Scanning of selection signature provides a glimpse into important economic traits in goats (Capra hircus)

Abstract

Goats (Capra hircus) are one of the oldest livestock domesticated species, and have been used for their milk, meat, hair and skins over much of the world. Detection of selection footprints in genomic regions can provide potential insights for understanding the genetic mechanism of specific phenotypic traits and better guide in animal breeding. The study presented here has generated 192.747G raw data and identified more than 5.03 million single-nucleotide polymorphisms (SNPs) and 334,151 Indels (insertions and deletions). In addition, we identified 155 and 294 candidate regions harboring 86 and 97 genes based on allele frequency differences in Dazu black goats (DBG) and Inner Mongolia cashmere goats (IMCG), respectively. Populations differentiation reflected by Fst values detected 368 putative selective sweep regions including 164 genes. The top 1% regions of both low heterozygosity and high genetic differentiation contained 239 (135 genes) and 176 (106 genes) candidate regions in DBG and IMCG, respectively. These genes were related to reproductive and productive traits, such as “neurohypophyseal hormone activity” and “adipocytokine signaling pathway”. These findings may be conducive to molecular breeding and the long-term preservation of the valuable genetic resources for this species.

Allele-specific expression reveals the phenotypic differences between thin- and fat-tailed sheep

“…2c, Additional file 4: TableS4). And the ratio of transition and transversion was 3:1, which is similar to the previous studies [48].…”

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

“…PRKAA1, protein kinase AMPactivated catalytic subunit alpha 1, served as an energy sensor that maintains energy homeostasis (Kahn et al, 2005;Krishan et al, 2014). And another gene, PARD3B with lower selection intensity here, had been identified with goat productive traits in another report (Guan et al, 2016).…”

“…Besides, there were few association analysis of single gene, for example, the SNPs of POU class 1 homeobox 1 (POU1F1) and KISS1 genes, insertion/deletion (indel) variants of lysine demethylase 6A (KDM6A) and β-Type platelet-derived growth factor receptor (PDGFRB), and transcript variants of catenin beta 1 (CTNNB1) had been reported to be associated with goat LS trait (An et al, 2013;Cui et al, 2018;Zhang X. et al, 2018;Yang et al, 2019;Zhu et al, 2019). Meanwhile, the genome-wide research on goat is also very lacking, only fewer reports showed some novel mutation sites affecting goat reproduction by whole-genome sequence (Guan et al, 2016;Lai et al, 2016). According to Guan et al (2016), the reproductionrelated genes regard to neurohypophysial hormone activity, including PAIP2B, CCDC64, and EPB41L5, had been identified.…”

“…Meanwhile, the genome-wide research on goat is also very lacking, only fewer reports showed some novel mutation sites affecting goat reproduction by whole-genome sequence (Guan et al, 2016;Lai et al, 2016). According to Guan et al (2016), the reproductionrelated genes regard to neurohypophysial hormone activity, including PAIP2B, CCDC64, and EPB41L5, had been identified. Also, Lai et al (2016) revealed a series of candidate genes for fecundity (number of lambs) in Laoshan dairy goats, such as synonymous mutation: MAP3K12, DNMT3B, and SMAD2 and non-synonymous mutation: SETDB2 and CDH26.…”

Whole-Genome Sequencing of Bamei Mutton Sheep for Screening the Genes and SNPs Associated with Litter Size under Selection

“…Regarding reproductive traits, using selection tests in pigs, previous studies demonstrated some strong selective signals belonging to the TGF-β signaling pathway (18,19). In addition, in goats, the genes regulating seasonal reproduction and litter size have been speci cally selected (20,21). Moreover, some fecundity-related genes revealed a strong selection signature in sheep from Ethiopia and Europe (22,23).…”