Genome-Wide Scan of Wool Production Traits in Akkaraman Sheep

The objective of this study was to uncover the genetic background of wool quality, a production trait, by estimating genomic heritability and implementing GWAS in Akkaraman sheep. The wool characteristics measured included fibre diameter (FD) and staple length (SL) at the age of 8 months and yearling fibre diameter (YFD), yearling staple length (YSL) and yearling greasy fleece weight (YGFW) at 18 months of age. Animals were genotyped using the Axiom 50 K Ovine Genotyping Array. Maximum likelihood estimations of a linear mixed model (LMM) were used to estimate genomic heritability, where GWAS was conducted following a score test of each trait. Genomic heritability estimates for the traits ranged between 0.22 and 0.63, indicating that phenotypes have a moderate range of heritability. One genome- and six chromosome-wide significant SNPs were associated with the wool traits in Akkaraman lambs. Accordingly, TRIM2, MND1, TLR2, RNF175, CEP290, TMTC3, RERE, SLC45A1, SOX2, MORN1, SKI, FAAP20, PRKCZ, GABRD, CFAP74, CALML6 and TMEM52 genes as well as nine uncharacterized regions (LOC101118971, LOC105609137, LOC105603067, LOC101122892, LOC106991694, LOC106991467, LOC106991455, LOC105616534 and LOC105609719) were defined as plausible candidates. The findings of this study shed light on the genetics of wool quality and yield for the Akkaraman breed and suggests targets for breeders during systematic breeding programmes.

Genetic variation in the ovine KAP22-1 gene and its effect on wool traits in Egyptian sheep

The objective of this study was to investigate the genetic polymorphisms in the keratin-associated protein (KAP22-1) gene in Barki (n=206), Rahmani (n=28) and Ossimi (n=28) as the three major sheep breeds in Egypt. Subsequently, the detected variants were correlated with important wool traits. The traits included greasy fleece weight (GFW, g), staple length (SL, cm), prickle factor (PF, %), medullated fiber (MF, %), fiber diameter (FD, µm), crimp percentage (CR, %) and the standard deviation of FD (SDfd, µm), as well as the subjectively assessed traits of kemp score (KS), handle grade (HG), greasy color grade (GCG), bulk grade (BG), luster grade (LG) and staple structure (SST). Animals were genotyped by polymerase chain reaction (PCR) – single strand conformation polymorphism (SSCP). Five SSCP banding patterns representing three different nucleotide variants (A, B and C) were detected. DNA sequencing confirmed three single nucleotide polymorphisms (SNPs). Animal age significantly affected GFW (P=0.007), SDfd (P=0.006), SL (P=0.002), CR (P=0.006), KS (P=0.001), LG (P=0.006) and SST (P=0.013). Likewise, the breed had a significant effect on all studied traits except HG and BG, which was not significant. Results showed significant associations between the KAP22-1 variants and CR (P=0.01), SL (P=0.012), KS (P<0.001) and GCG (P=0.01). Interestingly, animals with BB genotypes tended to produce more wool yield (1163.63±65.91 g) with high SL (8.38±0.20 cm), CR (8.38±0.21 %) and KS (1.98±1.88). Results of this study strongly recommend the KAP22-1 gene as a candidate gene for wool production traits in Egyptian sheep, with new useful insights into the visually assessed wool traits. The identified genetic markers may be incorporated into breeding strategies and genetic improvement programs of wool traits in Egyptian sheep.

Control of sheep flystrike: what's been tried in the past and where to from here

Flystrike remains a serious financial and animal welfare issue for the sheep industry in Australia despite many years of research into control methods. The present paper provides an extensive review of past research on flystrike, and highlights areas that hold promise for providing long-term control options. We describe areas where the application of modern scientific advances may provide increased impetus to some novel, as well as some previously explored, control methods. We provide recommendations for research activities: insecticide resistance management, novel delivery methods for therapeutics, improved breeding indices for flystrike-related traits, mechanism of nematode-induced scouring in mature animals. We also identify areas where advances can be made in flystrike control through the greater adoption of well-recognised existing management approaches: optimal insecticide-use patterns, increased use of flystrike-related Australian Sheep Breeding Values, and management practices to prevent scouring in young sheep. We indicate that breeding efforts should be primarily focussed on the adoption and improvement of currently available breeding tools and towards the future integration of genomic selection methods. We describe factors that will impact on the ongoing availability of insecticides for flystrike control and on the feasibility of vaccination. We also describe areas where the blowfly genome may be useful in providing impetus to some flystrike control strategies, such as area-wide approaches that seek to directly suppress or eradicate sheep blowfly populations. However, we also highlight the fact that commercial and feasibility considerations will act to temper the potential for the genome to act as the basis for providing some control options.

Whole-genome re-sequencing association study on yearling wool traits in Chinese fine-wool sheep

To investigate single nucleotide polymorphism (SNP) loci associated with yearling wool traits of fine-wool sheep for optimizing marker-assisted selection and dissection of the genetic architecture of wool traits, we conducted a genome-wide association study (GWAS) based on the fixed and random model circulating probability unification (FarmCPU) for yearling staple length (YSL), yearling mean fiber diameter (YFD), yearling greasy fleece weight (YGFW), and yearling clean fleece rate (YCFR) by using the whole-genome re-sequenced data (totaling 577 sheep) from the following four fine-wool sheep breeds in China: Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Qinghai fine-wool sheep (QHS), and Aohan fine-wool sheep (AHS). A total of 16 SNPs were detected above the genome-wise significant threshold (P = 5.45E-09), and 79 SNPs were located above the suggestive significance threshold (P = 5.00E-07) from the GWAS results. For YFD and YGFW traits, 7 and 9 SNPs reached the genome-wise significance thresholds, whereas 10 and 12 SNPs reached the suggestive significance threshold, respectively. For YSL and YCFR traits, none of the SNPs reached the genome-wise significance thresholds, whereas 57 SNPs exceeded the suggestive significance threshold. We recorded 14 genes located at the region of ±50-kb near the genome-wise significant SNPs and 59 genes located at the region of ±50-kb near the suggestive significant SNPs. Meanwhile, we used the Average Information Restricted Maximum likelihood algorithm (AI-REML) in the “HIBLUP” package to estimate the heritability and variance components of the four desired yearling wool traits. The estimated heritability values (h²) of YSL, YFD, YGFW, and YCFR were 0.6208, 0.7460, 0.6758, and 0.5559, respectively. We noted that the genetic parameters in this study can be used for fine-wool sheep breeding. The newly detected significant SNPs and the newly identified candidate genes in this study would enhance our understanding of yearling wool formation, and significant SNPs can be applied to genome selection in fine-wool sheep breeding.

Growth, body composition and body wrinkle are favourably correlated with reproductive performance in 2-8-year-old Merino sheep

Context Despite the increased economic importance of reproductive rate in Australian Merinos, there have been low genetic improvements in reproductive performance over the past several decades. Genetically improving reproductive traits through direct selection is restricted by low heritability, low selection intensity directly on reproductive traits, high recording costs and lack of accurate maternal pedigrees in the majority of industry breeding programs. However, indirect selection via correlated traits may be useful as a supplement to direct selection or even on its own where reproduction records are not collected. Aims The aims of the present study were to determine whether various production and quality traits have the potential to be used as indirect selection criteria for genetically improving lifetime reproductive rate, but also whether their selection could be detrimental to reproduction via unfavourable correlations. Methods Reproductive traits studied included pregnancy rate (ewes scanned pregnant per ewe joined), fetal number (number of fetuses scanned per ewe joined), number of lambs born (per ewe joined), number of lambs weaned (per ewe joined) and ewe rearing ability (number of lambs weaned per fetuses scanned). Using data from the SA Selection Demonstration Flocks project (1997–2005), reproductive traits were modelled against various visual and production traits to estimate correlations. Key results Favourable genetic correlations with reproductive traits were estimated with adult ewe bodyweight (0.37–0.50), hogget eye muscle depth (HEMD, 0.40–0.57), fat depth (HFAT, 0.27–0.48) and hogget body (HBWS) and neck wrinkle scores (–0.13 to –0.50). However, the estimates for genetic correlations with hogget eye muscle depth and fat depth were lower when bodyweight was fitted as a covariate, being 0.11–0.35 and 0.17–0.32 respectively. Genetic correlations with ewe rearing ability were generally unfavourable (except those with hogget body and neck wrinkle scores, which were –0.24 and –0.15 respectively), but were either negligible (adult ewe bodyweight, hogget eye muscle depth, fibre diameter and fleece weight) or low in magnitude(fat depth). Unfavourable genetic correlations were observed between fibre diameter and reproductive traits (0.13–0.33). Fleece weight had negligible genetic correlations with all reproductive traits studied (–0.08 to 0.10). Predictions of response to index selection using indirect criteria of one or more of yearling weight, HBWS, HEMD and HFAT measurements projected substantial genetic gains in the number of lambs weaned per ewe joined (NLW). Without reproduction records on the dams of candidates for selection, indirect selection using all four indirect criteria (yearling weight, HBWS, HEMD and HFAT) was predicted to achieve 112–168% of the genetic gains of direct selection for NLW. When all indirect and direct criteria for NLW are combined as part of index selection, even larger gains for NLW are predicted (from 164–215% of direct NLW genetic gains). Conclusions Findings from the present study suggest that bodyweight, HEMD and HFAT and HBWS could be potentially beneficial as indirect selection criteria for lifetime reproductive rate. Selection for reduced fibre diameter is potentially detrimental to reproductive performance; however, selection for improved fleece weight is unlikely to have any effect on genetic gain for reproductive traits. Implications Use of indirect selection for lifetime reproductive could allow for genetic gain when either used with or without the direct selection criteria of reproduction records.

Growth performance and carcass characteristics of Australian prime lambs supplemented with pellets containing canola oil or flaxseed oil

The objective of this study was to investigate the effects of enriched omega-3 oil supplemental pellets, breed and gender on lamb liveweight (LWT), body conformation and carcass characteristics, and to assess the relationships between body conformation and growth under an intensive finishing condition. Sixty ewe and wether prime lambs 7 months old were randomly allocated to one of five dietary treatments: no oil inclusion (Control); 2.5% canola oil; 5% canola oil; 2.5% flaxseed oil and 5% flaxseed oil, balanced by breed (purebred Merinos (M × M) and Corriedale × Merino (C × M) and White Suffolk × Corriedale (W × C) first crosses). Lambs were individually supplemented with 1 kg pellets per day and had free access to lucerne hay and water throughout the 7-week feeding trial, after a 3-week adaptation. Dietary oil inclusion did not cause significant differences in daily feed intake, growth performance and carcass characteristics (P > 0.05). However, first-cross W × C lambs had significantly higher feed intake, chest girth and body conformation score (P < 0.05) than M × M and C × M lambs. Carcass weight, dressing percentage and fat depth of crossbred lambs were significantly higher than those of M × M (P < 0.05). Significant interactions between oil inclusion and breed on average daily gain (ADG) and feed conversion ratio were observed. There were positive and highly significant correlations among LWT, ADG and body conformation measurements (P < 0.01). These findings suggest that prime lamb producers can better manage and match their breeding goals with feed resources by supplementing first-cross C × M lambs with pellets containing 5% canola oil or feeding first-cross W × C lambs with 5% flaxseed oil pellets during the 10-week intensive finishing period.

Genetic evaluation of adult ewe bodyweight and condition: relationship with lamb growth, reproduction, carcass and wool production

This paper reports on genetic variation in the growth, wool production, carcass, reproduction and the bodyweight and body condition of ewes managed in the Information Nucleus Flock (INF), with a focus on evaluating the potential value of including adult ewe bodyweight and condition change traits in the Australian national sheep genetic evaluations provided by Sheep Genetics. Data were collected over a 7-year period (2007–2013) at eight research sites across southern Australia. Approximately 13 700 ewes were weighed and condition scored with ewes on average mated four times during the study. Adult ewe weight and body condition were recorded across the production cycle and the impact of the physiological status and change in status of the ewe on the genetic relationships with lamb growth, carcass and wool production traits was evaluated. Strong genetic correlations between measurements across the production cycle for adult ewe bodyweight and condition, low heritability of change traits, along with weak genetic relationships between change traits and key production traits suggest that in production systems where nutritional challenges can be managed, change traits provide no improvement to the current practice of using static bodyweight and condition records. The genetic variation in weight and body condition and their genetic relationships with production traits were highly consistent across ages and the production cycle. As a result, the current practice by Sheep Genetics to treat adult weight as a single trait with repeat records is most likely sufficient. However, the inclusion of body condition within the Sheep Genetics evaluation has potential to assist in improving maternal performance, and the feed costs associated with maintaining ewe body condition.

The repeatability of textural wool handle

Merino breeders use textural greasy wool handle in ram buying and breeding decisions. The effectiveness of the current wool handle scoring system has not been objectively evaluated. The assessor repeatability of textural wool handle was quantified using three different methods of assessment (on the live animal, as a greasy wool mid-side sample, and as a clean (scoured) wool mid-side sample). The aim of the study was to determine which method of assessment is the most repeatable. Three separately defined repeatability estimates were calculated based on knowledge about the operator. The first estimate was based on the assessor repeatability from the operators used in this study. The second estimate was calculated using replicate values obtained from the same random assessor and the third estimate was based on two results from independent random assessors. The results demonstrated that the assessor repeatability was the greatest when handle was assessed on the clean wool mid-side method, followed by the greasy wool mid-side assessment, and least in the live-animal assessment. However, there was significant variation in the repeatability estimates between the four assessors used in the study. Accounting for fixed effects such as sex, sire group, birth type and rearing type, decreased the variation observed and thus had a negative impact on the assessor repeatability of textural wool handle. The results in this study indicate that non-wool constituents negatively impact on the ability of an assessor to consistently assign a score for textual handle in the greasy wool mid-side method. It is likely that the added cost and time required for scouring to assess handle in the clean state may not be economically viable in most situations. However, the increase in repeatability by assessing handle in greasy wool mid-side method compared with the live-animal assessment indicates that sheep producers should use this strategy when evaluating the trait on-farm.

Fabric and greasy wool handle, their importance to the Australian wool industry: a review

Handle-related properties of woollen fabrics have been demonstrated to be major factors affecting consumer buying attitudes. Handle is the combination of both textural and compressional attributes. Compressional handle has demonstrated processing advantages in woven and knitted fabrics. The handle of processing lots can be manipulated using a variety of technologies but direct manipulation of textural greasy wool handle pre-processing is still crude. On-farm, there is documented evidence that including handle assessment in a selection index provides additional improvements in genetic gain. However, the assessment of greasy wool handle is based on a tactile evaluation of the wool staple by sheep and wool classers, and its application is affected by a lack of framework that instructs assessors on a standard method of assessment. Once a reliable and repeatable protocol is developed, further understanding of the effect greasy wool handle has on final garment quality will be possible.

Genetic relationships between dagginess, breech bareness, and wool traits in New Zealand dual-purpose sheep

Genetic and phenotypic parameters were estimated for dagginess, breech, wool, and fiber traits from approximately 29,500 progeny born in 2009 and 2010 in New Zealand dual-purpose ram breeding sheep flocks. Dagginess is adherence of fecal matter to the wool, and this study investigates the genetic and phenotypic correlations between dagginess and breech and wool traits. Estimates for heritability were moderate (0.21 to 0.44) for the following traits: dag score at 3 and 8 mo (DAG3, DAG8), breech bareness, wool length, wool bulk (BULK), mean fiber diameter, mean fiber diameter SD, mean fiber diameter CV, curvature (CURV), weaning weight at 3 mo, and autumn BW. Heritability estimates for fleece weight at 12 mo and proportion of medullated fibers were high (0.49 and 0.53, respectively). Dag score at 3 mo and DAG8 had low genetic and phenotypic correlations with all traits. Breech bareness had positive genetic and phenotypic correlations with CURV and BULK and mostly negative genetic correlations with all other wool traits. In summary the quantity and attributes of wool were not primary causative factors in fecal accumulation, leaving fecal consistency and composition as the major factors.

Genetic (co)variances between wrinkle score and absence of breech strike in mulesed and unmulesed Merino sheep, using a threshold model

Heritability estimates for, and genetic correlations among neck wrinkle score, body wrinkle score, breech wrinkle score and the absence of breech strike were determined on 2918 16-month hoggets from a selection experiment with South African Merinos. Data were obtained from the lamb drops of 9 years between 1998 and 2007, born as the progeny of 247 sires and 1250 dams. All progeny born until 2002 were subjected to the Modified Mules operation as lambs (n = 1799). However, due to international pressure to phase out the Mules operation, animals from 2003 onwards were not mulesed (n = 1119). During both periods, the experimental animals were maintained in single flocks (separated on sex) after weaning. Progeny were subjected to visual appraisal of wrinkle scores (range) on the neck (1–6), body (1–5) and breech (1–6) at an age of ~16 months. The occurrence of blowfly strike in the breech area (breech strike) was recorded in all animals during the wool growth period of a year from shearing as weaners. Two four-trait animal models were fitted to obtain (co)variance components and ratios from the separate datasets with neck wrinkle score; body wrinkle score, breech wrinkle score and the absence of breech strike, all defined as threshold traits. Estimates of heritability for breech wrinkle score amounted to 0.27 and 0.45 for the mulesed and unmulesed groups, respectively. The absence of breech strike on the underlying scale was also heritable for the mulesed (0.33) and unmulesed (0.46) groups; translating to heritability estimates of 0.074 and 0.157, respectively, on the observed scale. The genetic correlations of wrinkle scores with absence of breech strike were generally favourable, but significant only for neck wrinkle score (–0.57) and breech wrinkle score (–0.45) in the unmulesed group. It was concluded that South African Merino sheep would respond to selection against breech strike under conditions of adequate challenge. Based on results from unmulesed sheep, selection for plainer sheep is also expected to result in a favourable correlated response in breech strike.

Will genetics offer a permanent solution to breech strike?

There are several options for managing flystrike other than mulesing. Breeding for plainer animals that do not require mulesing is an attractive, permanent long-term solution. Breech wrinkle is the key predisposing factor for breech and tail strike. Little effort has been made to reduce wrinkle score in sheep because mulesing was so successful and because there is a perception that reducing wrinkle score will reduce fleece weight. Fleece weight will be reduced if single-trait selection for wrinkle is applied, but if breech wrinkle is included in an index, the negative effect of wrinkle on other production traits can be minimised using the same method as that used to accommodate the negative correlation between fibre diameter and fleece weight. Breeding programs for reduced breech wrinkle should be used in combination with short-term tactical management strategies, especially during the initial stages of the breeding program. The need for tactical management will decrease as the program progresses. This approach can be applied using information that can be recorded easily and at low cost.

Can we breed Merino sheep with softer, whiter, more photostable wool?

Genetic parameters (heritability, phenotypic and genetic correlations) were estimated for a range of visual and measured wool traits recorded from the 2008 shearing of the initial cohort of Merino progeny born into the Sheep CRC’s Information Nucleus Flock. The aim of this initial analysis was to determine the feasibility of selectively breeding Merino sheep for softer, whiter, more photostable wool and to quantify the likely impact on other wool production and quality traits. The estimates of heritability were high for handle and clean colour (0.86 and 0.70, respectively) and moderate for photostability (0.18), with some evidence of maternal effects for both handle and photostability. The phenotypic correlations between handle and clean colour and between handle and photostability were close to zero, indicating that achieving the ‘triple’ objective of softer, whiter, more photostable wool in the current generation through phenotypic selection alone would be difficult. There was evidence of an antagonistic relationship between handle and photostability (–0.36), such that genetic selection for softer wool will produce less photostable wool that will yellow on exposure to UV irradiation. However genetic selection for whiter wool is complementary to photostability and will result in whiter wool that is less likely to yellow. Genetic selection to improve handle, colour and photostability can be achieved with few detrimental effects on other visual and measured wool traits, particularly if they are included in an appropriate selection index.

Predicted responses in Merino sheep from selection combining visually assessed and measured traits

Visually assessed traits for wool quality and ease of management are important to Merino sheep breeders and need to be considered in breeding programs. The present study reports on the predicted correlated responses in visual traits from selection using a range of standard MERINOSELECT™ indices available for use in Australian Merino breeding programs. The effect of including a visual trait in the index is also reported. The visual scored traits were classer grade, wool quality (handle, character and colour), conformation (neck and body wrinkle, front and back leg structure) and fleece rot. The indices covered a range of micron premiums of varying emphasis on increasing fleece weight and reducing fibre diameter. The indices were for Merino wool enterprises (Merino 14%, Merino 7% and Merino 3.5%) and Merino dual purpose wool and meat enterprises (Dual Purpose 7% and Dual Purpose 3.5%). The breeding objectives for the indices included fleece weight, fibre diameter, coefficient of variation of fibre diameter, staple strength, bodyweight and reproduction. Selection over 10 years using the standard MERINOSELECT™ indices is predicted to result in a small correlated improvement in the wool quality traits and classer grade, with a slight deterioration in fleece rot score. The improvement in wool handle, character and colour are greater with those indices that have a greater emphasis on reducing fibre diameter than with those increasing fleece weight. Indices with more emphasis on increased fleece weight than on reduced fibre diameter are predicted to result in small increases in neck and body wrinkle scores and a slight deterioration in wool colour. Inclusion of classer grade, handle, character or colour provided slight extra gains in fleece weight for indices that emphasised reduced fibre diameter through increased accuracy of selection.