Abstract
2 SNPs were discovered in our previous genome-wide association study (GWAS): s58995.1 (rs420767326 A>G) in MEF2B gene and OAR3_115712045.1 (rs401775061 A>C) in TRHDE gene, which were significantly associated with post-weaning gain in sheep. Herein, we performed a replication experiment to investigate single nucleotide polymorphisms (SNPs) within the MEF2B and TRHDE gene exons, the 5′untranslated regions (within 1000bp), the 3′ untranslated regions (within 1000bp) and their associations with Ujumqin sheep growth traits in 4-month age and 6-month age, respectively. Finally,3 SNPs were selected to be investigated including 1 SNP in 3′untranslated regions in MEF2B gene (rs417014745 A>G) and 2 SNPs in TRHDE gene (rs426980328 T>C and rs430810656 G>A).The χ2 test showed all the 3 variations were in Hardy–Weinberg equilibrium (P>0.05) status. Association analysis suggested that rs426980328 T>C was significantly associated with body weight and chest girth in 4-month age (P<0.05). rs430810656 G>A exhibited extremely significant association with body weight and chest girth in 4-month age (P<0.01). rs417014745 A>G was extremely significantly associated with body weight and chest girth in 4-month age and chest girth in 6-month age (P<0.01), and it was also significantly associated with body weight in 6-month age (P<0.05). Combined effect analysis indicated significant associations between the combinations of rs426980328-rs417014745, rs430810656-rs417014745 and several growth traits (P<0.05). These results suggested MEF2B and TRHDE genes affected growth traits in Ujumqin sheep and the combination effect of the two genes also played a significant effective role. These SNPs might have potential value as genetic markers for growth traits and it could be used in Ujumqin sheep breeding in future. Further studies are necessary to confirm our findings.
Highlights
Growth traits are significant economic traits in sheep, advances of molecular genetics have opened appealing perspectives for the identification of functional genes through genomics technology, single nucleotide polymorphisms (SNPs) have been widely used for QTL detection and localization for complex traits in many species[1]
TRHDE gene in goat was identified by the multiple genomic signatures of selection study, the results showed it could directly or indirectly influence traits for adaptation to hot arid environments[14].Based on these previous studies, further study on MEF2B and TRHDE genes were taken to investigate the relationship between SNPs within them and Ujumqin sheep growth traits, respectively, as well as their combined effect on Ujumqin sheep growth traits, in order to validate the genome-wide association study (GWAS) results and screen casual genetic variants as genetic markers that benefit for the sheep growth performance in an independent sheep population
DNA pool sequencing showed totally 2 SNPs were identified in MEF2B gene and 5 SNPs in the TRHDE gene, considering the compatibility of the primers used to extend the single site in the MALDI-TOF assay process, rs417014745 A>G in the 3’-UTR of MEF2B gene and 2 SNPs in the exon2, exon14 respectively were selected to be genotyped in a new Ujumqin sheep validation group including 343 samples
Summary
Growth traits are significant economic traits in sheep, advances of molecular genetics have opened appealing perspectives for the identification of functional genes through genomics technology, SNPs have been widely used for QTL detection and localization for complex traits in many species[1]. As a novel candidate gene for growth traits detected by GWAS, no study was found on associations between TRHDE gene and sheep growth traits.TRHDE is thyrotropinreleasing hormone degrading enzyme which encodes a member of the peptidase M1 family. It is reported TRHDE gene was associated with neuroglioma in human[9], OAR3_115712045.1 identified by our GWAS analysis was located within a QTL which was found to affect internal fat amount in Merino sheep[10]. TRHDE gene in goat was identified by the multiple genomic signatures of selection study, the results showed it could directly or indirectly influence traits for adaptation to hot arid environments[14].Based on these previous studies, further study on MEF2B and TRHDE genes were taken to investigate the relationship between SNPs within them and Ujumqin sheep growth traits, respectively, as well as their combined effect on Ujumqin sheep growth traits, in order to validate the GWAS results and screen casual genetic variants as genetic markers that benefit for the sheep growth performance in an independent sheep population
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