Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds †
by
, ,
Alexandra S. Abdelmanova
1,*, 
Alexander A. Sermyagin
1
,
Arsen V. Dotsev
1
,
Nikolay V. Bardukov
1,
Margaret S. Fornara
1,
Gottfried Brem
1,2 and
Natalia A. Zinovieva
1
1
L.K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy, Podolsk Municipal District, Moscow Region, 142132 Podolsk, Russia
2
Institute of Animal Breeding and Genetics, University of Veterinary Medicine (VMU), Veterinärplatz, A-1210 Vienna, Austria
*
Author to whom correspondence should be addressed.
†
Presented at the 2nd International Electronic Conference on Diversity (IECD 2022)—New Insights into the Biodiversity of Plants, Animals and Microbes, 15–31 March 2022; Available online: https://sciforum.net/event/IECD2022 .
Biol. Life Sci. Forum 2022, 15(1), 24; https://doi.org/10.3390/IECD2022-12415
Published: 15 March 2022
(This article belongs to the Proceedings of The 2nd International Electronic Conference on Diversity (IECD 2022)—New Insights into the Biodiversity of Plants, Animals and Microbes)
Abstract
:Cattle breeds used in industrial production tend to have a larger size compared to the local cattle, as the increased dairy and beef productivity is closely related to the stature. The aim of our work was to identify single nucleotide polymorphisms (SNPs), which are significantly associated with stature in diverse cattle breeds. Thirteen local and transboundary cattle breeds (n = 670) subjected to our study were divided in two groups according to the stature. The high-stature group included Angus, Ayrshire, Black-and-White, Holstein, Kholmogor, Yaroslavl, Tagil and Istoben breeds. The low-stature group comprised of Jersey, Kalmyk, Kyrgyz, Mongolian and Yakut cattle. The average height at withers was 136.3 ± 1.6 and 121.6 ± 2.8 cm in the high- and low-stature groups, respectively. The samples of 11 breeds were genotyped using high-density DNA arrays (Illumina Inc., USA). The genotypes of two remaining breeds were downloaded from the publicly available WIDDE database. Genome-wide association studies revealed four SNPs, which were strongly associated with the stature, including three SNPs at 77.3–77.8 cM on BTA4 (map53144-ss46525999, p < 7.747 × 10−101; BovineHD0400021479, p < 1.173 × 10−91; ARS-BFGL-NGS-116590, p < 7.665 × 10−105) and one SNPs at 25.2 cM on BTA14 (BovineHD1400007259, p < 1.324 × 10−109). Functional annotation showed the localization within identified regions of genes, which are responsible for growth, exterior characteristics, protein and lipid metabolism, and feed intake. Identified SNPs can be considered as useful DNA markers for marker-assistant cattle breeding aimed at increased stature. The study was funded by the Russian Ministry of Science and Higher Education No. 0445-2019-0024.
1. Introduction
Animals’ stature is closely related to the productivity. Many studies have been conducted, which revealed a large number of loci associated with body size in cattle [1,2]. The PLAG1 gene, which is located on chromosome 14 was the one of the most frequently detected genes in such studies [3,4,5]. However, the most studies were carried out on commercial breeds of cattle that have been subjected to the strong artificial selection pressures. Although comprehensive genome-wide studies of Russian local cattle breeds were carried out [6,7,8,9], the genetic basis of stature in these breeds was not investigated until now. Local breeds usually have lower productivity compared to commercial breeds but exceed them in adaptability to climate condition. Thus, they can be useful as a reserve of genetic diversity in breeding programs.
The aim of our work was to identify single nucleotide polymorphisms (SNPs), which are significantly associated with stature in commercial and local cattle breeds bred in Russia.
2. Materials and Methods
A total of 670 samples of thirteen local and transboundary cattle breeds, including Aberdeen-Angus (ANG, n = 39), Ayrshire (AYR, n = 144), Black-and-White (BLW, n = 50), Holstein (HLS, n = 184), Istoben (IST, n = 22), Jersey (JRS, n = 32), Kalmyk (KLM, n = 27), Kholmogor (KHL, n = 26), Kyrgyz (KRG, n = 24), Mongolian (MNG, n = 26), Tagil (TAG, n = 26), Yakut (YKT, n = 29) and Yaroslavl (YRS, n = 41), were subjected to our study.
Domestic Animal Diversity Information System (DAD-IS) [http://www.fao.org/dad-is/en (accessed on 1 October 2021)] maintained and developed by FAO was used to obtain the mean values for height at withers for studied breeds. Each breed was assigned the average breed value for the height at withers.
The samples of 11 breeds were genotyped using high-density DNA arrays (Illumina Inc., USA) in the L.K. Ernst Federal Research Center for Animal Husbandry. The genotypes of two remaining breeds were downloaded from the publicly available WIDDE database [http://widde.toulouse.inra.fr/wide (accessed on 1 October 2021)].
To identify SNPs that are significantly associated with height at withers we performed across-breed genome-wide association studies using a multivariate linear-mixed model implemented in the program PLINK 1.9.
3. Results and Discussion
Cattle breeds were divided in two groups according to the stature. The high-stature group included Angus, Ayrshire, Black-and-White, Holstein, Kholmogor, Yaroslavl, Tagil and Istoben breeds. The mean values for height at withers for these breeds exceeded the mean values calculated for all the studied breeds. The low-stature group comprised of Jersey, Kalmyk, Kyrgyz, Mongolian and Yakut cattle revealing the less height at withers comparing to the mean value calculated for the entire data set of breeds. The mean values for height at withers in the high- and low-stature groups were 136.3 ± 1.6 and 121.6 ± 2.8 cm, respectively (Figure 1).
Almost all low stature breeds (except Jersey) are meat type productivity. They were bred for the centuries by nomadic tribes in the harsh climate of steppes and semi-deserts of Central Asia. These breeds are able to survive under poor forage conditions in short dry summers and cold winters and be quickly fattened up with improved feeding. For this reason, the above mentioned breeds are traditionally bred in regions with severe climates and unstable forage resources.
Genome-wide association studies (Figure 2) revealed four SNPs, which are strongly associated with the stature, including three SNPs at 77.3–77.8 cM on BTA4 (map53144-ss46525999, p < 7.747 × 10−101; BovineHD0400021479, p < 1.173 × 10−91; ARS-BFGL-NGS-116590, p < 7.665 × 10−105) and one SNPs at 25.2 cM on BTA14 (BovineHD1400007259, p < 1.324 × 10−109).
The allele frequencies of significantly associated SNPs were calculated in each of two groups (Table 1).
Our results agree with the previous studies, indicated that 24.8–25.2 Mb region on BTA 14 is strongly related to body size [1,5,10]. Additionally, we identified the 77.3–77.8 Mb region on BTA 4, which was not shown to be associated with stature in previous studies [3,11,12]. The structural and functional annotation revealed the presence of genes, which are associated with metabolism, milk composition and synthesis as well as the average daily gain.
4. Conclusions
Identified SNPs can be considered as useful DNA markers for marker-assistant cattle breeding aimed at increased stature in diverse cattle breeds bred in Russia.
Author Contributions
Conceptualization, N.A.Z. and G.B.; methodology, A.S.A., and N.A.Z.; software, A.S.A. and A.V.D.; investigation, N.V.B., M.S.F.; provision of samples, A.A.S.; writing—original draft preparation, A.S.A. and N.A.Z.; writing—review and editing, A.V.D., A.A.S., G.B., and N.A.Z.; supervision, project administration, and funding acquisition, N.A.Z. All authors have read and agreed to the published version of the manuscript.
Funding
This research was funded by the Ministry of Science and Higher Education of the Russian Federation (theme No. FGGN-2022-0002).
Institutional Review Board Statement
The study was approved by the Ethics Commission of the L.K. Ernst Federal Research Center for Animal Husbandry (protocol No. 3 from the 19 January 2021).
Informed Consent Statement
Not applicable.
Data Availability Statement
Not applicable.
Acknowledgments
To conduct this study, we used the equipment of the Center for Collective Use “Bioresources and Bioengineering of Farm Animals” of L.K. Ernst Federal Research Center for Animal Husbandry.
Conflicts of Interest
The authors declare no conflict of interest. The funders had no role in the design of the study: in the collection, analyses, or interpretation of data; writing of the manuscript; or decision to publish the results.
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Figure 1.
Distribution of cattle breeds according to the mean values for the height at withers. Blue line indicates the mean values calculated for each of the studied breeds; orange line indicates the mean value calculated for the entire data set; the breeds are located clockwise from the breed having the lowest stature (Mongolian cattle) the breed revealing the greatest stature (Holsteins) as it is indicated by an arrow; the breeds’ abbreviations are deciphered in the Materials and Methods section.
Figure 1.
Distribution of cattle breeds according to the mean values for the height at withers. Blue line indicates the mean values calculated for each of the studied breeds; orange line indicates the mean value calculated for the entire data set; the breeds are located clockwise from the breed having the lowest stature (Mongolian cattle) the breed revealing the greatest stature (Holsteins) as it is indicated by an arrow; the breeds’ abbreviations are deciphered in the Materials and Methods section.
Figure 2.
Genome-wide association studies for the height at withers for studied breeds.
Table 1.
Frequencies of alternative alleles at the loci associated with the withers height.
| Localization | SNP | Allele | Allele Frequencies | |
|---|---|---|---|---|
| High-Stature Breeds | Low-Stature Breeds | |||
| Chr 4 | ARS-BFGL-NGS-116590 | T | 0.204 | 0.349 |
| G a | 0.796 | 0.651 | ||
| p b | *** | *** | ||
| Hapmap53144-ss46525999 | T a | 0.795 | 0.082 | |
| C | 0.205 | 0.918 | ||
| p | *** | ** | ||
| BovineHD0400021479 | A | 0.201 | 0.309 | |
| G a | 0.799 | 0.647 | ||
| p | *** | *** | ||
| Chr 14 | BovineHD1400007259 | T | 0.090 | 0.959 |
| G a | 0.910 | 0.041 | ||
| p | *** | ns | ||
a—alleles are associated with greater height at withers. b—** p < 0.01; *** p < 0.001; ns—not significant.
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Abdelmanova, A.S.; Sermyagin, A.A.; Dotsev, A.V.; Bardukov, N.V.; Fornara, M.S.; Brem, G.; Zinovieva, N.A. Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds. Biol. Life Sci. Forum 2022, 15, 24. https://doi.org/10.3390/IECD2022-12415
AMA Style
Abdelmanova AS, Sermyagin AA, Dotsev AV, Bardukov NV, Fornara MS, Brem G, Zinovieva NA. Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds. Biology and Life Sciences Forum. 2022; 15(1):24. https://doi.org/10.3390/IECD2022-12415
Chicago/Turabian StyleAbdelmanova, Alexandra S., Alexander A. Sermyagin, Arsen V. Dotsev, Nikolay V. Bardukov, Margaret S. Fornara, Gottfried Brem, and Natalia A. Zinovieva. 2022. "Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds" Biology and Life Sciences Forum 15, no. 1: 24. https://doi.org/10.3390/IECD2022-12415
APA StyleAbdelmanova, A. S., Sermyagin, A. A., Dotsev, A. V., Bardukov, N. V., Fornara, M. S., Brem, G., & Zinovieva, N. A. (2022). Genome-Wide Screening for SNPs Associated with Stature in Diverse Cattle Breeds. Biology and Life Sciences Forum, 15(1), 24. https://doi.org/10.3390/IECD2022-12415
