Genome-Wide Analysis of Positively Selected Genes in Seasonal and Non-Seasonal Breeding Species

Abstract

Some mammals breed throughout the year, while others breed only at certain times of year. These differences in reproductive behavior can be explained by evolution. We identified positively-selected genes in two sets of species with different degrees of relatedness including seasonal and non-seasonal breeding species, using branch-site models. After stringent filtering by sum of pairs scoring, we revealed that more genes underwent positive selection in seasonal compared with non-seasonal breeding species. Positively-selected genes were verified by cDNA mapping of the positive sites with the corresponding cDNA sequences. The design of the evolutionary analysis can effectively lower the false-positive rate and thus identify valid positive genes. Validated, positively-selected genes, including CGA, DNAH1, INVS, and CD151, were related to reproductive behaviors such as spermatogenesis and cell proliferation in non-seasonal breeding species. Genes in seasonal breeding species, including THRAP3, TH1L, and CMTM6, may be related to the evolution of sperm and the circadian rhythm system. Identification of these positively-selected genes might help to identify the molecular mechanisms underlying seasonal and non-seasonal reproductive behaviors.

DNAH1 gene mutations and their potential association with dysplasia of the sperm fibrous sheath and infertility in the Han Chinese population

“…The phenotype of MDHC7(À/À) mice is similar to that in some patients suffering from primary ciliary dyskinesia (PCD), which suggests that DNAH1 (HDHC7) gene mutations may also cause PCD in some patients (9). A study reported that DNAH1 is related to reproductive function, such as spermatogenesis and cell proliferation, in nonseasonal breeding species (10).…”

High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

“…The DCMS method detected selection sweeps near CMTM6 in Karakul and Edilbai sheep and near HTRA1 in Karakul, Tuva, and Buubei sheep. These genes are associated with off-season reproduction traits, such as year-around oestrous behavior in sheep (HTRA1 [82] and the evolution of sperm and the circadian rhythm systems in mammals (CMTM6 [83]). The DCMS method further reported narrow selection sweeps for multiple Russian sheep breeds in the areas of B4GALNT2 which was proposed as a strong candidate gene for ewe fertility [84].…”

Comparative transcriptome analysis reveals potential evolutionary differences in adaptation of temperature and body shape among four Percidae species

“…niloticus and D . rerio as references, so as to predict molecular insights into ecological niche partitioning and divergent adaptation involved in the evolutionary race [159, 160]. However, referring to Stepien et al’s comprehensive study on evolutionary and adaptive issues of perch [66], we realized that our study lacked sufficient geographic populations and phylogenetic species to emphasize more powerful and inherent mechanisms responsible for evolution.…”