Maize (Zea mays L.) is one of the main agricultural crops with the largest yield and acreage in the world. However, maize germplasm is very sensitive to low temperatures, mainly during germination, and low temperatures significantly affect plant growth and crop yield. Therefore, the identification of genes capable of increasing tolerance to low temperature has become necessary. In this study, fourteen phenotypic traits related to seed germination were used to assess the genetic diversity of maize through genome-wide association study (GWAS). A total of 30 single-nucleotide polymorphisms (SNPs) linked to low-temperature tolerance were detected (−log10(P) > 4), fourteen candidate genes were found to be directly related to the SNPs, further additional 68 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r2 ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then used to confirm the linkage between the candidate gene and low-temperature tolerance. A total of ten differentially expressed genes (DEGs) (|log2 fold change (FC)| ≥ 0.585, P < 0.05) were found within the set distance of LD decay (r2 ≥ 0.2). Among these genes, the expression of six DEGs was verified using qRT-PCR. Zm00001d039219 and Zm00001d034319 were putatively involved in ‘mitogen activated protein kinase (MAPK) signal transduction’ and ‘fatty acid metabolic process’, respectively, based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Thus, these genes appeared to be related to low-temperature signal transduction and cell membrane fluidity. Overall, by integrating the results of our GWAS and DEG analysis of low-temperature tolerance during germination in maize, we were able to identify a total of 30 SNPs and 82 related candidate genes, including 10 DEGs, two of which were involved in the response to tolerance to low temperature. Functional analysis will provide valuable information for understanding the genetic mechanism of low-temperature tolerance during germination in maize.

中文翻译：

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通过 GWAS 和 RNA-seq 方法鉴定玉米发芽过程中的候选低温耐受基因。


玉米（Zea mays L.）是世界上产量和面积最大的主要农作物之一。然而，玉米种质对低温非常敏感，主要是在发芽期间，低温显着影响植物生长和作物产量。因此，鉴定能够提高低温耐受性的基因已成为必要。在本研究中，利用与种子萌发相关的十四个表型性状，通过全基因组关联研究（GWAS）评估玉米的遗传多样性。共检测到30个与低温耐受性相关的单核苷酸多态性（SNP）（−log10（P）> 4），发现14个候选基因与SNP直接相关，进一步鉴定了68个基因。筛选扩展到包括与 SNP 的连锁不平衡 (LD) 衰减距离 r2 ≥ 0.2。然后使用RNA测序（RNA-seq）分析来确认候选基因与低温耐受性之间的联系。在设定的 LD 衰减距离（r2 ≥ 0.2）内，共发现 10 个差异表达基因（DEG）（|log2 倍数变化（FC）| ≥ 0.585，P < 0.05）。在这些基因中，使用 qRT-PCR 验证了 6 个 DEG 的表达。根据基因本体论 (GO) 和京都基因与基因组百科全书 (KEGG) 富集分析，Zm00001d039219 和 Zm00001d034319 被推定分别参与“丝裂原激活蛋白激酶 (MAPK) 信号转导”和“脂肪酸代谢过程”。因此，这些基因似乎与低温信号转导和细胞膜流动性有关。 总体而言，通过整合我们对玉米发芽过程中低温耐受性的 GWAS 和 DEG 分析结果，我们能够鉴定出总共 30 个 SNP 和 82 个相关候选基因，其中包括 10 个 DEG，其中两个参与了响应以适应低温。功能分析将为了解玉米发芽过程中耐低温的遗传机制提供有价值的信息。