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. 2023 Nov 29;45(12):9634-9655.
doi: 10.3390/cimb45120602.

Identification of Multiple Genetic Loci Related to Low-Temperature Tolerance during Germination in Maize (Zea maize L.) through a Genome-Wide Association Study

Tao Yu  1   2   3 , Jianguo Zhang  1   2   3 , Jingsheng Cao  1   2   3 , Shujun Li  1   2   3 , Quan Cai  1   2   3 , Xin Li  1   2 , Sinan Li  1   2 , Yunlong Li  1   2 , Changan He  2   4 , Xuena Ma  1   2
Affiliations

Identification of Multiple Genetic Loci Related to Low-Temperature Tolerance during Germination in Maize (Zea maize L.) through a Genome-Wide Association Study

Tao Yu et al. Curr Issues Mol Biol. .

Abstract

Low-temperature stress during the germination stage is an important abiotic stress that affects the growth and development of northern spring maize and seriously restricts maize yield and quality. Although some quantitative trait locis (QTLs) related to low-temperature tolerance in maize have been detected, only a few can be commonly detected, and the QTL intervals are large, indicating that low-temperature tolerance is a complex trait that requires more in-depth research. In this study, 296 excellent inbred lines from domestic and foreign origins (America and Europe) were used as the study materials, and a low-coverage resequencing method was employed for genome sequencing. Five phenotypic traits related to low-temperature tolerance were used to assess the genetic diversity of maize through a genome-wide association study (GWAS). A total of 14 SNPs significantly associated with low-temperature tolerance were detected (-log10(P) > 4), and an SNP consistently linked to low-temperature tolerance in the field and indoors during germination was utilized as a marker. This SNP, 14,070, was located on chromosome 5 at position 2,205,723, which explained 4.84-9.68% of the phenotypic variation. The aim of this study was to enrich the genetic theory of low-temperature tolerance in maize and provide support for the innovation of low-temperature tolerance resources and the breeding of new varieties.

Keywords: QTLs; abiotic stress; genome-wide association study (GWAS); low-temperature tolerance.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Variation in the clustering standard cross-entropy as the number of subgroups K increases.
Figure 2
Figure 2
The population structure of subgroups from K = 4 to K = 6. Note: (a) K = 4; (b) K = 5; and (c) K = 6.
Figure 3
Figure 3
The attenuation in maize chromosome LD with an increase in SNP distance.
Figure 4
Figure 4
Correlation analysis based on the relative germination index in 2018.
Figure 5
Figure 5
Correlation analysis based on the indoor relative germination index in 2018.
Figure 6
Figure 6
Correlation analysis based on the indoor relative germination index in 2019.
See this image and copyright information in PMC

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