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Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing

BACKGROUND: Quinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowledge on genomic variation, population structure, and genetic diversity and t...

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Autores principales: Zhang, Tifu, Gu, Minfeng, Liu, Yuhe, Lv, Yuanda, Zhou, Ling, Lu, Haiyan, Liang, Shuaiqiang, Bao, Huabin, Zhao, Han
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584319/
https://www.ncbi.nlm.nih.gov/pubmed/28870149
http://dx.doi.org/10.1186/s12864-017-4093-8
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author Zhang, Tifu
Gu, Minfeng
Liu, Yuhe
Lv, Yuanda
Zhou, Ling
Lu, Haiyan
Liang, Shuaiqiang
Bao, Huabin
Zhao, Han
author_facet Zhang, Tifu
Gu, Minfeng
Liu, Yuhe
Lv, Yuanda
Zhou, Ling
Lu, Haiyan
Liang, Shuaiqiang
Bao, Huabin
Zhao, Han
author_sort Zhang, Tifu
collection PubMed
description BACKGROUND: Quinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowledge on genomic variation, population structure, and genetic diversity and to develop novel Insertion/Deletion (InDel) markers for quinoa by whole-genome re-sequencing. RESULTS: We re-sequenced 11 quinoa accessions and obtained a coverage depth between approximately 7× to 23× the quinoa genome. Based on the 1453-megabase (Mb) assembly from the reference accession Riobamba, 8,441,022 filtered bi-allelic single nucleotide polymorphisms (SNPs) and 842,783 filtered InDels were identified, with an estimated SNP and InDel density of 5.81 and 0.58 per kilobase (kb). From the genomic InDel variations, 85 dimorphic InDel markers were newly developed and validated. Together with the 62 simple sequence repeat (SSR) markers reported, a total of 147 markers were used for genotyping the 129 quinoa accessions. Molecular grouping analysis showed classification into two major groups, the Andean highland (composed of the northern and southern highland subgroups) and Chilean coastal, based on combined STRUCTURE, phylogenetic tree and PCA (Principle Component Analysis) analyses. Further analysis of the genetic diversity exhibited a decreasing tendency from the Chilean coast group to the Andean highland group, and the gene flow between subgroups was more frequent than that between the two subgroups and the Chilean coastal group. The majority of the variations (approximately 70%) were found through an analysis of molecular variation (AMOVA) due to the diversity between the groups. This was congruent with the observation of a highly significant F(ST) value (0.705) between the groups, demonstrating significant genetic differentiation between the Andean highland type of quinoa and the Chilean coastal type. Moreover, a core set of 16 quinoa germplasms that capture all 362 alleles was selected using a simulated annealing method. CONCLUSIONS: The large number of SNPs and InDels identified in this study demonstrated that the quinoa genome is enriched with genomic variations. Genetic population structure, genetic core germplasms and dimorphic InDel markers are useful resources for genetic analysis and quinoa breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4093-8) contains supplementary material, which is available to authorized users.
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spelling pubmed-55843192017-09-06 Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing Zhang, Tifu Gu, Minfeng Liu, Yuhe Lv, Yuanda Zhou, Ling Lu, Haiyan Liang, Shuaiqiang Bao, Huabin Zhao, Han BMC Genomics Research Article BACKGROUND: Quinoa (Chenopodium quinoa Willd.) is a balanced nutritional crop, but its breeding improvement has been limited by the lack of information on its genetics and genomics. Therefore, it is necessary to obtain knowledge on genomic variation, population structure, and genetic diversity and to develop novel Insertion/Deletion (InDel) markers for quinoa by whole-genome re-sequencing. RESULTS: We re-sequenced 11 quinoa accessions and obtained a coverage depth between approximately 7× to 23× the quinoa genome. Based on the 1453-megabase (Mb) assembly from the reference accession Riobamba, 8,441,022 filtered bi-allelic single nucleotide polymorphisms (SNPs) and 842,783 filtered InDels were identified, with an estimated SNP and InDel density of 5.81 and 0.58 per kilobase (kb). From the genomic InDel variations, 85 dimorphic InDel markers were newly developed and validated. Together with the 62 simple sequence repeat (SSR) markers reported, a total of 147 markers were used for genotyping the 129 quinoa accessions. Molecular grouping analysis showed classification into two major groups, the Andean highland (composed of the northern and southern highland subgroups) and Chilean coastal, based on combined STRUCTURE, phylogenetic tree and PCA (Principle Component Analysis) analyses. Further analysis of the genetic diversity exhibited a decreasing tendency from the Chilean coast group to the Andean highland group, and the gene flow between subgroups was more frequent than that between the two subgroups and the Chilean coastal group. The majority of the variations (approximately 70%) were found through an analysis of molecular variation (AMOVA) due to the diversity between the groups. This was congruent with the observation of a highly significant F(ST) value (0.705) between the groups, demonstrating significant genetic differentiation between the Andean highland type of quinoa and the Chilean coastal type. Moreover, a core set of 16 quinoa germplasms that capture all 362 alleles was selected using a simulated annealing method. CONCLUSIONS: The large number of SNPs and InDels identified in this study demonstrated that the quinoa genome is enriched with genomic variations. Genetic population structure, genetic core germplasms and dimorphic InDel markers are useful resources for genetic analysis and quinoa breeding. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12864-017-4093-8) contains supplementary material, which is available to authorized users. BioMed Central 2017-09-05 /pmc/articles/PMC5584319/ /pubmed/28870149 http://dx.doi.org/10.1186/s12864-017-4093-8 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Zhang, Tifu
Gu, Minfeng
Liu, Yuhe
Lv, Yuanda
Zhou, Ling
Lu, Haiyan
Liang, Shuaiqiang
Bao, Huabin
Zhao, Han
Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing
title Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing
title_full Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing
title_fullStr Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing
title_full_unstemmed Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing
title_short Development of novel InDel markers and genetic diversity in Chenopodium quinoa through whole-genome re-sequencing
title_sort development of novel indel markers and genetic diversity in chenopodium quinoa through whole-genome re-sequencing
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5584319/
https://www.ncbi.nlm.nih.gov/pubmed/28870149
http://dx.doi.org/10.1186/s12864-017-4093-8
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