Signature selection analysis reveals candidate genes associated with production traits in Iranian sheep breeds

Abstract

Background Sheep were among the first animals to be domesticated. They are raised all over the world and produce a major scale of animal-based protein for human consumption and play an important role in agricultural economy. Iran is one of the important locations for sheep genetic resources in the world. Here, we compared the Illumina Ovine SNP50 BeadChip data of three Iranian local breeds (Moghani, Afshari and Gezel), as a population that does not undergone artificial breeding programs as yet, and five other sheep breeds namely East Friesian white, East Friesian brown, Lacaune, DorsetHorn and Texel to detect genetic mechanisms underlying economical traits and daptation to harsh environments in sheep. Results To identify genomic regions that have been targeted by positive selection, we used fixation index (Fst) and nucleotide diversity (Pi) statistics. Further analysis indicated candidate genes involved in different important traits such as; wool production included crimp of wool (PTPN3, NBEA and KRTAP20–2 genes), fiber diameter (PIK3R4 gene), hair follicle development (LHX2 gene), the growth and development of fiber (COL17A1 gene)), adaptation to hot arid environments (CORIN gene), adaptive in deficit water status (CPQ gene), heat stress (PLCB4, FAM107B, NBEA, PIK3C2B and USP43 genes) in sheep. Conclusions We detected several candidate genes related to wool production traits and adaptation to hot arid environments in sheep that can be applicable for inbreeding goals. Our findings not only include the results of previous researches, but also identify a number of novel candidate genes related to studied traits. However, more works will be essential to acknowledge phenotype- genotype relationships of the identified genes in our study.

Genomic adaptation to extreme climate conditions in beef cattle as a consequence of cross-breeding program

“…The pattern of LD decay can provide valuable insights into population history, including breeding systems and evolution of a population [42][43][44]. In this study, the LD values among SNPs decreased with increasing physical distance, which is in accordance with studies on different livestock species [42,45]. The relatively low levels of LD in the entire genome of cross-bred animals are probably the result of past admixture events between Red-Angus and Mongolian cattle that have been experienced due to genetic improvement of local cattle breeds for meat production traits.…”

Selection signatures for fiber production in commercial species: A review

“…This method is beneficial because it does not necessitate the availability of phenotypic records and may detect selection signals even when long‐term human‐mediated selection for wool qualities has resulted in total fixation of the desirable allele (Megdiche et al, 2019). Mohamadipoor Saadatabadi et al (2021) applied F ST and nucleotide diversity‐based statistical approaches to identify selection signals in genomic areas under selection pressure in three Iranian sheep breeds. The research revealed potential genes that regulate crimps in wool ( KRTAP20‐2 , PTPN3 , and NBEA genes), fiber fineness ( PIK3R4 gene), and the development of hair follicles ( LHX2 gene).…”

Genomic analysis of indigenous goats in Southwest Asia reveals evidence of ancient adaptive introgression related to desert climate

“…The most drought-affected regions of the Fertile Crescent are located in Iraq and Iran, which are also part of the hot-arid region of the Afro-Asian desert belt ( Ashraf et al, 2021 ; Kaniewski et al, 2012 ). As a result, indigenous domesticated animals of the region are well adapted to the local hot-desert environment ( Al-Thuwaini et al, 2019 ; Asadollahpour Nanaei et al, 2022 ; Saadatabadi et al, 2021 ).…”