Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice

Bahman Khahani,Elahe Tavakol,Fabio Fornara,Vahid Shariati

doi:10.1186/s12864-020-6702-1

Bahman Khahani, Elahe Tavakol + Show 2 more

Open Access

https://doi.org/10.1186/s12864-020-6702-1

Copy DOI

Abstract

BackgroundImproving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field trial conditions and effectively narrows down the confidence interval (CI) for identification of candidate genes (CG) and markers development.ResultsA comprehensive MQTL analysis was implemented on 1052 QTLs reported for yield (YLD), grain weight (GW), heading date (HD), plant height (PH) and tiller number (TN) in 122 rice populations evaluated under normal condition from 1996 to 2019. Consequently, these QTLs were confined into 114 MQTLs and the average CI was reduced up to 3.5 folds in compare to the mean CI of the original QTLs with an average of 4.85 cM CI in the resulted MQTLs. Among them, 27 MQTLs with at least five initial QTLs from independent studies were considered as the most stable QTLs over different field trials and genetic backgrounds. Furthermore, several known and novel CGs were detected in the high confident MQTLs intervals. The genomic distribution of MQTLs indicated the highest density at subtelomeric chromosomal regions. Using the advantage of synteny and comparative genomics analysis, 11 and 15 ortho-MQTLs were identified at co-linear regions between rice with barley and maize, respectively. In addition, comparing resulted MQTLs with GWAS studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits.ConclusionThis comprehensive analysis defines a genome wide landscape on the most stable loci associated with reliable genetic markers and CGs for yield and yield-related traits in rice. Our findings showed that some of these information are transferable to other cereals that lead to improvement of their breeding programs.

Highlights

Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals
candidate genes (CGs) were detected in the high confident MQTLs intervals
Comparing resulted MQTLs with Genome Wide Association Studies (GWAS) studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits

Summary

Introduction

Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Full list of author information is available at the end of the article. YLD and adaptation to different environments [3, 5,6,7]. These traits are continuously targeted in breeding programs for producing new high-yielding varieties [8]. Since these traits are governed by several genes named. 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 in a credit line to the data. The main problem faced by researchers in using QTL results are their dependency upon the population genetic backgrounds and the phenotyping environment that limit their applications in a wider range of populations or environments [10, 12]

Methods

Results

Conclusion