Abstract
Genetic Characteristics Analysis Using the Single Nucleotide
polymorphism Information among Pig Breeds
SANG MIN LEE
Department of Animal Science
The Grduate School
Chonbuk National University
This research is aime...
Abstract
Genetic Characteristics Analysis Using the Single Nucleotide
polymorphism Information among Pig Breeds
SANG MIN LEE
Department of Animal Science
The Grduate School
Chonbuk National University
This research is aimed to find out the genetic characteristics of breeds-Berkshire, Landrace, and Yorkshire owned by GGP farms in Korea to estimate the effective population size and to investigate the effect of SNP on the total number of piglets born, thereby providing the basis for the genome selection to improve breeding pigs. The results obtained from this research are summarized as follows:
1. In order to investigate the effect of the marker on the genetic characteristics of the purebred group, we obtained the genomic information of 3,710 heads of breeding pigs-1,615 heads of Berkshire, 1,401 heads of Landrace and 1,054 heads of Yorkshire-by using Porcine SNP 60k (v1, v2) manufactured by Illumina.
2. Data obtained 29,752 records of the total number of piglets born of 10,198 heads 3,622 heads of Berkshire (4,919 records), 2,970 heads of Landrace (10,629 records) and 3,606 heads of Yorkshire (14,214 records). The average total numbers of piglets born of Berkshire, Landrace and Yorkshire were 8.61±2.83 heads, 11.58±3.07 heads and 12.35±3.44 heads, respectively.
3. Using the result of the quality control (QC) of the SNP data we perfomed, we analyzed 1,585 heads of Berkshire, 1,038 heads of Landrace and 1,035 heads of Yorkshire, of which 25,921 pieces of common SNP genetic information were analyzed.
4. The numbers of SNPs of Berkshire, Landrace and Yorkshire having the minor allele frequency (MAF) less than 10% were 5,647 SNPs (21.8%), 3,819 SNPs (14.7%) and 3,632 SNPs (14.0%), respectively. The numbers of SNPs of Berkshire, Landrace and Yorkshire having MAF of 40% or more were 5,049 (19.5%), 6,070 (23.4%) and 6,199 (23.9%), respectively and generally low in Berkshire.
5. Averages of expected heterozygosities (HE) of Berkshire, Landrace, and Yorkshire were estimated at 0.33±0.15, 0.36±0.14 and 0.36±0.14, respectively, and averages of polymorphism information content (PIC) of Berkshire, Landrace and Yorkshire were estimated at 0.26±0.11, 0.28±0.10 and 0.29±0.10, respectively. Berkshire had the lowest average expected heterozygosity, whereas Landrace and Yorkshire has the most same heterozygosity which is similar in polymorphism information content.
6. As the result of conducting the pairwise T-test between breeds by using the HE and PIC between Berkshire (BB), Lanrace (LL), and Yorkshire (YY), averages of HE between BB and LL, BB and YY, and LL and YY were 0.0289, 0.327, and 0.0038, respectively, and averages of PIC thereof was 0.0211, 0.0236, and 0.0144, respectively. The result shows no significant difference between Landrace and Yorkshire, but there was a significant difference of Berkshire from Landrace and Yorkshire (p<0.01).
7. The total number of SNP pairs compared to estimate the linkage disequilibrium (r2) were 22,571,445, and average r2 of Berkshire, Landrace, and Yorkshire was the same as 0.41. The average r2 between adjacent marker pairs was highest in chromosome 1 (0.47) of Berkshire, chromosome 14 (0.49) of Landrace and chromosomes 1, 13 and 14 (0.47) of Yorkshire.
8. The effective population sizes from the 1st to 5th generation of Berkshire, Landrace and Yorkshire were estimated at 19.87 heads, 31.41 heads and 34.09 heads, respectively. The effective population size of the 5th to 10th generation of Berkshire, Landrace and Yorkshire was decreased maintaining the constant slope, and the effective population size was rapidly decreased recently since before the 10th generation.
9. Heritabilities of Berkshire, Landrace, and Yorkshire for the total number of piglets born were estimated at 0.081, 0.107 and 0.121, respectively, and the repeatabilities thereof were estimated at 0.186, 0.196 and 0.209, respectively.
10. The most markers had nearly zero SNP effect on the total number of piglets born, and only few markers had the high SNP effect.
11. The numbers of SNPs of Berkshire, Landrace and Yorkshire having 4×standard deviation of the total number of piglets born were 5 SNPs, 1 SNP and 10 SNPs, respectively. In addition, 2 SNPs of Yorkshire-ALGA0098882 (5.27), H3GA0009642 (5.11)-had more than 5×standard deviation.
12. When finding a protein-coding gene in the SNPs having 4×standard deviation of the total number of piglets born, we found protein-coding genes in all the 16 SNPs.
13. The protein-coding gene for reproductive traits affecting the production of breeding pigs was CD96 gene on chromosome 13, and the gene affecting the total number of piglets born was SEC23B gene.
keywords : Effective population size, F-statistics, Genetic Characteristics Analysis, Linkage disequilibrium (LD), Single Nucleotide Polymorphism (SNP)
Abstract
Genetic Characteristics Analysis Using the Single Nucleotide
polymorphism Information among Pig Breeds
SANG MIN LEE
Department of Animal Science
The Grduate School
Chonbuk National University
This research is aimed to find out the genetic characteristics of breeds-Berkshire, Landrace, and Yorkshire owned by GGP farms in Korea to estimate the effective population size and to investigate the effect of SNP on the total number of piglets born, thereby providing the basis for the genome selection to improve breeding pigs. The results obtained from this research are summarized as follows:
1. In order to investigate the effect of the marker on the genetic characteristics of the purebred group, we obtained the genomic information of 3,710 heads of breeding pigs-1,615 heads of Berkshire, 1,401 heads of Landrace and 1,054 heads of Yorkshire-by using Porcine SNP 60k (v1, v2) manufactured by Illumina.
2. Data obtained 29,752 records of the total number of piglets born of 10,198 heads 3,622 heads of Berkshire (4,919 records), 2,970 heads of Landrace (10,629 records) and 3,606 heads of Yorkshire (14,214 records). The average total numbers of piglets born of Berkshire, Landrace and Yorkshire were 8.61±2.83 heads, 11.58±3.07 heads and 12.35±3.44 heads, respectively.
3. Using the result of the quality control (QC) of the SNP data we perfomed, we analyzed 1,585 heads of Berkshire, 1,038 heads of Landrace and 1,035 heads of Yorkshire, of which 25,921 pieces of common SNP genetic information were analyzed.
4. The numbers of SNPs of Berkshire, Landrace and Yorkshire having the minor allele frequency (MAF) less than 10% were 5,647 SNPs (21.8%), 3,819 SNPs (14.7%) and 3,632 SNPs (14.0%), respectively. The numbers of SNPs of Berkshire, Landrace and Yorkshire having MAF of 40% or more were 5,049 (19.5%), 6,070 (23.4%) and 6,199 (23.9%), respectively and generally low in Berkshire.
5. Averages of expected heterozygosities (HE) of Berkshire, Landrace, and Yorkshire were estimated at 0.33±0.15, 0.36±0.14 and 0.36±0.14, respectively, and averages of polymorphism information content (PIC) of Berkshire, Landrace and Yorkshire were estimated at 0.26±0.11, 0.28±0.10 and 0.29±0.10, respectively. Berkshire had the lowest average expected heterozygosity, whereas Landrace and Yorkshire has the most same heterozygosity which is similar in polymorphism information content.
6. As the result of conducting the pairwise T-test between breeds by using the HE and PIC between Berkshire (BB), Lanrace (LL), and Yorkshire (YY), averages of HE between BB and LL, BB and YY, and LL and YY were 0.0289, 0.327, and 0.0038, respectively, and averages of PIC thereof was 0.0211, 0.0236, and 0.0144, respectively. The result shows no significant difference between Landrace and Yorkshire, but there was a significant difference of Berkshire from Landrace and Yorkshire (p<0.01).
7. The total number of SNP pairs compared to estimate the linkage disequilibrium (r2) were 22,571,445, and average r2 of Berkshire, Landrace, and Yorkshire was the same as 0.41. The average r2 between adjacent marker pairs was highest in chromosome 1 (0.47) of Berkshire, chromosome 14 (0.49) of Landrace and chromosomes 1, 13 and 14 (0.47) of Yorkshire.
8. The effective population sizes from the 1st to 5th generation of Berkshire, Landrace and Yorkshire were estimated at 19.87 heads, 31.41 heads and 34.09 heads, respectively. The effective population size of the 5th to 10th generation of Berkshire, Landrace and Yorkshire was decreased maintaining the constant slope, and the effective population size was rapidly decreased recently since before the 10th generation.
9. Heritabilities of Berkshire, Landrace, and Yorkshire for the total number of piglets born were estimated at 0.081, 0.107 and 0.121, respectively, and the repeatabilities thereof were estimated at 0.186, 0.196 and 0.209, respectively.
10. The most markers had nearly zero SNP effect on the total number of piglets born, and only few markers had the high SNP effect.
11. The numbers of SNPs of Berkshire, Landrace and Yorkshire having 4×standard deviation of the total number of piglets born were 5 SNPs, 1 SNP and 10 SNPs, respectively. In addition, 2 SNPs of Yorkshire-ALGA0098882 (5.27), H3GA0009642 (5.11)-had more than 5×standard deviation.
12. When finding a protein-coding gene in the SNPs having 4×standard deviation of the total number of piglets born, we found protein-coding genes in all the 16 SNPs.
13. The protein-coding gene for reproductive traits affecting the production of breeding pigs was CD96 gene on chromosome 13, and the gene affecting the total number of piglets born was SEC23B gene.
keywords : Effective population size, F-statistics, Genetic Characteristics Analysis, Linkage disequilibrium (LD), Single Nucleotide Polymorphism (SNP)
주제어
#Effective population size F-statistics Genetic Characteristics Analysis Linkage disequilibrium (LD) Single Nucleotide Polymorphism (SNP)
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