Identification of genomic regions affecting grain peroxidase activity in bread wheat using genome-wide association study

Zhengfu Zhou,Wenxu Li,Huiyue Guan,Shenghui Geng,Zhensheng Lei,Maomao Qin,Ziwei Zhang,Ziju Dai,Zhengqing Wu,Jinna Hou,Baoming Tian,Xia Shi,Congcong Liu

doi:10.1186/s12870-021-03299-6

Abstract

BackgroundPeroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Here, we performed a genome-wide association study (GWAS) on POD activity using an association population consisted with 207 wheat world-wide collected varieties. Our study also provide basis for the genetic improvement of flour color-based quality in wheat.ResultsTwenty quantitative trait loci (QTLs) were detected associated with POD activity, explaining 5.59–12.67% of phenotypic variation. Superior alleles were positively correlated with POD activity. In addition, two SNPs were successfully developed to KASP (Kompetitive Allele-Specific PCR) markers. Two POD genes, TraesCS2B02G615700 and TraesCS2D02G583000, were aligned near the QTLs flanking genomic regions, but only TraesCS2D02G583000 displayed significant divergent expression levels (P < 0.001) between high and low POD activity varieties in the investigated association population. Therefore, it was deduced to be a candidate gene. The expression level of TraesCS2D02G583000 was assigned as a phenotype for expression GWAS (eGWAS) to screen regulatory elements. In total, 505 significant SNPs on 20 chromosomes (excluding 4D) were detected, and 9 of them located within 1 Mb interval of TraesCS2D02G583000.ConclusionsTo identify genetic loci affecting POD activity in wheat grain, we conducted GWAS on POD activity and the candidate gene TraesCS2D02G583000 expression. Finally, 20 QTLs were detected for POD activity, whereas two QTLs associated SNPs were converted to KASP markers that could be used for marker-assisted breeding. Both cis- and trans-acting elements were revealed by eGWAS of TraesCS2D02G583000 expression. The present study provides genetic loci for improving POD activity across wide genetic backgrounds and largely improved the selection efficiency for breeding in wheat.

Highlights

Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour
POD activity is fairly variable, differing by 3–10 times [29]. These results suggest that POD activity could be altered through manipulating desired alleles by gene pyramiding
In this study, we used a population consisting of 207 wheat varieties to perform a genome-wide association study (GWAS) on POD activity at three locations

Summary

Introduction

Peroxidase (POD) activity plays an important role in flour-based product quality, which is mainly associated with browning and bleaching effects of flour. Multiple factors affect flour color, including yellow pigment content, oxidase activity, wheatgrain color, wet gluten content, water absorption, wheat bran content, and protein content. Class I is a group of intracellular enzymes that are extensively present in plants, bacteria, and yeast This class includes cytochrome C peroxidase (CCP), a soluble protein in the electron transport chain of mitochondria that prevents damage from toxic peroxides; ascorbate peroxidase (AP), which mainly functions to expend hydrogen peroxide in the chloroplast and cytosol of higher plants [9]; and bacterial catalaseperoxidase, which protects cells under oxidative stress [10]. Previous studies have shown that PODs are involved in various aspects of plant physiology, such as oxidizing compounds with hydrogen peroxide as an electron acceptor, defending against insect attack, generation and detoxification of active oxygen forms, lignin formation, and cell wall biosynthesis [13,14,15]

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