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. 2021 Jan 12;11(1):157.
doi: 10.3390/ani11010157.

Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep

Yaxin Yao  1 , Zhangyuan Pan  1 , Ran Di  1 , Qiuyue Liu  1 , Wenping Hu  1 , Xiaofei Guo  1   2 , Xiaoyun He  1 , Shangquan Gan  3 , Xiangyu Wang  1 , Mingxing Chu  1
Affiliations

Whole Genome Sequencing Reveals the Effects of Recent Artificial Selection on Litter Size of Bamei Mutton Sheep

Yaxin Yao et al. Animals (Basel). .

Abstract

Bamei mutton sheep is a Chinese domestic sheep breed developed by crossing German Mutton Merino sheep and indigenous Mongolian sheep for meat production. Here, we focused on detecting candidate genes associated with the increasing of the litter size in this breeds under recent artificial selection to improve the efficiency of mutton production. We selected five high- and five low-fecundity Bamei mutton sheep for whole-genome resequencing to identify candidate genes for sheep prolificacy. We used the FST and XP-EHH statistical approach to detect the selective sweeps between these two groups. Combining the two selective sweep methods, the reproduction-related genes JUN, ITPR3, PLCB2, HERC5, and KDM4B were detected. JUN, ITPR3, and PLCB2 play vital roles in GnRH (gonadotropin-releasing hormone), oxytocin, and estrogen signaling pathway. Moreover, KDM4B, which had the highest FST value, exhibits demethylase activity. It can affect reproduction by binding the promoters of estrogen-regulated genes, such as FOXA1 (forkhead box A1) and ESR1 (estrogen receptor 1). Notably, one nonsynonymous mutation (p.S936A) specific to the high-prolificacy group was identified at the TUDOR domain of KDM4B. These observations provide a new opportunity to research the genetic variation influencing fecundity traits within a population evolving under artificial selection. The identified genomic regions that are responsible for litter size can in turn be used for further selection.

Keywords: Bamei mutton sheep; breeding; litter size; selection signal analysis; whole-genome sequencing.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic and population structure of monotocous and polytocous sheep. (A) A neighbor-joining phylogenetic tree constructed using whole-genome SNP data. The scale bar represents the level of similarity; Monotocous (red) and polytocous (blue) samples are indicated. (B) A neighbor-joining phylogenetic tree constructed using SNP data selected based on FST score.
Figure 2
Figure 2
Selective sweep analysis of the monotocous and polytocous sheep. (A) Manhattan plot of FST among the monotocous and polytocous sheep. The FST was calculated for each 50 kb autosomal and X-chromosome window. The dashed line denotes a threshold of Z(FST) = 5; (B) Manhattan plot of XP-EHH among the monotocous and polytocous sheep. The XP-EHH value was calculated for each 50 kb autosomal and X-chromosome window. The dashed line denotes a threshold of |XP-EHH| > 2.
Figure 3
Figure 3
KDM4B mutation in the coding region. (A) Hp value around the KDM4B loci. Hp was calculated for each 10 kb window of the monotocous and polytocous sheep. The gene coordinates are based on Ensembl ID ENSOARG00000008388; (B) Percentages of homozygotes and heterozygotes in the monotocous and polytocous sheep. The reference and mutant alleles are represented by “+” and “−,” respectively. Besides the 10 sheep sequenced with Illumina technology, additional samples were genotyped by Sanger sequencing; (C) Evolutionary analysis of the p.S936A amino acid variant. The protein coordinates are based on Ensembl ID ENSOARP00000009005.1. The upper panel shows the domains of the protein. The orthologous protein sequences from 11 vertebrates are aligned with the mutant residues shown in red. The NJ tree derived from the multiple alignment is shown in the lower panel.
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