Association mapping, trait variation, interaction and population structure analysis in cucumber (Cucumis sativus L.)

In several regions of the world, low productivity in this crop is attributed to several factors including poor understanding of the genomic complexity of important traits associated with fruit quality and yield. Therefore, genome wide association analysis was performed for important traits using sim...

Full description

Saved in:
Bibliographic Details
Published in:Genetic resources and crop evolution 2022-06, Vol.69 (5), p.1901-1917
Main Authors: Kumar, Rahul, Das Munshi, Anilabh, Behera, Tusar Kanti, Jat, Gograj Singh, Choudhary, Harshawardhan, Talukdar, Akshay, Dash, Prasanta, Singh, Deepak
Format: Article
Language:English
Subjects:
Agriculture
Association analysis
Biomedical and Life Sciences
Chromosomes
Cucumbers
Food quality
Fruits
Gene mapping
Genomes
Genotypes
Genotyping
Life Sciences
Mapping
Markers
Nucleotide sequence
Plant Genetics and Genomics
Plant Physiology
Plant Sciences
Plant Systematics/Taxonomy/Biogeography
Population
Population structure
Populations
Research Article
Simple sequence repeats
Structural analysis
Variation
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:In several regions of the world, low productivity in this crop is attributed to several factors including poor understanding of the genomic complexity of important traits associated with fruit quality and yield. Therefore, genome wide association analysis was performed for important traits using simple sequence repeats (SSR) markers. Significant variation was recorded for all the studied traits in 78 cucumber genotypes under two environments (open field and net house) which indicated that the constituted association panel was suitable for association mapping. Genotyping was done using 60 highly polymorphic SSRs. By performing genome scanning out of 60 SSR markers, using mixed linear model (MLM) approach 4 and 6 markers explained an average of 23.93% and 17.37% of the trait variation under net house and open field condition, respectively. Based on MLM approach two markers on 3rd chromosome (UW084942) and 4th chromosome (UW062953) found to be associated with the average fruit weight (g) under both net house and open field condition. Population structure analysis revealed four distinct sub-populations that corroborated with the geographical origin as well as fruit quality and quantitative traits. The four sub-populations (A–D) had fixation index percentage equal to 24.35 29.48, 37.17 and 8.97 respectively, supporting the existence of moderate population structures. Therefore, the extensive phenotypic and genotypic characterization, population structure, and markers associated with important traits provided in this study will facilitate marker assisted improvement programs in cucumber.
ISSN:0925-9864
1573-5109
DOI:10.1007/s10722-022-01352-3