High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).

Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local g...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Bright Gyamfi Adu, Richard Akromah, Stephen Amoah, Daniel Nyadanu, Alex Yeboah, Lawrence Missah Aboagye, Richard Adu Amoah, Eva Gyamfuaa Owusu
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3198e4898fef44a0b3121ab36c56f267
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:3198e4898fef44a0b3121ab36c56f267
record_format	dspace
spelling	oai:doaj.org-article:3198e4898fef44a0b3121ab36c56f2672021-12-02T20:06:24ZHigh-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).1932-620310.1371/journal.pone.0255290https://doaj.org/article/3198e4898fef44a0b3121ab36c56f2672021-01-01T00:00:00Zhttps://doi.org/10.1371/journal.pone.0255290https://doaj.org/toc/1932-6203Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower's genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.Bright Gyamfi AduRichard AkromahStephen AmoahDaniel NyadanuAlex YeboahLawrence Missah AboagyeRichard Adu AmoahEva Gyamfuaa OwusuPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 16, Iss 7, p e0255290 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bright Gyamfi Adu Richard Akromah Stephen Amoah Daniel Nyadanu Alex Yeboah Lawrence Missah Aboagye Richard Adu Amoah Eva Gyamfuaa Owusu High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).
description	Cassava (Manihot esculenta Crantz) is an important industrial and staple crop due to its high starch content, low input requirement, and resilience which makes it an ideal crop for sustainable agricultural systems and marginal lands in the tropics. However, the lack of genomic information on local genetic resources has impeded efficient conservation and improvement of the crop and the exploration of its full agronomic and breeding potential. This work was carried out to obtain information on population structure and extent of genetic variability among some local landraces conserved at the Plant Genetic Resources Research Institute, Ghana and exotic cassava accessions with Diversity Array Technology based SilicoDArT and SNP markers to infer how the relatedness in the genetic materials can be used to enhance germplasm curation and future breeding efforts. A total of 10521 SilicoDArT and 10808 SNP markers were used with varying polymorphic information content (PIC) values. The average PIC was 0.36 and 0.28 for the SilicoDArT and SNPs respectively. Population structure and average linkage hierarchical clustering based on SNPs revealed two distinct subpopulations and a large number of admixtures. Both DArT platforms identified 22 landraces as potential duplicates based on Gower's genetic dissimilarity. The expected heterozygosity which defines the genetic variation within each subpopulation was 0.008 for subpop1 which were mainly landraces and 0.391 for subpop2 indicating the homogeneous and admixture nature of the two subpopulations. Further analysis upon removal of the duplicates increased the expected heterozygosity of subpop1 from 0.008 to 0.357. A mantel test indicated strong interdependence (r = 0.970; P < 0.001) between SilicoDArT and DArTSeq SNP genotypic data suggesting both marker platforms as a robust system for genomic studies in cassava. These findings provide important information for efficient ex-situ conservation of cassava, future heterosis breeding, and marker-assisted selection (MAS) to enhance cassava improvement.
format	article
author	Bright Gyamfi Adu Richard Akromah Stephen Amoah Daniel Nyadanu Alex Yeboah Lawrence Missah Aboagye Richard Adu Amoah Eva Gyamfuaa Owusu
author_facet	Bright Gyamfi Adu Richard Akromah Stephen Amoah Daniel Nyadanu Alex Yeboah Lawrence Missah Aboagye Richard Adu Amoah Eva Gyamfuaa Owusu
author_sort	Bright Gyamfi Adu
title	High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).
title_short	High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).
title_full	High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).
title_fullStr	High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).
title_full_unstemmed	High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).
title_sort	high-density dart-based silicodart and snp markers for genetic diversity and population structure studies in cassava (manihot esculenta crantz).
publisher	Public Library of Science (PLoS)
publishDate	2021
url	https://doaj.org/article/3198e4898fef44a0b3121ab36c56f267
work_keys_str_mv	AT brightgyamfiadu highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz AT richardakromah highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz AT stephenamoah highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz AT danielnyadanu highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz AT alexyeboah highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz AT lawrencemissahaboagye highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz AT richardaduamoah highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz AT evagyamfuaaowusu highdensitydartbasedsilicodartandsnpmarkersforgeneticdiversityandpopulationstructurestudiesincassavamanihotesculentacrantz
_version_	1718375353422970880

High-density DArT-based SilicoDArT and SNP markers for genetic diversity and population structure studies in cassava (Manihot esculenta Crantz).

Ejemplares similares