Abstract
Simple SummarySimple sequence repeats (SSRs) are present at high densities in regulatory elements, suggesting that they may affect gene function and phenotypic traits. Therefore, SSRs can be exploited in marker-assisted selection. In addition, they can be widely used as molecular markers to study genetic diversity, population structure, and evolution. While SSRs have been widely studied in many mammalian species, very little research has focused on genome-wide SSRs of miniature pigs, a small but special group of pigs that express the dwarf phenotype. Based on the SSR-enriched library building and sequencing, about 30,000 novel polymorphic SSRs for four miniature pig breeds were mapped to the Duroc pig reference genome. The four miniature pig breeds had different numbers and types of SSRs and distributions of repeat units. There were 2518 polymorphic SSRs in the intron or exon regions that were common to all four breeds and functional analyses revealed 17 genes that were associated with body size and other genes that were associated with growth and development. In conclusion, the SSRs detected in the miniature pigs in this study may provide useful genetic markers for the selection of farm animals and the polymorphic SSRs provide valuable insights into the determination of mature body size, as well as the immunity, growth and development of animals.Simple sequence repeats (SSRs) are commonly used as molecular markers in research on genetic diversity and discrimination among taxa or breeds because polymorphisms in these regions contribute to gene function and phenotypically important traits. In this study, we investigated genome-wide characteristics, repeat units, and polymorphisms of SSRs using sequencing data from SSR-enriched libraries created from Wuzhishan (WZS), Bama (BM), inbred Luchuan (LC) and Zangxiang (ZX) miniature pig breeds. The numbers and types of SSRs, distributions of repeat units and polymorphic SSRs varied among the four breeds. Compared to the Duroc pig reference genome, 2518 polymorphic SSRs were unique and common to all four breeds and functional annotation revealed that they may affect the coding and regulatory regions of genes. Several examples, such as FGF23, MYF6, IGF1R, and LEPROT, are associated with growth and development in pigs. Three of the polymorphic SSRs were selected to confirm the polymorphism and the corresponding alleles through fluorescence polymerase chain reaction (PCR) and capillary electrophoresis. Together, this study provides useful insights into the discovery, characteristics and distribution of SSRs in four pig breeds. The polymorphic SSRs, especially those common and unique to all four pig breeds, might affect associated genes and play important roles in growth and development.
Highlights
Simple sequence repeats (SSRs), known as microsatellites or short tandem repeats (STRs), consist of 2 to 6 base-pair motifs repeated several times in tandem
We discovered a total of 471,287 simple sequence repeat (SSR), including 290,373 dinucleotide repeats (Di-SSRs), 82,517 trinucleotide repeats (Tri-SSRs), 83,936 tetranucleotide repeats (Tetra-SSRs), 11,545 pentanucleotide repeats (Penta-SSRs)
Based on the SSR-enriched library, we obtained an average of 1,225,072 SSRs in the four pig breeds, which is less than the number of SSRs in the MicroSatellite DataBase (MSDB) [54]
Summary
Simple sequence repeats (SSRs), known as microsatellites or short tandem repeats (STRs), consist of 2 to 6 base-pair motifs repeated several times in tandem. As a consequence of their wide distribution and high mutation rate in eukaryotic genomes [1], SSRs have been used in genetic diversity and population structure studies [2,3,4,5], for discrimination among species or breeds [6,7], in marker-assisted selection [8,9,10] and in evolution analysis [11]. SSRs were predicted to be bound by protein-coding transcripts, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) and affect competing endogenous RNA crosstalk [12]. Besides being an important category of regulatory elements, polymorphic SSRs could quantitatively regulate the transcription of tissue-specific genes in the development of the frog embryo [13]. Another study showed that polymorphic SSRs play an important role in shaping splicing regulatory elements and lead to alternative splicing events in different stress environments [14]. An increasing number of studies on SSR discovery and functional analysis have been conducted, providing evidence for the importance of SSRs in gene function and complex traits [15]
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