GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data
Abstract
:1. Introduction
2. Results
2.1. Descriptive Statistics of Phenotypic Data
2.2. Genotype Imputation and Imputation Accuracy
2.3. Genome-Wide Association Studies
2.3.1. GWAS for Data before Imputation
2.3.2. GWAS for Data after Imputation
2.4. Bioinformatics Annotation Analysis
3. Discussion
3.1. Imputation of 50K Chip Data to WGS Data
3.1.1. Reference Population Size and Imputation Accuracy
3.1.2. Genetic Distance between Reference and Target Populations and Imputation Accuracy
3.1.3. Imputation Strategy and Imputation Accuracy
3.2. Potential Candidate Genes
4. Materials and Methods
4.1. Animals and Phenotype
4.2. SNP Chip Data
4.3. Reference Sequence Data
4.4. Genotype Imputation
4.5. Genome-Wide Association Studies
4.6. Bioinformatics Annotation Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Line | Trait | Samples Size | Mean | Standard Deviation | Minimum | Maximum |
---|---|---|---|---|---|---|
Canadian | TNB | 1403 | 14.42 | 1.97 | 8.10 | 22.30 |
French | 1252 | 14.29 | 1.72 | 7.85 | 21.03 | |
Canadian | NSB | 1403 | 1.26 | 0.85 | −0.21 | 4.65 |
French | 1252 | 1.16 | 0.74 | −0.19 | 5.73 | |
Canadian | GL | 1403 | 114.59 | 0.93 | 111.35 | 117.69 |
French | 1252 | 114.09 | 1.12 | 110.11 | 119.82 |
Trait | SSC | SNP Name | SNP Position (bp) | p (Canadian) | p (French) | p (Combined LW) | p (Meta) | Candidate Gene |
---|---|---|---|---|---|---|---|---|
TNB | 4 | WU_10.2_4_111043929 | 101,156,553 | 1.47 × 10−5 | 6.50 × 10−1 | 2.39 × 10−3 | 6.20 × 10−4 | NOTCH2 |
5 | ALGA0122851 | 79,145,588 | 1.11 × 10−4 | 3.71 × 10−2 | 4.26 × 10−5 | 2.22 × 10−5 | - | |
8 | H3GA0024679 | 30,016,379 | 1.69 × 10−6 | 4.62 × 10−1 | 9.30 × 10−5 | 6.75 × 10−5 | KLF3 | |
8 | Affx-114981021 | 56,076,247 | 4.95 × 10−4 | 4.44 × 10−6 | 1.61 × 10−8 | 1.30 × 10−8 | - | |
NSB | 1 | INRA0000573 | 9,677,339 | 1.37 × 10−5 | 1.35 × 10−2 | 1.54 × 10−5 | 1.20 × 10−6 | TMEM242 |
4 | ALGA0029239 | 123,733,425 | 7.90 × 10−6 | 7.47 × 10−1 | 6.98 × 10−4 | 2.46 × 10−3 | FNBP1L | |
4 | WU_10.2_4_136884741 | 125,301,443 | 1.94 × 10−3 | 6.29 × 10−4 | 1.78 × 10−6 | 4.20 × 10−6 | TGFBR3 | |
6 | WU_10.2_6_21881195 | 23,735,225 | 8.94 × 10−1 | 2.51 × 10−7 | 1.92 × 10−2 | 2.72 × 10−4 | - | |
10 | ASGA0046895 | 17,881,060 | 7.95 × 10−7 | 4.08 × 10−1 | 9.49 × 10−5 | 3.22 × 10−5 | - | |
11 | WU_10.2_11_78220891 | 70,923,126 | 6.20 × 10−4 | 1.30 × 10−3 | 1.08 × 10−5 | 2.65 × 10−6 | - | |
11 | ALGA0063609 | 70,551,880 | 5.29 × 10−3 | 9.79 × 10−4 | 2.05 × 10−5 | 1.77 × 10−5 | - | |
14 | MARC0062790 | 138,357,861 | 5.25 × 10−1 | 1.10 × 10−5 | 1.39 × 10−2 | 4.98 × 10−4 | - | |
18 | WU_10.2_18_6267059 | 5,909,015 | 1.71 × 10−5 | - | 8.92 × 10−6 | 1.71 × 10−5 | NUB1 | |
18 | MARC0056921 | 6,400,611 | 1.26 × 10−5 | 6.43 × 10−1 | 6.66 × 10−5 | 4.79 × 10−4 | GIMAP2 | |
GL | 1 | ASGA0104591 | 254,755,615 | 1.82 × 10−2 | 1.84 × 10−5 | 4.08 × 10−7 | 3.58 × 10−6 | COL27A1 |
6 | WU_10.2_6_144601434 | 156,647,853 | 8.97 × 10−6 | 1.21 × 10−1 | 2.60 × 10−1 | 3.05 × 10−2 | - | |
11 | ALGA0124549 | 25,293,190 | 9.56 × 10−1 | 3.24 × 10−6 | 3.60 × 10−4 | 1.26 × 10−3 | VWA8 | |
12 | WU_10.2_12_3290782 | 3,251,323 | 2.42 × 10−3 | 2.74 × 10−3 | 8.38 × 10−5 | 2.03 × 10−5 | - | |
14 | MARC0035949 | 61,937,863 | 4.86 × 10−2 | 1.48 × 10−3 | 1.18 × 10−5 | 2.98 × 10−4 | BICC1 |
SSC | SNP_R (Mb) | T_SNP_P (bp) | SNP_N | p (Canadian) | p (French) | p (Combined LW) | p (Meta) | Candidate Gene |
---|---|---|---|---|---|---|---|---|
1 | 261.86–261.90 | 261,882,219 | 4 | 4.42 × 10−1 | 7.79 × 10−7 | 2.41 × 10−2 | 4.60 × 10−3 | TTLL11 |
2 | 4.90–4.94 | 4,917,216 | 1 | 6.89 × 10−7 | - | 3.47 × 10−6 | 6.89 × 10−7 | UNC93B1/ALDH3B2 |
2 | 4.94–4.98 | 4,964,340 | 19 | 5.72 × 10−7 | 6.61 × 10−1 | 2.02 × 10−4 | 8.56 × 10−4 | TBX10/NDUFV1 |
2 | 127.88–127.92 | 127,904,283 | 13 | 4.21 × 10−6 | - | 8.20 × 10−5 | 4.21 × 10−6 | - |
3 | 6.81–6.85 | 117,058,450 | 1 | 3.78 × 10−4 | - | 4.61 × 10−6 | 3.78 × 10−4 | - |
3 | 117.04–117.08 | 6,831,554 | 1 | 6.12 × 10−4 | 1.65 × 10−3 | 1.08 × 10−5 | 3.29 × 10−6 | - |
4 | 117.63–117.67 | 117,647,397 | 1 | 9.90 × 10−1 | 4.47× 10−6 | 2.16 × 10−3 | 1.68 × 10−3 | CDC14A |
5 | 78.38–78.42 | 78,396,126 | 1 | 8.21 × 10−5 | 9.81 × 10−3 | 7.00 × 10−6 | 3.55 × 10−6 | COL2A1 |
5 | 78.40–78.44 | 78,424,002 | 1 | 4.34 × 10−6 | 3.17 × 10−3 | 1.08 × 10−7 | 8.03 × 10−8 | SENP1 |
5 | 78.53–78.57 | 78,554,745 | 1 | 1.14 × 10−5 | 3.20 × 10−3 | 2.80 × 10−7 | 1.84 × 10−7 | CCDC184 |
5 | 79.02–79.12 | 79,102,021 | 11 | 1.30 × 10−6 | 2.89 × 10−2 | 1.13 × 10−6 | 5.21 × 10−7 | - |
5 | 79.12–79.16 | 79,144,763 | 8 | 6.11 × 10−6 | 3.86 × 10−2 | 2.66 × 10−6 | 2.50 × 10−6 | - |
5 | 79.24–79.28 | 79,262,197 | 2 | 1.07 × 10−6 | 7.45 × 10−3 | 8.06 × 10−6 | 3.25 × 10−6 | KANSL2 |
5 | 79.24–79.29 | 79,271,540 | 7 | 1.38 × 10−6 | 2.44 × 10−2 | 5.50 × 10−7 | 4.31 × 10−7 | KANSL2, SNORA2C |
5 | 79.25–79.29 | 79,266,042 | 3 | 1.32 × 10−5 | 2.44 × 10−2 | 3.71 × 10−6 | 2.44 × 10−6 | KANSL2, SNORA2C |
5 | 79.70–79.74 | 79,716,662 | 1 | 4.02 × 10−7 | 4.12 × 10−2 | 1.97 × 10−7 | 3.66 × 10−7 | |
5 | 79.71–79.75 | 79,732,010 | 3 | 2.71 × 10−7 | 6.65 × 10−1 | 4.30 × 10−4 | 5.45 × 10−5 | SLC41A2 |
7 | 115.99–116.04 | 116,017,230 | 9 | 2.94 × 10−5 | 1.30 × 10−3 | 5.09 × 10−8 | 1.55 × 10−7 | GSC |
7 | 115.06–116.10 | 116,082,776 | 2 | 1.44 × 10−5 | 2.58 × 10−3 | 3.67 × 10−8 | 1.76 × 10−7 | GSC |
7 | 116.32–116.36 | 116,344,726 | 1 | 1.62 × 10−5 | - | 1.63 × 10−6 | 1.62 × 10−5 | - |
8 | 29.96–30.00 | 29,982,306 | 2 | 5.03 × 10−7 | - | 2.49 × 10−5 | 5.03 × 10−7 | - |
8 | 30.04–31.11 | 31,089,176 | 87 | 4.23 × 10−6 | 1.79 × 10−1 | 1.91 × 10−3 | 1.98 × 10−5 | KLF3, FAM114A1, TLR10, TLR1, TLR6, WDR19, PDS5A |
8 | 56.06–56.10 | 56,076,247 | 1 | 5.72 × 10−4 | 5.79 × 10−6 | 2.33 × 10−8 | 1.94 × 10−8 | - |
10 | 54.58–54.62 | 54,600,820 | 1 | 3.16 × 10−6 | 1.11 × 10−1 | 5.38 × 10−6 | 7.38 × 10−6 | PLXDC2 |
10 | 55.49-55.53 | 55,514,613 | 9 | 1.57 × 10−4 | 1.66 × 10−2 | 4.62 × 10−6 | 1.12 × 10−5 | - |
13 | 205.13–205.17 | 205,150,403 | 1 | 2.16 × 10−6 | 7.41 × 10−1 | 1.53 × 10−4 | 2.42 × 10−4 | RIPK4 |
15 | 2.20–2.28 | 2,257,349 | 4 | - | 3.69 × 10−5 | 4.41 × 10−6 | 3.69 × 10−5 | - |
15 | 2.24–2.35 | 2,325,462 | 4 | 5.96 × 10−3 | 3.20× 10−5 | 3.10 × 10−6 | 2.46 × 10−6 | - |
15 | 2.50–2.56 | 2,538,624 | 5 | - | 1.41 × 10−7 | 2.79 × 10−7 | 1.41× 10−7 | MMADHC |
15 | 2.54–2.60 | 2,578,548 | 6 | 1.56 × 10−1 | 3.42 × 10−7 | 1.96 × 10−6 | 2.10 × 10−5 | - |
15 | 2.57–2.61 | 2,586,649 | 2 | 8.65 × 10−1 | 8.25 × 10−7 | 9.70 × 10−5 | 4.51 × 10−4 | LYPD6 |
15 | 2.54–2.61 | 2,564,841 | 83 | - | 9.22 × 10−7 | 1.67 × 10−6 | 9.22 × 10−7 | LYPD6 |
15 | 2.65–2.69 | 2,671,075 | 1 | 2.53 × 10−3 | 3.27 × 10−4 | 6.97 × 10−6 | 3.13 × 10−6 | LYPD6 |
15 | 2.76–2.80 | 2,778,681 | 1 | - | 3.07 × 10−6 | 3.83 × 10−5 | 3.07 × 10−6 | LYPD6 |
15 | 2.68–2.81 | 2,779,384 | 11 | 9.87 × 10−1 | 2,779,3842.99 × 10−6 | 5.85 × 10−4 | 1.39 × 10−3 | LYPD6 |
15 | 2.90–2.95 | 2,933,736 | 6 | - | 7.06 × 10−6 | 3.30 × 10−6 | 5.68 × 10−6 | LYPD6B |
15 | 2.92–2.96 | 2,938,800 | 2 | - | 3.47 × 10−6 | 2.44 × 10−6 | 3.47 × 10−6 | LYPD6B |
15 | 3.24–3.28 | 3,264,770 | 1 | 4.51 × 10−1 | 4.48 × 10−6 | 6.54 × 10−5 | 2.17 × 10−4 | KIF5C |
15 | 3.26–3.30 | 3,278,046 | 2 | 9.74 × 10−2 | 1.03 × 10−5 | 3.90 × 10−6 | 2.29× 10−5 | KIF5C |
15 | 3.36–3.40 | 3,376,487 | 8 | 4.19 × 10−3 | 1.30 × 10−4 | 1.95 × 10−6 | 2.48 × 10−6 | KIF5C |
15 | 3.37–3.41 | 3,392,704 | 8 | 1.18 × 10−3 | 2.91 × 10−3 | 2.42 × 10−6 | 1.07 × 10−5 | - |
15 | 3.37–3.57 | 3,545,949 | 8 | 1.11 × 10−2 | 1.33 × 10−5 | 2.73 × 10−7 | 1.32 × 10−6 | EPC2 |
15 | 4.15–4.43 | 4,408,571 | 14 | 2.42 × 10−2 | 4.58× 10−5 | 3.03 × 10−6 | 9.11 × 10−6 | ORC4, ACVR2A |
15 | 4.79–4.88 | 4,857,043 | 20 | 3.63 × 10−1 | 1.07 × 10−6 | 5.46 × 10−3 | 7.16 × 10−3 | - |
SSC | SNP_R (Mb) | T_SNP_P (bp) | SNP_N | p (Canadian) | p (French) | p (Combined LW) | p (Meta) | Candidate Gene |
---|---|---|---|---|---|---|---|---|
1 | 9.04–9.42 | 9,404,407 | 12 | 3.60 × 10−5 | 1.11 × 10−2 | 1.07 × 10−5 | 2.06 × 10−6 | SYNJ2, ZDHHC14 |
1 | 9.38–9.43 | 9,411,440 | 57 | 3.57 × 10−5 | 6.68 × 10−4 | 3.87 × 10−7 | 9.23 × 10−8 | ZDHHC14 |
1 | 9.44–9.76 | 9,743,278 | 13 | 1.03 × 10−4 | 7.68 × 10−3 | 3.83 × 10−5 | 3.26 × 10−6 | ZDHHC14, TMEM242 |
3 | 5.44–5.49 | 5,470,408 | 5 | 1.25 × 10−2 | 2.52 × 10−5 | 8.38 × 10−6 | 2.48 × 10−6 | TECPR1, BRI3, BAIAP2L1 |
3 | 5.43–5.50 | 5,478,442 | 5 | 7.49 × 10−3 | 2.30 × 10−5 | 1.83 × 10−6 | 1.23 × 10−6 | TECPR1, BRI3, BAIAP2L1 |
3 | 126.29–126.42 | 126,396,984 | 9 | 1.62 × 10−6 | 5.71 × 10−1 | 6.02 × 10−5 | 1.06 × 10−4 | CYS1 |
3 | 126.38–126.43 | 126,405,359 | 6 | 6.22 × 10−6 | 4.31 × 10−2 | 3.09 × 10−6 | 2.96 × 10−6 | CYS1, KLF11 |
3 | 126.53–136.57 | 126,553,254 | 1 | 1.13 × 10−6 | 4.53 × 10−1 | 4.10 × 10−5 | 5.05 × 10−5 | TAF1B |
3 | 126.55–126.60 | 126,576,921 | 4 | 5.17 × 10−7 | 1.70 × 10−1 | 3.46 × 10−6 | 4.39 × 10−6 | TAF1B |
3 | 126.57–126.63 | 126,610,508 | 4 | 5.74 × 10−6 | 5.69 × 10−2 | 3.90 × 10−6 | 4.13 × 10−6 | TAF1B |
4 | 123.49–123.53 | 123,514,051 | 1 | 1.04 × 10−5 | - | 1.48 × 10−6 | 2.83 × 10−6 | BCAR3 |
4 | 123.48–123.54 | 123,515,536 | 5 | 3.21 × 10−5 | 7.62 × 10−1 | 1.48 × 10−6 | 6.79 × 10−6 | BCAR3 |
4 | 123.69–123.86 | 123,842,741 | 5 | 4.68 × 10−6 | 7.62 × 10−1 | 5.02 × 10−4 | 1.81 × 10−3 | FNBP1L, DR1 |
4 | 124.53–124.57 | 124,546,985 | 3 | 2.58 × 10−6 | - | 7.72 × 10−6 | 2.58 × 10−6 | EVI5 |
4 | 124.63–124.67 | 124,647,920 | 1 | 4.54 × 10−6 | 1.26 × 10−1 | 7.50 × 10−2 | 2.25 × 10−2 | GFI1 |
4 | 124.88–124.93 | 124,907,426 | 136 | 4.62 × 10−6 | - | 2.15 × 10−5 | 4.62 × 10−6 | BTBD8 |
4 | 124.84–124.93 | 124,912,144 | 83 | 2.38 × 10−6 | 6.77 × 10−1 | 4.03 × 10−5 | 2.03 × 10−4 | BTBD8 |
4 | 124.89–124.95 | 124,934,706 | 71 | 1.67 × 10−6 | 3.45 × 10−1 | 2.50 × 10−5 | 3.62 × 10−5 | BTBD8 |
4 | 124.93–124.97 | 124,946,497 | 7 | 2.48 × 10−8 | 5.10 × 10−1 | 1.05 × 10−6 | 6.64 × 10−6 | BTBD8, EPHX4 |
4 | 124.92–125.00 | 124,977,862 | 102 | 1.55 × 10−6 | 8.97 × 10−1 | 5.50 × 10−4 | 6.65 × 10−4 | BTBD8, EPHX4 |
4 | 124.96–125.00 | 124,978,259 | 3 | 2.88 × 10−6 | - | 2.79 × 10−6 | 2.88 × 10−6 | EPHX4 |
4 | 125.08–125.29 | 125,266,938 | 27 | 2.59 × 10−3 | 9.16 × 10−4 | 3.54 × 10−6 | 7.94 × 10−6 | TGFBR3 |
4 | 125.25–125.29 | 125,266,999 | 1 | 3.98 × 10−6 | 9.16 × 10−4 | 1.28 × 10−8 | 1.81 × 10−8 | TGFBR3 |
4 | 125.25–125.33 | 125,314,460 | 38 | 1.39 × 10−3 | 9.61 × 10−4 | 2.35 × 10−6 | 4.41 × 10−6 | TGFBR3 |
6 | 10.13–10.21 | 10,185,432 | 61 | 2.66 × 10−6 | 9.08 × 10−1 | 8.04 × 10−2 | 8.57 × 10−4 | NUDT7 |
6 | 23.63–24.55 | 24,525,703 | 151 | 6.56 × 10−1 | 5.10 × 10−8 | 2.09 × 10−3 | 4.81 × 10−5 | - |
8 | 135.32–135.43 | 135,411,117 | 3 | 2.64 × 10−6 | 5.19 × 10−1 | 5.40 × 10−3 | 2.97 × 10−3 | LIN54, THAP9, SEC31A |
10 | 17.51–17.56 | 17,535,810 | 2 | - | 1.29 × 10−3 | 1.05 × 10−6 | 1.29 × 10−3 | - |
11 | 70.38–70.93 | 70,913,213 | 48 | 4.86 × 10−3 | 5.62 × 10−5 | 3.14 × 10−6 | 1.48 × 10−6 | FGF14 |
11 | 70.89–70.94 | 70,915,607 | 13 | 8.02 × 10−3 | 5.62 × 10−5 | 8.92 × 10−6 | 2.68 × 10−6 | - |
14 | 31.82–31.86 | 31,835,585 | 1 | 5.00 × 10−2 | 6.43 × 10−5 | 4.63 × 10−6 | 3.06 × 10−5 | ARPC3, GPN3, FAM216A |
15 | 2.24–3.42 | 3,396,362 | 8 | 2.72 × 10−4 | 3.87 × 10−3 | 2.77 × 10−6 | 3.65 × 10−6 | - |
15 | 3.39–3.43 | 3,411,573 | 1 | 2.08 × 10−1 | 1.14 × 10−6 | 3.24 × 10−6 | 2.06 × 10−5 | EPC2 |
15 | 3.53–3.57 | 3,545,949 | 1 | 2.09 × 10−4 | 1.65 × 10−3 | 1.79 × 10−7 | 1.20 × 10−6 | EPC2 |
18 | 1.70–1.74 | 1,721,220 | 1 | 3.82 × 10−3 | 5.29 × 10−5 | 4.73 × 10−6 | 1.07 × 10−6 | MNX1 |
18 | 1.69–1.78 | 1,758,722 | 4 | 4.17 × 10−3 | 2.37 × 10−4 | 2.26 × 10−5 | 4.09 × 10−6 | MNX1, HOM1 |
18 | 4.16–5.70 | 5,675,281 | 71 | 1.88 × 10−6 | 1.12 × 10−1 | 1.94 × 10−2 | 1.77 × 10−2 | PRKAG2 |
18 | 5.68–5.84 | 5,822,905 | 19 | 6.15 × 10−6 | - | 4.08 × 10−6 | 6.15 × 10−6 | PRKAG2, RHEB, CRYGN |
18 | 6.15–6.21 | 6,190,743 | 63 | 2.31 × 10−6 | - | 8.90 × 10−7 | 2.31 × 10−6 | AGAP3, FASTK, SLC4A2, ASIC3, ABCB8, ATG9B, NOS3 |
18 | 6.18–6.25 | 6,231,446 | 52 | 1.16 × 10−6 | - | 2.01 × 10−6 | 1.16 × 10−6 | ASIC3, ABCB8, ATG9B, NOS3, KCNH2 |
18 | 6.21–6.25 | 6,232,825 | 4 | 3.93 × 10−6 | - | 5.27 × 10−6 | 3.93 × 10−6 | NOS3, KCNH2 |
18 | 6.21–6.27 | 6,246,190 | 25 | 3.93 × 10−6 | - | 1.32 × 10−6 | 3.93 × 10−6 | NOS3, KCNH2 |
18 | 6.23–7.09 | 7,071,468 | 10 | 2.47 × 10−6 | 7.24 × 10−1 | 3.10 × 10−4 | 2.46 × 10−4 | KCNH2, GIMAP2, TAS2R39 |
18 | 9.84–9.98 | 9,961,849 | 7 | 1.34 × 10−4 | 1.43 × 10−2 | 4.47 × 10−6 | 8.26 × 10−6 | TBXAS1, HIPK2 |
SSC | SNP_R (Mb) | T_SNP_P (bp) | SNP_N | p (Canadian) | p (French) | p (Combined LW) | p (Meta) | Candidate Gene |
---|---|---|---|---|---|---|---|---|
1 | 254.70–254.77 | 254,753,857 | 15 | 9.06 × 10−2 | 2.19 × 10−5 | 4.87 × 10−6 | 3.40 × 10−5 | AMBP, KIF12, COL27A1 |
1 | 254.73–254.78 | 254,756,216 | 10 | 6.79 × 10−2 | 7.84 × 10−6 | 1.31 × 10−6 | 4.91 × 10−6 | COL27A1 |
1 | 254.74–254.78 | 254,757,687 | 5 | 3.92 × 10−2 | 3.23 × 10−6 | 7.39 × 10−7 | 1.77 × 10−6 | COL27A1 |
2 | 148.22–148.26 | 148,238,122 | 1 | 6.20 × 10−1 | 3.91 × 10−6 | 4.08 × 10−4 | 4.16 × 10−4 | PPP2R2B |
6 | 156.54–156.58 | 156,564,691 | 2 | 5.73 × 10−4 | 8.95 × 10−4 | 1.06 × 10−5 | 1.71 × 10−6 | - |
6 | 156.55–156.60 | 156,578,616 | 2 | 3.48 × 10−6 | 6.73 × 10−2 | 2.07 × 10−1 | 3.43 × 10−2 | - |
6 | 159.28–159.49 | 159,467,436 | 4 | 3.98 × 10−3 | 5.68 × 10−4 | 3.85 × 10−6 | 2.45 × 10−6 | ZYG11B, PODN |
10 | 54.75–54.79 | 54,772,721 | 1 | 7.92 × 10−3 | 7.50 × 10−4 | 4.94 × 10−6 | 2.19 × 10−5 | MALRD1 |
11 | 24.70–24.78 | 24,756,403 | 2 | - | 5.31 × 10−7 | 3.65 × 10−6 | 5.31 × 10−7 | AKAP11 |
11 | 24.73–24.78 | 24,763,839 | 30 | - | 3.39 × 10−7 | 5.11 × 10−5 | 1.05 × 10−5 | AKAP11 |
11 | 24.75–24.87 | 24,848,044 | 15 | - | 6.15 × 10−7 | 1.90 × 10−3 | 1.64 × 10−3 | DGKH |
11 | 24.93–25.02 | 24,996,968 | 3 | - | 3.98 × 10−7 | 6.50 × 10−8 | 3.98 × 10−7 | DGKH |
11 | 25.04–25.09 | 25,069,836 | 59 | - | 2.85 × 10−6 | 2.19 × 10−4 | 1.09 × 10−4 | VWA8 |
11 | 25.05–25.09 | 25,072,777 | 5 | - | 5.46 × 10−7 | 8.49 × 10−8 | 5.46 × 10−7 | VWA8 |
11 | 25.08–25.25 | 25,229,257 | 10 | - | 1.72 × 10−6 | 1.71 × 10−5 | 1.72 × 10−6 | VWA8 |
11 | 25.21–25.33 | 25,306,498 | 58 | - | 8.50 × 10−6 | 3.40 × 10−6 | 8.50 × 10−6 | VWA8 |
11 | 25.30–25.37 | 51,268,401 | 6 | - | 2.57 × 10−6 | 1.87 × 10−7 | 2.57 × 10−6 | VWA8 |
11 | 51.25–51.29 | 51,268,401 | 1 | 2.87 × 10−6 | 4.07 × 10−1 | 6.18 × 10−2 | 4.61 × 10−3 | - |
14 | 61.85–62.44 | 62,420,628 | 46 | 2.87 × 10−2 | 2.29 × 10−4 | 3.67 × 10−6 | 2.30 × 10−4 | BICC1 |
17 | 46.30–46.38 | 46,358,876 | 4 | 4.03 × 10−6 | 9.01 × 10−1 | 5.28 × 10−3 | 5.89 × 10−4 | GTSF1L |
18 | 45.35–45.39 | 45,371,853 | 1 | 4.60 × 10−4 | 1.55 × 10−3 | 3.95 × 10−6 | 2.36 × 10−6 | HOXA13, HOXA11 |
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Wang, X.; Wang, L.; Shi, L.; Zhang, P.; Li, Y.; Li, M.; Tian, J.; Wang, L.; Zhao, F. GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data. Int. J. Mol. Sci. 2022, 23, 13338. https://doi.org/10.3390/ijms232113338
Wang X, Wang L, Shi L, Zhang P, Li Y, Li M, Tian J, Wang L, Zhao F. GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data. International Journal of Molecular Sciences. 2022; 23(21):13338. https://doi.org/10.3390/ijms232113338
Chicago/Turabian StyleWang, Xiaoqing, Ligang Wang, Liangyu Shi, Pengfei Zhang, Yang Li, Mianyan Li, Jingjing Tian, Lixian Wang, and Fuping Zhao. 2022. "GWAS of Reproductive Traits in Large White Pigs on Chip and Imputed Whole-Genome Sequencing Data" International Journal of Molecular Sciences 23, no. 21: 13338. https://doi.org/10.3390/ijms232113338