Identification and Functional Verification of Cold Tolerance Genes in Spring Maize Seedlings Based on a Genome-Wide Association Study and Quantitative Trait Locus Mapping.

Yukun Jin,Yongjing Xi,Piwu Wang,Jing Qu,Zhongren Zhang,Shuyan Guan,Rengui Zhao,Zhifeng Xiao,Zhou Yang

doi:10.3389/fpls.2021.776972

Yukun Jin, Yongjing Xi + Show 7 more

Open Access

https://doi.org/10.3389/fpls.2021.776972

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Abstract

Maize (Zea mays L.) is a tropical crop, and low temperature has become one of the main abiotic stresses for maize growth and development, affecting many maize growth processes. The main area of maize production in China, Jilin province, often suffers from varying degrees of cold damage in spring, which seriously affects the quality and yield of maize. In the face of global climate change and food security concerns, discovering cold tolerance genes, developing cold tolerance molecular markers, and creating cold-tolerant germplasm have become urgent for improving maize resilience against these conditions and obtaining an increase in overall yield. In this study, whole-genome sequencing and genotyping by sequencing were used to perform genome-wide association analysis (GWAS) and quantitative trait locus (QTL) mapping of the two populations, respectively. Overall, four single-nucleotide polymorphisms (SNPs) and 12 QTLs were found to be significantly associated with cold tolerance. Through joint analysis, an intersection of GWAS and QTL mapping was found on chromosome 3, on which the Zm00001d002729 gene was identified as a potential factor in cold tolerance. We verified the function of this target gene through overexpression, suppression of expression, and genetic transformation into maize. We found that Zm00001d002729 overexpression resulted in better cold tolerance in this crop. The identification of genes associated with cold tolerance contributes to the clarification of the underlying mechanism of this trait in maize and provides a foundation for the adaptation of maize to colder environments in the future, to ensure food security.

Highlights

Various abiotic stresses, such as low temperature, drought, and high salinity, significantly affect the normal growth and yield of plants
Three standards were used for the screening of single-nucleotide polymorphisms (SNPs): first, in the offspring typing, there may be a few base types that did not appear in the parents, and we considered them as deletions; second, included genotypes covered at least 80% of SNPs in the offspring; 2h ttp://treesoft.sourceforge.net/ 3h ttps://yanglab.westlake.edu.cn/software/gcta/#Overview 4h ttp://www.uniprot.org/ 5h ttp://clovr.org/docs/clusters-of-orthologous-groups-cogs/ 6h ttp://geneontology.org/ 7h ttps://www.genome.jp/kegg/ 8h ttps://www.ncbi.nlm.nih.gov/
We demonstrated that cold-tolerant maize had higher POD activity than cold-sensitive maize

Summary

Introduction

Various abiotic stresses, such as low temperature, drought, and high salinity, significantly affect the normal growth and yield of plants. Cold stress has had an impact on the growth, yield, and spatial distribution of crops, including maize (Zea mays L.). Cold tolerance in maize is a complex quantitative hereditary trait, controlled by multiple genes; different periods of this crop are controlled by different genetic mechanisms, which are affected by environmental factors (Hodges et al, 1997; Gao et al, 2009). Many studies have shown that cold tolerance at the germination and seedling stages of maize is a quantitative trait, controlled by multiple genes (Trzcinska-Danielewicz et al, 2009); studies have shown that epistasis and additive and dominant gene effects in maize germination under low temperature significantly affect tolerance (Ma et al, 2007)

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