QTL affecting fleece traits in Angora goats

Small Ruminant Research 71 (2007) 158–164

QTL affecting fleece traits in Angora goats E.M. Cano a , G. Marrube c , D.L. Roldan a , F. Bidinost b , M. Abad b , D. Allain d , D. Vaiman e , H. Taddeo b , M.A. Poli a,∗ a

b

INTA, Instituto de Gen´etica, CICVyA, cc 25, 1712-Castelar, Buenos Aires, Argentina INTA, Estaci´on Experimental Agropecuaria Bariloche, cc 277, 8400-San Carlos de Bariloche, R´ıo Negro, Argentina c Facultad de Ciencias Veterinarias U.B.A., Area de Gen´ etica, Av. Chorroar´ın 280, 1427-Buenos Aires, Argentina d INRA, Station d’Am´ elioration G´en´etique des Animaux, BP27, 31326 Castanet Tolosan, France e Laboratoire de G´ ´ en´etique des Pathologies Placentaires, INSERM-U361, Pavillon Baudelocque, en´etique et Epig´ 123 Bd Port-Royal, 75014 Paris, France Received 8 March 2006; received in revised form 26 May 2006; accepted 6 June 2006 Available online 25 July 2006

Abstract With the aim to detect chromosome segment (quantitative traits loci, QTL) affecting fleece traits in Angora goats, a genome scan using 76 microsatellite markers spanning 1261 cM on 21 chromosomes was conducted. Eight paternal half-sib families were used, which included a total of 288 kids from a dispersed nucleus herd. Mid-side mohair samples were taken from kids at 4 months of age and eight phenotypic fleece traits were measured. We found putatives QTL for coefficient of variation of average fiber diameter (CVAFD) in chromosome 1 and 13, for kemp fiber (KEMP) in chromosome 5 and for discontinuous medullated fibers (DISC) and staple length (SL) in chromosome 2. These results demonstrate the segregation of quantitative traits involved in mohair production. Further studies will concentrate on these regions to characterize the variation of these QTL. © 2006 Elsevier B.V. All rights reserved. Keywords: QTL; Fleece traits; Angora goats; Microsatellites

1. Introduction In the last 10 years many livestock genetic genome maps were developed (Bishop et al., 1994; Rohrer et al., 1996; Crawford et al., 1992; Vaiman et al., 1996; Schibler et al., 1998; Maddox et al., 2001). Microsatellite markers from these maps are used to identify inheritance patterns of linked segments of the genome in structured pedigree populations

∗ Corresponding author. Tel.: +54 11 4621 3316/1683; fax: +54 11 44811316. E-mail address: [email protected] (M.A. Poli).

0921-4488/$ – see front matter © 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.smallrumres.2006.06.002

(Georges et al., 1995). Associations of marker allele with the phenotype of interest indicate the presence of a quantitative traits loci (QTL). Detection of QTL is the first step towards the identification of genes and causal polymorphisms for traits of importance in agriculture (Seaton et al., 2002). Development of reasonably dense microsatellite linkage map for the caprine genome (Vaiman et al., 1996; Schibler et al., 1998) together with the development of efficient and robust linear regression methods to detect and mapping of QTL in simple and complex pedigrees (e.g. Haley and Knott, 1992; Haley et al., 1994; Knott et al., 1996, 1998; de Koning et al., 1998, 2001) have made possible the chromosomal location of loci influencing QTL.

E.M. Cano et al. / Small Ruminant Research 71 (2007) 158–164

The only documented QTL study in goats is related with a highly variable ␣sl-casein polymorphism, whose variants were associated to different rates of protein synthesis (Barbieri et al., 1995; Suarez, 2004). Mohair production in Argentina is located mostly on the northern area of Patagonia (Neuqu´en, Rio Negro and Chubut provinces). Flocks have an average of 150 goats with low individual mohair production (1–2 kg/goat/year). Quality of fleece is characterized by a high proportion of medullated fiber contamination (10% medullated fiber in average), and goods or adequate fiber diameters and staple length. A breeding programme has been established. Abad et al. (2002) used a dispersed nucleus scheme to improve both quantity and quality of mohair produced by Angora goats. The population used by Abad et al. (2002) was used to detect QTL for fleece traits. In this paper, we present the first results of an initial genome-wide scan, using 76 microsatellite markers spanning 1261 cM on 21 chromosomes in 8 half-sibs Angora goat families, with the aim to detect chromosome segment affecting fleece traits. 2. Materials and methods 2.1. Animals and phenotype traits Two hundred and eighty-eight kids from eight Angora bucks were used. The numbers of half-sib offspring per buck ranged from 24 to 71 and were created in two years (2000 and 2001). In the first step the eight bucks were run for a panel of 120 microsatellites. In the second step and taking into account the allele number, polymorphic information content (PIC) (Botstein et al., 1980) and heterozygocity by microsatellite, a panel of 76 markers was chosen to type all progeny in the 21 autosomes. Mid-side mohair samples were taken from kids at 4 months of age and analyzed at the Textile Fibers Laboratory of INTA Bariloche. Eight phenotypic fleece traits were measured: average fiber diameter (AFD; ␮m), coefficient of variation of AFD (CVAFD; %), the percentage of fiber with diameter over 30 ␮m (F30), percentage of kemp fiber (KEMP; %), percentage of continuous medullated fibers (CONT; %), percentage of discontinuous medullated fibers (DISC; %), staple length (SL; mm) and the average curvature of fiber (ACF; ◦ /mm). The samples were analyzed according to IWTO-8-97 and IWTO-12-03. The staple length was measured with a calliper.

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2.2. Microsatellite genotyping DNA was isolated from blood using IsoCode® Stix kit according to the instruction by the supplier (Schleicher & Schuell, USA). Genotypes were generated using microsatellite primers forward labeled with [␥ 32 P]. The PCR reactions were performed using as DNA template 5 ␮l IsoCode® Stix eluate in a final volume of 15 ␮l containing 3 pmol of each primer, 200 ␮M dNTP, 1.5 mM MgCl, 50 mM KCl, 10 mM Tris–Cl, 1.0% (v/v) Triton X-100 and 2 Units of Taq DNA polymerase (Promega, Madison, USA). The reactions were carried out in a PTC-100 thermocycler (MJ-Research Inc., USA) under the following conditions: 95 ◦ C for 3 min followed by a hot-start and a touchdown of 1 ◦ C for cycle from 60 to 53 ◦ C; then 28 cycles of 95 ◦ C for 45 s, 53 ◦ C for 45 s and 72 ◦ C for 1 min and a final extension step of 5 min at 72 ◦ C. PCR products were run on 6% polyacrylamide gel using electrophoresis and the gels dried and autoradiographied. The films were scored independently by two researchers and the results incorporated in a database containing marker genotype and phenotypic data. A panel of 120 microsatellite distributions on 29 autosomes from the goat genetic map (Vaiman et al., 1996; Schibler et al., 1998; http://locus.jouy.inra.fr/) was chosen and used in this study. 2.3. Statistical analysis 2.3.1. Interval analysis These analyses were performed under a half-sib model (Knott et al., 1996) using QTL Express program (Seaton et al., 2002), at http://qtl.cap.ed.ac.uk/. The fixed effects included in the analysis were sex, year of birth (2000 or 2001), birth type (single or twin) and flock (eight levels). Appropriate F-statistic thresholds for chromosome-wise type 1 error rate were generated by permutation test of 10,000 iterations (Churchill and Doerge, 1994; Doerge and Churchill, 1996). To estimate the confidence intervals (CI) of the QTL locations the LOD drop-off method developed by Lander and Botstein (1989) was used. 3. Results In Table 1 phenotypic data for the eight families are shown. In all families the means for the AFD, CVAFD, F30 and ACF traits were quite similar. It is clear that family 8 has high value in almost all traits, mainly for CONT and DISC traits. Family 3 shows the lowest staple length (68.0 mm).

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Table 1 Phenotype data (means ± S.D.) of the progeny at the age of 4 months of the eight Angora goat families Trait AFD (␮m) Family 1 (25) Family 2 (71) Family 3 (28) Family 4 (24) Family 5 (42) Family 6 (31) Family 7 (41) Family 8 (26)

23.9 23.3 23.2 22.7 23.2 23.6 23.4 23.6

± ± ± ± ± ± ± ±

2.5 1.7 1.8 1.1 1.6 1.6 1.5 2.5

CVAFD (%) 27.8 27.4 29.0 28.8 26.7 27.3 28.9 30.7

± ± ± ± ± ± ± ±

2.8 3.8 4.0 2.6 2.7 2.5 3.0 3.4

F30 (%) 17.0 12.1 12.7 11.1 12.2 13.9 14.6 18.3

± ± ± ± ± ± ± ±

KEMP (%)

10.5 8.0 8.1 5.1 7.2 6.9 8.4 10.1

0.8 3.0 1.1 0.9 2.7 1.7 1.9 2.3

± ± ± ± ± ± ± ±

0.9 3.3 1.2 0.9 2.7 3.0 2.6 3.8

CONT (%) 1.3 4.1 2.9 2.5 4.4 3.7 4.2 15.0

± ± ± ± ± ± ± ±

1.1 6.9 3.3 2.0 5.7 3.9 4.0 11.2

DISC (%) 0.7 1.9 1.4 0.6 2.5 2.4 2.0 7.3

± ± ± ± ± ± ± ±

0.9 3.6 1.7 0.9 3.5 2.8 2.2 7.1

SL (mm) 90.0 90.0 68.0 76.0 96.1 93.4 90.5 –

± ± ± ± ± ± ±

11.8 10.5 12.0 16.0 10.9 10.2 11.5

ACF (◦ /mm) 34.6 34.4 34.4 33.9 32.7 33.9 33.9 33.6

± ± ± ± ± ± ± ±

2.8 3.6 1.6 1.9 2.8 3.5 2.7 2.5

(n) Progeny number; AFD, average fiber diameter; CVAFD, coefficient of variation of AFD; F30, the proportion of fiber with diameter over 30 ␮m; KEMP, kemp fiber; CONT, continuous medullated fibers; DISC, discontinuous medullated fibers; SL, staple length; ACF, average curvature of fiber. (–) Data not available.

Table 2 shows the markers used and the bucks heterozygous average by chromosome. Based on the goat genetic map (Schibler et al., 1998) the estimate genome coverage was 1261 cM.

In Table 3, the putative QTL found in this analysis are summarized. By chromosome (CHI) are listed traits with its closest markers associated anywhere in map position in cM.

Table 2 Goat genome coverage by chromosome CHI

No. of markers

CHI lengtha (cM)

Coverageb (cM)

Proportion of heterozygous siresc

Markers (distance, cM)d ILSTS004 (66), BM1312 (30), LSCV06 (16), CSSM32 (27), CSSM19 (17), BM3205 INRA40 (31), ILSTS030 (32), ILSTS082 (46), LSCV37 (32), IDVGA64 (26), OarFCB011 McM58 (37), CSSM54 BMS1788 (19), McM218 (70), LSCV15 (20), OarHH35 OarFCB005 (15), LSCV25 (19), BMS1248 (20), ILSTS034 (21), BM2830 OarAE101 (19), BM0143 (18), BM4621 (21), BM0415 INRA129 (30), McM064 (45), HEL04 (30), CSSM47 INRA127 (6), BM2504 (38), TGLA073 (18), BM4208 (15), INRA144 TGLA272 (12), TGLA378 (25), TGLA102 INRA177 (28), ILSTS049 (78), ILSTS045 BMS0712 (35), BM6404 (26), INRA005 (8), OarVH117 ILSTS059 (32), IL2RA CSSM66 (46), BM0302 (37), BM2934 INRA224 (40), LSCV05 (34), TGLA075 OarVH098 (34), ILSTS058 HAUT14 (30), SCRD232 (20), INRA210 BMS0745 (20), BMS1920 (17), LSCV36 (35), McM210 (30), MAP2 TGLA304 (31), INRA036 (25), ILSTS072 OarCP73 (21), BM1258 (19), OLA-DRB (12), OarHH56 BM4005 (19), BP28 LSCV41 (11), INRAMTT183 (35), OarJMP58

1

6

186

57

0.50

2

6

180

167

0.50

3 4 5

2 4 5

102 140 79

38 38 75

0.31 0.75 0.58

6 8 9

4 4 5

94 137 77

58 60 77

0.70 0.70 0.45

10 11 12 13 14 15 17 18 19

3 3 4 2 3 3 2 3 5

55 156 108 32 119 98 76 74 97

38 28 61 32 83 74 34 50 97

0.67 0.67 0.46 0.50 0.50 0.80 0.63 0.71 0.63

20 23 25 27

3 4 2 3

114 87 40 84

56 52 40 46

0.40 0.50 0.63 0.30

76

2601

1261

0.57

Total

Number of markers used, chromosome length, proportion of buck heterozygous and markers name by chromosome used. a CHI length: chromosome length from goat genetic map (Schibler et al., 1998). b Coverage (in cM) taking into account markers intervals. c Proportion of bucks heterozygous averaged over all markers by chromosome. d The first marker is the closest to the centromere and between brackets the distance (in cM) between markers.

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Table 3 Putative QTL significant at the P < 0.05 and <0.01 chromosome-wise level for four traits by chromosome

Closest markers Position (cM) Confidence intervals (cM)b F-Statistic F-Threshold Number of informative families QTL variance (%) Effect/S.D.

CHI 1

CHI 2

CVAFDa

DISCa

LSCV06 96 12–112 2.9 2.4* 2 5.0 1.6/1.2

ILSTS030 32 22–46 4.2 4.1* 1 9.0 3.9

CHI 5

CHI 13

SLa

KEMPa

CVAFDa

ILSTS082 64 52–92 2.8 2.8* 1 6.6 1.9

LSCV25 20 16–47 2.4 2.2* 2 7.5 0.9/1.5

IL2RA 32 20–32 2.6 2.3* 1 11.3 1.1

Closest markers, position, estimated significance levels (F-statistic), number of informative families, the QTL variance (%), and the effect/standard deviation. CVAFD, coefficient of variation of AFD; AFD, average fiber diameter; DISC, discontinuous medullated fibers; SL, staple length; KEMP, kemp fiber. Chromosome-wise F-statistic threshold at the * P < 0.05 level QTL, as determined by permutation test 10,000 iterations, each 4 centiMorgan (cM). a Trait. b 95% LOD drop-off confidence interval.

The chromosome-wide, F-statistics and threshold of the 0.05 significant level with the 95% of the confidence intervals (LOD drop-off method) are shown. In the best situations they ranged from 12 to 40 cM but they frequently exceeded 50 cM and sometimes included the complete chromosome. QTL were found for four traits. Putative QTL for CVAFD were detected on chromosomes 1 and 13. On

chromosome 5 a putative QTL affected KEMP were present. For DISC and for SL traits two putative QTL were detected on chromosome 2. Estimates of QTL contributions to the QTL variance (%) (the percentage by which trait variance is reduced when a QTL is included the model within each of the sire family) ranged from 5 to 11.3%. The effect/standard deviation (the QTL effect scaled by the standard devia-

Fig. 1. Map of the F-statistics depicting the positions of putative QTL in Angora goat by chromosome. On the chromosome (CHI) the underlined microsatellites markers were used. The level is provided for P < 0.05 (dashed line) chromosome-wise significance.

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Fig. 1. (Continued ).

tion of the trait) ranged from 0.9 to 3.9 genetic standard deviation and is shown in the last row of Table 3. In all cases, the number of informative bucks (heterozygous for the QTL) ranged from 1 to 2 out of 8. In Fig. 1 the plot of the F-statistics for putative QTL grouped by chromosome are shown. 4. Discussion Here were reported several putatives QTL for CVAFD (CHI 1, 13), KEMP (CHI 5), DISC and SL (CHI 2). Until now no other reports on QTL associated with mohair fiber traits in Angora goat have been published before. Nevertheless, in sheep several reports of linkage between genes and QTL with wool production traits are available (Parsons et al., 1994; Henry et al., 1998; Ponz et al., 2001; Rogers et al., 1994; Allain et al., 1998; Cockett et al., 2001; Bray et al., 2002; Purvis and Franklin, 2005). Due to the homology between sheep and goat maps (Maddox, 2005), putatives QTL for CVAFD and KEMP found in the Angora goat on chromosomes 1 and 5 could be related with those keratin (KRT) and keratine-associated protein (KRTAP) family genes as pointed out by McLaren et al. (1997). In sheep on chromosome 1 several high-glycine–tyrosine keratin associated proteins (KRTAP6.1, KRTAP7 and KRTAP8) genes

were mapped by McLaren et al. (1997). Another important wool follicle protein trichohyalin (THH), encoded by a single gene, was also mapped in the chromosome 1 (McLaren et al., 1997), although this protein is also expressed in other epidermal tissues (O’Keefe et al., 1993). The KRT2, KRT2.13 and KRT2.10 genes (Hediger et al., 1991; McLaren et al., 1997) mapped on chromosome 3 in sheep, four keratin family genes (KRT8 and KRT1B) have been assigned to chromosome 5 in cattle (Fries et al., 1991), and one of these genes KRT was assigned to chromosome 5 in the goat (Schibler et al., 1998; Pinton et al., 2000); all of them could be related with those QTL found here on goat chromosome 5. Similarly, the localization of the QTL on the chromosome 4 in sheep for CVAFD (Allain et al., 1998; Ponz et al., 2001) could be associated to the putative QTL observed on the chromosome 4 (data not shown). Moreover, in sheep, a linkage between highglycine–tyrosine keratin gene loci and wool fiber diameter has been previously demonstrated (Parsons et al., 1994). Thus, such KRTAPs and KRT gene could be good candidates for the associated QTL on goat chromosomes 1 and 5. With the proposal of diminishing the confidence interval we have increased the number of kids by family on previous step to fine mapping on the candidate regions.

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