Whole Genome Resequencing of Heugu (Korean Black Cattle) for the Genome-Wide SNP Discovery

Choi, Jung‐Woo; Chung, Won‐Hyong; Lee, Kyung-Tai; Choi, Jae-Won; Jung, Kyoung-Sub; Cho, Yong-Min; Kim, Namshin

doi:10.5851/kosfa.2013.33.6.715

Cited by 3 publications

(1 citation statement)

References 31 publications

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“…Currently, four Korean native cattle breeds are registered with the Domestic Animal Diversity Information Service through the Food and Agriculture Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu ( FAO, 2014 ). With recent advances in WGS technology, a representative individual per each of the four breeds was recently resequenced and yielded a substantial number of SNPs ( Choi et al, 2013a ; 2013b ; 2014 ; Lee et al, 2013 ). However, there are overall few publications available that investigated the native genome resources at the population level.…”

Section: Introductionmentioning

confidence: 99%

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

Choi

Lee³

et al. 2015

Molecules and Cells

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Over the last 30 years, Hanwoo has been selectively bred to improve economically important traits. Hanwoo is currently the representative Korean native beef cattle breed, and it is believed that it shared an ancestor with a Chinese breed, Yanbian cattle, until the last century. However, these two breeds have experienced different selection pressures during recent decades. Here, we whole-genome sequenced 10 animals each of Hanwoo and Yanbian cattle (20 total) using the Illumina HiSeq 2000 sequencer. A total of approximately 3.12 and 3.07 billion sequence reads were mapped to the bovine reference sequence assembly (UMD 3.1) at an average of approximately 10.71- and 10.53-fold coverage for Hanwoo and Yanbian cattle, respectively. A total of 17,936,399 single nucleotide polymorphisms (SNPs) were yielded, of which 22.3% were found to be novel. By annotating the SNPs, we further retrieved numerous nonsynonymous SNPs that may be associated with traits of interest in cattle. Furthermore, we performed whole-genome screening to detect signatures of selection throughout the genome. We located several promising selective sweeps that are potentially responsible for economically important traits in cattle; the PPP1R12A gene is an example of a gene that potentially affects intramuscular fat content. These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

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Section: Introductionmentioning

confidence: 99%

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

Choi

Lee³

et al. 2015

Molecules and Cells

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Current Status of Cattle Genome Sequencing and Analysis using Next Generation Sequencing

Choi¹,

Chai²,

Yu³

et al. 2015

Journal of Life Science

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Thanks to recent advances in next-generation sequencing (NGS) technology, diverse livestock species have been dissected at the genome-wide sequence level. As for cattle, there are currently four Korean indigenous breeds registered with the Domestic Animal Diversity Information System of the Food and Agricultural Organization of the United Nations: Hanwoo, Chikso, Heugu, and Jeju Heugu. These native genetic resources were recently whole-genome resequenced using various NGS technologies, providing enormous single nucleotide polymorphism information across the genomes. The NGS application further provided biological such that Korean native cattle are genetically distant from some cattle breeds of European origins. In addition, the NGS technology was successfully applied to detect structural variations, particularly copy number variations that were usually difficult to identify at the genome-wide level with reasonable accuracy. Despite the success, those recent studies also showed an inherent limitation in sequencing only a representative individual of each breed. To elucidate the biological implications of the sequenced data, further confirmatory studies should be followed by sequencing or validating the population of each breed. Because NGS sequencing prices have consistently dropped, various population genomic theories can now be applied to the sequencing data obtained from the population of each breed of interest. There are still few such population studies available for the Korean native cattle breeds, but this situation will soon be improved with the recent initiative for NGS sequencing of diverse native livestock resources, including the Korean native cattle breeds. -Review -

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Genetic variation analysis of Guanling cattle based on whole-genome resequencing

Xu,

Wang,

et al. 2024

Anim Biosci

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Objective: The objective of this study was to unravel the genetic traits of Guanling cattle, pinpoint genes advantageous for muscle growth, and lay a foundation for the preservation of genetic diversity and further analysis of regulation mechanism of important economic traits in local cattle breed.Methods: In this study, we sequenced the whole genome of 3 Guanling cattle in Guizhou province using the Illumina HiSeq cBo sequencing platform. And, high- multiplex polymerase chain reaction technology was employed to detect high-quality single nucleotide polymorphism (SNP) sites of other 55 Guanling cattle.Results: Our study identified 166,411 non-synonymous SNPs (nsSNPs) and 42,423 insertions and deletions (indels). Through SNP annotation, gene function enrichment analysis, and comparing with Simmental, Angus, and Limousin cattle, we identified six genes (LEPR, AKAP9, SIX4, SPIDR, PRG4, FASN) which are potentially influential on meat quality traits, playing crucial roles in muscle growth, fat metabolism, and bodily support. We also examined polymorphisms at seven SNP sites in Guanling cattle and found that all seven were in Hardy–Weinberg equilibrium.Conclusion: These findings suggested that these gene sites are stable and widespread in the Guanling cattle population. Our research lays the groundwork for future genetic enhancement and variety identification of Guanling cattle.

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Whole Genome Resequencing of Heugu (Korean Black Cattle) for the Genome-Wide SNP Discovery

Cited by 3 publications

References 31 publications

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

Whole-Genome Resequencing Analysis of Hanwoo and Yanbian Cattle to Identify Genome-Wide SNPs and Signatures of Selection

Current Status of Cattle Genome Sequencing and Analysis using Next Generation Sequencing

Genetic variation analysis of Guanling cattle based on whole-genome resequencing

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