Whole-genome selective sweeps analysis in Pakistani Kamori goat

Rashid Saif,Tania Mahmood,Aniqa Ejaz,Safdar Ali Fazlani,Saeeda Zia

doi:10.1016/j.genrep.2021.101429

Rashid Saif, Tania Mahmood + Show 3 more

Open Access

https://doi.org/10.1016/j.genrep.2021.101429

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Abstract

Natural and artificial selection fix certain genomic regions of reduced heterozygosity which is an initial process in breed development. The primary goal of the current study is to identify the genomic selection signatures under positive selection and underlying genes in the Pakistani Kamori goat breed. High throughput whole-genome pooled-seq of Kamori (n = 12) and Bezoar (n = 8) was carried out. Raw fastq files underwent quality checks, trimming, mapping against reference genome, SNPs calling against Bezoar goat and allele frequency calculation. Selection sweeps were identified by applying pooled heterozygosity (Hp) and Tajima's D (TD) on Kamori while regions under divergent selection between Kamori & Bezoar were observed by Fixation Index (FST) analysis. Genome sequencing yielded 619,031,812 reads of which, 616,624,284 were successfully mapped. A total of 98,574 autosomal selection signals were detected; 32,838 from Hp and 32,868 from each FST & TD statistics. Annotation of the regions (with threshold −ZHp > 5, −ZTD > 2.5 & -ZFST < −4.5) detected 92 candidate genes. The top hits harbor Chr.6, 8, 12 & 26 having genes associated with body weight (GLIS3), coat color (DOCK8) and multidrug resistance-associated protein 4-like (LOC102179751 & LOC102180583). Other significant windows harbor milk production, immunity, adaptation and reproduction trait related genes. Current findings highlighted the genomic regions under-selection in Kamori breed which are likely to be associated with its vested traits that can be ameliorated further, by exploring the full genetic potential of this valued species. These may also be propagated to other undefined goat breeds by adopting targeted breeding policies.

Highlights

Domestic goat breeds have been under well documented and strong selection for several years through natural and artificial methods for various quantitative traits especially meat, milk and reproduction
3.2 Candidate selection signals and harbor genes The windows under positive selection in Kamori goat obtained after setting thresholds (−ZHp ≥ 5, Tajima’s D (TD) ≤ -2.72 and FST ≤ 0.09) on the basis of previously published data and rationale observation of our own data, are further finemapped and annotated which revealed genes related to body mass, coat color, wool type, milk production, immunity, adaptation to environment, body height and reproduction (Table 2)
This genome wide selection scan presents the results of regions under positive selection using complementary statistical tests, – ZHp and TD on Kamori breed and of genomic diversity analysis applied on Kamori vs. Bezoar using FST approach

Summary

Introduction

Domestic goat breeds have been under well documented and strong selection for several years through natural and artificial methods for various quantitative traits especially meat, milk and reproduction. Whole genome analysis based on population genetic statistics have been developed that significantly asses the selective sweeps in all livestock species without known phenotypes. Kamori is famous for its long ears, neck and unique coat colors usually dark brown with small dark or coffee colored patches over its entire body. They are medium to large size milch breed mainly found in Nawabshah, Dadu and Larkana districts in Sindh province of Pakistan. The primary goal of this research was to identify genomic regions and underlying candidate genes affected by selection in Kamori goat

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