SERPINA1 gene identified in RNA-Seq showed strong association with milk protein concentration in Chinese Holstein cows

PeerJ
Cong LiShengli Zhang

Abstract

The detection of candidate genes and mutations associated with phenotypic traits is important for livestock animals. A previous RNA-Seq study revealed that SERPINA1 gene was a functional candidate that may affect milk protein concentration in dairy cows. To further confirm the genetic effect of SERPINA1 on milk protein traits, genetic polymorphisms were identified and genotype-phenotype associations were performed in a large Chinese Holstein cattle population. The entire coding region and the 5'-regulatory region (5'-UTR) of SERPINA1 was sequenced using pooled DNA of 17 unrelated sires. Association studies for five milk production traits were performed using a mixed model with a population encompassing 1,027 Chinese Holstein cows. A total of four SNPs were identified in SERPINA1, among which rs210222822 and rs41257068 presented in exons, rs207601878 presented in an intron, and rs208607693 was in the 5'-UTR. Analyses of pairwise D' measures of linkage disequilibrium (LD) showed strong linkage among these four SNPs (D' = 0.99-1.00), and a 9 Kb haplotype block involving three main haplotypes with GTGT, CCCC and CCGT was inferred. An association study revealed that all four single SNPs and their haplotypes had significant genetic e...Continue Reading

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Datasets Mentioned

BETA
X63129

Methods Mentioned

BETA
RNA-Seq
electrophoresis
genotyping
PCR

Software Mentioned

Haploview
SAS
BLAST
Beagle3
Primer3web Program

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