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Assessment of positional candidate genes myf5 and igf1 for growth on bovine chromosome 5 in commercial lines of Bos taurus¹

C. Li^*, J. Basarab, W. M. Snelling, B. Benkel, B. Murdoch^*, C. Hansen^* and S. S. Moore^*

^* Department of Agricultural, Food, and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada T6G 2P5; and Lacombe Research Centre, AAFRD, Lacombe, Alberta, Canada T4L 1W1; and USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166; and and Agriculture and Agri-Food Canada, Lethbridge Research Center, Alberta, Canada TIJ 4B1

Abstract

Quantitative trait loci for growth traits in beef cattle have been previously reported and fine-mapped in three chromosomal regions of 0 to 30 cM, 55 to 70 cM, and 70 to 80 cM of bovine chromosome 5. In this study, we further examined the association between gene-specific single nucleotide polymorphisms (SNP) of two positional candidate genes, bovine myogenic factor 5 (myf5) and insulin-like growth factor-1 (igf1), in the QTL regions and the birth weight (BWT), preweaning average daily gain (PWADG), and average daily gain on feed (ADGF) in commercial lines of Bos taurus. The QTL regions for the growth traits identified using a haplotype association analysis, which included the gene-specific SNP markers for both genes in this study, were in agreement with previous studies. The gene-specific SNP marker association analysis indicated that the SNP in myf5 had a significant additive effect on PWADG in the M1 line of Beefbooster Inc. (P < 0.10), and a significant additive effect (P < 0.05) and a significant dominance effect (P < 0.10) on ADGF in the M3 line of Beefbooster Inc. When the data from the two commercial lines were pooled, the SNP in myf5 showed a significant association with PWADG (P < 0.10) and with ADGF (P < 0.05). The association between the SNP and BWT, however, did not reach a significance level in the M1 line, the M3 line, or across the lines. For igf1, no significant association between the SNP and the growth traits was detected in either the M1 line or the M3 line, whereas there was only a significant dominance effect (P < 0.10) on BWT detected for the SNP in igf1 when the data from the two commercial lines were pooled. These results suggest that myf5 is a strong candidate gene that influences PWADG and ADGF in beef cattle. The SNP of igf1 may not be a causative or close to the causative mutation that affects the three growth traits in the populations of beef cattle examined in this study. Other SNP of igf1 and myf5 or other genes in their respective chromosomal regions, however, should also be studied.

Key Words: Cattle • Growth Traits • Marker Genes • Quantitative Trait Loci

Introduction

Quantitative trait loci for growth traits in beef cattle have been reported in a number of studies (Davis et al., 1998; Stone et al., 1999; Casas et al., 2000). Recently, we fine-mapped QTL for birth weight (BWT), preweaning average daily gain (PWADG), and average daily gain on feed (ADGF) on bovine chromosome 5 (Li et al., 2002a,b). Three chromosomal regions (0 to 30 cM, 55 to 70 cM, and 70 to 80 cM) were identified as having significant associations with the growth traits. In previous studies, two genes, bovine myogenic factor 5 (myf5) and insulin-like growth factor-1 (igf1), were both considered to be positional candidate genes underlying two of the three chromosomal regions (0 to 30 cM and 70 to 80 cM) as they were mapped at the chromosomal locations of 19.0 cM and 73.5 cM, respectively (Grosse et al., 1999). The myf5 gene plays a role in myogenic lineage determination and/or myocyte differentiation (Braun et al., 1989). In bovine, the gene has a length of 5,219 bp, with three exons and two introns (Gene Bank accession. No. M95684; Barth et al., 1993). A mutation of A/G was identified for myf5 at the 1948 bp position of the intron 2 region (Drogemuller and Kempers, 2000). The examination of the association between this single nucleotide polymorphism (SNP) and growth traits in beef cattle has not been reported. The igf1 gene is also considered to be a factor that regulates growth, differentiation, and the maintenance of differentiated function in numerous tissues and in specific cell types of mammals through binding to a family of specific membrane-associated glycoprotein receptors (Werner et al., 1994). A transition of T/C was identified for igf1 at 512 bp 5' to the first codon of the first exon (Gene Bank Accession No. AF017143; Ge et al., 1997). The objective of this study was to examine the associations between the two SNP of myf5 and igf1 and BWT, PADG, and ADGF in commercial lines of Bos taurus.

Materials and Methods

Animals and Phenotypic Data
Animals were from the M1 and the M3 lines of Beefbooster Inc. (Calgary, Canada) and born in 1998. The M1 line was developed from an Angus base. The M3 line was developed from small cows of various breeds. The two lines have been under selection for over 30 yr, and the selection criteria for the lines are based on indices described by MacNeil and Newman (1994). In the spring of 1998, male calves were identified and calf BWT were taken at or near birth. A 10-mL blood sample was collected by venipuncture from each male calf and the potential sires, and the DNA from each blood sample was extracted and kept for later parentage identification. Sire identification was carried out by the Saskatchewan Research Council Canada using DNA microsatellite markers. Meanwhile, cows and calves were placed on tame pastures from May through to mid-September and October. In the fall of 1998, the calves were weaned and weighed between September 16 and October 20. The PWADG was calculated by the difference between weaning weight and BWT, divided by days between weaning date and birth date. Over one-third (38.6%) of the bull calves with the lowest PWADG were then culled. The remaining male calves were placed in feedlot pens for postweaning performance testing. Briefly, animals were first placed in one of the feedlot pens where they were adjusted to diet and environment over 21 to 29 d before the test. During the adjustment period, animals were fed a diet consisting of 50.5% barley silage, 15.0% chopped hay, 21.1% rolled barley grain, 10.0% wheat mill run pellets, and 3.4% calf supplement (as-fed basis). After the adjustment, animals were placed on a 120-d growth performance test. During the first 17-d test, the animals were fed the same diet as in the adjustment period, followed by a 22-d test in which they were fed a diet consisting of 72.0% barley silage, 5.2% rolled barley grain, 20.0% wheat mill run pellets, and 2.8% calf supplement (as-fed basis). During the last 81-d test, the animals were fed a diet consisting of 87.5% barley silage, 10.1% wheat mill run pellets, and 2.4% calf supplement (as-fed basis). The ADG on feed was then calculated by the difference between weight when the test started and weight when the test ended, divided by the days of test.

Genotyping
One hundred seventy-six male calves and their 12 respective sires (9 to 30 calves from each sire) of the M1 line and another 170 male calves and their 14 sires (5 to 29 calves from each sire) of the M3 line were genotyped for the myf5 and igf1 gene-specific markers. In a previous study, 16 microsatellite loci on bovine chromosome 5 were genotyped for the same animals of the M1 line, and nine microsatellite loci were genotyped for the same animals of the M3 line (Li et al., 2002a,b).

Genotyping of the myf5 SNP marker was carried out using the PCR–RFLP method and allele discrimination with the 5' nuclease assay (Applied Biosystems, Streetsville, Canada). The PCR–RFLP method started with a primary PCR amplification of genomic DNA using primers MYF5F2 (5'-CCT ATC TGG TCC AGA AAG AGC AG-3') and MYF5R (5'-TAT ATA AGT TAA GCA TTG CAA CAA-3'), followed by a nested PCR using primers MYF5F3 (5'-GAG CAG CAG TTT TGA CAG CG-3') and MYF5R3 (5'-AGC ATT GCA ACA AAC TAC CT-3'). The PCR products were then digested using TaqI (T/CGA) (New England Biolabs, Pickering, Canada) by incubation at 37°C for 2 h. The fragments were separated on 1.5% agarose gels (Sigma, Oakville, Canada) by electrophoresis with 1x TBE buffer and stained using ethidium bromide. The genotype of each animal was determined based on the fragment profile, with allele "1" uncut and allele "2" cut. The primers used in the PCR–RFLP method were designed based on the sequence of myf5 (GenBank Accession No. M95684). The allele discrimination using the 5' nuclease assay was performed using an ABI Prism 7700 sequence detector. Briefly, a forward primer (5'-CAA ATT TCT ACC AGG CTT TCT GTG A-3') and a reverse primer (5'-GCT TAT TCG GCC GCT TAA ACT-3') were designed to amplify the SNP region (CAA/CGA) of myf5 at the 1,948 bp position of intron 2 (GenBank Accession No. M95684). Two fluorogenic probes were also designed to target the two alleles, with VIC reporter dye for allele "1" (CAA) and FAM reporter dye for allele "2" (CGA). The sequences of the probes for allele "1" and allele "2" detection were 5'-TTG GGT TTC AAA GGT-3' and 5'-TGG GTT TCG AAG GTG-3', respectively. A perfect match of a probe sequence to the target sequence will result in the cleavage and release of the reporter dye. Thus, a substantial increase in either VIC or FAM dye fluorescence indicates homozygosity for the VIC-specific allele (allele "1") or for the FAM-specific allele (allele "2"), respectively. An increase in both signals indicates heterozygosity. A subset of samples were genotyped using the PCR–RFLP method and allele discrimination with the 5' nuclease assay to confirm that the two methods generated the same genotypes.

The genotyping of the igf1 SNP marker was performed as described by Ge et al. (2001), with some modifications. First, a template for nested PCR was prepared by amplification of genomic DNA with primers IGF485F (5'-CAG TGG GAA AAT GAT TTG CCT CTC-3') and IGF1325R (5'-TTA AAT AAT TGG GTT GGA AGA CTG C-3'). The nested PCR was carried out with primers IGF677F (5' ATT ACA AAG CTG CCT GCC CC-3') and IGF897R (5'-ACC TTA CCC GTA TGA AAG GAA TAT ACG T-3'). The PCR products were then digested using SnaBI (TAC/GTA) (New England Biolabs) by incubation at 37°C for 2 h. The fragments were separated on 1.5% agarose gels (Sigma) by electrophoresis with 1x TBE buffer and stained using ethidium bromide. The genotype of each animal was determined based on the fragment profile, with allele "A" cut and allele "B" uncut (Ge et al., 2001).

Haplotype Association Analysis
Haplotypes (linkage phases) involving myf5 and igf1 in the chromosomal regions of 0 to 30 cM and 70 to 80 cM were constructed. The loci used for haplotype construction in the region of 0 to 30 cM were BM6026, BP1, myf5, and BL23 for both the M1 line and the M3 line. In the region of 70 to 80 cM, the loci used for haplotype construction were ETH10, igf1 gene SNP locus (IGF1), igf-1 microsatellite locus (IGF-1M), and BM1819 for the M1 line, and BMS490, igf1 gene SNP locus (IGF1), igf-1 microsatellite locus (IGF-1M), and BM1819 for the M3 line. Haplotypes were constructed as previously described (Li et al., 2002b). Briefly, genotypes of the six microsatellites and the two gene-specific SNP of each of the 176 male calves in the M1 line and genotypes of the six microsatellites and the two gene-specific SNP of each of the 170 male calves in the M3 line were checked against the calf's sire to verify sire inheritance. Alleles of each locus contributed by the sire (as well as by the dam) were identified for each calf by examining the genotype of their sires. The haplotypes (allele linkage phases) of each male calf were then established along the chromosomal regions.

Haplotype association analyses were carried out separately for the M1 line and the M3 line for each of the most commonly observed haplotypes of two adjacent loci with a frequency greater than 8.0%, and the BWT, PWADG, and ADGF, using the multiple trait derivative-free restricted maximum likelihood (MTDFREML) program (Boldman et al., 1993), with animal models including two generations of pedigrees. Haplotypes that extended more than two loci were not included in the final haplotype association analysis because their low frequencies in the data set in comparison to that of haplotypes of two adjacent loci. The animal model for the M1 line included fixed effects of haplotype (1, 0), herd (1, 2), interaction effect between haplotype and herd, random animal additive, age of dam as a covariate, and residual effects. Because the number of animals carrying two copies of a haplotype was small in the data set, animals carrying two copies of a haplotype were grouped with animals carrying one copy of a haplotype as haplotype class "1," and animals without the haplotype under test was coded as class "0." Animals with uncertain haplotypes were considered to be missing values and were deleted from the analysis. The animal model for the M3 line was a reduced model with the fixed effect of herd and interaction effect between haplotype and herd removed because the animals in the M3 line were from only one herd. The contrasts and tests between means of haplotypes were performed as described by Boldman et al. (1993), and the haplotype effect in standard deviations was estimated by the difference between means of the two haplotype classes, divided by the standard deviation.

Gene-Specific SNP Marker Association Analysis
Association analysis between the genotype of the genes myf5 and igf1 and the growth traits was first analyzed separately for the M1 line and the M3 line using the respective animal model as defined in the haplotype association analysis, with the fixed effect of haplotype substituted with fixed effect of animal genotype for the myf5 (11, 12, or 22) or for the igf1 genotypes (AA, AB, or BB). Additive effects were estimated by the difference between the two homozygous genotypes and the dominance effects were estimated by subtracting the average of solutions for homozygous genotypes from that for heterozygous genotype. The contrasts and tests among or between means of genotypes were performed as described by Boldman et al. (1993).

The single-locus association analysis was also carried out across the M1 and the M3 lines using the same procedure, with the data from the two lines combined; the animal model included fixed effects of genotype, line, herd, an interaction effect between genotype and line, random animal additive, age of dam as a covariate, and residual effects.

Results

Four hapotypes with alleles of myf5 in the chromosomal region of 19.0 to 28.6 cM and three haplotypes with alleles of igf1 in the chromosomal region of 70.0 to 77.6 cM were found to have significant effects on the growth traits in the M1 line (Table 1). Haplotype myf5-1, BL23-3 had a significant negative effect on BWT, decreasing it by 0.83 SD. Haplotype myf5-2, BL23-4, however, had a significant positive effect on BWT, increasing it by 0.61 SD. In the same chromosomal region, haplotype myf5-2, BL23-3 showed significant positive effects on both PWADG and ADGF, increasing them by 0.50 SD and 0.47 SD, respectively. In the chromosomal region of 70.0 to 77.6 cM, haplotypes ETH10-4, igf1-A, and igf1-B, BM1819-5 had significant positive effects on ADGF, increasing it by 0.67 and 0.63 SD, respectively. Haplotype igf1-A, BM1819-5, however, had a significant negative effect on PWADG, decreasing it by 0.41 SD.

Results of the gene-specific SNP marker association analysis for the myf5 and igf1 are shown in Tables 2 and 3, respectively. For the SNP of myf5, a significant additive effect on the PWADG was detected in the M1 line (P < 0.10) (Table 2). Calves with the genotype "22" gained 0.05 kg more than did calves with the "11" genotype. The additive effects and dominance effects of the SNP of myf5 on BWT and ADGF were, however, not significant in the M1 line. In the M3 line, the SNP of myf5 had both a significant additive effect (P < 0.05) and a dominance effect (P < 0.10) on the ADGF (Table 2). Calves with the genotype "22" gained 0.083 kg more than calves with the "11" genotype, and calves with the genotype "12" gained 0.059 kg less than the average of calves with the genotype "11" or "22." However, the additive and dominance effects of the SNP of myf5 on BWT and PWADG were not significant in the M3 line. When the data from the M1 and the M3 line were pooled, it was found that the SNP of myf5 had a significant additive effect on average daily gain on feed (P < 0.05) and a significant additive effect on PWADG (P < 0.10; Table 2). Calves with the genotype "22" gained 0.032 kg and 0.072 kg more than calves with the genotype "11" for PWADG and ADGF, respectively. The association between the SNP of myf5 and BWT was still not significant at the threshold of P < 0.10, although there was a trend that calves with the genotype "22" had a higher BWT than did calves with the genotype "11."

Discussion

Birth weight, PWADG, and ADGF are three growth traits that have an important impact on the profitability in the beef cattle industry. Therefore, breeding for optimal BWT and larger gains is a major consideration in beef cattle breeding programs. Mapping of QTL and identification of causative genes that affect growth traits will greatly enhance the progress towards this goal.

We previously fine-mapped three chromosomal regions on bovine chromosome 5 (0 to 30 cM, 55 to 70 cM, and 70 to 80 cM) that had significant associations with BWT, PWADG, and ADGF in commercial lines of Bos taurus (Li et al., 2002a,b). In this study, we examined the association between two positional candidate genes for two of the above three chromosomal regions, myf5 for the chromosomal region of 0 to 30 cM and igf1 for the chromosomal region of 70 to 80 cM, and the growth traits in two commercial lines of Bos taurus. In the haplotype association analysis, four haplotypes with an allele of the gene myf5 in the M1 line and one haplotype with an allele of the gene myf5 in the M3 line were found to have significant effects on the growth traits. In the other chromosomal region, three haplotypes with an allele of gene igf1 in the M1 line and three haplotypes with an allele of igf1 in the M3 line showed significant associations with the growth traits. These results confirm the QTL regions identified previously using the identical by descent haplotype sharing analysis (Li et al., 2002a,b).

The further single gene-specific SNP marker association analysis in this study detected a significant additive genetic effect on PWADG in the M1 line and significant additive and dominance effects on ADGF in the M3 line for the SNP of myf5. The additive effects of the SNP in myf5 on the PWADG and on the ADGF were confirmed when the pooled data from the two commercial lines were analyzed, with the genotype "22" significantly associated with higher PWADG and higher ADGF. These results are also supported by the haplotype association analysis, in which the haplotypes of myf5 with an allele "2" were significantly associated with higher PWADG and higher ADGF (Table 1).

The association between the SNP of myf5 and BWT, however, did not reach a significance level either when data were analyzed separately in the M1 or in the M3 line, even though animals with the genotype "22" had a higher BWT than did calves with the genotype "11" in both lines. When data were analyzed across the lines, the significance level of the association between the SNP of myf5 and birth weight was found to be marginal (P = 0.112), but still did not reach the threshold (P < 0.10). It is conceivable that the association between the SNP in myf5 and BWT would be significant if a relatively larger number of animals had been used, given the fact that two haplotypes with an allele of myf5 in the M1 line and one haplotype in the M3 line had significant effects on BWT, and the haplotypes with an allele "2" were significantly associated with higher BWT in the populations of beef cattle examined in this study (Table 1). However, other SNP in myf5 may also have effects on BWT.

The two commercial lines, M1 and M3, have experienced selection for varying objectives. The M1 line was developed as a moderate, intermediate framed strain with emphasis on mothering ability and sound udders. The M3 line, however, was developed as a light- and small-framed line to ensure easy calving for heifers with a BWT restriction of 33.6 kg or less. As a result of selection, the M1 and M3 lines were significantly different in BWT, PWADG, and ADGF (P < 0.001, Table 4). The BWT, PWADG, and ADGF of the M1 line were significantly higher than those of the M3 line. Accordingly, the genotype frequencies and allele frequencies of myf5 between the two lines were also significantly different (P < 0.01), with higher frequencies of genotype "22" and "12," as well as higher frequency of allele "2" present in the M1 line (Table 4). These results may also suggest the existence of a strong association between the genotypes of myf5 and the growth traits in consideration of different selection emphasis placed on growth between the two lines.

The igf1 gene has also been considered to be one of the genes that affect growth in mammals. In beef cattle, Moody et al. (1994, 1996) reported that igf1 was significantly associated with weaning weight, yearling weight, and BWT. In a study by Ge et al. (2001), the genotype "BB" of igf1 was found to have higher weight gain during the first 20 d after weaning and higher on-test weight. A dominance effect of the marker on postweaning gain was also detected in the low-igf1 line that was selected for low blood serum igf1 concentration (Ge et al., 2001). The association between the SNP of igf1 and the growth traits, however, was not significant in the high-igf1 line (Ge et al., 2001). In our study, no genetic effects of the SNP of igf1 on any of the traits were detected in either the M1 or the M3 line. A significant dominance effect on BWT was found for the SNP of igf1 only when the data from the two lines were pooled, with the genotype "AB" associated with lower BWT. Genotype "BB" showed an inconsistent trend toward higher BWT, higher PWADG, and higher ADGF in both the M1 and the M3 lines (Table 3). Furthermore, in the haplotype analyses, the haplotypes with allele "B" or "A" did not demonstrate a consistent trend toward a positive or negative effect on the growth traits (Table 1). In an attempt to correct for the linkage phase when the data from the two lines were pooled for the single gene-specific SNP association analysis, the genotypes of igf1 in the M3 line were reverse coded (i.e., "AA" was coded as "BB" and "BB" was coded as "AA"). The genotype effect, however, still did not reach the significant level (data not shown). The genotype frequencies and allele frequencies of igf1 between the two lines were not significantly different (P > 0.05, Table 4), suggesting that the SNP of igf1 is not associated with the growth traits. Moreover, the interaction effect between igf1 and myf5 was also examined. That effect, however, was not significant (data not shown). The relatively small sample size used in this study may lack the power of detecting the association between igf1 and the growth traits. Nevertheless, the results may also suggest that the SNP of igf1 is not a causative or may not be close to the causative mutation that affects the three growth traits in the populations of beef cattle examined in this study. Thus, other SNP of igf1 or other genes in the chromosomal regions should be studied.

Implications

The associations between two single nucleotide polymorphisms of genes myf5 and igf1 and growth traits were examined in commercial lines of Bos taurus. It was found that the genotype "22" or allele "2" of myf5 was significantly associated with higher preweaning average daily gain and higher average daily gain on feed. The results provide a valuable reference for further candidate gene research and marker-assisted selection.

Footnotes

¹ The authors thank D. Van Vleck and Z. Wang for their comments and help with MTDFREML computer programs. This work was supported through grant No. ACC-99AB343 awarded to B. Benkel and S. S. Moore through the Canada-Alberta Beef Industry Development Fund.

² Correspondence: 4-10 Ag/For Building (phone: 780-492-0169; fax: 780-492-4265; e-mail: stephen.moore{at}ualberta.ca).

Received for publication April 29, 2003. Accepted for publication August 27, 2003.

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