Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle

Abstract. Jakaria, Ulum MF, Lestari D, Akwila S, Sihite DEWT, Priyanto R, Muladno, Sumantri C. 2020. Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle. Biodiversitas 21: 2971-2976. The present investigation aims to explore specific SNPs of Bali cattle, focusing mainly on CAS...

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Autores principales:	Jakaria Jakaria Jakaria, MOKHAMAD FAKHRUL ULUM, DEWI LESTARI, SAMUEL AKWILA, DIAN ERMA WARU TIDOLF SIHITE, RUDY PRIYANTO, MULADNO, CECE SUMANTRI
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2020
Materias:	bali cattle, 5’utr, meat quality, polymorphism Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/9bba561a390d4fac9d90a80087269911
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spelling	oai:doaj.org-article:9bba561a390d4fac9d90a800872699112021-11-22T00:40:52ZInvestigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle1412-033X2085-472210.13057/biodiv/d210713https://doaj.org/article/9bba561a390d4fac9d90a800872699112020-06-01T00:00:00Zhttps://smujo.id/biodiv/article/view/5371https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Abstract. Jakaria, Ulum MF, Lestari D, Akwila S, Sihite DEWT, Priyanto R, Muladno, Sumantri C. 2020. Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle. Biodiversitas 21: 2971-2976. The present investigation aims to explore specific SNPs of Bali cattle, focusing mainly on CAST, CAPN, and SCD genes in 5'UTR. DNA of Bali cattle (25 individuals) from Breeding Centre of Bali cattle in Bali Province, Indonesia, were extracted according to the protocol of GenAID. Amplification of the CAST, CAPN, and SCD genes were designed using the Primer3 program based on reference sequences (access numbers AH014526.2, AH009246.3, and AY241932). Furthermore, the PCR product was sequenced through forward primer sequencing. The data sequence results were analyzed using the Bioedit, MEGA7, Popgen 3.2, and DnaSP6 V6 programs. The results showed that SNPs were detected at g.921C>T and g.922T>G in 5'UTR for the CAST gene between the reference of GenBank AH014526.2 and Bali cattle, but it was monomorphic within the population. The high polymorphism of SNPs was found in g.232G>T for the CAPN gene and g.134A>del for the SCD gene. However, the SNP g.246C>del SCD gene was detected as monomorphic in this region. Moreover, this result shows that low nucleotide diversities (Pi) for CAST, CAPN, and SCD genes in 5'UTR of Bali cattle were 0.00422, 0.00632, and 0.00449, respectively. This finding was important for developing marker-assisted selection (MAS) to improve the meat quality of Bali cattle.Jakaria Jakaria JakariaMOKHAMAD FAKHRUL ULUMDEWI LESTARISAMUEL AKWILADIAN ERMA WARU TIDOLF SIHITERUDY PRIYANTOMULADNOCECE SUMANTRIMBI & UNS Soloarticlebali cattle, 5’utr, meat quality, polymorphismBiology (General)QH301-705.5ENBiodiversitas, Vol 21, Iss 7 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	bali cattle, 5’utr, meat quality, polymorphism Biology (General) QH301-705.5
spellingShingle	bali cattle, 5’utr, meat quality, polymorphism Biology (General) QH301-705.5 Jakaria Jakaria Jakaria MOKHAMAD FAKHRUL ULUM DEWI LESTARI SAMUEL AKWILA DIAN ERMA WARU TIDOLF SIHITE RUDY PRIYANTO MULADNO CECE SUMANTRI Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
description	Abstract. Jakaria, Ulum MF, Lestari D, Akwila S, Sihite DEWT, Priyanto R, Muladno, Sumantri C. 2020. Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle. Biodiversitas 21: 2971-2976. The present investigation aims to explore specific SNPs of Bali cattle, focusing mainly on CAST, CAPN, and SCD genes in 5'UTR. DNA of Bali cattle (25 individuals) from Breeding Centre of Bali cattle in Bali Province, Indonesia, were extracted according to the protocol of GenAID. Amplification of the CAST, CAPN, and SCD genes were designed using the Primer3 program based on reference sequences (access numbers AH014526.2, AH009246.3, and AY241932). Furthermore, the PCR product was sequenced through forward primer sequencing. The data sequence results were analyzed using the Bioedit, MEGA7, Popgen 3.2, and DnaSP6 V6 programs. The results showed that SNPs were detected at g.921C>T and g.922T>G in 5'UTR for the CAST gene between the reference of GenBank AH014526.2 and Bali cattle, but it was monomorphic within the population. The high polymorphism of SNPs was found in g.232G>T for the CAPN gene and g.134A>del for the SCD gene. However, the SNP g.246C>del SCD gene was detected as monomorphic in this region. Moreover, this result shows that low nucleotide diversities (Pi) for CAST, CAPN, and SCD genes in 5'UTR of Bali cattle were 0.00422, 0.00632, and 0.00449, respectively. This finding was important for developing marker-assisted selection (MAS) to improve the meat quality of Bali cattle.
format	article
author	Jakaria Jakaria Jakaria MOKHAMAD FAKHRUL ULUM DEWI LESTARI SAMUEL AKWILA DIAN ERMA WARU TIDOLF SIHITE RUDY PRIYANTO MULADNO CECE SUMANTRI
author_facet	Jakaria Jakaria Jakaria MOKHAMAD FAKHRUL ULUM DEWI LESTARI SAMUEL AKWILA DIAN ERMA WARU TIDOLF SIHITE RUDY PRIYANTO MULADNO CECE SUMANTRI
author_sort	Jakaria Jakaria Jakaria
title	Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
title_short	Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
title_full	Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
title_fullStr	Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
title_full_unstemmed	Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle
title_sort	investigating new snps of cast, capn and scd genes in 5’utr of bali cattle
publisher	MBI & UNS Solo
publishDate	2020
url	https://doaj.org/article/9bba561a390d4fac9d90a80087269911
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Investigating new SNPs of CAST, CAPN and SCD genes in 5’UTR of Bali cattle

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