QTL mapping and candidate gene analysis of peduncle vascular bundle related traits in rice by genome-wide association study

Laiyuan Zhai,Yun Wang,Xinyu Wang,Shu Wang,Tianqing Zheng,Zhikang Li,Kai Chen,Jianlong Xu

doi:10.1186/s12284-018-0204-7

Abstract

BackgroundThe vascular bundle especially in the peduncle is one of crucial limiting factors of rice yield, and it determines how plants efficiently transport photosynthetic products, mineral nutrients and water from leaf and root to panicle. However, the genetic base of rice vascular bundle related traits in the peduncle still remains unknown.ResultsThe 423 panel showed substantial natural variations of peduncle vascular bundle. In total, 48 quantitative trait loci/locus (QTL) affecting the eight traits were identified throughout the genome by applying a significance threshold of P < 1.0 × 10− 4. Combined determining linkage disequilibrium (LD) blocks associated with significant SNPs and haplotype analyses allowed us to shortlist six candidate genes for four important QTL regions affecting the peduncle vascular bundle traits, including one cloned gene (NAL1) and three newly identified QTL (qLVN6, qSVN7, and qSVA8.1). Further the most likely candidate genes for each important QTL were also discussed based on functional annotation.ConclusionsGenetic base on peduncle vascular bundle related traits in rice was systematically dissected, and most likely candidate genes of the known gene NAL1 and the three newly identified QTL (qLVN6, qSVN7, and qSVA8.1) were analyzed. The results provided valuable information for future functional characterization and rice breeding for high yield through optimizing transportation efficiency of photosynthetic products by marker-assisted selection.

Highlights

The vascular bundle especially in the peduncle is one of crucial limiting factors of rice yield, and it determines how plants efficiently transport photosynthetic products, mineral nutrients and water from leaf and root to panicle
It is of importance to study the genetic basis of peduncle vascular bundle to provide useful information for the genetic improvement of rice yield potential using heterosis between indica and japonica
We reported the first Genomewide association study (GWAS) for vascular bundle system in any agricultural crop using a panel of germplasm resources with a broad genetic diversity

Summary

Introduction

The vascular bundle especially in the peduncle is one of crucial limiting factors of rice yield, and it determines how plants efficiently transport photosynthetic products, mineral nutrients and water from leaf and root to panicle. Vascular bundles, which interconnect all parts of the plant, extending from the stem into leaves, and down into the root system It consists of xylem and phloem, two differentiated conductive tissues, as well as. The capacity of the vascular bundle system for efficiently transporting assimilates from the source to the sink has been shown as a limiting factor for yield potential realization (Housley and Peterson 1982). It is of importance to study the genetic basis of peduncle vascular bundle to provide useful information for the genetic improvement of rice yield potential using heterosis between indica and japonica

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Discussion

Conclusion