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

Choi JW, Choi BH, Lee SH, Lee SS, Kim HC, Yu D, Chung WH, Lee KT, Chai HH, Cho YM, Lim D - Mol. Cells (2015)

Bottom Line: 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.These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

View Article: PubMed Central - PubMed

Affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.

ABSTRACT
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.

No MeSH data available.


Distribution of ZHp scores across all 29 Bos taurus autosomes for HAN and YAN. The upper and lower plots indicate the ZHp score distribution of Hanwoo and Yanbian cattle, respectively. Even numbered chromosomes are presented in gray and odd numbered chromosomes are black. The blue and red horizontal lines indicate ZHp thresholds of −4 and −5 that could be strong candidates of selective sweeps in this study.
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f3-molce-38-5-466: Distribution of ZHp scores across all 29 Bos taurus autosomes for HAN and YAN. The upper and lower plots indicate the ZHp score distribution of Hanwoo and Yanbian cattle, respectively. Even numbered chromosomes are presented in gray and odd numbered chromosomes are black. The blue and red horizontal lines indicate ZHp thresholds of −4 and −5 that could be strong candidates of selective sweeps in this study.

Mentions: Using all of the WGS-derived SNPs from this study, we scanned the whole genome to detect regions with high degrees of fixation, which are indicative of signature of selection, in each breed. We applied 50% overlapping sliding windows that were 150 kb along all 29 autosomes; however, 30 windows with fewer than 10 SNPs were excluded. A total of 33,482 windows were used to calculate the Z transformations of the pooled heterozygosity (ZHp) in each window. The ZHp scores ranged from −7.95 to 1.54 and from −10.96 to 1.61, with median values of 0.24 and 0.22 for HAN and YAN, respectively (Fig. 3, Supplementary Tables S3 and S4). Because extremely low ZHp scores indicate putative selective sweeps because of excess homozygosity, we focused on the ZHp score in the extreme lower end of the distribution. We observed 195 and 173 windows with ZHp values of less than or equal to −4 in HAN and YAN, respectively, whereas 73 and 68 windows showed ZHp scores less than −5 that corresponded to approximately the lowest 0.2% for HAN and YAN, respectively.


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

Choi JW, Choi BH, Lee SH, Lee SS, Kim HC, Yu D, Chung WH, Lee KT, Chai HH, Cho YM, Lim D - Mol. Cells (2015)

Distribution of ZHp scores across all 29 Bos taurus autosomes for HAN and YAN. The upper and lower plots indicate the ZHp score distribution of Hanwoo and Yanbian cattle, respectively. Even numbered chromosomes are presented in gray and odd numbered chromosomes are black. The blue and red horizontal lines indicate ZHp thresholds of −4 and −5 that could be strong candidates of selective sweeps in this study.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4443289&req=5

f3-molce-38-5-466: Distribution of ZHp scores across all 29 Bos taurus autosomes for HAN and YAN. The upper and lower plots indicate the ZHp score distribution of Hanwoo and Yanbian cattle, respectively. Even numbered chromosomes are presented in gray and odd numbered chromosomes are black. The blue and red horizontal lines indicate ZHp thresholds of −4 and −5 that could be strong candidates of selective sweeps in this study.
Mentions: Using all of the WGS-derived SNPs from this study, we scanned the whole genome to detect regions with high degrees of fixation, which are indicative of signature of selection, in each breed. We applied 50% overlapping sliding windows that were 150 kb along all 29 autosomes; however, 30 windows with fewer than 10 SNPs were excluded. A total of 33,482 windows were used to calculate the Z transformations of the pooled heterozygosity (ZHp) in each window. The ZHp scores ranged from −7.95 to 1.54 and from −10.96 to 1.61, with median values of 0.24 and 0.22 for HAN and YAN, respectively (Fig. 3, Supplementary Tables S3 and S4). Because extremely low ZHp scores indicate putative selective sweeps because of excess homozygosity, we focused on the ZHp score in the extreme lower end of the distribution. We observed 195 and 173 windows with ZHp values of less than or equal to −4 in HAN and YAN, respectively, whereas 73 and 68 windows showed ZHp scores less than −5 that corresponded to approximately the lowest 0.2% for HAN and YAN, respectively.

Bottom Line: 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.These discoveries provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds.

View Article: PubMed Central - PubMed

Affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Korea.

ABSTRACT
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.

No MeSH data available.