Genome-wide association analysis of nine reproduction and morphological traits in three goat breeds from Southern China
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Objective: This study aimed to investigate the significant single nucleotide polymorphisms (SNPs) and genes associated with nine reproduction and morphological traits in three breed populations of Chinese goats. Methods: The genome-wide association of nine reproduction and morphological traits (litter size, nipple number, wattle, skin color, coat color, black dorsal line, beard, beard length, and hind leg hair) were analyzed in three Chinese native goat breeds (n = 336) using an Illumina Goat SNP50 Beadchip. Results: A total of 17 genome-wide or chromosome-wide significant SNPs associated with one reproduction trait (litter size) and six morphological traits (wattle, coat color, black dorsal line, beard, beard length, and hind leg hair) were identified in three Chinese native goat breeds, and the candidate genes were annotated. The significant SNPs and corresponding putative candidate genes for each trait are as follows: two SNPs located on chromosomes 6 (CSN3) and 24 (TCF4) for litter size trait; two SNPs located on chromosome 9 (KATNA1) and 1 (UBASH3A) for wattle trait; three SNPs located on chromosome 26 (SORCS3), 24 (DYM), and 20 (PDE4D) for coat color trait; two SNPs located on chromosome 18 (TCF25) and 15 (CLMP) for black dorsal line trait; four SNPs located on chromosome 8, 2 (PAX3), 5 (PIK3C2G), and 28 (PLA2G12B and OIT3) for beard trait; one SNP located on chromosome 18 (KCNG4) for beard length trait; three SNPs located on chromosome 17 (GLRB and GRIA2), 28 (PGBD5), and 4 for hind leg hair trait. In contrast, there were no SNPs identified for nipple number and skin color. Conclusion: The significant SNPs or genes identified in this study provided novel insights into the genetic mechanism underlying important reproduction and morphological traits of three local goat breeds in Southern China as well as further potential applications for breeding goats.
Abstract
Objective: This study aimed to investigate the significant single nucleotide polymorphisms (SNPs) and genes associated with nine reproduction and morphological traits in three breed populations of Chinese goats. Methods: The genome-wide association of nine reproduction and morphological traits (litter size, nipple number, wattle, skin color, coat color, black dorsal line, beard, beard length, and hind leg hair) were analyzed in three Chinese native goat breeds (n = 336) using an Illumina Goat SNP50 Beadchip. Results: A total of 17 genome-wide or chromosome-wide significant SNPs associated with one reproduction trait (litter size) and six morphological traits (wattle, coat color, black dorsal line, beard, beard length, and hind leg hair) were identified in three Chinese native goat breeds, and the candidate genes were annotated. The significant SNPs and corresponding putative candidate genes for each trait are as follows: two SNPs located on chromosomes 6 (CSN3) and 24 (TCF4) for litter size trait; two SNPs located on chromosome 9 (KATNA1) and 1 (UBASH3A) for wattle trait; three SNPs located on chromosome 26 (SORCS3), 24 (DYM), and 20 (PDE4D) for coat color trait; two SNPs located on chromosome 18 (TCF25) and 15 (CLMP) for black dorsal line trait; four SNPs located on chromosome 8, 2 (PAX3), 5 (PIK3C2G), and 28 (PLA2G12B and OIT3) for beard trait; one SNP located on chromosome 18 (KCNG4) for beard length trait; three SNPs located on chromosome 17 (GLRB and GRIA2), 28 (PGBD5), and 4 for hind leg hair trait. In contrast, there were no SNPs identified for nipple number and skin color. Conclusion: The significant SNPs or genes identified in this study provided novel insights into the genetic mechanism underlying important reproduction and morphological traits of three local goat breeds in Southern China as well as further potential applications for breeding goats.
참고문헌 (33)
- Luigi-Sierra MG, "A genome-wide association analysis for body, udder, and leg conformation traits recorded in Murciano-Granadina goats", J Dairy Sci, 103, pp.11605~11617 (2020)[DOI]
- Saleh AA, "Evaluation of morphological traits and physiological variables of several Chinese goat breeds and their crosses", Trop Anim Health Prod, 53, pp.74~ (2021)[DOI]
- Rabiul Islam, "Genome-wide association analysis reveals the genetic locus for high reproduction trait in Chinese Arbas Cashmere goat", Genes & Genomics, 42(8), pp.893~899 (2020), 한국유전학회[DOI]
- Abdoli R, "Genomewide association study of first lambing age and lambing interval in sheep", Small Rumin Res, 178, pp.43~45 (2019)[DOI]
- Peng WF, "A genome-wide association study reveals candidate genes for the supernumerary nipple phenotype in sheep(Ovis aries)", Anim Genet, 48, pp.570~579 (2017)[DOI]
- Ghaffarilaleh V, "Variation and frequency of supernumerary teats, litter size, histological features and the fibroblast growth factor 2(FGF-2)gene expression pattern in goats", Theriogenology, 179, pp.141~148 (2022)[DOI]
- Martin P, "Heritability and genome-wide association mapping for supernumerary teats in French Alpine and Saanen dairy goats", J Dairy Sci, 99, pp.8891~8900 (2016)[DOI]
- Nazari-Ghadikolaei A, "Genomewide association studies identify candidate genes for coat color and mohair traits in the Iranian Markhoz goat", Front Genet, 9, pp.105~ (2018)[DOI]
- Eugenio Jara, "Revealing the genetic basis of eyelid pigmentation in Hereford cattle", Journal of Animal Science, 100(5) (2022), Oxford University Press (OUP)[DOI]
- García-Gámez E, "Using regulatory and epistatic networks to extend the findings of a genome scan : identifying the gene drivers of pigmentation in merino sheep", PLoS One, 6, pp.e21158~ (2011)[DOI]
- Wang FH, "Genome-wide association study of fleece traits in Inner Mongolia Cashmere goats", Anim Genet, 52, pp.375~379 (2021)[DOI]
- Zhao BR, "Integration of a singlestep genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep", Genet Sel Evol, 53, pp.56~ (2021)[DOI]
- Reber I, "Wattles in goats are associated with the FMN1", GREM1 region on chromosome 10, 2015, pp.46, 316~320
- Tosser-Klopp G, "Design and characterization of a 52K SNP chip for goats", PLoS One, 9, pp.e86227~ (2014)[DOI]
- Purcell S, "PLINK : a tool set for whole-genome association and population-based linkage analyses", Am J Hum Genet, 81, pp.559~575 (2007)[DOI]
- Aulchenko YS, "GenABEL : An R library for genome-wide association analysis", Bioinformatics, 23, pp.1294~1296 (2007)[DOI]
- Alexander DH, "Fast model-based estimation of ancestry in unrelated individuals", Genome Res, 9, pp.1655~1664 (2009)[DOI]
- Rout PK, "Post translational modifications of milk proteins in geographically diverse goat breeds", Sci Rep, 11, pp.5619~ (2021)[DOI]
- Lan XY, "Relationship between polymorphisms of CSN3, CSN1S2 and β-lg genes and litter sizes of Xinong Saanen dairy goat", Scientia Agricultura Sinica, 38, pp.2333~2338 (2005)
- Lan R, "Genome-wide association study of lambing number in goat", Acta Vet Zootec Sin, 46, pp.549~554 (2015)[DOI]
- Islam R, "Genome-wide runs of homozygosity, effective population size, and detection of positive selection signatures in six Chinese goat breeds", Genes(Basel), 10, pp.938~ (2019)[DOI]
- Tao L, "Genome-wide screening of candidate genes for litter size in Yunshang Black goats", pp.2021
- Xin D, "Insertion", deletion variants within the IGF2BP2 gene identified in reported genome-wide selective sweep analysis reveal a correlation with goat litter size, 2021, pp.22, 757~766
- Hardwick LJA, "Size of supernumerary teats in sheep correlates with complexity of the anatomy and microenvironment", J Anat, 236, pp.954~962 (2020)[DOI]
- Tao L, "Identification of genes associated with litter size combining genomic approaches in Luzhong mutton sheep", Anim Genet, 52, pp.545~549 (2021)[DOI]
- Subkhangulova A, "SORCS1 and SORCS3 control energy balance and orexigenic peptide production", EMBO Rep, 19, pp.e44810~ (2018)[DOI]
- Marchesi JAP, "Exploring the genetic architecture of feed efficiency traits in chickens", Sci Rep, 11, pp.4622~ (2021)[DOI]
- Henkel J, "Introgression of ASIP and TYRP1 alleles explains coat color variation in valais goats", J Hered, 112, pp.452~457 (2021)[DOI]
- Wang XW, "Quantitative analysis of mRNA expression of Tan sheep coat color candidate genes MC1R and TCF25", Acta Agric Zhejiangensis, 32, pp.1351~1356 (2020)[DOI]
- Yang KX, "Copy number variation in HOXB7 and HOXB8 involves in the formation of beard trait in chickens", Anim Genet, 51, pp.958~963 (2020)[DOI]
- Zuñiga-Garcia S, "Does size matters? Relationships among social dominance and some morphometric traits upon out-of-season reproductive outcomes in anestrus dairy goats treated with P4 + eCG", Biology (Basel), 9, pp.354~ (2020)[DOI]
- Ren H, "Comparative transcriptome and histological analyses provide insights into the prenatal skin pigmentation in goat(Capra hircus)", Physiol Genomics, 49, pp.703~711 (2017)[DOI]
- Peñagaricano F, "Gene expression analysis identifies new candidate genes associated with the development of black skin spots in Corriedale sheep", J Appl Genet, 53, pp.99~106 (2012)[DOI]
