Given that the polymorphisms in the four genes described above are considered to be the most associated with economically advantageous traits, each gene and its SNPs should be considered in more detail. GH is considered a principal regulatory factor for somatic growth, metabolism, and lactation in mammals. This polypeptide hormone, comprising 191 amino acids and encoded by a gene approximately 1800 base pairs in length, exerts lactogenic, lipolytic, and galactopoietic effects and significantly influences cattle reproductive performance [48–51]. The bovine GH gene, which is located in the 19q26 chromosomal region, comprises five exons and four introns [52, 53].

Numerous polymorphic variants have been identified within the GH gene. While the majority of these variants are located in non-translated intronic regions, a small number of these variants are found in exons. However, a specific C>G transversion in the fifth exon (position 2141), which results in the substitution of leucine amino acid by valine, has been identified as a primary focus of research investigating associations with productivity traits in cattle [54]. This polymorphism has been previously described in the literature as the L/V polymorphism, which indicates the amino acid transition present in the hormone. Furthermore, GH polymer-phisms, characterized by the substitution of CTG (allele A) to GTG (allele B) in codon 127 and ACG (alleles A and B) to ATG (allele C) in codon 172, have been demonstrated to influence carcass traits and fatty acid profile [55].

Extensive research has identified numerous other polymorphisms associated with key economic traits within GH. The following single-nucleotide polymorphisms have been identified: c.457C>G, linked to backfat thickness [55, 56], and c.2141C>G, a substitution caused by a polymorphism in exon 5, associated with fatty acid composition and subcutaneous fat deposition [57–60].

A total of 63 single-nucleotide polymorphisms (SNPs) have been identified in the bovine GH, with three located in the coding region and the remaining 60 in the 5′ and 3′ untranslated regions (UTRs) and introns [61].

The identification of polymorphisms, such as c.2141C>G, is a valuable tool for marker-assisted selection, allowing for the prediction of productivity potential and meat amino acid composition [62]. Research on Hereford bull calves has demonstrated that the GH c.2141C>G polymorphism significantly alters the amino acid profile of meat, although its effects are subject to breed and population specificity [63, 64].

The genetic composition of the Kalmyk cattle population with respect to the GH gene has been the focus of substantial research, which has revealed considerable variability. A study conducted to monitor the development of the novel “Aduchi” beef breed, presented by a crossbreeding between Kalmyk and American Aberdeen-Angus in the Republic of Kalmykia, documented an increase in the frequency of the desirable VV genotype from 2.2% (n = 46) to 19.7% (n = 112) between 2018 and 2022, indicating the efficacy of targeted selection [36, 37].

A comprehensive comparative analysis of the GH c.2141C>G polymorphism across Asian steppe breeds revealed that the Kalmyk breed (n = 60) exhibited the highest frequency of the preferred VV genotype (78.3%) [38]. This result was analogous to that of the Mongolian breed (75%) and significantly higher than that of Kazakh Whiteheaded cattle of Kazakhstani (49%) and Russian (63%) selection. The minimal discrepancy between the Kalmyk and Mongolian breeds substantiates their close genetic relationship [38].

However, other studies have reported a significantly lower V allele prevalence within specific Kalmyk subpopulations. An analysis of animals from two breeding farms in Kalmykia, SPK Plodovitoye and NAO Kirovsky, found a VV genotype frequency of only 2% at both locations [39]. Despite its low frequency, VV homozygous bulls exhibited the highest live weight at 16 months, with a notable difference of 7 kg between farms, confirming a reliable association between genotype and live weight [39]. This finding of the extreme rarity of the V allele is corroborated by several other studies. Research conducted in the Stavropol Territory revealed the complete absence of the V allele, which is considered desirable, in Kalmyk cattle [40]. This finding is consistent with the results of earlier genotyping of breeding bulls, which showed a 94% prevalence of the LL genotype [41]. A subsequent investigation documented a higher frequency of the VV genotype in the Kalmyk breed, such as 42% [42]. However, a recent analysis from Stavropol breeding farms substantiated the low proportion, as only 2% of Kalmyk animals were homozygous for VV. Notably, a considerable proportion of patients were found to be heterozygous LV (43%) [43]. Another study investigating the GH c.2141C>G polymorphism in a population of 156 Kalmyk breed cattle in the Stavropol region established that the desirable VV genotype was present at a frequency of 25% [44].

Thus, GH gene polymorphisms show significant variability and impact key traits in Kalmyk cattle. The role of the TG gene, another important marker for meat quality, is explored in the following section.

TG is a high-molecular-weight glycoprotein synthesized in the follicular cells of the thyroid gland. It functions as a pivotal precursor and carrier molecule in the synthesis of the thyroid hormones triiodothyronine and thyroxine. These hormones play a critical role in regulating metabolism and influencing the tendency of tissues to accumulate fat [64]. The bovine TG gene, particularly its 5′ UTR, is one of the most extensive DNA regions in mammals. It is located in the chromosome 14 centromeric region and comprises 37 exons [65]. A well-characterized mutation in this gene, c.-422C>T, occurs in the 5′-promoter region and involves a substitution of cytosine for thymine at nucleotide position −422 [64].

The TG polymorphism X05380.1:g.-422C>T, identified in the 5′-UTR of the TG gene, is characterized by a C-to-T transition. This specific SNP has been used as a genetic marker to predict higher marbling scores in beef cattle, thereby enhancing meat quality. The T allele of the TG c.-422C>T polymorphism is associated with enhanced lipogenesis and reduced protein synthesis in muscle tissue. These effects are more pronounced in the homozygous state [58]. Animals with the homozygous TT genotype exhibit an augmented capacity to synthesize intramuscular fat, resulting in a substantially elevated marbling score compared with those with other genotypes [64–66].

In addition to the c.-422C>T polymorphism, further variations in this region have been identified. A thorough review of extant Chinese studies revealed four novel SNPs (c.275A>G, c.277C>G, c.280A>G, and c.281G>C) in the 5′-flanking region of the TG gene. The association analyses indicated that these SNPs exhibited a significant correlation with average daily gain, demonstrating a high level of significance (p < 0.01) with c.275A>G and c.277C>G and a moderate level (p < 0.05) with c.280A>G and c.281G>C [67].

An investigation into the genetic composition of Kalmyk cattle in relation to the TG gene revealed a series of dynamic alterations in response to selective pressures. Research on a herd forming a new high-productivity beef type, which is a crossbreed between Kalmyk cattle and American Aberdeen-Angus in the Republic of Kalmykia, documented a notable increase in the frequency of the desirable TT genotype, from 6.5% (n = 46) in 2018 to 13.4% (n = 112) in 2022 [36, 37]. This twofold increase serves as a robust indicator of the efficacy of direct or indirect selection for traits associated with this genotype, particularly enhanced growth rate, live weight, and meat quality metrics, during the development of this novel beef type.

However, comparative analyses across beef breeds demonstrated considerable variation in TT frequency, underscoring population-specific differences. An investigation of genotype frequency among cattle in the Stavropol region revealed the highest prevalence of the TT genotype in Kalmyk cattle (12.5%), based on a sample of 40 animals [40]. This frequency exceeded that observed in the Kazakh Whiteheaded, Hereford, Aberdeen-Angus, and Simmental breeds at 6.3%, 0%, 3.03%, and 7.7%, respectively, with sample sizes of 16, 37, 33, and 39 animals, respectively [40].

Conversely, a separate study of herds in the same region reported a substantially lower frequency of this genotype in the Kalmyk breed, with a frequency of 4% from a sample of 96 animals [42]. This result placed it below the frequencies reported for Hereford cattle at 16% and Kazakh Whiteheaded cattle at 6% [42]. This pronounced discrepancy in reported genotype frequencies is likely attributable to factors such as geographical isolation, distinct breeding objectives and histories, and genetic drift within different subpopulations of the same breed.

Interpretation and limitations

In contrast to the TG gene polymorphism c.-422C>T, which is probably a key genetic marker for marbling in beef cattle, the effect of polymorphisms in other genes might be unclear.

The LEP gene, which encodes the adipokine hormone leptin, plays a pivotal role in regulating energy homeostasis, feed intake, adipogenesis, and reproductive function in cattle [68]. The bovine LEP gene, which spans over 15 kilobases (kb), is located on chromosome 4q32 and comprises three exons and two introns [69, 70].

The polymorphism LEP c.466C>T, also known as LEP73, R4C, and R25C, is of particular interest. It is located 73 base pairs from the start of exon 2 and causes an amino acid substitution of arginine for cysteine at position 4 of the mature leptin protein [71]. The T allele of this single-nucleotide polymorphism is associated with increased leptin messenger ribonucleic acid expression. This directly influences feeding behavior, determines the highest feed efficiency, and consequently results in the formation of carcasses with high fat content. In contrast, the C allele has been linked to reduced carcass fat deposition, leading to leaner carcasses in animals carrying this genotype [72].

The LEP c.528T>C polymorphism is located in the 5′ UTR and has been shown to have a positive influence on marbling and meat yield in beef cattle. Additionally, the study describes the LEP c.73 polymorphism T>C, which is located in exon 2, has been shown to have a positive effect on adipose tissue formation and carcass quality [51, 73, 74].

Polymorphism c.95A>T, also known as Y7F, is located in the coding part of the LEP gene within exon 2, resulting from the nucleotide substitution A>T at position 95,689,996 bp [75]. The paucity of research on this subject is primarily attributable to the rarity of non-YY genotypes within populations [76]. Researchers in Ireland have demonstrated a correlation between the LEP Y7F polymorphism in cattle and increased energy accumulation in the form of adipose tissue deposits [74]. In contrast, Japanese studies have identified a relationship between this polymorphism and its influence on carcass weight [77].

Significant associations between novel exonic SNPs and enhanced carcass traits in Chinese Simmental cattle have been identified. These SNPs, specifically 169T>C and 299T>A in exon 2 and exon 3, respectively, have been shown to impact characteristics such as slaughter weight, marbling score, and intramuscular fat [78]. A subsequent review of polymorphisms associated with beef traits emphasized the role of LEP SNPs in meat flavor, fat thickness, and meat yield [79].

The most comprehensive genotyping study in Kalmyk cattle (n = 156) identified c.73T>C as a key LEP polymorphism [45]. Allele frequencies for c.73T>C were C: 0.52 and T: 0.48. Robust association analyses were conducted: individuals heterozygous CT or homozygous CC for the c.73T>C polymorphism exhibited a 7.3% and 9.5% greater live weight, respectively, than TT homozygous counterparts [45].

The genetic architecture of the LEP locus in Kalmyk cattle demonstrates considerable population-specific variation, reflecting diverse breeding histories and selection pressures. An investigation of a novel high-productivity crossbreed beef type of Kalmyk and Aberdeen-Angus in the Republic of Kalmykia revealed a high prevalence of the TT genotype for the c.314C>T polymorphism; therefore, 49.1% out of 112 animals were TT homozygous, suggesting that this allele was selected for active or inadvertent selection during herd formation [37]. The polymorphism is frequently characterized by an amino acid change at position A80V, resulting in the following genotypes: AA, AV, and VV.

The highest frequency of reliable genotypes was observed in the Kalmyk cattle population from the Stavropol region, with a sample size of 46. In this group, 79% of the animals possessed the AA genotype at the c.314C>T locus, whereas 83% were homozygous for the YY genotype at the c.95A>T position [43]. In stark contrast, a study of 96 Kalmyk animals from the Stavropol region reported a markedly low frequency, with only 1% having a desirable LEP TT haplotype at position 140 of exon 3, which was considerably more common in contemporary Hereford (12%) and Kazakh Whiteheaded (10%) populations from the same region [42]. This discrepancy underscores the presence of significant genetic stratification within the Kalmyk breed, likely attributable to geographical isolation and divergent breeding objectives.

These findings provide compelling evidence of a significant association between specific LEP alleles and growth traits in Kalmyk cattle. However, the contradictory results regarding allele frequencies across studies highlight the lack of population homogeneity and preclude a definitive consensus. Consequently, while the LEP gene represents a promising candidate for marker-assisted selection in Kalmyk cattle, further validation in larger, well-defined cohorts is essential to confirm its utility and to account for population substructure, genotype-by-environment interactions, and potential epistatic effects before its implementation in breeding programs.

The CAPN1 gene, located on chromosome 29, encodes the catalytic large subunit of the μ-calpain protease, a calcium-dependent enzyme critically involved in post-mortem proteolysis and meat tenderization [80]. The bovine CAPN1 gene comprises 19 exons and 17 introns spanning 11,055 base pairs [81]. Several polymorphisms within this gene have been extensively characterized for their impact on meat quality traits [82].

Several SNPs within CAPN1 are considered key molecular markers for meat tenderness. These include substitutions at codon 316 (c.4568G>C, Gly/Ala) in exon 9 [83, 84], codon 530 (c.654A>G, Ile/Val) in exon 14 [84], and intronic polymorphisms at positions 4751 and 5331 [85]. Meta-analyses have consistently identified the C allele of 316G>C, the G allele of 530A>G, and the C allele at position 4751 as favorable markers associated with reduced shear force and improved meat tenderness [58, 83]. Among these, the 316G>C polymorphism in exon 9 exerts the most pronounced effect on meat tenderness across diverse cattle breeds [86, 87]. The C allele is considered advantageous as it significantly improves meat tenderness [88].

Within the coding region of CAPN1, a nonsynonymous nucleotide substitution g.43405875C>G results in the replacement of glycine with alanine at amino acid position 316 (rs17872000). The C316 allele is considered the desirable allelic variant associated with increased meat tenderness. Animals homozygous for this allele are of particular interest for selection aimed at improving meat quality. Cattle carrying the alanine variant demonstrate markedly higher meat tenderness compared with carriers of the glycine allele, with reported improvements exceeding 30%.

The biological mechanism underlying this association involves the role of μ-calpain in post-mortem degradation of myofibrillar proteins, particularly Z-disks, leading to weakening of sarcomere structures and enhanced tenderization [89–91].

Investigations into the CAPN1 genetic structure of Kalmyk cattle reveal substantial heterogeneity and an overall low prevalence of favorable alleles. In a newly developed high-productivity crossbred beef type of Kalmyk and Red Angus in the Republic of Kalmykia, the frequency of the preferred CC genotype ranged from 3% to 12%, with a strong predominance of the GG genotype (69%–77%) [36]. Similar patterns were observed in the Stavropol region, where the CC genotype frequency was only 5% among 42 Kalmyk animals [46], comparable to Hereford (5%) and Kazakh Whiteheaded (6%) cattle from the same region. Other studies reported CC genotype frequencies of 6% in small Kalmyk cohorts (n = 16 [41] and n = 46 [43]) and 3% in a larger sample of 96 animals [42].

Pronounced subpopulation stratification has been identified within the Kalmyk breed. A comparative analysis of two breeding farms in Kalmykia, SPK Plodovitoye and NAO Kirovsky, revealed higher frequencies of the desirable c.4568G>C CC genotype at SPK Plodovitoye compared with NAO Kirovsky (22% vs. 18%). Bulls from SPK Plodovitoye carrying the favorable genotype also exhibited a higher live weight at 16 months (489.3 kg), exceeding those from NAO Kirovsky by 7.1 kg, suggesting a potential pleiotropic effect or linked selection for growth traits [39]. In the Orenburg region, a relatively higher CC genotype frequency (19.7%) was reported among 122 Kalmyk cattle, exceeding that observed in other local breeds [47], highlighting the influence of regional breeding strategies on allele distribution.

In conclusion, while CAPN1 is a well-established molecular marker for meat tenderness in global beef cattle populations, its practical application in Kalmyk cattle breeding programs is constrained by the low overall frequency of favorable alleles and marked inter-herd variability. Associations between CAPN1 genotypes and economically important traits in Kalmyk cattle require further validation in larger, well-controlled cohorts to account for population structure and environmental interactions before reliable implementation in marker-assisted selection strategies.