Identification of genetic markers associated with wool quality traits in merino sheep

A candidate gene approach was used to identify potential genetic markers associated with wool quality traits including mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), coefficient of variation of fibre diameter (CVD), prickle factor, curvature, yellowness, brightness, staple strength, staple length, yield, greasy fleece weight (GFW) and clean fleece weight (CFW). Inheritance of potential genetic markers was studied in two half-sib Merino families and assessed for association with the wool quality traits. The sire for one of the half-sib families is referred to as MV144-58-00, and wool measurements from its progeny were taken at 12 (n = 131), 24 (n =128) and 36 (n = 37) months of age. The sire for the second half-sib family is referred to as Stoneyhurst, and wool measurements from its progeny (n = 35) were taken at 12 months of age. Genes that code for the keratin intermediate-filament proteins (KRTs) (KRT1.2, KRT2.10) and the keratin intermediate-filament-associated proteins (KAPs) (KAPl.1, KAPl.3, KAP3.2, KAP6.1, KAP 7, KAP8) were targeted for this investigation, along with the beta 3-adrenergic receptor (ADRB3) gene and microsatellites BfMS and OarFCB193. Polymerase chain reaction (PCR) was used to amplify specific DNA fragments from each locus and PCR- single strand conformational polymorphism (PCR-SSCP) analysis was used to detect polymorphism within the half-sib families for all the loci, except for the KAP1.1 gene, where length polymorphism was detected using agarose gel electrophoresis. Only the loci that were heterozygous for the sire (KAP1.1, KAP1.3, KRT1.2, ADRB3, KAP8) and hence were informative, were genotyped in the progeny. The total number of alleles observed at the KAP1.1, KAP1.3, KRT1.2, KAP8 and the ADRB3 loci were four, ten, six, five and six, respectively. Analysis of each of the informative loci revealed allelic associations with various wool traits. In the MV144-58-00 (genotypes KAP1.1 AB; KAP1.3 BD; KRT1.2 AB; ADRB3 CE) half-sib, inheritance of the KAP1.1 A allele was associated with a higher yield at 24 months of age (P = 0.037). This trend also observed at 36 months of age (P = 0.078). At 12 months of age, the KAP1.1 A allele tended to be associated with increased staple length (P = 0.08). At 36 months of age, the inheritance of the KAP1.1 B allele tended towards being associated with whiter wool (P = 0.080). The MV144-58-00 KAP1.3 D allele tended to be associated with increased yield at 24 and 36 months of age (P = 0.091 and 0.059, respectively), and with lower FDSD at 12 months of age (P = 0.055). The sire KAP1.3 B allele was associated with whiter wool colour at 36 months of age (P = 0.045). The inheritance of the MV144-58-00 KR T1.2 B allele was associated with or tended to be associated with a smaller FDSD (P = 0.040), an increase in staple strength (P = 0.025) and an increase in GFW (P = 0.069) at 12 months of age. At 24 months of age, the KR T1.2 B allele tended to be associated with increased yield (P = 0.057). At 36 months of age, the KRTl.2 A allele was associated with whiter wool (P = 0.019) and tended to be associated with increased crimp within the wool fibre (P = 0.089). In the Stoneyhurst (genotypes KAP1.1 BC; KAP1.3 CJ; KRT1.2 DE; ADRB3 CE) half-sib, inheritance of the KAP1.1 B allele was associated with longer staple length (P = 0.018) and a decrease in wool brightness (P = 0.039). In contrast, KAP1.1 C allele was associated with lowest staple length (P = 0.018) and brighter wool colour (P = 0.039). Associations observed with the inheritance of Stoneyhurst KAP 1.1 alleles were similar to the inheritance ofKAPl.3 alleles. Stoneyhurst KAP1.3 J allele was associated with longer staple length (P = 0.017) and a decrease in wool brightness (P = 0.010). In contrast, KAP1.3 C allele was associated with lowest staple length (P = 0.017) and brighter wool colour (P = 0.010). The Stoneyhurst KRT12 D allele was associated with longer staple length and a decrease in wool brightness (P = 0.033). In contrast, KRT1.2 E allele was associated with lowest staple length (P = 0.033) and brighter wool colour (P = 0.022). Sire alleles at the ADRB3 gene locus were associated with variation in staple strength (P = 0.025) for MV144-58-00's progeny, and with variation in yield (P = 0.023) for Stoneyhurst's progeny. The results obtained in this thesis are consistent with KAP1.1, KAP1.3 and KRT1.2 being clustered on one chromosome because both sires in this study passed on two major KAP1.1-KAP1.3-KRT1.2 haplotypes to their progeny, and the associations with wool traits were very similar for all the three loci. The major sire derived KAP1.1 – KAP1.3 - KRT1.2 haplotypes observed within the MV144-58-00 half-sib were: BBA (frequency of 43.4%; n = 43) and ADB (frequency of 44.4%; n = 44). Other minor haplotypes observed were: ADA (frequency of 4.0%; n = 4); BDA (frequency of 2.0%; n = 2); BBB (frequency of 3.0%; n = 3) and BDB (frequency of 3.0%; n = 3). In the Stoneyhurst half-sib, major sire-derived KAP 1.1 - KAP 1.3 - KR Tl.2 haplotypes observed were CCE (frequency of 53.1 %; n = 17) and BJD (frequency of 40.6%; n = 13). The minor haplotype BJE (frequency of 6.3%; n = 2) was also observed. Statistical analyses within the MVI44-58-00 half-sib showed that KAP1.1 AKAP1.3 D - KRT1.2 B haplotype was associated with increased yield (P = 0.023) and tended towards whiter wool colour (P = 0.059), smaller FDSD (P = 0.081) and stronger staple strength (P = 0.092). In the Stoneyhurst half-sib, the KAP1.1 B - KAP1.3 J - KRT1.2 D haplotype was associated with longer staple length (P = 0.010), while the KAP1.1 C - KAP1.3 C - KRT1.2 E haplotype showed a strong trend with increased wool brightness (P = 0.096). Result from this study indicated that the keratin genes on chromosome 11 are recombining relatively frequently at recombination "hotspots". A high rate of recombination among loci that impact on wool traits would make breeding for consistent wool quality very difficult. The results presented in this thesis suggest that genes coding for the KRTs and KAPs have the potential to impact on wool quality. KAP1.1, KAP1.3 and KRT1.2 could potentially be exploited in gene marker-assisted selection programmes within the wool industry to select for animals with increased staple length, 'increased staple strength, higher yield and brighter wool. This study was however limited to two half-sib families, and further investigation is required.