Pereira Guilherme L, Malheiros Jessica M, Ospina Alejandra M T, Chardulo Luis Artur L, Curi Rogério A
Department of Animal Breeding and Nutrition, College of Veterinary and Animal Science, São Paulo State University (UNESP), Rubião Junior District, Botucatu, São Paulo, 18618-970, Brazil.
Department of Animal Science, College of Agriculture and Veterinary Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil.
J Appl Genet. 2019 Feb;60(1):79-86. doi: 10.1007/s13353-019-00483-1. Epub 2019 Jan 21.
Among horses selected for speed, the racing line of Quarter Horses is characterized by high performance in sprint races, with these animals being considered the fastest horses in the world. However, few studies have investigated in more detail the polymorphisms and genes that act on this trait. The objective of this study was to analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing performance. Genotypic and phenotypic records from 360 animals of the racing line of Quarter Horses, previously genotyped with an SNP chip to obtain individual genomic estimated breeding values for performance, were used for the formation and sequencing of two groups of animals with contrasting racing performance (20 animals with superior SImax and 20 with inferior SImax). Two rapid runs were performed using two pools of libraries containing 20 and 19 samples randomly chosen among the 40 samples with contrasting SIs. A total of 1203 variants (1105 SNPs and 93 InDels) were identified in 33 regions of interest obtained previously by GWAS. Twenty-nine of the polymorphisms (24 SNPs and 5 InDels) were considered to be important based on three different and independent approaches: SIFT scores classified as deleterious (< 0.05), degree of impact on the consensus region of each polymorphism, and different allele frequencies identified by Fisher's exact test (p < 0.01) between the groups of horses with contrasting SImax. Thus, eight genes described as functional and positional candidates in previous studies (ABCG5, COL11A1, GEN1, SOCS3, MICAL1, SPTBN1, EPB41L3, and SHQ1) and nine new candidate genes (AKNA, ARMC2, FKBP15, LHX1, NOL10, TMEM192, ZFP37, FIG4, and HNRNPU), some of them with known function, were related to racing performance in Quarter Horses.
在被选作追求速度的马匹中，夸特马的赛马品系以在短跑比赛中的高性能为特征，这些动物被认为是世界上跑得最快的马。然而，很少有研究更详细地调查影响这一性状的多态性和基因。本研究的目的是分析夸特马中先前通过全基因组关联研究（GWAS）与该性状相关区域的外显子组和非翻译区（UTR），探寻与赛马性能相关或处于强连锁不平衡状态的因果基因多态性。从360匹夸特马赛马品系的动物中获取基因型和表型记录，这些动物先前已用SNP芯片进行基因分型以获得个体基因组性能估计育种值，用于组建和测序两组具有对比性赛马性能的动物（20匹SImax值高的动物和20匹SImax值低的动物）。使用从40个具有对比性SIs的样本中随机选择的20个和19个样本组成的两个文库池进行了两次快速测序。在先前通过GWAS获得的33个感兴趣区域中总共鉴定出1203个变异（1105个单核苷酸多态性（SNP）和93个插入缺失（InDel））。基于三种不同且独立的方法，29个多态性（24个SNP和5个InDel）被认为是重要的：SIFT评分归类为有害（<0.05）、对每个多态性共有区域的影响程度，以及通过费舍尔精确检验（p<0.01）在具有对比性SImax的马组之间鉴定出的不同等位基因频率。因此，先前研究中描述为功能和位置候选基因的8个基因（ABCG5、COL11A1、GEN1、SOCS3、MICAL1、SPTBN1、EPB41L3和SHQ1）以及9个新的候选基因（AKNA、ARMC2、FKBP15、LHX1、NOL10、TMEM192、ZFP37、FIG4和HNRNPU），其中一些具有已知功能，与夸特马的赛马性能相关。
