The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia

Abstract. Herlina L, Istiaji B. 2020. The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia. Biodiversitas 21: 4677-4685. One of the most important diseases and become challenge in breeding resistant variety of shallots in Indonesia i...

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Autores principales:	Lina Herlina, BONJOK ISTIAJI
Formato:	article
Lenguaje:	EN
Publicado:	MBI & UNS Solo 2020
Materias:	crx genes, effector, foc, fusarium, phylogenetic analysis, six genes Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/10e961061ef04db7aa47fed2714d06cf
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spelling	oai:doaj.org-article:10e961061ef04db7aa47fed2714d06cf2021-11-22T00:51:09ZThe use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia1412-033X2085-472210.13057/biodiv/d211029https://doaj.org/article/10e961061ef04db7aa47fed2714d06cf2020-09-01T00:00:00Zhttps://smujo.id/biodiv/article/view/6699https://doaj.org/toc/1412-033Xhttps://doaj.org/toc/2085-4722Abstract. Herlina L, Istiaji B. 2020. The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia. Biodiversitas 21: 4677-4685. One of the most important diseases and become challenge in breeding resistant variety of shallots in Indonesia is Fusarium disease, caused by Fusarium oxysporum f.sp. cepae (FOC). To discriminate the F. oxysporum into forma speciales is uneasy, often managed through laborious and time-intensive disease assays., therefore molecular approaches become the most relevant choice. FOCs from Indonesia were examined by molecular criteria based on putative and effector genes-based markers, i.e.: SIX-genes, C5-gene, and CRX1-2-genes. The alignment analysis discovered some regions which sequences highly contained conserved bases, while amplification result bands vary in size, between 400 - 500 bp. The combined of 7 SIX-genes primers and 3 effector primers (C5 and CRX1-2) used in the clustering analysis of 15 FOC isolates in this study showed that they succeeded in separating 15 FOC isolates into 4 groups through NTSys. Clustering analysis showed that those markers succeeded in grouping 15 FOC isolates into different clades (by coefficient of similarity: 0.69). Phylogenetic analysis based on CRX genes sequence as putative effector genes confirmed that CRX1 and CRX2 genes were able to classify the FOC into their forma speciales. Those effectors genes are potential to serve as marker-templates to facilitate identification of FOC which infested shallots in Indonesia.Lina HerlinaBONJOK ISTIAJIMBI & UNS Soloarticlecrx genes, effector, foc, fusarium, phylogenetic analysis, six genesBiology (General)QH301-705.5ENBiodiversitas, Vol 21, Iss 10 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	crx genes, effector, foc, fusarium, phylogenetic analysis, six genes Biology (General) QH301-705.5
spellingShingle	crx genes, effector, foc, fusarium, phylogenetic analysis, six genes Biology (General) QH301-705.5 Lina Herlina BONJOK ISTIAJI The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia
description	Abstract. Herlina L, Istiaji B. 2020. The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia. Biodiversitas 21: 4677-4685. One of the most important diseases and become challenge in breeding resistant variety of shallots in Indonesia is Fusarium disease, caused by Fusarium oxysporum f.sp. cepae (FOC). To discriminate the F. oxysporum into forma speciales is uneasy, often managed through laborious and time-intensive disease assays., therefore molecular approaches become the most relevant choice. FOCs from Indonesia were examined by molecular criteria based on putative and effector genes-based markers, i.e.: SIX-genes, C5-gene, and CRX1-2-genes. The alignment analysis discovered some regions which sequences highly contained conserved bases, while amplification result bands vary in size, between 400 - 500 bp. The combined of 7 SIX-genes primers and 3 effector primers (C5 and CRX1-2) used in the clustering analysis of 15 FOC isolates in this study showed that they succeeded in separating 15 FOC isolates into 4 groups through NTSys. Clustering analysis showed that those markers succeeded in grouping 15 FOC isolates into different clades (by coefficient of similarity: 0.69). Phylogenetic analysis based on CRX genes sequence as putative effector genes confirmed that CRX1 and CRX2 genes were able to classify the FOC into their forma speciales. Those effectors genes are potential to serve as marker-templates to facilitate identification of FOC which infested shallots in Indonesia.
format	article
author	Lina Herlina BONJOK ISTIAJI
author_facet	Lina Herlina BONJOK ISTIAJI
author_sort	Lina Herlina
title	The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia
title_short	The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia
title_full	The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia
title_fullStr	The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia
title_full_unstemmed	The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia
title_sort	use of effector gene based-markers to facilitate identification of fusarium sp. infected shallot in java, indonesia
publisher	MBI & UNS Solo
publishDate	2020
url	https://doaj.org/article/10e961061ef04db7aa47fed2714d06cf
work_keys_str_mv	AT linaherlina theuseofeffectorgenebasedmarkerstofacilitateidentificationoffusariumspinfectedshallotinjavaindonesia AT bonjokistiaji theuseofeffectorgenebasedmarkerstofacilitateidentificationoffusariumspinfectedshallotinjavaindonesia AT linaherlina useofeffectorgenebasedmarkerstofacilitateidentificationoffusariumspinfectedshallotinjavaindonesia AT bonjokistiaji useofeffectorgenebasedmarkerstofacilitateidentificationoffusariumspinfectedshallotinjavaindonesia
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The use of effector gene based-markers to facilitate identification of Fusarium sp. infected shallot in Java, Indonesia

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