Molecular Biology Reports

, Volume 37, Issue 1, pp 429–434 | Cite as

A novel polymorphism of GDF5 gene and its association with body measurement traits in Bos taurus and Bos indicus breeds

  • Yong Feng Liu
  • Lin Sen Zan
  • Kui Li
  • Shuan Ping Zhao
  • Ya Ping Xin
  • Qing Lin
  • Wan Qiang Tian
  • Zhi Wei Wang


Body measurement traits, influenced by genes and environmental factors, play numerous important roles in the value assessment of productivity and economy. Growth differentiate factor 5 (GDF5), involved in the development and maintenance of bone and cartilage, is an important candidate gene for body measurement traits selection through marker-assisted selection (MAS). In this study, based on the PCR-RFLP technology, we discovered and evaluated the potential association of the single nucleotide polymorphism (SNP) (T586C in exon 1) of the bovine GDF5 gene with body measurement traits in 985 Bos taurus breed, 42 Bos indicus breed and 76 Bos indicus × Bos taurus individuals. As the SNP marker, there were the significant effects on the Body length (BL) in the Bos taurus (BT) and Bos indicus × Bos taurus (BMY) populations (P < 0.05). In BT population, animals with the genotype TT had lower mean values for BL and Hip width (HW) than these with the TC and CC genotype (P < 0.01). In BMY population, animals with the genotype TC had lower mean values for BL than these with the genotype CC (P < 0.05). These results suggest that the SNP of the GDF5 gene could be a very useful genetic marker for body measurement traits in the bovine reproduction and breeding.


Cattle GDF5 gene SNP polymorphism PCR-RFLP Body measurement 


Growth differentiate factor 5 (GDF5), known as cartilage-derived morphogenetic protein 1 (CDMP1), is a member of the transforming growth factor-b (TGF-b) superfamily and also closely related to the subfamily of bone morphogenetic proteins (BMPs) [1]. The role of GDF5 in the development and maintenance of bone and cartilage has been recognized recently [2, 3, 4, 5, 6]. The expression of GDF5 was observed in the regions between skeletal elements where joints formed later [7, 8]. It plays a crucial role in the morphogenesis of tendon, ligament and bone. A null mutation of GDF5 could cause developmental failure of skeletal structure and intra-articular ligaments in mice [9, 10]. Besides, GDF5 can express in the regions of future joints during early development, which indicates it could be involved in joint formation [3, 11]. The previous reports have demonstrated that the mutants of GDF5 in both mouse and human GDF5 led to abnormal joint development [7, 8]. There are observations of thick and enlarged cartilage components of the appendicular skeleton in GDF5 transgenic mice [12, 13], which further provides the evidence of the chondrogenic possibility of GDF5 in vivo [14, 15]. In humans, GDF5 is present in adult articular cartilage and able to stimulate proteoglycan synthesis in articular cartilage explants [14]. To our knowledge, there is no information about polymorphisms of bovine GDF5 gene to be studied so far.

Based on the important roles of the GDF5 in chondrogenesis and proteoglycan synthesis as determined in mouse and human, GDF5 could be an attractive candidate gene for body measurement traits in bovine. Therefore, the objective of this study is to detect SNPs in bovine GDF5 gene and to explore their possible association with body measurement traits in Bos taurus and Zebu (Bos indicus).

Materials and methods

DNA samples and data collections

A total of 1,103 adult animals were randomly selected from breeding populations and used to analyze the GDF5 allelic frequencies, including Qinchuan (QC, n = 393, Shaanxi province), Qinchuan improvement steers (QI, n = 240, Shaanxi province), Nanyang (NY, n = 62, Henan province), Jiaxian red (JR, n = 77, Henan province), Xia’nan (XN, n = 78, Henan province), Luxi (LX, n = 79, Shandong province), Simmental and Luxi crossbred steers (SL, n = 56, Shandong province), Brahma (Bos indicus) (BH, n = 42, Yunnan province) and BMY (Brahma crossed with descendant of male murry grey and female Yunnan yellow cattle) (BMY, n = 76, Yunnan province). The following traits were measured as described previously [16], including Body length (BL), Withers height (WH), Hip height (HH), Rump length (RL) and Hip width (HW). In order to minimize systematic error, single person was assigned to measure one of the five traits in all animals.

DNA samples were extracted from leukocytes and tissue samples using standard phenol–chloroform protocol [17].

PCR amplification and sequencing

According to the sequence of bovine GDF5 gene (GenBank accession No. NC_007311), one pair of primers (5′-TGT CCG ATG CTG ACA GAA AGG-3′ and 5′-GAG TGA GGT TAA TCC CAG ATA CCA-3′) was designed to amplify a 235 bp product of the GDF5 exon 1 and its intron region. Polymerase chain reaction (PCR) amplifications were performed in 20 μl reaction mixture containing 50 ng mixed DNA template (DNA template was mixed nine DNA samples from nine different breeds with the same volume, respectively), 10 pM of each primer, 0.20 mM dNTP, 2.5 mM MgCl2 and 0.5 U Taq DNA polymerase (TaKaRa, Dalian, China). The PCR protocol was 95°C for 5 min followed by 32 cycles of 94°C for 30 s, 60°C annealing for 30 s, and 72°C for 30 s, and a final extension at 72°C for 10 min. The products were purified by using a Wizard Prep PCR purification kit (Shanghai Bioasia Biotechnology, P. R. China) and sequenced (Beijing Aolaibo Biotechnology, P. R. China; Applied Biosystems 3730xl DNA sequencer, Foster city, CA, USA).

Genotyping of MvaI GDF5 allele by PCR-RFLP

Aliquots of 20 μl PCR products were digested with 10 U MvaI (MBI, Fermentas) at 37°C for 5 h following the supplier’s manual. The digested products were detected by electrophoresis in 2.5% agarose gel stained with ethidium bromide. To confirm the results based on the PCR-RFLP technique, the PCR products from the mix DNA template were sequenced in both directions (Beijing Aolaibo Biotechnology, P. R. China; Applied Biosystems 3730xl DNA sequencer, Foster city, CA, USA).

Statistical analyses

The following items were statistically analyzed according to the previous approaches [18, 19], including genotypic frequencies, allelic frequencies, Hardy–Weinberg equilibriums, gene homozygosity, gene heterozygosity, effective allele numbers and polymorphism information (PIC) content. The association between SNP marker genotypes of the GDF5 gene and records of body measurement traits (BL, WH, HH, RL and HW) was analyzed by the least-squares method as applied in the GLM procedure of SAS (SAS Institute Inc., Cary, NC, USA) according to the following statistical linear model:
$$ Y_{ijkl} = \mu + G_{i} + S_{j} + {\text{BF}}_{k} + {\text{Ma}}_{l} + \varepsilon_{ijkl} , $$
where Y ijkl is observation for the body measurement trait, μ is overall mean for each trait, G i is genotype effect, S j is fixed effect of sex, BF k is fixed effect of breed and farm, Ma l is regression variable for measure age, ε ijkl is random environment effect.

Results and discussion

After a 235 bp product of the GDF5 gene was amplified and sequenced, we found a SNP, named T586C, in the GDF5 gene. The T586C mutation, a synonymous mutation of leucine, was also observed at position 586 of the exon 1 which creates the MvaI restriction site (CC^WGG).

For the T586C SNP in the populations that we analyzed in this study, three size variants of restriction fragments were identified, namely: 235, 181 and 54 bp. Subsequently, we analyzed the localization of migration bands of the restriction fragments and found out three genotypes of “mutation T > C”. Our data in Fig. 1 shows that the genotype TT represents the occurrence of one band of 235 bp, genotype TC represents three restriction fragment bands of 235, 181 and 54 bp, and genotype CC represents two bands of 181 and 54 bp.
Fig. 1

Agarose gel electrophoresis of MvaI PCR-RFLP and DNA sequencing maps in both directions at bovine GDF5 locus. Note: TT genotype demonstrates one fragment (235 bp), TC genotype shows three fragments (235, 181, and 54 bp) and CC genotype shows two fragments (181 and 54 bp). Although 54 bp fragment is not long enough to be visible in 2.5% agarose gel electrophoresis, 235 and 181 bp fragments can exactly classify the different genotypes (e.g., TT, TC and CC)

Moreover, allele frequencies of the SNP were investigated and performed by χ 2 test in the all populations of bovine in our study (Table 1). The data shown here demonstrate that the range of frequencies of GDF5-T and C allele was from 0.1694 to 0.5076 among seven different subpopulations of Bos taurus (BT) population, and there was significant difference in the allelic frequency only among QC populations in the SNP (P < 0.05). Furthermore, frequencies of T/C alleles were 0.4198/0.5802, 0.0238/0.9762 and 0.1447/0.8553 in BT, BH and BMY population, respectively; and only BT population was not in Hardy–Weinberg equilibrium (P < 0.05). The frequencies of TT genotype were low in the seven Bos taurus population (Table 1). The possibility of this observation is the occurrence of gene random drift due to the low frequency of allele T. In addition, we did not find TT genotype in the Bos indicus (BH) population and Bos indicus × Bos taurus (BMY) population (shown in Table 1). There are a couple of possibilities for this observation in these populations, including: (1) TT genotype possibly exists in the Zebu pedigrees population, but the individuals are not enough in our study, and (2) the animals with TT genotype do not exist in the Bos indicus breed and their crossbreed.
Table 1

Genotype frequencies (%) at the GDF5 gene for the SNP in bovine populations


Observed genotypes (number)


Allelic frequencies

χ2 (HW *)

P value (HW*)







0.2036 (80)

0.6081 (239)

0.1883 (74)







0.1333 (32)

0.5583 (134)

0.3083 (74)







0.0161 (1)

0.3065 (19)

0.6774 (42)







0.1299 (10)

0.6234 (48)

0.2468 (19)







0.0769 (6)

0.4231 (33)

0.5000 (39)







0.0759 (6)

0.5823 (46)

0.3418 (27)







0.0714 (4)

0.5357 (30)

0.3929 (22)







0.1411 (139)

0.5574 (549)

0.3015 (297)







0.0000 (0)

0.0476 (2)

0.9524 (40)







0.0000 (0)

0.2895 (22)

0.7105 (54)






Note: BT, population including QC, QI, NY, JR, XN, LX and SL population

HW Hardy–Weinberg equilibrium

Gene heterozygosity, effective allele numbers and PIC (Polymorphism Information Content) of bovine GDF5 locus in seven populations of Bos taurus breed varied from 0.2813 to 0.4999, 1.3915 to 1.9995, 0.2418 to 0.3749, respectively, which were higher values than these in BH and BMY population (Table 2). Generally, PIC is classified into the following three types: low polymorphism (PIC value < 0.25), median polymorphism (0.25 < PIC value < 0.5), and high polymorphism (PIC value > 0.5). According to this classification of PIC, all Bos taurus population, except NY population, belongs to the median polymorphism level. However, BH and BMY population belong to the low polymorphism level. Therefore, our data indicate that the high frequency of GDF5-C allele at bovine GDF5 locus could be used to characterize Bos taurus breeds. Moreover, the further analysis also reveals the rare polymorphism of bovine GDF5 locus in Bos indicus population compared to Bos taurus population.
Table 2

Population genetic indexes at the GDF5 locus in bovine populations


Gene homozygosity

Gene heterozygosity

Effective allele numbers




















































Then, five body measurement traits were analyzed by the comparison between the genotypes of 1,103 individuals and their phenotypic data. The results of association analysis of the gene-specific SNP marker are shown in Table 3. At the SNP marker there are significant effects on the BL in the two populations (P < 0.05). In BT population, animals with the genotype TT have lower mean values for BL and HW than these with the TC and CC genotype (P < 0.01). In QC population, animals with the genotype TT have lower mean values for BL, WH and HW than these with the TC and CC genotype (P < 0.01). In QI population, animals with the genotype TT have lower mean values for BL and HW than these with the TC and CC genotype (P < 0.05). In BMY population, animals with the genotype TC have lower mean values for BL than these with the genotype CC (P < 0.05). No significant correlations were observed between any of the marker genotypes at T586C and other traits. Moreover, the T > C synonymous mutation of leucine results in the increase of the part of phenotypic variation, especially on the BL and HW phenotypes in Bos taurus. Therefore, we assumed that the mutation for T586C could has the important influence on many minor genes, which involve in body length and hip width in bovine.
Table 3

Associations of T586C SNP genotypes with body measurement traits at bovine GDF5 gene



Traits (cm, Mean ± SE)








143.40 ± 0.96A

131.00 ± 0.91

133.44 ± 0.82

44.42 ± 0.48

47.02 ± 0.56A


146.71 ± 0.54B

132.13 ± 0.44

133.94 ± 0.42

45.04 ± 0.22

49.02 ± 0.29B


147.44 ± 0.79B

132.65 ± 0.66

134.11 ± 0.61

45.27 ± 0.33

48.95 ± 0.40B

P value








118.52 ± 0.67a

112.34 ± 1.24

120.59 ± 1.18

40.73 ± 0.91

38.25 ± 0.79


122.49 ± 1.21b

114.21 ± 0.79

120.35 ± 0.69

41.89 ± 0.32

38.02 ± 0.51

P value








131.70 ± 1.18A

120.69 ± 1.07A

124.71 ± 0.96

43.44 ± 0.53

40.50 ± 0.67A


138.89 ± 0.73B

128.10 ± 0.59B

128.29 ± 0.52

45.27 ± 0.28

44.39 ± 0.35B


138.57 ± 1.33B

127.51 ± 1.08B

128.25 ± 1.09

45.28 ± 0.56

44.50 ± 0.75B

P value








145.93 ± 1.66a

137.48 ± 1.22

135.91 ± 1.45a

47.37 ± 1.11

47.48 ± 1.12A


149.93 ± 0.90b

138.15 ± 0.56

139.65 ± 0.55b

48.32 ± 0.45

51.39 ± 0.52B


151.57 ± 1.23b

138.27 ± 0.91

138.19 ± 0.78ab

48.40 ± 0.58

50.94 ± 0.60B

P value






a,bMeans with different superscripts were significantly different (P < 0.05)

A,BMeans with different superscripts were significantly different (P < 0.01)

The body measurement traits are affected by many factors, such as genotype, sex, age, breed, herd, location and other random environment factors. But, we have established the new statistical model in which the three factors (breed, herd, and location) were involved and then we have employed the least-squares method in GLM procedure of SAS software to do the related analysis. However, we did not find the significant difference (P > 0.05) (data not shown).

A number of studies have recently demonstrated that the functional SNP in GDF5 gene has a plausible biological role in height, sitting height and other stature indexes in human [20, 21, 22, 23]. The research work by Sanna et al. [21] has shown that the GDF5 gene has the significant influence on the height and two SNPs, rs6060369 and rs143383, frequently occur in human GDF5. Furthermore, the previous reports by Chang et al. [24] and Chujo et al. [25] have revealed that GDF5 is involved in bone growth and differentiation in both adult and embryonic tissues. Meanwhile, Chujo et al. [25] have also investigated the function of GDF5 in restoration of vertebral disc height through enhancing production of extra cellular matrix in the rabbit model of disc degeneration [24]. These studies have shown that GDF5 expression was easily detected in the primordial cartilage of long bones rather than in the vertebrae and ribs. And lower expression of GDF5 would logically lead to a reduction in limb bone growth, consistent with decreased height. Lower transcription of GDF5 may influence the amount of cartilage in the vertebrae, limb proportions or joint angles, resulting in both a modest decrease in stature [25]. Voight et al. [26] reported that GDF5 and UQCC have been found to show strong evidence for selection in a genome-wide search for regions that have undergone recent selection. Above all, although many studies focus on association of GDF5 gene variants with body measurement traits in human, the available studies on bovine and other livestock have never been reported. Therefore, based on these results of the genome-wide approach in human, considering the evolutionarily conservation between cattle and human, we apply the research results of human GDF5 to analyze polymorphism and genetic effect on cattle GDF5 gene locus. And the present study firstly shows that the T586C SNP of bovine GDF5 is significantly associated with Body length and Hip width (Table 3) in the bovine. These results are consistent with the findings reported in human.

In conclusion, we identified one SNP in the GDF5 gene and investigated its association in different bovine breed populations. Our results provide evidence that the GDF5 gene might have potential effects on body measurement traits in the bovine. Therefore, further work will be necessary to use the SNP for marker-assisted selection (MAS) in larger population. It is also significant to investigate whether the GDF5 gene plays a role on development of those traits and whether it involves in linkage disequilibrium with other causative mutations.



This work was supported by the China National “863” Program (2006AA10Z1A1), the National Eleventh “Five-Year” Science and Technology Support Project (2006BAD01A10-3), the “13115” Scientific and Technological Innovation Program of Shaanxi Province (2007ZDCY-01), National 973 Program (2006CB102105) and Talent Foundation for Northwest A&F University. Moreover, the bovine populations were supported by Qinchuan beef cattle breeding center of Shaanxi province, Nanyang, Jiaxian and Xianan cattle breeding center of Henan province, Luxi cattle breeding center of Shandong province and Yunnan beef cattle & pasture research center (P. R. China).


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Copyright information

© Springer Science+Business Media B.V. 2009

Authors and Affiliations

  • Yong Feng Liu
    • 1
  • Lin Sen Zan
    • 1
    • 3
  • Kui Li
    • 2
  • Shuan Ping Zhao
    • 1
  • Ya Ping Xin
    • 1
  • Qing Lin
    • 1
  • Wan Qiang Tian
    • 1
  • Zhi Wei Wang
    • 2
  1. 1.College of Animal Science and TechnologyNorthwest A & F UniversityYanglingPeople’s Republic of China
  2. 2.Key Laboratory for Farm Animal Genetic Resources and Utilization of Ministry of Agriculture of China, Institute of Animal ScienceChinese Academy of Agricultural SciencesBeijingPeople’s Republic of China
  3. 3.National Beef Cattle Improvement Centre of ChinaYanglingPeople’s Republic of China

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