Application of GWAS and mGWAS in Livestock and Poultry Breeding
Abstract
:Simple Summary
Abstract
1. Introduction
2. Research Progress of GWAS in Genetic Breeding of Livestock and Poultry
3. Research Progress of mGWAS in Genetic Breeding of Livestock and Poultry
4. The Advantages and Disadvantages of GWAS
5. The Advantages and Disadvantages of mGWAS
6. Conclusions and Perspective
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Species | Variety | Research Traits | Candidate Gene | References |
---|---|---|---|---|
Cattle | Indonesian cattle | Body weight | SUGT1, SF3A3, DSCAM | [17] |
Canadian Holstein cattle | Reproduction | CSh, FSTCc, NRRh | [18] | |
Qinchuan cattle | Body conformation | ADAMTS17, ALDH1A3, CHSY1, MAGEL2, MEF2A, SYNM, CNTNAP5, CTNNA3 | [19] | |
Holstein cattle | Heifer livability | MOG, OR12D2E, OR12D3, OR2H1, OR5V1, OR5V1C, OR5V2, TRIM10, TRIM15 | [20] | |
Hawaiian beef cattle | Carcass weight | RGS20, TCEA1, LYPLA1, MRPL15, EIF5 | [21] | |
Brazilian beef cattle | Carcass and meat quality traits | CAST, PLAG1, XKR4, PLAGL2, AQP3/AQP7, MYLK2, WWOX, CARTPT, PLA2G, etc. | [22] | |
Simmental Holstein cattle | Hair color and birth weight | RNF41, ZC3H10, ERBB3, PMEL, OR10A7 | [23] | |
Sheep | Spanish Merino sheep | Quality wool | EDN2, COL18A1, LRP1B, FGF12, ADAM17 | [24] |
U.S. rangeland ewes | Longevity and reproduction | LPL, ANOS1, ARHGEF26, ASIC2, ASTN2, ATP8A2, CAMK2D, etc. | [25] | |
High mountain Merino sheep | 14 months live weight | FAM184B, NCAPG, MACF1, ANKRD44, DCAF16, FUK, LCORL, SYN3 | [26] | |
Hu sheep | Shape | KITLG, CADM2, MCTP1, COL4A6 | [27] | |
Merino sheep | Fiber and skin wrinkles | ALX4, EIF2AK2, ESRP1, HAS2, MC5R, MX2 | [28] | |
5 varieties including Wadi, Icelandic, Finnsheep, etc. | Litter size | CASK, PLCB4, RPTOR, GRIA2, PLCB1 | [29] | |
Colombian Creole hair sheep | Meat quality | ELOVL2, ARAP2, IBN2, TPM2, etc. | [30] | |
Pig | Jinhua × Piétrain | Meat color | ZBTB17, FAM131C, KIFC3, NTPCR, etc. | [31] |
Large White × Tongcheng pigs | Intramuscular fat traits in longissimus dorsi muscle | NR2F2, MCTP2, MTLN, ST3GAL5, NDUFAB1, etc. | [32] | |
Duroc × (Landrace × Yorkshire) pigs | Somatic skeletal traits | OPRM1, SLC44A5, WASHC4, NOPCHAP1, RHOT1, etc. | [33] | |
Yorkshire pigs | Reproductive traits | ELMO1, AOAH, INSIG2, NUP205, LYPLAL1, etc. | [34] | |
Duroc, Changbai, Dabai | Growth traits | SKAP2, SATB1, PDE7B, PPP1R16B, WNT3, WNT9B | [35] | |
Duroc × Landrace × Yorkshire | Economic characteristics of carcass | TIMP2, EML1, SMN1 | [36] | |
Duroc × Saba, Yorkshire × (Landrace × Saba) | Meat quality traits | GRM8, ANKRD6, MACROD2, CDYL2, CHL1, etc. | [37] | |
Duroc, Yorkshire, Landrace | Pig fatness trait | MC4R, PPARD, SLC27A1, PHLPP1, NUDT3, ILRUN, RELCH, KCNQ5, ITPR3, and U3 | [38] | |
Birds | Wenchang chickens | Feed efficiency and growth traits | PLCE1, LAP3, MED28, QDPR, LDB2 and SEL1L3 | [39] |
Italian local chickens | Shank and eggshell color | MTAP, CDKN2A, CDKN2B, SLC7A11 and MITF | [40] | |
Wenshang Barred, Recessive White, Luxi Mini | Body weight and size | LCORL, LDB2, and PPARGC1A | [41] | |
Rhode Island Red chickens | Eggshell strength | FRY and PCNX2 | [42] | |
Ogye x White Leghorn | Skin color | MTAP, FEM1C, GNAS and EDN3 | [43] | |
Lingnan Yellow chicken×Chinese Huiyang Bearded | Body weight | CAB39L, RCBTB1 | [44] | |
Arbor Acres broiler× Baier layer | Skeletal muscle production traits | LRCH1, CDADC1, CAB39L, FOXO1, NBEA, GPALPP1, etc. | [45] | |
Tibetan chicken, Wenchang chicken, etc. | Chest muscle fatty acid composition | ENO1, ADH1, ASAH1, ADH1C, PIK3CD, WISP1, AKT1, PANK3, C1QTNF2 | [46] | |
NEAUHLF | Growth traits | ACTA1, IGF2BP1, TAPT1, LDB2, PRKCA, TGFBR2, GLI3, SLC16A7, INHBA, BAMBI, GATA4, etc. | [47] |
Species | Variety | Research Contents | Candidate Gene | References |
---|---|---|---|---|
Cattle | Canadian hybrid beef cattle | Heritability of plasma metabolites | CTNNA2 | [16] |
Charolais, Hereford–Angus crosses, and a Beefbooster composite breed | Feed efficiency traits | PLSCR1, AQP9, NEDD4, PRTG, PYGO1, CUX2, NOS1, etc. | [59] | |
Charolais, Hereford–Angus crosses, and a Beefbooster composite breed | Carcass merit traits | CDH13, KMT5B, NDUFS8, ALDH3B1, CHKA, TCIRG1 | [60] | |
Guangxi Buffalo | Buffalo milk traits | ATG16L1 | [61] | |
Pigs | Duroc pig, Landrace pig | Genetic variation in feed efficiency | LRRC4C, SH2D4A, MBOAT1 | [62] |
Birds | Beijing Duck × Liancheng Duck | Skeletal muscle metabolism | AOX1, ACBD5, GADL1, CARNMT2 | [63] |
High-quality chicken strain A03 × Huiyang Bearded Chicken | Chicken blood metabolites from the Qing Dynasty | TDH, AASS, ABCB1, CD36 | [64] |
mGWAS | GWAS | |
---|---|---|
Principle | Metabolite genome association analysis is conducted, utilizing sample metabolomic data as the phenotype [72]. | Phenotypic trait information was gathered from samples, followed by an association analysis between the phenotype and the genome [1]. |
Characteristic | Among different varieties or individuals, the types and contents of metabolites exhibit significant variation, characterized by rich data and precise identification. | Traditional phenotypes exhibit fewer types, are challenging to quantify, and are heavily influenced by environmental factors, leading to elevated rates of false positives. |
Summary | The increased availability of phenotypic data enables the identification of a broader spectrum of gene phenotypes that can be quantified. Enhanced quantification accuracy corresponds to more precise SNP localization. Moreover, ample data facilitate the identification of rare SNP loci. | The localization of genes is relatively limited in terms of quantity, and their localization effect is often poor. Additionally, there can be simultaneous associations with multiple genes, making it challenging to distinguish the main gene responsible. |
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Ren, J.; Gao, Z.; Lu, Y.; Li, M.; Hong, J.; Wu, J.; Wu, D.; Deng, W.; Xi, D.; Chong, Y. Application of GWAS and mGWAS in Livestock and Poultry Breeding. Animals 2024, 14, 2382. https://doi.org/10.3390/ani14162382
Ren J, Gao Z, Lu Y, Li M, Hong J, Wu J, Wu D, Deng W, Xi D, Chong Y. Application of GWAS and mGWAS in Livestock and Poultry Breeding. Animals. 2024; 14(16):2382. https://doi.org/10.3390/ani14162382
Chicago/Turabian StyleRen, Jing, Zhendong Gao, Ying Lu, Mengfei Li, Jieyun Hong, Jiao Wu, Dongwang Wu, Weidong Deng, Dongmei Xi, and Yuqing Chong. 2024. "Application of GWAS and mGWAS in Livestock and Poultry Breeding" Animals 14, no. 16: 2382. https://doi.org/10.3390/ani14162382
APA StyleRen, J., Gao, Z., Lu, Y., Li, M., Hong, J., Wu, J., Wu, D., Deng, W., Xi, D., & Chong, Y. (2024). Application of GWAS and mGWAS in Livestock and Poultry Breeding. Animals, 14(16), 2382. https://doi.org/10.3390/ani14162382