Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm

Chinese jujube (<i>Ziziphus jujuba</i> Mill.) is an economically important fruit tree with outstanding adaptability to marginal lands and a broad range of climate conditions. There are over 800 cultivars, mostly landraces from China. However, a high rate of mislabeling in Chinese jujube...

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Autores principales:	Lihua Song, Bing Cao, Yue Zhang, Lyndel W. Meinhardt, Dapeng Zhang
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	genetic integrity genetic redundancy gene bank mislabeling DNA fingerprinting molecular markers Agriculture S
Acceso en línea:	https://doaj.org/article/5b55908df7db4c16aec796538dbe02ca
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spelling	oai:doaj.org-article:5b55908df7db4c16aec796538dbe02ca2021-11-25T16:10:58ZMining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm10.3390/agronomy111123032073-4395https://doaj.org/article/5b55908df7db4c16aec796538dbe02ca2021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4395/11/11/2303https://doaj.org/toc/2073-4395Chinese jujube (<i>Ziziphus jujuba</i> Mill.) is an economically important fruit tree with outstanding adaptability to marginal lands and a broad range of climate conditions. There are over 800 cultivars, mostly landraces from China. However, a high rate of mislabeling in Chinese jujube germplasm restricts the sharing of information and materials among jujube researchers and hampers the use of jujube germplasm in breeding. In the present study, we developed a large panel of single nucleotide polymorphism (SNP) markers and validated 288 SNPs by genotyping 114 accessions of Chinese jujube germplasm. The validation resulted in the designation of a set of 192 polymorphic SNP markers that revealed a high rate of synonymous mislabeling in the jujube germplasm collection in Ningxia, China. A total of 17 groups of duplicates were detected, encompassing 49 of the 114 Chinese jujube cultivars. Model-based population stratification revealed two germplasm groups, and the core members of the two groups showed a significant genetic differentiation (Fst = 0.16). The results supported the hypothesis that the cultivated Chinese jujube had multiple origins and multiple regions of domestication. The Neighbor-Joining dendrogram further revealed that this collection is comprised of multiple sub-groups, each including 1-13 closely related cultivars. Parentage analysis of cultivars with known pedigree information proved the efficacy of using these SNP markers for parentage verification. A subset of 96 SNPs with high information index was selected for future downstream application including gene bank management, verification of pedigrees in breeding programs, quality control for propagation of planting materials and support of the traceability and authentication of jujube products.Lihua SongBing CaoYue ZhangLyndel W. MeinhardtDapeng ZhangMDPI AGarticlegenetic integritygenetic redundancygene bankmislabelingDNA fingerprintingmolecular markersAgricultureSENAgronomy, Vol 11, Iss 2303, p 2303 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	genetic integrity genetic redundancy gene bank mislabeling DNA fingerprinting molecular markers Agriculture S
spellingShingle	genetic integrity genetic redundancy gene bank mislabeling DNA fingerprinting molecular markers Agriculture S Lihua Song Bing Cao Yue Zhang Lyndel W. Meinhardt Dapeng Zhang Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm
description	Chinese jujube (<i>Ziziphus jujuba</i> Mill.) is an economically important fruit tree with outstanding adaptability to marginal lands and a broad range of climate conditions. There are over 800 cultivars, mostly landraces from China. However, a high rate of mislabeling in Chinese jujube germplasm restricts the sharing of information and materials among jujube researchers and hampers the use of jujube germplasm in breeding. In the present study, we developed a large panel of single nucleotide polymorphism (SNP) markers and validated 288 SNPs by genotyping 114 accessions of Chinese jujube germplasm. The validation resulted in the designation of a set of 192 polymorphic SNP markers that revealed a high rate of synonymous mislabeling in the jujube germplasm collection in Ningxia, China. A total of 17 groups of duplicates were detected, encompassing 49 of the 114 Chinese jujube cultivars. Model-based population stratification revealed two germplasm groups, and the core members of the two groups showed a significant genetic differentiation (Fst = 0.16). The results supported the hypothesis that the cultivated Chinese jujube had multiple origins and multiple regions of domestication. The Neighbor-Joining dendrogram further revealed that this collection is comprised of multiple sub-groups, each including 1-13 closely related cultivars. Parentage analysis of cultivars with known pedigree information proved the efficacy of using these SNP markers for parentage verification. A subset of 96 SNPs with high information index was selected for future downstream application including gene bank management, verification of pedigrees in breeding programs, quality control for propagation of planting materials and support of the traceability and authentication of jujube products.
format	article
author	Lihua Song Bing Cao Yue Zhang Lyndel W. Meinhardt Dapeng Zhang
author_facet	Lihua Song Bing Cao Yue Zhang Lyndel W. Meinhardt Dapeng Zhang
author_sort	Lihua Song
title	Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm
title_short	Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm
title_full	Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm
title_fullStr	Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm
title_full_unstemmed	Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm
title_sort	mining single nucleotide polymorphism (snp) markers for accurate genotype identification and diversity analysis of chinese jujube (<i>ziziphus jujuba</i> mill.) germplasm
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/5b55908df7db4c16aec796538dbe02ca
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Mining Single Nucleotide Polymorphism (SNP) Markers for Accurate Genotype Identification and Diversity Analysis of Chinese Jujube (<i>Ziziphus jujuba</i> Mill.) Germplasm

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