D. Allain

Effects of non-genetic factors on production traits of Inner Mongolia cashmere goats in China

Abstract The effects of age, sex, age of dam, year of production, herd, and type of birth on cashmere weight, fiber diameter, fiber length, body weight at birth, weaning and yearling in goats, were based on 12 years data from an Inner Mongolia Albas cashmere goat stock farm. The year of production had significant influence on cashmere weight, fiber diameter and length, and body weight of yearlings and adult goats. Year had no significant effect on weaning weight. In the yearling, males produced more cashmere and were heavier in body weights at birth, weaning and 1 year of age than the females. Adult males were significantly heavier than adult females in cashmere weight, fiber diameter and length, and body weight. In the yearling, age of dam had a significant effect on cashmere weight, fiber diameter and length, body weights at birth, weaning and 1 year of age. In the adult, age of dam also had a significant effect on fiber diameter and body weight. Dams aged 2–4 years produced offsprings with a higher cashmere production than those at older ages. In the yearling, type of birth had significant effects on body weight at birth, weaning and 1 year of age, and fiber length. The herd-within-year effects were significant for all traits studied whereas sex×year effects were significant for cashmere weight and body weights at birth, weaning and 1 year of age. These results indicate that the estimation of breeding value in a selection scheme for cashmere production would be more precise following adjustment for age structures, age of dam, sex, type of birth, herd and significant interactions.

Assessment of genetic variation explained by markers for wool traits in sheep via a segment mapping approach.

A first step towards the genetic dissection of quantitative traits is to perform a genome scan with DNA markers evenly spaced throughout the genome. However, and despite recent advancements in typing technology, a dense genome scan remains a lengthy and very expensive task. An alternative approach is to perform a preliminary typing with a reduced number of markers, not necessarily covering all chromosomes, in order to assess the fraction of total genetic variation explained by typed markers and to identify the most relevant chromosomes to pursue genotyping. The segment mapping strategy (Pe ́rez-Enciso and Varona 2000) is particularly well suited to this end, as it allows us to analyze simultaneously the whole genome. In short, the method consists of partitioning the genome into a series of segments, delimiting specific genome regions that we are interested in analyzing. The method allows us to model the segment as a fixed effect, as in crosses between inbred lines, as a random effect, e.g., in purebred analysis, or as a mixed model, which is useful in analyzing crosses between divergent breeds. The fraction of total genetic variance explained by each segment is subsequently estimated. In this approach, the most relevant question is the fraction of genetic variance explained by the whole segment; we are not interested so much in how many quantitative trait loci (QTLs) there are or in their exact position. We illustrate the proposed strategy in a halfsib design experiment in sheep for QTL detection in wool traits (Allain et al. 1998). The population analyzed came from the synthetic breed INRA401. This breed is a composite Romanov (prolific breed) and Berrichon du Cher (meat breed). It was created in France in 1980 (Ricordeau et al. 1992). The main selection objective is reproductive performance, and there is no selection on wool characteristics. The experimental resource population for the QTL study comprised 30 rams and 690 ewes, which produced 1109 lambs (694 males and 415 females). The number of offspring per sire ranged from 31 to 45. The number of ewes mated to a given ram also ranged from 31 to 45. Most of the ewes were mated to a single ram, but 78 of them were mated to two different rams. Thus, all individuals in the pedigree were indirectly related. Mid-side wool samples were taken from the offspring lambs at a fixed weight, 32 and 38 kg for females and males respectively (about 3 months of age). Staple length (SL) was measured. Then, after a washing treatment, wool samples were analyzed in a textile laboratory (ITF, France) by Optical Fiber Diameter Analysis for determining the mean (MFD) and the coefficient of variation (CVFD) of the fiber diameter. Fiber diameter was assessed according to the IWTO-4795 standard method. In total, 4000 fiber snippets per individual were measured. All sires, dams, and offspring were typed for the 40 microsatellites listed in Fig. 1, distributed among 20 out of the 26 ovine autosomes. The total length covered by all markers was about 600 cM, plus eight chromosomes where only one marker was available. The total length of the sheep genome is about 2500 cM. DNA was extracted from the blood, and PCR-amplified microsatellites were analyzed on a capillary electrophoresis equipment with fluorescent detection. Genetic distances between microsatellites within the same linkage group were estimated with the CRIMAP software. The linear model used to analyze the data was:

Genetics of fibre production and fleece characteristics in small ruminants, Angora rabbit and South American camelids.

This paper reviews genetics of fibre production and fleece characteristics in small ruminants, Angora rabbit and South American camelids with a special distinction between single-coated (SC) and double-coated (DC) species. Considering the biology of fibre production, there are variations in coat composition and structure, fibre growth pattern and fibre structure and quality between these two main kinds of fibre-producing animals. In SC species, all fibres are nearly similar in dimensions and are produced from individual follicles that have a very long period, essentially permanent, of active growth without a synchronous phase of rest between follicles. In contrast, in DC species the fleece comprises a coarse outer coat and a fine inner coat with variations of coat composition and structure, and fibre growth pattern according to the season with a well-defined duration of fibre growth. Genetic basis of hair growth pattern, coat composition and fibre structure are different between species. In small ruminants, these coat characters are additive and because of several genes whereas in rabbit, several autosomal recessive genes determine fibre growth, coat composition and structure. In alpaca, the fleece type (Suri or Huacaya) is determined by a single dominant gene. This paper also reviews genetic parameters of fibre production traits in Angora goat, Angora rabbit and alpaca in which many aspects of the genetic basis of fibre production are analogous. There are many traits controlling both fibre quality and fibre quantity, and most of these traits tend to be moderately to strongly inherited so that a rapid genetic progress in any traits is possible and indeed has been achieved. However, there are differences in breeding programmes. In DC Angora rabbit, selection for one single trait, the easy measurable total fleece weight has general beneficial effects on fleece quality. However, because of antagonistic relations between qualitative and quantitative traits in SC species, achieving this goal requires a multi-trait selection index approach. Gene mapping studies have recently identified several putative quantitative trait loci and major genes affecting fibre and fleece characteristics in sheep, goat and rabbit are reviewed. The whole genome sequence of sheep and rabbit will be available in the near future and the use of high-density single nucleotide polymorphism chip will allow fine mapping and dissection of the genetic basis of many production traits including fibre production and fleece characteristics. The application of these techniques will thus contribute to improving the efficiency, profitability and sustainability of small ruminant and rabbit fibre production.

Genetic parameter estimates of production traits of Angora goats in Argentina

Abstract The objective of this study was to estimate genetic parameters for fleece traits in an experimental Angora goat flock. The fleece traits analyzed in this study were: greasy fleece weight (GFW), average fiber diameter (AFD), percentage of medullated fiber (MF) and corrected greasy fleece weight (CGFW). Direct and maternal variance components and resulting heritabilities were estimated using an animal model and DFREML procedures on the first shearing. Six different animal models were fitted ranging from a simple model with animals as the only random effect to the most comprehensive model allowing for both genetic and environmental maternal effects and a genetic correlation between genetic direct and maternal effects. The models were tested by the Likelihood Ratio Test which indicated that the maternal effects (genetic and environmental) can be ignored. Direct heritabilities estimated with a single trait model were 0.26±0.06, 0.33±0.06, 0.10±0.04 and 0.22±0.06 for GFW, AFD, MF and CGFW, respectively. Genetic correlations were estimated with a multivariate model. The pattern of correlations showed that GFW was positively correlated with AFD and CGFW, 0.51 and 0.53 respectively and negatively correlated with MF −0.72. AFD was negatively correlated with MF and CGFW (−0.18 and −0.37, respectively) and MF was negatively correlated with CGFW −0.65. The repeatability estimates were based upon other files containing information on all shearings. The repeatabilities were 0.64, 0.70, 0.58 and 0.68 for GFW, AFD, MF and CGFW, respectively. Genetic parameters estimated in this study appear reliable and provide a better basis for the Argentina genetic Angora goat improvement program. The moderate heritability level for CGFW added to the negative genetic correlation with AFD may be an alternative solution for selection programs based on a single trait. The high levels of repeatability estimates confirm the benefits of the selection program based on objective measurements observed at the age of year.

Merino sheep: a further look at quantitative trait loci for wool production

A quantitative trait loci (QTL) analysis of wool traits from experimental half-sib data of Merino sheep is presented. A total of 617 animals distributed in 10 families were genotyped for 36 microsatellite markers on four ovine chromosomes OAR1, OAR3, OAR4 and OAR11. The markers covering OAR3 and OAR11 were densely spaced, at an average distance of 2.8 and 1.2 cM, respectively. Body weight and wool traits were measured at first and second shearing. Analyses were conducted under three hypotheses: (i) a single QTL controlling a single trait (for multimarker regression models); (ii) two linked QTLs controlling a single trait (using maximum likelihood techniques) and (iii) a single QTL controlling more than one trait (also using maximum likelihood techniques). One QTL was identified for several wool traits on OAR1 (average curvature of fibre at first and second shearing, and clean wool yield measured at second shearing) and on OAR11 (weight and staple strength at first shearing, and coefficient of variation of fibre diameter at second shearing). In addition, one QTL was detected on OAR4 affecting weight measured at second shearing. The results of the single trait method and the two-QTL hypotheses showed an additional QTL segregating on OAR11 (for greasy fleece weight at first shearing and clean wool yield trait at second shearing). Pleiotropic QTLs (controlling more than one trait) were found on OAR1 (clean wool yield, average curvature of fibre, clean and greasy fleece weightand staple length, all measured at second shearing).

Quantitative trait loci linked to PRNP gene controlling health and production traits in INRA 401 sheep

In this study, the potential association of PrP genotypes with health and productive traits was investigated. Data were recorded on animals of the INRA 401 breed from the Bourges-La Sapinière INRA experimental farm. The population consisted of 30 rams and 852 ewes, which produced 1310 lambs. The animals were categorized into three PrP genotype classes: ARR homozygous, ARR heterozygous, and animals without any ARR allele. Two analyses differing in the approach considered were carried out. Firstly, the potential association of the PrP genotype with disease (Salmonella resistance) and production (wool and carcass) traits was studied. The data used included 1042, 1043 and 1013 genotyped animals for the Salmonella resistance, wool and carcass traits, respectively. The different traits were analyzed using an animal model, where the PrP genotype effect was included as a fixed effect. Association analyses do not indicate any evidence of an effect of PrP genotypes on traits studied in this breed. Secondly, a quantitative trait loci (QTL) detection approach using the PRNP gene as a marker was applied on ovine chromosome 13. Interval mapping was used. Evidence for one QTL affecting mean fiber diameter was found at 25 cM from the PRNP gene. However, a linkage between PRNP and this QTL does not imply unfavorable linkage disequilibrium for PRNP selection purposes.

A Deletion in Exon 9 of the LIPH Gene Is Responsible for the Rex Hair Coat Phenotype in Rabbits (Oryctolagus cuniculus)

The fur of common rabbits is constituted of 3 types of hair differing in length and diameter while that of rex animals is essentially made up of amazingly soft down-hair. Rex short hair coat phenotypes in rabbits were shown to be controlled by three distinct loci. We focused on the “r1” mutation which segregates at a simple autosomal-recessive locus in our rabbit strains. A positional candidate gene approach was used to identify the rex gene and the corresponding mutation. The gene was primo-localized within a 40 cM region on rabbit chromosome 14 by genome scanning families of 187 rabbits in an experimental mating scheme. Then, fine mapping refined the region to 0.5 cM (Z = 78) by genotyping an additional 359 offspring for 94 microsatellites present or newly generated within the first defined interval. Comparative mapping pointed out a candidate gene in this 700 kb region, namely LIPH (Lipase Member H). In humans, several mutations in this major gene cause alopecia, hair loss phenotypes. The rabbit gene structure was established and a deletion of a single nucleotide was found in LIPH exon 9 of rex rabbits (1362delA). This mutation results in a frameshift and introduces a premature stop codon potentially shortening the protein by 19 amino acids. The association between this deletion and the rex phenotype was complete, as determined by its presence in our rabbit families and among a panel of 60 rex and its absence in all 60 non-rex rabbits. This strongly suggests that this deletion, in a homozygous state, is responsible for the rex phenotype in rabbits.

Genetic Diversity and Population Structure in South African, French and Argentinian Angora Goats from Genome-Wide SNP Data

The Angora goat populations in Argentina (AR), France (FR) and South Africa (SA) have been kept geographically and genetically distinct. Due to country-specific selection and breeding strategies, there is a need to characterize the populations on a genetic level. In this study we analysed genetic variability of Angora goats from three distinct geographical regions using the standardized 50k Goat SNP Chip. A total of 104 goats (AR: 30; FR: 26; SA: 48) were genotyped. Heterozygosity values as well as inbreeding coefficients across all autosomes per population were calculated. Diversity, as measured by expected heterozygosity (HE) ranged from 0.371 in the SA population to 0.397 in the AR population. The SA goats were the only population with a positive average inbreeding coefficient value of 0.009. After merging the three datasets, standard QC and LD-pruning, 15 105 SNPs remained for further analyses. Principal component and clustering analyses were used to visualize individual relationships within and between populations. All SA Angora goats were separated from the others and formed a well-defined, unique cluster, while outliers were identified in the FR and AR breeds. Apparent admixture between the AR and FR populations was observed, while both these populations showed signs of having some common ancestry with the SA goats. LD averaged over adjacent loci within the three populations per chromosome were calculated. The highest LD values estimated across populations were observed in the shorter intervals across populations. The Ne for the Angora breed was estimated to be 149 animals ten generations ago indicating a declining trend. Results confirmed that geographic isolation and different selection strategies caused genetic distinctiveness between the populations.

Factors affecting fleece traits of Angora goat in Argentina

Information collected over a fifteen-year period on an experimental flock were analyzed to evaluate the effect of year, age of dam, sex, and type of birth on the characteristics of the fleece at first shearing and the effects of year, age at shearing, and sex on the characteristics of the fleece at subsequent shearings. The variables analyzed were greasy fleece weight (GFW), average fiber diameter (AFD), percentage of medullated fibers (MF) and corrected greasy fleece weight (CGFW). At first shearing significant statistical differences were detected (P<0.05) for year, dams age, sex, and type of birth for GFW and CGFW. For AFD and MF, solely the shearing year was significant (P<0.05). Data collected from the second and following shearings showed differences (P<0.05) due to year of production, age at shearing time, and sex for the four variables analyzed. GFW increases to a maximum at 3–4 years of age, while CGFW is practically constant between 2 to 4 years of age, thus suggesting that the increase in fleece weight is due to an increase of AFD. On the other hand, MF shows a positive tendency related to age, for the analyzed interval of ages. In general, assuming comparisons are conducted within years of production, the results showed the importance of adjusting for age of dam, sex and type of birth for fleece weight, for traits collected at 12 months of age. For traits recorded at the second and later shearings adjustment for sex and age effects would be necessary for fleece weight, fiber diameter and log-transformed percent medullation. This result indicated, that to improve the estimation of breeding values in a selection scheme, it is necessary to use different models to adjust the data according to the yearly sequence of shearings.

A frameshift mutation in the melanophilin gene causes the dilute coat colour in rabbit (Oryctolagus cuniculus) breeds

In rabbit, the dilute locus is determined by a recessive mutated allele (d) that causes the dilution of both eumelanic and pheomelanic pigmentations. In mice, similar phenotypes are determined by mutations in the myosin VA, Rab27a and melanophilin (MLPH) genes. In this study, we investigated the rabbit MLPH gene and showed that a mutation in this gene appears responsible for the dilute coat colour in this species. Checkered Giant F1 families segregating for black and grey (diluted or blue) coat colour were first genotyped for a complex indel in intron 1 of the MLPH gene that was completely associated with the coat colour phenotype (θ = 0.00; LOD = 4.82). Then, we sequenced 6357 bp of the MLPH gene in 18 rabbits of different coat colours, including blue animals. A total of 165 polymorphisms were identified: 137 were in non-coding regions and 28 were in coding exons. One of them was a frameshift deletion in exon 5. Genotyping the half-sib families confirmed the complete cosegregation of this mutation with the blue coat colour. The mutation was analysed in 198 rabbits of 23 breeds. All Blue Vienna and all other blue/grey/ash rabbits in other breeds (Californian, Castor Rex, Checkered Giant, English Spot, Fairy Marburg and Fairy Pearly) were homozygous for this deletion. The identification of MLPH as the responsible gene for the dilute locus in rabbit provides a natural animal model for human Griscelli syndrome type 3 and a new mutant to study the role of this gene on pigmentation.