转座子引起的猪ktn1基因结构变异及其与生产性能的关联分析

Structural variations caused by transposons in porcine ktn1 gene and their association with production traits

为探明转座子对猪的ktn1基因及其侧翼区结构变异的贡献,从全基因组测序(WGS)数据库中获取14个猪基因组中的ktn1基因序列和侧翼序列,通过ClustalX多序列比对和RepeatMasker转座子注释,全面解析转座子对ktn1的影响。通过PCR检测到一个SINEA1转座子插入多态,在苏姜猪群体中与相关性状进行关联分析。结果显示,ktn1基因及其侧翼区中含有至少77个转座子片段,其中绝大部分(98.70%)为SINE类转座子,并鉴定到9个小结构变异和4个由转座子引起的大结构变异,表明转座子是基因变异的重要来源。其中一个SINEA1插入多态引起的结构变异,在不同品种中呈现丰富的多态性,且无插入个体(SINE-/-)苏姜猪的断奶窝重((64.20±10.6) kg)比纯合有插入个体(SINE+/+)((74.14±9.0) kg)和杂合有插入个体(SINE+/-)((69.71±7.7) kg)轻(P<0.05),表明基于转座子插入多态研发分子标记具有可行性,提示转座子插入多态分子标记在分子辅助育种中具有较强的应用潜力。

In order to determine the effect of transposons on the sequence and structural variations of the porcine ktn1 gene and its flanking regions, we obtained 14 ktn1 sequences(including genic region, 5-kb 5′ flank and 3-kb 3′ flanking regions) from the WGS database in NCBI, multiple sequence alignment by ClustalX and transposon annotation by RepeatMasker. Then we analyzed the effect of transposons on ktn1. A SINEA1 insertion polymorphism was detected by PCR, and correlation was analyzed with related traits in the Sujiang pig population. The ktn1 gene and its flanking regions contained at least 77 transposon fragments, the majority(98.70%) of which was SINE insertions. We observed 9 small structural variations and 4 large structural variations caused by transposons, indicating that transposons were an important source of genetic variations. One of the structural variations caused by SINEA1 insertion polymorphism showed rich polymorphism in different breeds, and in Sujiang pigs, the weaned litter weight of non-inserted individuals(SINE-/-)((64.20±10.6) kg) was lighter than homozygous insertionindividuals(SINE+/+)((74.14±9.0) kg) and heterozygous insertion individuals(SINE+/-)((69.71±7.7) kg)(P<0.05). It is feasible to develop molecular marker based on the transposon insertion polymorphism to provide application potential in molecular-assisted breeding.