Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animals, Genotyping, and Data Editing
2.3. Statistical Analysis
2.4. Candidate Gene Detection
3. Results
3.1. Genome-wide Association Study and FST
3.2. Canonical Discriminant Analysis
3.3. Candidate Gene Detection
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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SNP | GWAS | Raw CC | ||
---|---|---|---|---|
BTA 1 | Disease 2 | Can1 | Can2 | |
ARS-BFGL-NGS-13673 | 1 | Ma | 0.63 | 0.52 |
ARS-USDA-AGIL-chr2-17084934-000418 | 2 | Ma | 0.27 | 0.59 |
ARS-USDA-AGIL-chr4-114395607-000108 | 4 | Ar, Ma | −0.19 | 0.05 |
ARS-USDA-AGIL-chr7-12174899-000752 | 7 | Ar | −0.18 | −0.14 |
Hapmap44668-BTA-119022 | 7 | Ar | 0.62 | −0.26 |
ARS-USDA-AGIL-chr7-18201332-000761 | 7 | Ma | 0.66 | 0.88 |
ARS-USDA-AGIL-chr8-84099468-000783 | 8 | Ar | −0.15 | −0.72 |
ARS-USDA-AGIL-chr10-25594159-000176 | 10 | Ar, Ma | −0.37 | 0.15 |
ARS-USDA-AGIL-chr11-36809347-000009 | 11 | Ar, Ma | −0.16 | 0.22 |
ARS-BFGL-NGS-15423 | 16 | Ma | 0.02 | 0.02 |
BovineHD1600007856 | 16 | Ma | 0.37 | 0.25 |
BovineHD4100012725 | 16 | Ma | 0.72 | −0.11 |
ARS-USDA-AGIL-chr17-6999864-000318 | 17 | Ma | −0.09 | −0.17 |
ARS-USDA-AGIL-chr22-32285822-000477 | 22 | Ar, Ma | 0.19 | −0.08 |
BovineHD2400015279 | 24 | Ar | −0.57 | 0.56 |
ARS-USDA-AGIL-chr24-25995108-000530 | 24 | Ar, Ma | −0.17 | −0.47 |
ARS-USDA-AGIL-chr25-1930875-000536 | 25 | Ar | −0.12 | 0.45 |
BovineHD4100017966 | 26 | Ma | −0.02 | −0.78 |
BovineHD2600011259 | 26 | Ma | 0.31 | 0.42 |
BovineHD2600011282 | 26 | Ma | 0.42 | 0.5 |
BovineHD2600014129 | 26 | Ma | 0.59 | 0.85 |
BovineHD2800000629 | 28 | Ar | 0.56 | −1.17 |
ARS-USDA-AGIL-chr29-39842168-000583 | 29 | Ar | −0.40 | −0.65 |
Within-class average | ||||
Arthrogryposis | Ar | 1.23 | −1.55 | |
Macroglossia | Ma | 2.03 | 1.13 | |
Healthy control | He | −1.62 | 0.16 |
BTA | SNP | Gene | |||
---|---|---|---|---|---|
Name | Position | Symbol | Name | Location | |
4 | ARS-USDA-AGIL-chr4-114395607-000108 | 113,596,650 | KCNH2 | Potassium voltage-gated channel, sub-family H, member 2 | 113,526,185..113,562,025 |
NOS3 | Nitric oxide synthase 3 | 113,577,075..113,595,527 | |||
ATG9B | Autophagy-related 9B | 113,594,821..113,605,878 | |||
ABCB8 | ATP binding cassette subfamily B member 8 | 113,605,775..113,623,178 | |||
ASIC3 | acid sensing ion channel subunit 3 | 113,624,088..113,629,085 | |||
7 | ARS-USDA-AGIL-chr7-12174899-000752 | 11,085,449 | ZNF333 | zinc finger protein 333 | 11,071,151..11,102,144 |
ADGRE3 | adhesion G protein-coupled receptor E3 | 11,116,555..11,181,632 | |||
Hapmap44668-BTA-119022 | 85,227,970 | // | no genes in the considered interval | ||
8 | ARS-USDA-AGIL-chr8-84099468-000783 | 82,677,581 | ERCC6L2 | ERCC excision repair 6 like 2 | 82,557,942..82,712,671 |
10 | ARS-USDA-AGIL-chr10-25594159-000176 | 25,539,231 | OR4E2 | olfactory receptor, family 4, subfamily E, member 2 | 25,539,229..25,540,170 |
OR10G2 | olfactory receptor, family 10, subfamily G, member 2 | 25,587,007..25,587,963 | |||
11 | ARS-USDA-AGIL-chr11-36809347-000009 | 36,957,396 | ACYP2 | acylphosphatase 2 | 36,831,155..37,010,456 |
TSPYL6 | TSPY like 6 | 36,954,224..36,957,858 | |||
22 | ARS-USDA-AGIL-chr22-32285822-000477 | 32,169,050 | FRMD4B | FERM domain containing 4B | 32,022,767..32,382,939 |
24 | ARS-USDA-AGIL-chr24-25995108-000530 | 25,684,356 | DSG2 | desmoglein 2 | 25,602,973..25,653,973 |
DSG3 | desmoglein 3 | 25,666,298..25,699,081 | |||
DSG4 | desmoglein 4 | 25,725,711..25,755,364 | |||
BovineHD2400015279 | 53,288,962 | // | no genes in the considered interval | ||
25 | ARS-USDA-AGIL-chr25-1930875-000536 | 1,929,340 | CCNF | cyclin F | 1,947,654..1,965,422 |
TEDC2 | tubulin epsilon and delta complex 2 | 1,966,625..1,970,947 | |||
NTN3 | netrin 3 | 1,975,804..1,978,415 | |||
28 | BovineHD2800000629 | 2,661,658 | // | no genes in the considered interval | |
29 | ARS-USDA-AGIL-chr29-39842168-000583 | 39,215,494 | PAG9 | pregnancy-associated glycoprotein 9 | 39,237,412..39,246,707 |
BTA | SNP | Gene | |||
---|---|---|---|---|---|
Name | Position | Symbol | Name | Location | |
1 | ARS-BFGL-NGS-13673 | 86,784,250 | // | no genes in the considered interval | |
2 | ARS-USDA-AGIL-chr2-17084934-000418 | 17,077,000 | ZNF385B | zinc finger protein 385B | 16,957,646..17,442,243 |
TRNAC-ACA | transfer RNA cysteine | 17,082,352..17,082,423 | |||
4 | ARS-USDA-AGIL-chr4-114395607-000108 | 113,596,650 | KCNH2 | potassium voltage-gated channel, sub-family H, member 2 | 113,526,185..113,562,025 |
NOS3 | nitric oxide synthase 3 | 113,577,075..113,595,527 | |||
ATG9B | autophagy related 9B | 113,594,821..113,605,878 | |||
ABCB8 | ATP binding cassette subfamily B member 8 | 113,605,775..113,623,178 | |||
ASIC3 | acid-sensing ion channel subunit 3 | 113,624,088..113,629,085 | |||
7 | ARS-USDA-AGIL-chr7-18201332-000761 | 16,970,401 | CERS4 | ceramide synthase 4 | 16,897,965..16,933,292 |
CD320 | CD320 molecule | 16,952,355..16,957,071 | |||
NDUFA7 | NADH:ubiquinone oxidoreductase subunit A7 | 16,960,703..16,967,936 | |||
RPS28 | ribosomal protein S28 | 16,968,061..16,969,193 | |||
KANK3 | KN motif and ankyrin repeat domains 3 | 16,969,360..16,980,814 | |||
ANGPTL4 | angiopoietin like 4 | 17,005,585..17,012,655 | |||
10 | ARS-USDA-AGIL-chr10-25594159-000176 | 25,539,231 | OR4E2 | olfactory receptor, family 4, subfamily E, member 2 | 25,539,229..25,540,170 |
OR10G2 | olfactory receptor, family 10, subfamily G, member 2 | 25,587,007..25,587,963 | |||
11 | ARS-USDA-AGIL-chr11-36809347-000009 | 36,957,396 | ACYP2 | acylphosphatase 2 | 36,831,155..37,010,456 |
TSPYL6 | TSPY like 6 | 36,954,224..36,957,858 | |||
16 | BovineHD1600007856 | 27,494,192 | NVL | nuclear valosin-containing protein-like | 27,322,130..27,502,627 |
CNIH4 | cornichon family AMPA receptor auxiliary protein 4 | 27,529,034..27,543,276 | |||
ARS-BFGL-NGS-15423 | 72,258,249 | KCNH1 | potassium voltage-gated channel subfamily H member 1 | 72,205,829..72,642,416 | |
BovineHD4100012725 | 72,266,300 | ||||
17 | ARS-USDA-AGIL-chr17-6999864-000318 | 7,013,884 | LRBA | lipopolysaccharide responsive beige-like anchor protein | 6,799,299..7,556,716 |
22 | ARS-USDA-AGIL-chr22-32285822-000477 | 32,169,050 | FRMD4B | FERM domain containing 4B | 32,022,767..32,382,939 |
24 | ARS-USDA-AGIL-chr24-25995108-000530 | 25,684,356 | DSG2 | desmoglein 2 | 25,602,973..25,653,973 |
DSG3 | desmoglein 3 | 25,666,298..25,699,081 | |||
DSG4 | desmoglein 4 | 25,725,711..25,755,364 | |||
26 | BovineHD4100017966 | 40,441,709 | PLPP4 | phospholipid phosphatase 4 | 40,509,729..40,656,785 |
BovineHD2600011259 | 40,460,199 | ||||
BovineHD2600011282 | 40,517,972 | ||||
BovineHD2600014129 | 48,680,201 | // | no genes in the considered interval |
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Di Stasio, L.; Albera, A.; Pauciullo, A.; Cesarani, A.; Macciotta, N.P.P.; Gaspa, G. Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed. Animals 2020, 10, 1732. https://doi.org/10.3390/ani10101732
Di Stasio L, Albera A, Pauciullo A, Cesarani A, Macciotta NPP, Gaspa G. Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed. Animals. 2020; 10(10):1732. https://doi.org/10.3390/ani10101732
Chicago/Turabian StyleDi Stasio, Liliana, Andrea Albera, Alfredo Pauciullo, Alberto Cesarani, Nicolò P. P. Macciotta, and Giustino Gaspa. 2020. "Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed" Animals 10, no. 10: 1732. https://doi.org/10.3390/ani10101732
APA StyleDi Stasio, L., Albera, A., Pauciullo, A., Cesarani, A., Macciotta, N. P. P., & Gaspa, G. (2020). Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed. Animals, 10(10), 1732. https://doi.org/10.3390/ani10101732