Genome-wide analysis reveals selection for Chinese Rongchang pigs

doi:10.15302/J-FASE-2017161

Front. Agr. Sci. Eng.

2017, Vol. 4

Issue (3) : 319-326 https://doi.org/10.15302/J-FASE-2017161

RESEARCH ARTICLE

Genome-wide analysis reveals selection for Chinese Rongchang pigs

Lei CHEN¹, Shilin TIAN², Long JIN², Zongyi GUO¹, Dan ZHU¹, Lan JING¹, Tiandong CHE², Qianzi TANG², Siqing CHEN¹, Liang ZHANG¹, Tinghuan ZHANG¹, Zuohua LIU¹, Jinyong WANG¹(

), Mingzhou LI²(

)

¹. Key Laboratory of Pig Industry Sciences, Ministry of Agriculture, Chongqing Academy of Animal Sciences, Chongqing 402460, China
². Institute of Animal Genetics and Breeding/College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China

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Abstract

Livestock have undergone domestication and consequently strong selective pressure on genes or genomic regions that control desirable traits. To identify selection signatures in the genome of Chinese Rongchang pigs, we generated a total of about 170 Gb of DNA sequence data with about 6.4-fold coverage for each of six female individuals. By combining these data with the publically available genome data of 10 Asian wild boars, we identified 449 protein-coding genes with selection signatures in Rongchang pigs, which are mainly involved in growth and hormone binding, nervous system development, and drug metabolism. The accelerated evolution of these genes may contribute to the dramatic phenotypic differences between Rongchang pigs and Chinese wild boars. This study illustrated how domestication and subsequent artificial selection have shaped patterns of genetic variation in Rongchang pigs and provides valuable genetic resources that can enhance the use of pigs in agricultural production and biomedical studies.

Keywords domestication genome pig re-sequencing selection

Corresponding Author(s): Jinyong WANG,Mingzhou LI

Just Accepted Date: 16 May 2017 Online First Date: 05 June 2017 Issue Date: 12 September 2017

Cite this article:

Lei CHEN,Shilin TIAN,Long JIN, et al. Genome-wide analysis reveals selection for Chinese Rongchang pigs[J]. Front. Agr. Sci. Eng. , 2017, 4(3): 319-326.

URL:

https://academic.hep.com.cn/fase/EN/10.15302/J-FASE-2017161
https://academic.hep.com.cn/fase/EN/Y2017/V4/I3/319

Fig.1 Phylogenetic relationship of Rongchang pigs. (a) Neighbor-joining phylogenetic tree of pig breeds. The scale bar represents p-distance; (b) two-way principle component plot of pig breeds. The fractions of the variance explained are 12.2% and 5.74% for eigenvectors 1 and 2, respectively, with a Tracy-Widom P value<10⁻⁷⁸ (Table S5).

Fig.2 Genomic regions with strong selective sweep signals in Rongchang pigs. (a) Genome-wide distribution of pooled heterozygosity values (Hp), genetic differentiation (F_ST), and corresponding Z transformations (Z(Hp)) and Z(F_ST), which were calculated in 100-kb windows with 10-kb steps (n = 229772, contain≥100 SNPs). Data points located to the right of the vertical line (where Z(F_ST) is 2) and below the horizontal line (where Z(Hp) is −2) were identified as selected regions in Rongchang pigs (red points). m, mean; s, standard deviation; (b) violin plot of Z(Hp)_Rongchang, Z(F_ST), and |Tajima’s D_{Rongchang pigs} – Tajima’s D_{Asian wild boars}| in genomic regions with strong selective sweep signals for Rongchang pigs compared with the whole genome. Out of 229772 100-kb windows that contained≥100 SNPs with 10-kb steps across the pig reference genome (gray violin), 1852 windows were picked out as regions with strong selective sweep signals (green violin). Each violin with the width depicting a 90°-rotated kernel density trace and its reflection. Vertical black boxes denote the interquartile range between the first and third quartiles (25th and 75th percentiles, respectively) and the white point inside denotes the median. Vertical black lines denote the lowest and highest values within a 1.5 times interquartile range from the first and third quartiles, respectively. The statistical significance was calculated by the Mann–Whitney U test; (c) phylogenetic tree (scale bar represents p-distance); (d) two-way principle component plot of Rongchang pigs (n = 6) and Asian wild boars (n = 10) based on SNPs in regions with strong selective sweep signals with 25.0% of variance explained for eigenvector 1, (P = 0.030, Tracy-Widom test) and 13.7% for eigenvector 2 (P = 0.277, Tracy-Widom test).

Tab.1 Functional gene categories enriched for genes affected by selection in Rongchang pigs

Fig.3 Genes related to nervous system development that show selective sweep signatures in Rongchang pigs. (a) Z(Hp), Z(F_ST), and Tajima’s D values are plotted using a 10-kb sliding window. Genomic regions located above the upper horizontal dashed red line (Z(F_ST) = 2) and below the lower horizontal dashed black line (Z(Hp) = −2) were considered regions with strong selective sweep signals for Rongchang pigs (beige regions). Genome annotations are shown at the bottom (black bar: coding sequences, blue bar: genes). The boundaries of genes related to nervous system development are marked in red; (b) the gene trees for 10 genes related to nervous system development of 10 Asian wild boars and six Rongchang pigs.

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