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. 2021 Jun 11:12:662846.
doi: 10.3389/fgene.2021.662846. eCollection 2021.

Whole-Exome Sequencing Analysis of Human Semen Quality in Russian Multiethnic Population

Semyon Kolmykov  1   2 , Gennady Vasiliev  1 , Ludmila Osadchuk  1 , Maxim Kleschev  1 , Alexander Osadchuk  1
Affiliations

Whole-Exome Sequencing Analysis of Human Semen Quality in Russian Multiethnic Population

Semyon Kolmykov et al. Front Genet. .

Abstract

The global trend toward the reduction of human spermatogenic function observed in many countries, including Russia, raised the problem of extensive screening and monitoring of male fertility and elucidation of its genetic and ethnic mechanisms. Recently, whole-exome sequencing (WES) was developed as a powerful tool for genetic analysis of complex traits. We present here the first Russian WES study for identification of new genes associated with semen quality. The experimental 3 × 2 design of the WES study was based on the analysis of 157 samples including three ethnic groups-Slavs (59), Buryats (n = 49), and Yakuts (n = 49), and two different semen quality groups-pathozoospermia (n = 95) and normospermia (n = 62). Additionally, our WES study group was negative for complete AZF microdeletions of the Y-chromosome. The normospermia group included men with normal sperm parameters in accordance with the WHO-recommended reference limit. The pathozoospermia group included men with impaired semen quality, namely, with any combined parameters of sperm concentration <15 × 106/ml, and/or progressive motility <32%, and/or normal morphology <4%. The WES was performed for all 157 samples. Subsequent calling and filtering of variants were carried out according to the GATK Best Practices recommendations. On the genotyping stage, the samples were combined into four cohorts: three sets corresponded to three ethnic groups, and the fourth set contained all the 157 whole-exome samples. Association of the obtained polymorphisms with semen quality parameters was investigated using the χ2 test. To prioritize the obtained variants associated with pathozoospermia, their effects were determined using Ensembl Variant Effect Predictor. Moreover, polymorphisms located in genes expressed in the testis were revealed based on the genomic annotation. As a result, the nine potential SNP markers rs6971091, rs557806, rs610308, rs556052, rs1289658, rs278981, rs1129172, rs12268007, and rs17228441 were selected for subsequent verification on our previously collected population sample (about 1,500 males). The selected variants located in seven genes FAM71F1, PPP1R15A, TRIM45, PRAME, RBM47, WDFY4, and FSIP2 that are expressed in the testis and play an important role in cell proliferation, meiosis, and apoptosis.

Keywords: Buryats; Slavs; Yakuts; association analysis; normospermia; pathozoospermia; semen quality; whole-exome sequencing.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

FIGURE 1
FIGURE 1
Whole-exome genotype data filtering pipeline.
FIGURE 2
FIGURE 2
Sperm quality (normospermia and pathozoospermia) and ethnic effects on semen quality parameters. (A) Sperm concentration, (B) total sperm count, (C) progressive sperm motility, and (D) normal sperm morphology in the preselected sample. Blue columns—normospermia, yellow columns—pathozoospermia. The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
FIGURE 3
FIGURE 3
Visualization of the first two components of the results of the multidimensional scaling analysis of 157 samples in the context of other populations.
FIGURE 4
FIGURE 4
Graphical summary of the results of the association analysis of 157 samples. Plot of –log10(p-values) of the χ2 test. Polymorphisms with p-value < 10–2 and high or moderate impact based on the VEP results located in the genes expressed in the testis (>1NX) are highlighted.
FIGURE 5
FIGURE 5
Graphical summary of the results of the association analysis of the ethnic-specific sets of polymorphisms. Plot of –log10 (p-values) of the χ2 test. (A) Buryats; (B) Slavs; and (C) Yakuts. Polymorphisms with p-value < 10–2 and high or moderate impact based on the VEP results located in the genes expressed in the testis (>1NX) are highlighted.
FIGURE 6
FIGURE 6
Coordinated allelic effects of the SNP marker rs6971091 of the FAM71F1 gene on semen quality parameters. (A) Sperm concentration, (B) total sperm count, and (C) proportion of motile, and (D) morphologically normal sperm. All the allelic differences were highly significant (p < 0.0025). The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
FIGURE 7
FIGURE 7
Coordinated allelic effects of the SNP marker rs557806 of the PPP1R15A gene on semen quality parameters. (A) Sperm concentration, (B) total sperm count, and (C) proportion of motile, and (D) morphologically normal sperm. All the allelic differences were highly significant (p < 0.005). The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
FIGURE 8
FIGURE 8
Coordinated allelic effects of the SNP marker rs4844247 of the TEX11 gene on semen quality parameters. (A) Sperm concentration, (B) total sperm count, and (C) proportion of motile, and (D) morphologically normal sperm. All the allelic differences were highly significant (p < 0.005). The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
FIGURE 9
FIGURE 9
Coordinated allelic effects of the SNP marker rs12268007 of the WDFY4 gene on semen quality parameters. (A) Sperm concentration, (B) total sperm count, and (C) proportion of motile, and (D) morphologically normal sperm. All the allelic differences were highly significant (p < 0.005). The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
FIGURE 10
FIGURE 10
Coordinated allelic effects of the SNP marker rs17228441 of the FSIP2 gene on semen quality parameters. (A) Sperm concentration, (B) total sperm count, and (C) proportion of motile, and (D) morphologically normal sperm. All the allelic differences were highly significant (p < 0.005). The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
FIGURE 11
FIGURE 11
Coordinated allelic effects of the SNP marker rs278981 of the RBM47 gene on semen quality parameters. (A) Sperm concentration, (B) total sperm count, and (C) proportion of motile, and (D) morphologically normal sperm. All the allelic differences were highly significant (p < 0.005). The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
FIGURE 12
FIGURE 12
Coordinated allelic effects of the SNP marker rs1129172 of the PRAME gene on semen quality parameters. (A) Sperm concentration, (B) total sperm count, and (C) proportion of motile, and (D) morphologically normal sperm. All the allelic differences were highly significant (p < 0.05). The red lines indicate the WHO reference limits for different normal semen parameters [World Health Organization (WHO), 2010].
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