Variation of the calpain 1 p.Ala316Gly genotypes in Turkish Grey Steppe and Anatolian Black bulls

Abstract

Calpain 1 (CAPN1) gene is known as the micromolar calcium-activated neutral protease gene and it degrades calcium-dependent cysteine protease, μ-calpain, which reduces myofibrillar proteins in postmortem conditions. This gene has important effects on muscle metabolism and development. Although this gene has been widely studied among various cattle breeds, there is limited information on Turkish native cattle. Therefore, the present study aimed at determining the genetic variability of the CAPN1 p.Ala316Gly polymorphism in some Turkish native cattle breeds. In this respect, 99 Turkish Grey Steppe and 41 Anatolian Black bulls were genotyped by the PCR-RFLP. The genotypic and allelic frequencies, the Hardy-Weinberg equilibrium (HWE), the population genetic parameters including gene heterozygosity (He), the polymorphism information content (PIC), the effective allele numbers (Ne), the fixation index (Fıs), and the level of possible variability realization (%V) were evaluated in this study. Moreover, biodiversity indexes including the Shannon-Weaver diversity index, Simpson's dominance index, and Gini coefficient were calculated. Results revealed that the GG genotype was remarkably predominant in both native breeds. On the other hand, it was observed that the CC genotype was absent in the total population. This resulted in notably low C allele frequency (0.13 and 0.12 in Turkish Grey Steppe and Anatolian Black, respectively). The Fisher’s exact test showed a deviation from HWE and population genetics parameters indicated remarkably low genetic variabilities in the studied breeds. This observation was supported by the low levels of biodiversity. Taken together, the CAPN1 marker showed low informativeness in Turkish Grey Steppe and Anatolian Black cattle but further analyzes are needed for the genetic characterization of the native cattle breeds in Turkey. Molecular genetic studies on native breeds should be encouraged to reveal broader perspectives regarding significant biological processes and to achieve a better understanding of complex traits such as growth, muscle development, and feed efficiency.

Keywords

• Turkish Grey Steppe cattle
• Anatolian Black cattle
• CAPN1
• single nucleotide polymorphism
• population genetics

Boz ve Yerli Kara Irkı Sığırlarda Kalpain 1 p.Ala316Gly Genotiplerine Ait Genetik Varyasyonun Değerlendirilmesi

Abstract

Kalpain 1 (CAPN1) geni, mikromolar kalsiyum–aktive nötral proteaz geni olarak bilinir ve postmortem koşullarda miyofibriler proteinleri indirgeyen kalsiyum bağımlı sistein proteazı, μ-kalpaini ayrıştırır. Bu genin kas metabolizması ve gelişimi üzerinde önemli etkileri vardır. Bu gen, çeşitli sığır ırkları arasında geniş çapta çalışılmış olmasına rağmen, Türk yerli sığırları hakkında sınırlı bilgi bulunmaktadır. Bu nedenle bu çalışma, bazı Türk yerli sığır ırklarında CAPN1 p.Ala316Gly polimorfizmine ait genetik varyasyonu belirlemeyi amaçlamıştır. Bu kapsamda 99 Boz ve 41 Yerli Kara ırkı erkek sığır PCR-RFLP metodu kullanılarak genotiplendirilmiştir. Genotipik ve alelik frekanslar, Hardy-Weinberg dengesi (HWE), heterozigotluk (He), polimorfizm bilgi içeriği (PIC), efektif alel sayısı (Ne), fiksasyon indeksi (Fıs), olası varyasyon gerçekleşme düzeyi (%V) dahil olmak üzere popülasyon genetik parametreleri değerlendirilmiştir. Ayrıca Shannon-Weaver indeksi, Simpson dominantlık indeksi ve Gini katsayısını içeren biyoçeşitlilik indeksleri hesaplanmıştır. Sonuçlar, GG genotipinin her iki yerli ırkta da oldukça baskın olduğunu ortaya koydu. Öte yandan, toplam popülasyonda CC genotipinin bulunmadığı gözlenmiştir. Bu durum dikkate değer düzeyde düşük C allel frekansıyla sonuçlanmıştır (Boz ve Yerli Kara için sırasıyla 0.13 ve 0.12). Fisher’ın kesin testi, HWE’den sapma oldğunu, popülasyon genetiği parametreleri ise, incelenen ırklarda oldukça düşük bir genetik varyasyon düzeyi olduğunu göstermiştir. Bu gözlem, düşük seviyedeki biyolojik çeşitlilik seviyeleri ile desteklenmiştir. Nitekim CAPN1 markörü, Boz ve Yerli Kara sığırları için düşük seviyede bilgilendiricilik göstermiştir ancak Türkiye’deki yerli sığır ırklarının genetik karakterizasyonu hakkında ileride yapılacak çalışmalara ihtiyaç vardır. Yerli ırklarda yapılacak moleküler genetik çalışmalar, önemli biyolojik süreçlerle ilgili daha geniş perspektifleri ortaya koymak ve büyüme, kas gelişimi ve yem verimliliği gibi kompleks özelliklerin daha iyi anlaşılmasını sağlamak için teşvik edilmelidir.

Keywords

• Boz ırk
• Yerli Kara
• CAPN1
• tek nükleotit polimorfizmi
• popülasyon genetiği

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