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A whole genome sequence association study for puberty in a large Duroc × Erhualian F2 population
Author(s) -
Xin W. S.,
Zhang F.,
Yan G. R.,
Xu W. W.,
Xiao S. J.,
Zhang Z. Y.,
Huang L. S.
Publication year - 2018
Publication title -
animal genetics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.756
H-Index - 81
eISSN - 1365-2052
pISSN - 0268-9146
DOI - 10.1111/age.12623
Subject(s) - biology , genetics , quantitative trait locus , whole genome sequencing , population , candidate gene , genetic association , snp , genome wide association study , genome , single nucleotide polymorphism , gene , genotype , demography , sociology
Summary A large proportion of gilts and sows are culled from reproduction populations because of anestrus and pubertal reproductive failure. Selecting early onset of puberty gilts has a favorable effect on sows’ reproductivity. However, age at puberty is hard to be routinely measured in commercial herds. With molecular genetic predictors, identifying individuals that have a propensity for early onset of puberty can be simplified. We previously performed genome scanning and a genome‐wide association study for puberty in an F2 resource population using 183 microsatellites and 62 125 SNP s respectively. The detection power and resolution of identified quantitative trait loci were very low. Herein, we re‐sequenced 19 founders of the F2 resource population in high coverage, and whole genome sequences of F2 individuals were imputed to perform an association study for reproductive traits. A total of 2339 SNP s associated with pubertal reproductive failure were identified in the region of 30.94–40.74 Mb on SSC 7, with the top one, positioned at 33.36 Mb, explaining 16% of the phenotypic variances. We improved the magnitude of the P‐ value by 10E+5 to 10E+7 using the whole genome sequence rather than using low/middle density markers as in previous studies, and we narrowed down the QTL confidence interval to 5.25 Mb. Combining the annotation of gene function, RAB 23 and BAK 1 were perceived as the most compelling candidate genes. The identified loci may be useful in culling sows failing to show estrus by marker‐assisted selection to increase reproductive efficiency of swine herds.