171 b)Imputabilidad, es decir, que las instituciones educativas den cuenta a la sociedad de su

7.3.5.1 Selection of daggy Romneys

The DAG3 and DAG8 breeding values were calculated by SIL as described in section 7.3.4.3. The average of the DAG3 and DAG8 breeding values were used to identify the top 60 most daggy Romneys. There were 43 purebred Romneys in the top 60 and these were selected for comparing with the 40 genotyped Arapawas. Twenty- seven of the selected Romneys had been genotyped at AgResearch, Invermay, and the remainder at Illumina.

7.3.5.2 Quality control

Genotypes were quality checked before analysis. The SNPs were discarded if the minor allele frequency across both groups (Romney and Arapawa) were less than 2%. Genotypes were also discarded if the call rate in either group was less than 95%. The SNPs were aligned to Ovine genome v2.0. SNPs that were on an unknown chromosome or chromosome Y were discarded. The first 2 principal components were plotted for quality assurance.

7.3.5.3 Wright’s FST

Wright’s fixation index FST (Wright, 1931; 1943; 1965) was calculated for each

SNP using Microsoft Office Excel 2007 and the smoothed results plotted by chromosome. For each SNP, firstly, the observed heterozygosity in each population (Hobs1: Romney and Hobs2: Arapawa) was estimated as the number of heterozygotes in

the population divide by the number of animals with genotypes for that SNP in that population. Secondly, the expected heterozygosity was calculated for each population (Hexp1: Romney and Hexp2: Arapawa) as 2pq, where p and q were the frequency of the

first and second allele in the population. Thirdly, the expected heteroygosity for the subpopulation (HS) was calculated as (Hobs1*n1 + Hobs2*n2) / ntotal, where n1 and n2 are

the number of Romney and Arapawa sheep with genotypes, respectively for that SNP, respectively and ntotal is the number of Romney plus Arapawa animals with genotypes

for that SNP. Fourthly, the expected heterozygosity for the overall total population (HT)

was calculated as 2݌ሶݍሶ where ݌ሶ and ݍሶ are the frequencies of allele 1 and 2, respectively for Romney and Arapawa as one population. Finally, FST was calculated as (HT–HS) /

195 The fixation index is the difference in expected heterozygosity between the subpopulations relative to the total population, i.e. the extent of genetic differentiation between subpopulations. The results range from 0 (no differentiation) to 1 (complete differentiation, where subpopulations are fixed for the alternative allele). Smoothed estimates were calculated as the moving average with a window of 5 (WIN5) SNPs. This enables discovery of selection peaks across the 5 marker regions to be identified rather than one-off extreme values. A significance level of a WIN5 FST value greater

than 0.30 was set and identified regions were aligned to the Ovine genome v2 to identify underlying genes. Detailed methods are described in Moradi et al. (2012). Empirical P values were calculated by ranking the WIN5 FST values and dividing the

rank of the top individual SNP in the significant region by the number of SNPs with a WIN5 value (n = 46,907).

The resulting FST values were plotted against the average FST values from the ovine

HapMap study (Kijas et al., 2012a), and the correlation calculated.

7.4 Results

7.4.1 GWAS

7.4.1.1 Quality control

After quality control checks, there were 47,084 SNPs retained for the GWAS. Figure 7.1 shows the minor allele frequency distribution of the final SNPs. The mean minor allele frequency was 0.29. There were 154 monomorphic SNPs and 6 with loss of heterozygote (K. Dodds Pers. Comm.).

7.4.1.2 Data summary

The average reliability after selecting those animals with a reliability greater or equal to 0.8h2 ranged from 0.48 to 0.58 for the production and wool traits (Table 7.1), and 0.24 to 0.42 for the fibre traits. Table 7.1 shows a summary of the number of animals, heritability, reliability cut off and resulting average and maximum reliabilities of the EBVs for each trait used in the analysis.

196

Figure 7.1: Minor allele frequency (MAF) for the Ovine 50K SNP chip, following removal of quality control checks, for the 8579 animals retained for GWAS. Arrow indicates mean MAF.

Table 7.1: Summary table of the number of animals (n), heritability (h2_{), reliability cut off} (0.8h2), average and maximum reliability (Av Rel, Max Rel) of breeding values used in the analysis.

Trait1 _{n h}2 _0.8h2 _{Av Rel Max Rel}

WWT 8599 0.177 0.142 0.546 0.998 WWTm 4284 0.115 0.092 0.611 0.980 LW8 8185 0.400 0.320 0.675 0.998 FW12 7088 0.350 0.280 0.582 0.998 DAG3 2800 0.334 0.267 0.474 0.980 DAG8 2114 0.309 0.247 0.514 0.980 BBREECH 1047 0.369 0.295 0.570 0.942 BULK 1245 0.436 0.348 0.545 0.938 LENGTH 1244 0.447 0.358 0.552 0.939 MFD 195 0.418 0.334 0.412 0.644 FDSD 83 0.253 0.203 0.279 0.514 FDCV 105 0.231 0.184 0.263 0.514 CURV 92 0.292 0.233 0.323 0.567 MED% 93 0.202 0.161 0.238 0.485

1_{WWT: weaning weight; WWTm: WWT maternal; LW8: autumn live weight; FW12: fleece weight at 12}

months; DAG3, DAG8: dag score at 3 and 8 months; BBREECH: breech bareness; BULK: wool bulk, LENGTH: wool length; MFD, mean fibre diameter; FDSD: standard deviation of MFD; FDCV: coefficient of variation of MFD; CURV: curvature; MED%: proportion of medullated fibres.

197 Table 7.2: The breed genotypic variance explained by the first 6 principal components (PC) for each trait. Note differences between traits are due to number and selection of animals genotyped that are relevant to the specific analysis.

Trait1 PC1 PC2 PC3 PC4 PC5 PC6 Total WWT 0.521 0.122 0.049 0.036 0.027 0.021 0.775 WWTm 0.467 0.178 0.042 0.021 0.020 0.015 0.744 LW8 0.527 0.124 0.051 0.036 0.024 0.019 0.780 FW12 0.530 0.086 0.053 0.046 0.027 0.021 0.764 DAG3 0.513 0.114 0.036 0.020 0.017 0.015 0.716 DAG8 0.471 0.133 0.032 0.023 0.022 0.021 0.702 BBREECH 0.441 0.060 0.027 0.024 0.018 0.014 0.584 BULK 0.572 0.050 0.021 0.017 0.013 0.012 0.685 LENGTH 0.571 0.051 0.021 0.017 0.013 0.012 0.685 MFD 0.346 0.064 0.037 0.034 0.030 0.022 0.532 FDSD 0.135 0.088 0.076 0.047 0.039 0.033 0.418 FDCV 0.144 0.098 0.070 0.047 0.033 0.026 0.418 CURV 0.147 0.099 0.077 0.046 0.038 0.029 0.436 MED% 0.146 0.105 0.077 0.040 0.035 0.029 0.432

1_{WWT: weaning weight; WWTm: WWT maternal; LW8: autumn live weight; FW12: fleece weight at 12}

months; DAG3, DAG8: dag score at 3 and 8 months; BBREECH: breech bareness; BULK: wool bulk, LENGTH: wool length; MFD, mean fibre diameter; FDSD: standard deviation of MFD; FDCV: coefficient of variation of MFD; CURV: curvature; MED%: proportion of medullated fibres.

7.4.1.3 Principal components

Fitting the first 6 PCs accounted for the majority of the population structure. The first 4 PCs for WWT are shown in Figure 7.2. Table 7.2 shows the proportion of genetic variation contained in the genomic relationship matrix explained by the first PC and the additional variance explained by the second to sixth PCs for each trait. The majority of the variance (above 44%) is explained by the first PC for the production and wool traits LENGTH and BULK. For the fibre traits the first PC only explains 14-15 %, except MFD where it explains 35%.

198

Figure 7.2: The first 4 principal components (PC) calculated from the G matrix for weaning weight. Romney (blue), Coopworth (green), Texel (yellow), Perendale (purple) and others (grey).

7.4.1.4 QQ plots

The observed distribution of -log10(P) values were plotted against the expected

distribution (exponential) under the null hypothesis of no genetic association and no LD between SNPs. The QQ plots for WWT, FW12, DAG3 and DAG8 are shown in Figure 7.3 and for the remaining traits in Appendix 6. The slopes (lambda) for all traits were less than 1 (Table 7.3). The right hand tail deviated above the slope for FW12 (Figure 7.3, B), DAG8 (Figure 7.3, D), and the fibre traits; MFD, FDSD, FDCV, CURV and MED% (Appendix 6). The best SNPs of these traits may be considered significantly above the noise.

199 Table 7.3: Estimate of lambda (slope), and their standard error (s.e.) of the linear regression of the observed -log10(P) on the expected -log10(P)(QQ plot) for each trait.

Trait lambda s.e. Weaning weight 0.66 0.00007 Maternal weaning weight 0.73 0.00006 Live weight at 8 months 0.27 0.00009 Fleece weight at 12 months 0.45 0.00008 Dag score at 3 months 0.58 0.00009 Dag score at 8 months 0.67 0.00011 Breech bareness 0.73 0.00006 Wool bulk 0.70 0.00008 Wool length 0.75 0.00007 Mean fibre diameter (MFD) 0.96 0.00004 Standard deviation of MFD 0.96 0.00012 Coefficient of variation of MFD 0.98 0.00009 Curvature 0.98 0.00014 Proportion of medullated fibres 1.04 0.00006

Figure 7.3: QQ plot for weaning weight (A), fleece weight at 12 months (B), dag score at 3 months (C) and 8 months (D) -log10(P) values. The 0-1 line is in black and the linear regression in red.

A B