An assessment of population stratification and haplotype based Genome-wide association for wool quality traits in Zandi sheep breed

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MOHAMMADI H.; RAFAT S.A.; MORADI SHAHREBABAK H.; SHODJA J.; MORADI M.H.

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Journal: ANIMAL SCIENCE RESEARCHES (FACULTY OF AGRICULTURE, UNIVERSITY OF TABRIZ) Year:2018 | Volume:28 | Issue:2 Page(s): 193-204

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Title

An assessment of population stratification and haplotype based Genome-wide association for wool quality traits in Zandi sheep breed

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Keywords

Candidate geneQ1

Genome-wide association studyQ1

Population stratificationQ1

Wool qualityQ1

Zandi sheepQ1

Abstract

Introduction: Identifying of genes with large effects on economically important traits, has been one of the important goals in sheep breeding. Over the last decade, by the advent of genome-wide panels of single nucleotide polymorphisms (SNPs), it has become possible to identify and localize QTLs for complex traits in many livestock species. One important obstacle in association studies is the confounding effect of population structure. Because this effect generally increases in proportion to population size, population structure remains a major concern in association analyses. To date, 98 QTLs for wool traits have been reported via genome scan based on marker-QTL linkage analyses (http: //cn. animalgenome. org/cgi-bin/QTLdb/OA/index, 27 Aug, 2017). Compared with traditional QTL mapping strategies, a GWAS has major advantages both in its power to detect causal variants with modest effects and in defining narrower genomic regions harboring causal variants for economically important traits. In this study, we assessed Population stratification and performed a Genome-wide association study (GWAS) of Wool quality traits in Zandi sheep. Material and methods: A total of 96 Iranian Zandi sheep was used in the study. The following four traits were analyzed: staple length (SL), mean fiber diameter (MFD), fiber diameter coefficient of variation (FDCV), and the proportion of fiber that was equal or more than 30 µ m (F≥ 30). Animals were genotyped using 50 K SNPChip panel. Quality control of the genotype data consisted in removing SNPs with a call rate less than 95 %, SNPs with a minor allele frequency (MAF) less than 5 %, SNPs with more than x % missing genotypes, and SNPs that deviated strongly from Hardy– Weinberg equilibrium (P < 10 − 6 ). The PLINK was used to generate the matrix using the GLM algorithm. In this study, although the resources of this breed were very clear, we still examined the distribution of the test statistics obtained from the numerous association tests. We also assessed their deviation from the expected distribution of no SNPs being associated with the trait of interest using a quantile-quantile (Q-Q) plot, which is commonly used to analyze Population stratification in GWAS. We use SNPEVG tool to show the (Q-Q) plot. The Bonferroni method was used to adjust for multiple testing from the number of SNP loci detected. We declared a significant SNP at the genomewide significance level if the raw P-value was0. 05/N, here N is the number of SNP loci tested in the analysis. The exact positions of the annotated genes were extracted from the latest sheep genome Oar_v4. 0 assembly along with the NCBI annotation release 102 of the sheep genome. To investigate if the significant SNPs detected in this study were within the range of previously identified QTL for relevant traits, we searched for meat or production QTL in the Animal QTLdb within a 1-Mb region on both sides of each significant haplotype. Results and discussion: After quality control, 2 individuals were excluded, leaving 94 sheep for the association analysis. Additionally, we removed 1070 SNPs with call rates less than 95% and 7717 SNPs with MAF less than 0. 05. A total of 40, 879 SNPs passed these quality-control filters and were retained in the dataset. These SNPs were distributed across 26 autosomes, with the number of SNPs per chromosome ranging from 747 to 5694, and with a mean distance between adjacent SNPs ranging from 50. 4 to 68. 7 kb. Wool MFD was 29. 85± 0. 03 µ m with an individual sheep range of 22. 4-39. 04 µ m. The overall coefficient of variation of fiber diameter was 43. 12%± 0. 7% with an individual sheep range of 19. 7%– 68. 0%. The average percentages of fiber that had equal or more than 30 µ m were 27. 04± 0. 03% with an individual sheep range of 12. 04-43. 10%. Average wool staple length was 11. 25± 0. 03 cm with an individual sheep range of 6-19 cm. The result from genomic control showed weak Population stratification for SL, MDF, FDCV and F≥ 30 between populations of Zandi sheep. The genomic inflation factors (λ gc) for the four traits were equal to 1. 127, 1. 101, 1. 059, and 1. 009 for MDF, FDCV, FD≥ 30 and SL, respectively. However, the Q-Q plots clearly showed there was no evidence of any systematic bias due to population structure or analytical approach in our case. Overally, two significant SNPs at the genome-wise level were identified for FD, and FDCV. No significant SNPs was identified for SLor FD≥ 30. Two Haplotype region within ERBB2 and GNAS genes previously reported in human growth and development hair and skin. Haplotypes were located with previously QTL reported to affect fiber diameter and fiber diameter coefficient of variation in Merino and INRA401 breed sheep. The functions of all of the above genes are directly or indirectly related to skin and hair development. Hair follicles are skin appendages and produce hair; therefore, we hypothesize that these genes control hair follicle development and fiber diameter trait. Conclusion: The results of this study could provide a suite of novel SNP markers and Candidate genes associated with wool traits and hence, may play an important role in understanding the biology of wool traits in fat-tailed sheep.

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APA: Copy

MOHAMMADI, H., RAFAT, S.A., MORADI SHAHREBABAK, H., SHODJA, J., & MORADI, M.H.. (2018). An assessment of population stratification and haplotype based Genome-wide association for wool quality traits in Zandi sheep breed. ANIMAL SCIENCE RESEARCHES (FACULTY OF AGRICULTURE, UNIVERSITY OF TABRIZ), 28(2 ), 193-204. SID. https://sid.ir/paper/370090/en

Vancouver: Copy

MOHAMMADI H., RAFAT S.A., MORADI SHAHREBABAK H., SHODJA J., MORADI M.H.. An assessment of population stratification and haplotype based Genome-wide association for wool quality traits in Zandi sheep breed. ANIMAL SCIENCE RESEARCHES (FACULTY OF AGRICULTURE, UNIVERSITY OF TABRIZ)[Internet]. 2018;28(2 ):193-204. Available from: https://sid.ir/paper/370090/en

IEEE: Copy

H. MOHAMMADI, S.A. RAFAT, H. MORADI SHAHREBABAK, J. SHODJA, and M.H. MORADI, “An assessment of population stratification and haplotype based Genome-wide association for wool quality traits in Zandi sheep breed,” ANIMAL SCIENCE RESEARCHES (FACULTY OF AGRICULTURE, UNIVERSITY OF TABRIZ), vol. 28, no. 2 , pp. 193–204, 2018, [Online]. Available: https://sid.ir/paper/370090/en

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