Identification of the Gene Diversity of MSTN
According to the mixed DNA pool sequence, 29 single nucleotide polymorphic sites were identified in the
MSTN sequence (Table 4). Among them, one single nucleotide mutation site was in the 52 UTR, two were in exon 1, one was in exon 2, five were in intron 1 and the 20 remaining single nucleotides were in intron 2. Twenty disparate sites were found between Dazu and Boer goats. One mutation site was in the regulatory region and the 19 remaining mutation sites were in the intron region.
Haplotype Distribution
Statistical analysis revealed that polymorphism appeared in 20 out of 29 mutation sites in all the four goat breeds. About 18–20 SNP sites were detected in Nubian and local Chinese goats and only five SNPs were found in Boer goats (Table 5).
Among the 148 goats, 20 mutation sites constituting 18 haplotypes were found. The haplotypes in different breeds had diverse frequency and distribution. For instance, haplotype H_2 in the four populations accounted for 54.05% of the total number of haplotypes. However, most of the haplotypes did not have high frequencies. Only 1/3 of the haplotypes in one population were unique and the rest had excessively low frequencies. H_18 only appeared in Dazu black goats and its frequency was 0.3%. According to the types of haplotypes in each goat population, the Nubian goats carried the most haplotypes of up to 15. Among them, H_9, H_12, H_13 and H_14 were unique and constituted less than 1% of the total sample in Nubian goats. Dazu black goats possessed eight haplotypes among which H_17 and H_18 were unique with frequencies of 1.0% and 0.3%, respectively. Boer goats had six haplotypes; among them, H_3 only appeared in this breed and accounted for 1% of the total number. Youzhou black goats had five haplotypes and no unique haplotype (Table 6 to8 ).
Haplotype network and phylogeny clustering distribution maps revealed that the 18 haplotypes could be divided into two clusters (Best Fitting Model, Table S1). Cluster I included 10 haplotypes, namely, H_1, H_2, H_3, H_4, H_5, H_6, H_10, H_11, H_1 and H_15. Cluster II included eight haplotypes, namely, H_7, H_8, H_9, H_12, H_13, H_16, H_17 and H_18. According to their distribution, the haplotypes in Boer goats were classified as Cluster I and those carried by Nubian goats, Dazu black goats and Youzhou black sheep belonged to both clusters (Fig 1).
The genetic diversity of
MSTN in goats has been widely studied. However, the polymorphism of
MSTN varies in different goat populations.
Li et al. (2006a) detected seven polymorphic loci in the intron 2 of 24 goat populations.
Liu (2006) discovered eight polymorphic loci in Chinese local breeds. One polymorphic locus is in 52 UTR, one is in exon 1 and six are in intron 2.
Li et al. (2006b) found eight SNPs in intron 2 and exon 3 of 22 goat breeds and they include seven SNPs in intron 2 and one SNP in exon 3. Some scholars revealed only 1 to 2 polymorphic sites in exon 3 of local and commercial goat breeds here and abroad
(Khichar et al., 2016; Min et al., 2015; Wang et al. 2008). All these reports are in accordance with the present findings. Most polymorphic loci are assembled in intron 2. Other sequences, especially in exon 2, where no mutation sites have been found, are rarely mutated. This finding indicated differences in the conservative property of diverse
MSTN regions. With respect to the total number of SNPs, the number of SNPs in
MSTN of Nubian goats, Youzhou black goats and Dazu black goats is higher than that of Boer goats and others. These three breeds had rich genetic diversity and hence had a high breeding value
.
MSTN gene polymorphic loci play an important role in the growth of goats. Mutations in nucleotides at different positions in
MSTN sequence result in disparate characters in goats. For instance, a polymorphic locus detected in the
MSTN gene of Boer and Anhui white goats is associated with goat weight at 12 months of age, body length and height at withers
(Zhang et al. 2013). For the T/C mutation at base 3783 in intron 2 of
MSTN of Haimen goats, its polymorphism substantially influences the goat’s birth weight (
p<0.01;
Zhang 2009). Furthermore, the function of the same polymorphic locus differs in various goat populations. The insertion and deletion of 5 bp TTTTA in the 5¢ UTR of
MSTN are observed in Boer goats, Inner Mongolia White Cashmere goats and Shaanbei White Cashmere Goat and this mutation site is prominently relevant to the growth of goats, especially to the chest depth, height and chest circumference of Inner Mongolia White Cashmere goats and Shaanbei White Cashmere goats. However, studies have yet to determine if the site has the same genetic effect in other populations
(Bi et al., 2020a; Bi et al., 2020b; Zhang et al., 2012). These studies have illustrated that
MSTN plays an important role in the growth and development of goats and is inseparable from the multifunctional polymorphic sites crucial in goat breeding. Additionally,
MSTN has abundant genetic diversity, which is important in breeding various types of goats.
A large number of
MSTN gene polymorphic loci functioning in goat growth should be explored in detail. However, polymorphic loci follow the general distribution pattern after haplotypes in Boer goats, Nubian goats, Youzhou black goats and Dazu black goats are constructed. The haplotype distribution in Boer goats is concentrated, whereas the distribution in the three other goat breeds is highly scattered. A similar situation is observed in sheep. Fifteen SNP sites with 12 haplotypes are detected in
MSTN of local Chinese sheep breeds (9) and imported sheep breed. Haplotype VIII is a haploid homozygous in all-meat or meat/wool sheep. Haplotype I is only distributed in skin type and skin/meat type goat breeds
(Gong et al., 2009). Polymorphic loci are discovered in
MSTN of Yanqi horse and Yili horse and they have three genotypes: AA, AG and GG. This site deviates from the Hardy–Weinberg equilibrium. The correlation analysis of different genotypes and body size traits shows that the chest circumference of GG and AG types of Yanqi horse is significantly longer than that of AA type (
p<0.05). The body length of the GG-type Yili horse is longer than that of AA type. The chest circumference of the GG type is remarkably longer than that of the AG and AA types
(Han 2015). Meanwhile, 11 polymorphic loci with 12 haplotypes are found in
MSTN of commercial and local breed chickens. Haplotypes are closely related to the body weight of chicken on days 1, 14, 28 and 42 and carcass traits on day 42
(Dushyanth et al., 2016). The ~622 bp A/T mutation in the 52 UTR of
MSTN is associated with the economic traits of Boer goats and three other local goats (Lubei White, Laoshan Dairy and Wendeng Dairy goats). The CC genotype is primarily concentrated in the Boer goat population and TT is mainly concentrated in the three local populations; the weaning weight and net meat weight of the CC-type individuals are significantly higher than those of TT types
(Min et al., 2015).
Different genotypes or haplotypes have disparate distributions in animal populations with different production types. This result implies that a dominant genotype is gradually achieved. This finding is consistent with the breeding expectations of long-term artificial selection. Boer goat is the best meat goat breed in the world and its haplotypes related to economic traits accumulate through long-term artificial selection. As local indigenous goat breeds, Dazu and Youzhou black goats are bred through natural selection and environmental adaptability without powerful manual selection. The lactation and meat performance of Nubian goats, as a milk/meat dual type, are achieved through artificial breeding
(Kholif et al., 2018). However, the emphasis on production speed and meat production is weaker than the selection pressure of Boer goats because they are bred for their meat and milk. As a result, the genetic diversity of the selected genomic regions related to traits varies.
