| Transposable elements（TEs）are vital component of eukaryotic genomes,occupying30%-50%of mammalian genomes.They shape both the entire genome and genes that not only play a key role in genome sizes,speciation,diversity but also regulating gene expression and altering gene activity to produce phenotypic variation or disease.Furthermore,the TIP molecular marker of SINE with a larger insert fragment has more great impact on gene expression compared with SNP,and could be effective genotyped just by simple PCR amplification,has been already widely used in plants and humans,but there are few related studies on pigs.Based on this,the article explored the composition,distribution and age that the critical attributes of pig TEs by genome annotation,and established the TEs polymorphism library in"Zhuangxiang Black"pigs so as to screen meat quality traits related polymorphic SINE combined with eQTL analysis,which has provided new molecular markers for the genetic improvement of meat quality.The main results of this research are as follows:（1）Retrotransposons are abundant in pig genomes,occupying 36.8%（920.83MB）,of which LINE account for 17.76%（444.40MB）,mainly the L1 family;SINE account for12.91%（323.04MB）,and 84.03%originate from t RNAs;LTR account for 6.13%（153.39MB）,mainly the ERV family.（2）A total of 24,698 retrotransposons polymorphic loci were identified in“Zhuangxiang Black”pigs,which were widely distributed in non-coding regions,including 186 cases across exons;Poly SINE occupy 83.27%of all polymorphic events,and there were Indel,Dup,Inv that the three polymorphic types,the Indel type is the majority,SINE polymorphic frequency are significantly related to their age,and the youngest SINE,pre0-ss contribute to the most poly loci in the population;L1 and ERV are the only families showing polymorphism of LINE and LTR respectively,it is speculated that there may be live L1,ERV and SINE/t RNA transposons in pigs.（3）Combined with eQTL analysis,we identified the following 4 potential SINE molecular markers for genetic improvement of meat quality traits in the"Zhuangxiang Black"pigs:1)The AIDA gene expression levels increase sharply（p=4.23548E-12）with the insertion of a 274bp SINE transposon located in the 6th intron of AIDA（denoted as Indel＿10:11439826＿11440099）,and the polymorphism is significantly associated with pH24（p=0.00128）.2)The RNLS gene expression levels are decreased significantly among the SINE-/-,SINE+/-,SINE+/+genotypes due to the indel of a 258bp SINE transposon in the 5th intron of RNLS（denoted as Indel＿14:100386929＿100387186）,and the polymorphism is dramatic significantly associated with pH24（p=0.00904）and drip loss（p=0.00717）.3)The indel of a 281bp SINE transposon in the 8th intron of the HSDL2 gene（denoted as Indel＿1:253174645＿253174925）shows remarkably differences in the expression level of HSDL2 gene between the SINE+/+,SINE+/-genotypes（6.91227E-13）,and the polymorphism is significantly associated with marbling（p=0.04599）.4)A segment located in the 3th intron of the CENPS gene that contains an indel of a 297bp SINE transposon（denoted as Indel＿6:70706599＿70707103）shows extremely notable differences in the expression level of CENPS between the SINE+/+,SINE+/-genotypes（p=1.23123E-15）,and the polymorphism is greatly associated with flesh color（p=0.01126）and eye muscle area（p=0.00305）.This study has annotated and analyzed the classification,composition,distribution,age that the some critical attributes of TEs in the pig genome,offering a reference for further understanding of pig TEs,and first identified all TE polymorphisms in the"Zhuangxiang Black"pig population,furtherly unearthed four poly SINE associated with some vital meat quality traits combined with eQTL analysis,which provided a new type of molecular markers for genetic improvement of meat quality traits. |
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