Balancing selection at a premature stop mutation in themyostatingene underlies a recessive leg weakness syndrome in pigs

Abstract

12Balancing selection provides a plausible explanation for the maintenance of deleterious 13 alleles at moderate frequency in livestock, including lethal recessives exhibiting 14 heterozygous advantage in carriers. In the current study, a leg weakness syndrome 15 causing mortality of piglets in a commercial line showed monogenic recessive 16 inheritance, and a region on chromosome 15 associated with the syndrome was identified 17 by homozygosity mapping. Whole genome resequencing of cases and controls identified 18 a mutation coding for a premature stop codon within exon 3 of the porcine Myostatin 19 (MSTN) gene, similar to those causing a double-muscling phenotype observed in several 20 mammalian species. The MSTN mutation was in Hardy-Weinberg equilibrium in the 21 population at birth, but significantly distorted amongst animals still in the herd at 110 kg, 22 due to an absence of homozygous mutant genotypes. In heterozygous form, the MSTN 23 mutation was associated with a major increase in muscle depth and decrease in fat depth, 24 suggesting that the deleterious allele was maintained at moderate frequency due to 2 25 heterozygous advantage. Knockout of the porcine MSTN by gene editing has previously 26 been linked to problems of low piglet survival and lameness. This MSTN mutation is an 27 example of putative balancing selection in livestock, providing a plausible explanation 28 for the lack of disrupting MSTN mutations in pigs despite many generations of selection 29 for lean growth. 30 Introduction 32 Leg weakness is heterogeneous condition causing lameness in pigs, and has negative 33 impacts on both animal welfare and productivity [1, 2]. Significant heritability estimates 34 have been reported for leg weakness traits [reviewed in 3], with moderate to high 35 estimates in certain pig breeds, e.g. h 2 = 0.45 in Landrace [4]. Several quantitative trait 36 loci (QTL) have been identified for these traits, albeit they are generally not consistent 37 across studies and breeds [5-8], which may be partly due to the heterogeneity of this 38 condition. Interestingly, significant genetic correlations between leg weakness and other 39 production traits (such as growth and muscle depth) have been detected [4]. Further, in a 40 divergent selection experiment in Duroc lines, selection for high leg weakness was 41 associated with a significant increase in muscle length and weight [9]. Taken together, 42 these results suggest a degree of antagonistic genetic relationship between leg weakness 43 and muscle growth traits in pigs, potentially explaining increases in the syndrome 44 observed with intense selection for lean growth in recent decades. 45 Deleterious alleles can be maintained at relatively high frequency in commercial livestock 46 populations due to heterozygous advantage for traits under selection [10]. Examples of 47 65mass and reduced fat depth than wild type homozygotes. Therefore, we propose that the 66 MSTN mutant allele is highly deleterious in this population in homozygous form, but was 67 maintained ...

Whole-Genome Resequencing Reveals Genetic Structure and Introgression in Chinese Pudong White Pigs

“…The whole-genome resequencing data of 320 individuals from 27 populations, including 18 Chinese indigenous breeds (Jinhua (JH), Erhualian (EHL), Meishan (MS) Wannan Black (WNB), Wuzhishan (WZS), Luchuan (LUC), Bamaxiang (BMX), Baoshan (BS), RC, Neijiang (NJ), Hetao (HT), Laiwu Black (LWH), Min (MIN), Bamei (BAM), Tibet Tibetan (TT), Sichuan Tibetan (SCT), Yunnan Tibetan (YNT), Gansu Tibetan (GST), n = 181), CWB (n = 13), six European domestic breeds (Duroc (DU), French Large White (FLW), English Large White (ELW), Korean Landrace (KLR), Danish Landrace (DLR), Pietrain (PI), n = 113), EWB (n = 21) and OUT (Phacochoerus africanus, Sus cebifrons, Sus celebensis, Sus verrucosus, Sus barbatus, Sumatras wild boars, n = 7) were downloaded from NCBI public database (Access No. PRJNA398176 [26], PRJNA213179 [25], PRJNA488327 [27], PRJNA550237 [28], PRJEB9922 [29], PRJEB1683 [23], PRJNA553106 [30], PRJNA231897 [31], PRJNA239399 [32], PRJNA506339 [33] and PRJNA260763 [34], Table S1). The whole-genome sequencing raw data of 335 pigs was ltered by the following steps: (i) removing the paired reads if the content of N contained in a single-end sequencing read exceeded 10% of the length of the read; (ii) ltering the paired reads if the number of low-quality (Q < = 5) bases contained in a single-end sequencing read exceeded 50% of the length of the read; (iii) removal of the adapter paired-end reads.…”