Genome-wide association study uncovers new genetic loci and candidate genes underlying seed chilling-germination in maize

Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis

KEY MESSAGE

Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.

Sweet corn association panel and genome-wide association analysis reveal loci for chilling-tolerant germination

Sweet corn is highly susceptible to the deleterious effects of low temperatures during the initial stages of growth and development. Employing a 56K chip, high-throughput single-nucleotide polymorphism (SNP) sequencing was conducted on 100 sweet corn inbred lines. Subsequently, six germination indicators-germination rate, germination index, germination time, relative germination rate, relative germination index, and relative germination time-were utilized for genome-wide association analysis. Candidate genes were identified via comparative analysis of homologous genes in Arabidopsis and rice, and their functions were validated using quantitative real-time polymerase chain reaction (qRT-PCR). The results revealed 35,430 high-quality SNPs, 16 of which were significantly correlated. Within 50 kb upstream and downstream of the identified SNPs, 46 associated genes were identified, of which six were confirmed as candidate genes. Their expression patterns indicated that Zm11ΒHSDL5 and Zm2OGO likely play negative and positive regulatory roles, respectively, in the low-temperature germination of sweet corn. Thus, we determined that these two genes are responsible for regulating the low-temperature germination of sweet corn. This study contributes valuable theoretical support for improving sweet corn breeding and may aid in the creation of specific germplasm resources geared toward enhancing low-temperature tolerance in sweet corn.

Protoplast transient expression-based RNA-sequencing: A simple method to screen transcriptional regulation in plants

Protoplast transient expression-based RNA-sequencing identifies Opaque2 targets supported by molecular evidence and expression quantitative trait loci.

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

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.

Genetic and molecular exploration of maize environmental stress resilience: Toward sustainable agriculture

Global climate change exacerbates the effects of environmental stressors, such as drought, flooding, extreme temperatures, salinity, and alkalinity, on crop growth and grain yield, threatening the sustainability of the food supply. Maize (Zea mays) is one of the most widely cultivated crops and the most abundant grain crop in production worldwide. However, the stability of maize yield is highly dependent on environmental conditions. Recently, great progress has been made in understanding the molecular mechanisms underlying maize responses to environmental stresses and in developing stress-resilient varieties due to advances in high-throughput sequencing technologies, multi-omics analysis platforms, and automated phenotyping facilities. In this review, we summarize recent advances in dissecting the genetic factors and networks that contribute to maize abiotic stress tolerance through diverse strategies. We also discuss future challenges and opportunities for the development of climate-resilient maize varieties.

Genetic variation in ZmWAX2 confers maize resistance to Fusarium verticillioides

Fusarium verticillioides (F. verticillioides) is a widely distributed phytopathogen that incites multiple destructive diseases in maize, posing a grave threat to corn yields and quality worldwide. However, there are few reports of resistance genes to F. verticillioides. Here, we reveal that a combination of two single nucleotide polymorphisms (SNPs) corresponding to ZmWAX2 gene associates with quantitative resistance variations to F. verticillioides in maize through a genome-wide association study. A lack of ZmWAX2 compromises maize resistance to F. verticillioides-caused seed rot, seedling blight and stalk rot by reducing cuticular wax deposition, while the transgenic plants overexpressing ZmWAX2 show significantly increased immunity to F. verticillioides. A natural occurrence of two 7-bp deletions within the promoter increases ZmWAX2 transcription, thus enhancing maize resistance to F. verticillioides. Upon Fusarium stalk rot, ZmWAX2 greatly promotes the yield and grain quality of maize. Our studies demonstrate that ZmWAX2 confers multiple disease resistances caused by F. verticillioides and can serve as an important gene target for the development of F. verticillioides-resistant maize varieties.

Integration of GWAS and RNA-Seq Analysis to Identify SNPs and Candidate Genes Associated with Alkali Stress Tolerance at the Germination Stage in Mung Bean

Soil salt-alkalization seriously impacts crop growth and productivity worldwide. Breeding and applying tolerant varieties is the most economical and effective way to address soil alkalization. However, genetic resources for breeders to improve alkali tolerance are limited in mung bean. Here, a genome-wide association study (GWAS) was performed to detect alkali-tolerant genetic loci and candidate genes in 277 mung bean accessions during germination. Using the relative values of two germination traits, 19 QTLs containing 32 SNPs significantly associated with alkali tolerance on nine chromosomes were identified, and they explained 3.6 to 14.6% of the phenotypic variance. Moreover, 691 candidate genes were mined within the LD intervals containing significant trait-associated SNPs. Transcriptome sequencing of alkali-tolerant accession 132-346 under alkali and control conditions after 24 h of treatment was conducted, and 2565 DEGs were identified. An integrated analysis of the GWAS and DEGs revealed six hub genes involved in alkali tolerance responses. Moreover, the expression of hub genes was further validated by qRT-PCR. These findings improve our understanding of the molecular mechanism of alkali stress tolerance and provide potential resources (SNPs and genes) for the genetic improvement of alkali tolerance in mung bean.

QTL-seq and transcriptomic integrative analyses reveal two positively regulated genes that control the low-temperature germination ability of MTP-maize introgression lines

KEY MESSAGE

Two candidate genes (ZmbZIP113 and ZmTSAH1) controlling low-temperature germination ability were identified by QTL-seq and integrative transcriptomic analyses. The functional verification results showed that two candidate genes positively regulated the low-temperature germination ability of IB030. Low-temperature conditions cause slow maize (Zea mays L.) seed metabolism, resulting in slow seedling emergence and irregular seedling emergence, which can cause serious yield loss. Thus, improving a maize cultivar's low-temperature germination ability (LTGA) is vital for increasing yield production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant of cold stress and can thus be used to improve the LTGA of maize. In a previous study, the genetic bridge MTP was constructed (from maize, T. dactyloides, and Z. perennis) and used to obtain a highly LTGA maize introgression line (IB030) by backcross breeding. In this study, IB030 (Strong-LTGA) and Mo17 (Weak-LTGA) were selected as parents to construct an F₂ offspring. Additionally, two major QTLs (qCS1-1 and qCS10-1) were mapped. Then, RNA-seq was performed using seeds of IB030 and the recurrent parent B73 treated at 10 °C for 27 days and 25 °C for 7 days, respectively, and two candidate genes (ZmbZIP113 and ZmTSAH1) controlling LTGA were located using QTL-seq and integrative transcriptomic analyses. The functional verification results showed that the two candidate genes positively regulated LTGA of IB030. Notably, homologous cloning showed that the source of variation in both candidate genes was the stable inheritance of introgressed alleles from Z. perennis. This study was thus able to analyze the LTGA mechanism of IB030 and identify resistance genes for genetic improvement in maize, and it proved that using MTP genetic bridge confers desirable traits or phenotypes of Z. perennis and tripsacum essential to maize breeding systems.

Genomic-regions associated with cold stress tolerance in Asia-adapted tropical maize germplasm

Maize is gaining impetus in non-traditional and non-conventional seasons such as off-season, primarily due to higher demand and economic returns. Maize varieties directed for growing in the winter season of South Asia must have cold resilience as an important trait due to the low prevailing temperatures and frequent cold snaps observed during this season in most parts of the lowland tropics of Asia. The current study involved screening of a panel of advanced tropically adapted maize lines to cold stress during vegetative and flowering stage under field conditions. A suite of significant genomic loci (28) associated with grain yield along and agronomic traits such as flowering (15) and plant height (6) under cold stress environments. The haplotype regression revealed 6 significant haplotype blocks for grain yield under cold stress across the test environments. Haplotype blocks particularly on chromosomes 5 (bin5.07), 6 (bin6.02), and 9 (9.03) co-located to regions/bins that have been identified to contain candidate genes involved in membrane transport system that would provide essential tolerance to the plant. The regions on chromosome 1 (bin1.04), 2 (bin 2.07), 3 (bin 3.05-3.06), 5 (bin5.03), 8 (bin8.05-8.06) also harboured significant SNPs for the other agronomic traits. In addition, the study also looked at the plausibility of identifying tropically adapted maize lines from the working germplasm with cold resilience across growth stages and identified four lines that could be used as breeding starts in the tropical maize breeding pipelines.

GWAS across multiple environments and WGCNA suggest the involvement of ZmARF23 in embryonic callus induction from immature maize embryos

Combined GWAS, WGCNA, and gene-based association studies identified the co-expression network and hub genes for maize EC induction. ZmARF23 bound to ZmSAUR15 promoter and regulated its expression, affecting EC induction. Embryonic callus (EC) induction in immature maize embryos shows high genotype dependence, which limits the application of genetic transformation in transgenic breeding and gene function elucidation in maize. Herein, we conducted a genome-wide association mapping (GWAS) for four EC induction-related traits, namely rate of embryonic callus induction (REC), increased callus diameter (ICD), ratio of shoot formation (RSF), and length of shoot (LS) across different environments. A total of 77 SNPs were significantly associated these traits under three environments and using the averages (across environments). Among these significant SNPs, five were simultaneously detected under multiple environments and 11 had respective phenotypic variation explained > 10%. A total of 257 genes were located in the linkage disequilibrium decay of these REC- and ICD-associated SNPs, of which 178 were responsive to EC induction. According to the expression values of the 178 genes, we performed a weighted gene co-expression network analysis (WGCNA) and revealed an EC induction-associated module and five hub genes. Hub gene-based association studies uncovered that the intragenic variations in GRMZM2G105473 and ZmARF23 influenced EC induction efficiency among different maize lines. Dual-luciferase reporter assay indicated that ZmARF23 bound to the promoter of a known causal gene (ZmSAUR15) for EC induction and positively regulated its expression on the transcription level. Our study will deepen the understanding of genetic and molecular mechanisms underlying EC induction and contribute to the use of genetic transformation in maize.

Genome-wide association study identifies GhSAL1 affects cold tolerance at the seedling emergence stage in upland cotton (Gossypium hirsutum L.)

Genomic analysis of upland cotton revealed that cold tolerance was associated with ecological distribution. GhSAL1 on chromosome D09 negatively regulated cold tolerance of upland cotton. Cotton can undergo low-temperature stress at the seedling emergence stage, which adversely affects growth and yield; however, the regulatory mechanism underlying cold tolerance remains nebulous. Here, we analyze the phenotypic and physiological parameters in 200 accessions from 5 ecological distributions under constant chilling (CC) and diurnal variation of chilling (DVC) stresses at the seedling emergence stage. All accessions were clustered into four groups, of which Group IV, with most germplasms from the northwest inland region (NIR), had better phenotypes than Groups I-III under the two kinds of chilling stresses. A total of 575 significantly associated single-nucleotide polymorphism (SNP) were identified, and 35 stable genetic quantitative trait loci (QTL) were obtained, of which 5 were associated with traits under CC and DVC stress, respectively, while the remaining 25 were co-associated. The accumulation of dry weight (DW) of seedling was associated with the flavonoid biosynthesis process regulated by Gh_A10G0500. The emergence rate (ER), DW, and total length of seedling (TL) under CC stress were associated with the SNPs variation of Gh_D09G0189 (GhSAL1). GhSAL1^HapB was the elite haplotype, which increased ER, DW, and TL by 19.04%, 11.26%, and 7.69%, respectively, compared with that of GhSAL1^HapA. The results of virus-induced gene silencing (VIGS) experiment and determination of metabolic substrate content preliminarily illustrated that GhSAL1 negatively regulated cotton cold tolerance through IP₃-Ca²⁺ signaling pathway. The elite haplotypes and candidate genes identified in this study could be used to improve cold tolerance at the seedling emergence stage in future upland cotton breeding.

Impact of climate perturbations on seeds and seed quality for global agriculture

In agriculture, seeds are the most basic and vital input on which croplands productivity depends. These implies a good starting material, good production lines and good storage options. High-quality seed lots must be free of pests and pathogens and contain a required degree of genetic purity. Seeds need also to be stored in good condition between harvest and later sowing, to insure later on the field a good plant density and higher crop yield. In general, these parameters are already widely accepted and considered in many countries where advanced technologies evaluate them. However, the more and more frequently devastating climate changes observed around the world has put seed quality under threat, and current seeds may not be adapted to hazardous and unpredictable conditions. Climate-related factors such as temperature and water availability directly affect seed development and later germination. For these reasons, investigating seed quality in response to climate changes is a step to propose new crop varieties and practices that will bring solutions for our future.

Chilling Tolerance in Maize: Insights into Advances—Toward Physio-Biochemical Responses’ and QTL/Genes’ Identification

Maize, a major staple cereal crop in global food supply, is a thermophilic and short-day C4 plant sensitive to low-temperature stress. A low temperature is among the most severe agro-meteorological hazards in maize-growing areas. This review covers the latest research and progress in the field of chilling tolerance in maize in the last 40 years. It mainly focuses on how low-temperature stress affects the maize membrane and antioxidant systems, photosynthetic physiology, osmoregulatory substances and hormone levels. In addition, the research progress in identifying cold-tolerance QTLs (quantitative trait loci) and genes to genetically improve maize chilling toleranceis comprehensively discussed. Based on previous research, this reviewprovides anoutlook on potential future research directions and offers a reference for researchers in the maize cold-tolerance-related field.

GWAS and transcriptome analysis reveal MADS26 involved in seed germination ability in maize

MADS26 affecting maize seed germination was identified by GWAS and transcriptomics. Gene-based association analyses revealed three variations within MADS26 regulating seed germination traits. Overexpressed MADS26 in Arabidopsis improved seed germination. Seed germination ability is extremely important for maize production. Exploring the genetic control of seed germination ability is useful for improving maize yield. In this study, a genome-wide association study (GWAS) was conducted to excavate the significant SNPs involved in seed germination ability based on an association panel consisting of 300 lines. A total of 11 SNPs and 75 candidate genes were significantly associated with the seed germination traits. In addition, we constructed 24 transcriptome libraries from maize seeds at four germination stages using two inbred lines with contrasting germination rates. In total, 15,865 differentially expressed genes were induced during seed germination. Integrating the results of GWAS and transcriptome analysis uncovered four prioritized genes underlying maize seed germination. The variations located in the promoter of Zm00001d017932, a MADS-transcription factor 26 (MADS26), were verified to affect the seed germination, and the haplotype TAT was determined as a favorable haplotype for high-germination capability. MADS26 was induced to express by ethylene during seed germination in maize and overexpressing MADS26 increased the seed germination ability in Arabidopsis. These findings will contribute to understanding of the genetic and molecular mechanisms on seed germination and the genetic modification of seed germination ability in maize.

The Importance of a Genome-Wide Association Analysis in the Study of Alternative Splicing Mutations in Plants with a Special Focus on Maize

Alternative splicing is an important mechanism for regulating gene expressions at the post-transcriptional level. In eukaryotes, the genes are transcribed in the nucleus to produce pre-mRNAs and alternative splicing can splice a pre-mRNA to eventually form multiple different mature mRNAs, greatly increasing the number of genes and protein diversity. Alternative splicing is involved in the regulation of various plant life activities, especially the response of plants to abiotic stresses and is also an important process of plant growth and development. This review aims to clarify the usefulness of a genome-wide association analysis in the study of alternatively spliced variants by summarizing the application of alternative splicing, genome-wide association analyses and genome-wide association analyses in alternative splicing, as well as summarizing the related research progress.

Screening of stable resistant accessions and identification of resistance loci to Barley yellow mosaic virus disease

Background

The disease caused by Barley yellow mosaic virus (BaYMV) infection is a serious threat to autumn-sown barley (Hordeum vulgare L.) production in Europe, East Asia and Iran. Due to the rapid diversification of BaYMV strains, it is urgent to discover novel germplasm and genes to assist breeding new varieties with resistance to different BaYMV strains, thus minimizing the effect of BaYMV disease on barley cropping.

Methods

A natural population consisting of 181 barley accessions with different levels of resistance to BaYMV disease was selected for field resistance identification in two separate locations (Yangzhou and Yancheng, Jiangsu Province, China). Additive main effects and multiplicative interaction (AMMI) analysis was used to identify accessions with stable resistance. Genome-wide association study (GWAS) of BaYMV disease resistance was broadly performed by combining both single nucleotide polymorphisms (SNPs) and specific molecular markers associated with the reported BaYMV disease resistance genes. Furthermore, the viral protein genome linked (VPg) sequences of the virus were amplified and analyzed to assess the differences between the BaYMV strains sourced from the different experimental sites.

Results

Seven barley accessions with lower standardized Area Under the Disease Progress Steps (sAUDPS) index in every environment were identified and shown to have stable resistance to BaYMV disease in each assessed location. Apart from the reported BaYMV disease resistance genes rym4 and rym5, one novel resistance locus explaining 24.21% of the phenotypic variation was identified at the Yangzhou testing site, while two other novel resistance loci that contributed 19.23% and 19.79% of the phenotypic variation were identified at the Yancheng testing site, respectively. Further analysis regarding the difference in the VPg sequence of the predominant strain of BaYMV collected from these two testing sites may explain the difference of resistance loci differentially identified under geographically distinct regions. Our research provides novel genetic resources and resistance loci for breeding barley varieties for BaMYV disease resistance.

Identification of the Potential Genes Regulating Seed Germination Speed in Maize

Seed germination is the crucial stage in plant life cycle. Rapid and uniform germination plays an essential role in plant development and grain yield improvement. However, the molecular mechanism underlying seed germination speed is largely unknown due to the complexity of the dynamic process and the difficulty in phenotyping. Here, we conducted a time-series comparative transcriptome study of two elite maize inbred lines, 72-3 and F9721, with striking difference in seed germination speed, and identified a major locus underlying maize germination speed through genome-wide association analysis (GWAS) of an F₂ segregation population. Comparative transcriptome study identified 12 h after imbibition (HAI) as the critical stage responsible for the variation in germination speed. The differentially expressed genes (DEGs) between 72-3 and F9721 were mainly enriched in metabolic pathways, biosynthesis of secondary metabolites, oxidoreductase activity pathways, hormone signal transduction, and amino acid transporter activity pathways. GWAS revealed that germination speed was controlled by a major locus on chromosome 1 with the leading SNP as AX-91332814, explaining 10.63% of phenotypic variation. A total of 87 proposed protein-coding genes surrounding the locus were integrated with DEGs. Combined with evidence from the gene expression database and gene synteny with other model species, we finally anchored three genes as the likely candidates regulating germination speed in maize. This study provides clues for the further exploration of genes controlling the maize seed germination speed, thus facilitating breeding of rapid germinated elite lines through marker assistant selection.

QTL Mapping Low-Temperature Germination Ability in the Maize IBM Syn10 DH Population

Chilling injury poses a serious threat to seed emergence of spring-sowing maize in China, which has become one of the main climatic limiting factors affecting maize production in China. It is of great significance to mine the key genes controlling low-temperature tolerance during seed germination and study their functions for breeding new maize varieties with strong low-temperature tolerance during germination. In this study, 176 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, which comprised 6618 bin markers, were used for QTL analysis of low-temperature germination ability. The results showed significant differences in germination related traits under optimum-temperature condition (25 °C) and low-temperature condition (10 °C) between two parental lines. In total, 13 QTLs were detected on all chromosomes, except for chromosome 5, 7, 10. Among them, seven QTLs formed five QTL clusters on chromosomes 1, 2, 3, 4, and 9 under the low-temperature condition, which suggested that there may be some genes regulating multiple germination traits at the same time. A total of 39 candidate genes were extracted from five QTL clusters based on the maize GDB under the low-temperature condition. To further screen candidate genes controlling low-temperature germination, RNA-Seq, in which RNA was extracted from the germination seeds of B73 and Mo17 at 10 °C, was conducted, and three B73 upregulated genes and five Mo17 upregulated genes were found by combined analysis of RNA-Seq and QTL located genes. Additionally, the variations of Zm00001d027976 (GLABRA2), Zm00001d007311 (bHLH transcription factor), and Zm00001d053703 (bZIP transcription factor) were found by comparison of amino sequence between B73 and Mo17. This study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of low-temperature germination tolerance in maize.

Association mapping uncovers maize ZmbZIP107 regulating root system architecture and lead absorption under lead stress

Lead (Pb) is a highly toxic contaminant to living organisms and the environment. Excessive Pb in soils affects crop yield and quality, thus threatening human health via the food chain. Herein, we investigated Pb tolerance among a maize association panel using root bushiness (BSH) under Pb treatment as an indicator. Through a genome-wide association study of relative BSH, we identified four single nucleotide polymorphisms (SNPs) and 30 candidate genes associated with Pb tolerance in maize seedlings. Transcriptome analysis showed that four of the 30 genes were differentially responsive to Pb treatment between two maize lines with contrasting Pb tolerance. Among these, the ZmbZIP107 transcription factor was confirmed as the key gene controlling maize tolerance to Pb by using gene-based association studies. Two 5' UTR_variants in ZmbZIP107 affected its expression level and Pb tolerance among different maize lines. ZmbZIP107 protein was specifically targeted to the nucleus and ZmbZIP107 mRNA showed the highest expression in maize seedling roots among different tissues. Heterologous expression of ZmbZIP107 enhanced rice tolerance to Pb stress and decreased Pb absorption in the roots. Our study provided the basis for revelation of the molecular mechanism underlying Pb tolerance and contributed to cultivation of Pb-tolerant varieties in maize.

Recent Advances in the Analysis of Cold Tolerance in Maize

Maize (Zea mays L.) is an annual grass that originated in tropical and subtropical regions of the New World. Maize is highly sensitive to cold stress during seed gemination and the seedling phase, which can lead to reductions in plant vigor and grain production. There are large differences in the morphological and physiological changes caused by cold stress among maize varieties. In general, cold tolerant varieties have a stronger ability to maintain such changes in traits related to seed germination, root phenotypes, and shoot photosynthesis. These morphological and physiological characteristics have been widely used to evaluate the cold tolerance of maize varieties in genetic analyses. In recent years, considerable progress has been made in elucidating the mechanisms of maize in response to cold tolerance. Several QTL, GWAS, and transcriptomic analyses have been conducted on various maize genotypes and populations that show large variations in cold tolerance, resulting in the discovery of hundreds of candidate cold regulation genes. Nevertheless, only a few candidate genes have been functionally characterized. In the present review, we summarize recent progress in molecular, physiological, genetic, and genomic analyses of cold tolerance in maize. We address the advantages of joint analyses that combine multiple genetic and genomic approaches to improve the accuracy of identifying cold regulated genes that can be further used in molecular breeding. We also discuss the involvement of long-distance signaling in plant cold tolerance. These novel insights will provide a better mechanistic understanding of cold tolerance in maize.