this chip averaged 98.17%. A significant association signal for slaughter weight and carcass length was identified on 37.3–41.5 Mb of chromosome 6, pinpointing the NCAPG‐LCORL locus. This locus has previously been associated with meat and carcass traits in cattle. Additionally, novel candidate regions were identified around 3.4 Mb of chromosome 13 and 73.5 Mb of chromosome 8, significantly correlated with hip height and marbling score, respectively. We compared the accuracy of genomic estimated breeding values between the Illumina BovineHD BeadChip and this chip. The results demonstrated that the Cattle110K capture chip had a comparable ability in genomic prediction to the Illumina BovineHD BeadChip. Advances in using the cost‐effective liquid capture chip are expected to accelerate the genetic progress of cattle in the coming years.

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