Functional mutation allele mining of plant architecture and yield-related agronomic traits and characterization of their effects in wheat

Huijun Guo,Linshu Zhao,Luxiang Liu,Shirong Zhao,Hongchun Xiong,Jiayu Gu,Yuping Ding,Yongdun Xie

doi:10.1186/s12863-019-0804-2

Huijun Guo, Linshu Zhao + Show 6 more

Open Access

https://doi.org/10.1186/s12863-019-0804-2

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Abstract

BackgroundWheat mutant resources with phenotypic variation have been developed in recent years. These mutants might carry favorable mutation alleles, which have the potential to be utilized in the breeding process. Plant architecture and yield-related features are important agronomic traits for wheat breeders and mining favorable alleles of these traits will improve wheat characteristics.ResultsHere we used 190 wheat phenotypic mutants as material and by analyzing their SNP variation and phenotypic data, mutation alleles for plant architecture and yield-related traits were identified, and the genetic effects of these alleles were evaluated. In total, 32 mutation alleles, including three pleiotropic alleles, significantly associated with agronomic traits were identified from the 190 wheat mutant lines. The SNPs were distributed on 12 chromosomes and were associated with plant height (PH), tiller number, flag leaf angle (FLA), thousand grain weight (TGW), and other yield-related traits. Further phenotypic analysis of multiple lines carrying the same mutant allele was performed to determine the effect of the allele on the traits of interest. PH-associated SNPs on chromosomes 2BL, 3BS, 3DL, and 5DL might show additive effects, reducing PH by 10.0 cm to 31.3 cm compared with wild type, which means that these alleles may be favorable for wheat improvement. Only unfavorable mutation alleles that reduced TGW and tiller number were identified. A region on chromosome 5DL with mutation alleles for PH and TGW contained several long ncRNAs, and their sequences shared more than 90% identity with cytokinin oxidase/dehydrogenase genes. Some of the mutation alleles we mined were colocalized with previously reported QTLs or genes while others were novel; these novel alleles could also result in phenotypic variation.ConclusionOur results demonstrate that favorable mutation alleles are present in mutant resources, and the region between 409.5 to 419.8 Mb on chromosome 5DL affects wheat plant height and thousand grain weight.

Highlights

Wheat mutant resources with phenotypic variation have been developed in recent years
single nucleotide polymorphism (SNP) potentially associated with plant architecture- and yield-related traits under different environments The principal component analysis (PCA) indicated that the population was divided into five subpopulations (Additional file 1: Figure S1)
One hundred ninety advanced phenotypic wheat mutants were genotyped by 660 K SNP assay, and 10 agronomic traits were investigated under 5 environments

Summary

Introduction

Wheat mutant resources with phenotypic variation have been developed in recent years. These mutants might carry favorable mutation alleles, which have the potential to be utilized in the breeding process. In the past few decades, mutation induction has been used to improve crop varieties Using this procedure, more than 3200 new mutant plant varieties have been bred from over 200 species worldwide Using an M2 population and reverse-genetic methodologies, such as TILLING (Targeting Induced Local Lesions in Genomes), novel alleles of known genes have been identified and functionally characterized in several plant species including wheat [4,5,6,7,8]. Various mutations affecting plant architecture, spike morphology, and yield-related traits have been identified, and there are many novel mutant genes/alleles available. A new methodology that could identify mutated genes/QTLs directly from the mutants should be developed which would be helpful in accelerating the gene mining process

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