The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm

Abstract. Saputra TI, Roberdi, Nugroho YA, Artutiningsih W, Purba OS, Maryanto SD, Yono D, Utomo C, Liwang T. 2021. The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm. Biodiversitas 22: 3356-3362. The unlabeled probes-high resolution m...

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Autores principales:	TENGKU IMAM SAPUTRA, ROBERDI ROBERDI, YOGO ADHI NUGROHO, WULAN ARTUTININGSIH, OLIVIA S. PURBA, SIGIT DWI MARYANTO, DWI YONO, CONDRO UTOMO, TONY LIWANG
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2021
Materias:	hrm, interspecific hybrid, molecular markers, oil palm, snps genotyping. Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/81189e56a89f4266bc8cd1d8551b6071
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spelling	oai:doaj.org-article:81189e56a89f4266bc8cd1d8551b60712021-11-22T12:14:18ZThe development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm1412-033X2085-472210.13057/biodiv/d220642https://doaj.org/article/81189e56a89f4266bc8cd1d8551b60712021-06-01T00:00:00Zhttps://smujo.id/biodiv/article/view/8288https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Abstract. Saputra TI, Roberdi, Nugroho YA, Artutiningsih W, Purba OS, Maryanto SD, Yono D, Utomo C, Liwang T. 2021. The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm. Biodiversitas 22: 3356-3362. The unlabeled probes-high resolution melting (UP-HRM) marker is a useful tool for detecting of single nucleotide polymorphisms (SNPs). The objectives of this study were to develop UP-HRM markers to differentiate specific SNPs patterns on oil palm. The marker was developed and tested with Elaeis guineensis (Eg), Elaeis oleifera (Eo), Eo x Eg (hybrid), and was validated with 53 individuals of BC1F1 populations ((Eo x Eg) x Eg). Four UP-HRM markers were developed based on 2 SNPs in the stearoyl-acyl-carrier-protein 9-desaturase (EgSAD), 1 SNP in the auxin-responsive protein IAA27-like (EgIAA27), and 1 SNP in the 1-amino cyclopropane-1-carboxylate oxidase (EgACC) genes. The SNP discovery result showed that Eg was represented a reference homozygote genotype, while Eo was represented as an alternative homozygote genotype and the Eo x Eg hybrid was represented as a heterozygote genotype in all genes. The typical UP-HRM melt curve graph was successfully generated. This result was consistent with each genotype model for all four markers. The UP-HRM markers can distinguish each genotype according to the single-pass sequencing results. Furthermore, dendrogram analysis on validation divided 53 BC1F1 samples into three cluster groups.TENGKU IMAM SAPUTRAROBERDI ROBERDIYOGO ADHI NUGROHOWULAN ARTUTININGSIHOLIVIA S. PURBASIGIT DWI MARYANTODWI YONOCONDRO UTOMOTONY LIWANGMBI & UNS Soloarticlehrm, interspecific hybrid, molecular markers, oil palm, snps genotyping.Biology (General)QH301-705.5ENBiodiversitas, Vol 22, Iss 6 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	hrm, interspecific hybrid, molecular markers, oil palm, snps genotyping. Biology (General) QH301-705.5
spellingShingle	hrm, interspecific hybrid, molecular markers, oil palm, snps genotyping. Biology (General) QH301-705.5 TENGKU IMAM SAPUTRA ROBERDI ROBERDI YOGO ADHI NUGROHO WULAN ARTUTININGSIH OLIVIA S. PURBA SIGIT DWI MARYANTO DWI YONO CONDRO UTOMO TONY LIWANG The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm
description	Abstract. Saputra TI, Roberdi, Nugroho YA, Artutiningsih W, Purba OS, Maryanto SD, Yono D, Utomo C, Liwang T. 2021. The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm. Biodiversitas 22: 3356-3362. The unlabeled probes-high resolution melting (UP-HRM) marker is a useful tool for detecting of single nucleotide polymorphisms (SNPs). The objectives of this study were to develop UP-HRM markers to differentiate specific SNPs patterns on oil palm. The marker was developed and tested with Elaeis guineensis (Eg), Elaeis oleifera (Eo), Eo x Eg (hybrid), and was validated with 53 individuals of BC1F1 populations ((Eo x Eg) x Eg). Four UP-HRM markers were developed based on 2 SNPs in the stearoyl-acyl-carrier-protein 9-desaturase (EgSAD), 1 SNP in the auxin-responsive protein IAA27-like (EgIAA27), and 1 SNP in the 1-amino cyclopropane-1-carboxylate oxidase (EgACC) genes. The SNP discovery result showed that Eg was represented a reference homozygote genotype, while Eo was represented as an alternative homozygote genotype and the Eo x Eg hybrid was represented as a heterozygote genotype in all genes. The typical UP-HRM melt curve graph was successfully generated. This result was consistent with each genotype model for all four markers. The UP-HRM markers can distinguish each genotype according to the single-pass sequencing results. Furthermore, dendrogram analysis on validation divided 53 BC1F1 samples into three cluster groups.
format	article
author	TENGKU IMAM SAPUTRA ROBERDI ROBERDI YOGO ADHI NUGROHO WULAN ARTUTININGSIH OLIVIA S. PURBA SIGIT DWI MARYANTO DWI YONO CONDRO UTOMO TONY LIWANG
author_facet	TENGKU IMAM SAPUTRA ROBERDI ROBERDI YOGO ADHI NUGROHO WULAN ARTUTININGSIH OLIVIA S. PURBA SIGIT DWI MARYANTO DWI YONO CONDRO UTOMO TONY LIWANG
author_sort	TENGKU IMAM SAPUTRA
title	The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm
title_short	The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm
title_full	The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm
title_fullStr	The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm
title_full_unstemmed	The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm
title_sort	development of unlabeled probes-high resolution melting (up-hrm) marker on sad, iaa27 and acc genes of oil palm
publisher	MBI & UNS Solo
publishDate	2021
url	https://doaj.org/article/81189e56a89f4266bc8cd1d8551b6071
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The development of unlabeled probes-high resolution melting (UP-HRM) marker on SAD, IAA27 and ACC genes of oil palm

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