QTL-By-Environment Interaction in the Response of Maize Root and Shoot Traits to Different Water Regimes

Genomic basis determining root system architecture in maize

KEY MESSAGE

A total of 389 and 344 QTLs were identified by GWAS and QTL mapping explaining accumulatively 32.2-65.0% and 23.7-63.4% of phenotypic variation for 14 shoot-borne root traits using more than 1300 individuals across multiple field trails. Efficient nutrient and water acquisition from soils depends on the root system architecture (RSA). However, the genetic determinants underlying RSA in maize remain largely unexplored. In this study, we conducted a comprehensive genetic analysis for 14 shoot-borne root traits using 513 inbred lines and 800 individuals from four recombinant inbred line (RIL) populations at the mature stage across multiple field trails. Our analysis revealed substantial phenotypic variation for these 14 root traits, with a total of 389 and 344 QTLs identified through genome-wide association analysis (GWAS) and linkage analysis, respectively. These QTLs collectively explained 32.2-65.0% and 23.7-63.4% of the trait variation within each population. Several a priori candidate genes involved in auxin and cytokinin signaling pathways, such as IAA26, ARF2, LBD37 and CKX3, were found to co-localize with these loci. In addition, a total of 69 transcription factors (TFs) from 27 TF families (MYB, NAC, bZIP, bHLH and WRKY) were found for shoot-borne root traits. A total of 19 genes including PIN3, LBD15, IAA32, IAA38 and ARR12 and 19 GWAS signals were overlapped with selective sweeps. Further, significant additive effects were found for root traits, and pyramiding the favorable alleles could enhance maize root development. These findings could contribute to understand the genetic basis of root development and evolution, and provided an important genetic resource for the genetic improvement of root traits in maize.

Characterization and Effect of a Nematophagous Fungus Talaromyces cystophila sp. nov. for the Biological Control of Corn Cyst Nematode

The dynamic of plant-parasitic nematode populations in soil is closely related to soil microorganisms. Fungi from Heterodera zeae cysts were isolated to explore the phenomenon of decline in the H. zeae population in the soil. Phylogenetic study of partial ITS, BenA, CaM, and RPB2 gene sequences, in addition to morphological investigations, was utilized to identify a nematode-destroying fungus. The nematicidal activity of a novel strain GX1 against H. zeae was assessed in vitro and in the greenhouse. Our findings revealed that strain GX1 is a new species of Talaromyces, named Talaromyces cystophila. It has a strong parasitic and lethal effect on H. zeae cysts, with 91.11% parasitism on cysts at 3 days after treatment. The contents of second-stage juveniles (J2s) and eggs inside the cysts were degraded and formed dense vacuoles, and the damaged eggs could not hatch normally. The spore suspension exhibited high nematophagous activity against nematodes, and fermentation filtrate exhibited marked inhibition of egg hatching and nematicidal activities on J2s. The hatching inhibition rates of eggs exposed to 1 × 108 CFU/ml spore suspensions or 20% 1-week fermentation filtrate (1-WF) for 15 days were 98.56 and 100%, respectively. The mortality of J2s exposed to 1 × 108 CFU/ml spore suspension reached 100% at 24 h; exposure to 50% 2-WF was 98.65 and 100% at 24 and 48 h, respectively. Greenhouse experiments revealed that the spore suspension and fermentation broth considerably decreased H. zeae reproduction by 56.17 to 78.76%. T. cystophila is a potential biocontrol strain with nematophagous and nematicidal activity that deserves attention and application.

Root responses to abiotic stress: a comparative look at root system architecture in maize and sorghum

Under all environments, roots are important for plant anchorage and acquiring water and nutrients. However, there is a knowledge gap regarding how root architecture contributes to stress tolerance in a changing climate. Two closely related plant species, maize and sorghum, have distinct root system architectures and different levels of stress tolerance, making comparative analysis between these two species an ideal approach to resolve this knowledge gap. However, current research has focused on shared aspects of the root system that are advantageous under abiotic stress conditions rather than on differences. Here we summarize the current state of knowledge comparing the root system architecture relative to plant performance under water deficit, salt stress, and low phosphorus in maize and sorghum. Under water deficit, steeper root angles and deeper root systems are proposed to be advantageous for both species. In saline soils, a reduction in root length and root number has been described as advantageous, but this work is limited. Under low phosphorus, root systems that are shallow and wider are beneficial for topsoil foraging. Future work investigating the differences between these species will be critical for understanding the role of root system architecture in optimizing plant production for a changing global climate.

Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences

Large-scale genotype and phenotype data have been increasingly generated to identify genetic markers, understand gene function and evolution and facilitate genomic selection. These datasets hold immense value for both current and future studies, as they are vital for crop breeding, yield improvement and overall agricultural sustainability. However, integrating these datasets from heterogeneous sources presents significant challenges and hinders their effective utilization. We established the Genotype-Phenotype Working Group in November 2021 as a part of the AgBioData Consortium (https://www.agbiodata.org) to review current data types and resources that support archiving, analysis and visualization of genotype and phenotype data to understand the needs and challenges of the plant genomic research community. For 2021-22, we identified different types of datasets and examined metadata annotations related to experimental design/methods/sample collection, etc. Furthermore, we thoroughly reviewed publicly funded repositories for raw and processed data as well as secondary databases and knowledgebases that enable the integration of heterogeneous data in the context of the genome browser, pathway networks and tissue-specific gene expression. Based on our survey, we recommend a need for (i) additional infrastructural support for archiving many new data types, (ii) development of community standards for data annotation and formatting, (iii) resources for biocuration and (iv) analysis and visualization tools to connect genotype data with phenotype data to enhance knowledge synthesis and to foster translational research. Although this paper only covers the data and resources relevant to the plant research community, we expect that similar issues and needs are shared by researchers working on animals. Database URL: https://www.agbiodata.org.

A simulation-based assessment of the efficiency of QTL mapping under environment and genotype x environment interaction effects

The objective of this simulation-based study was to assess how genes, environments, and genotype x environment (GxE) interaction affect the quantitative trait loci (QTL) mapping efficiency. The simulation software performed 50 samplings of 300 recombinant inbred lines (RILs) from a F2, which were assessed in six environments. The RILs were genotyped for 977 single nucleotide polymorphisms (SNP) and phenotyped for grain yield. The average SNP density was 2 cM. We defined six QTLs and 190 minor genes. The trait heritability ranged from 30 to 80%. We fitted the single QTL model and the multiple QTL model on multiple phenotypes. The environment and complex GxE interaction effects led to a low correlation between the QTL heritability and power. The single- and across-environment analyses allowed all QTLs be declared, with an average power of 28 to 100%. In the across-environment analysis, five QTLs showed average power in the range 46 to 82%. Both models provided a good control of the false positive rate (6%, on average) and a precise localization of the QTLs (bias of 2 cM, on average). The QTL power in each environment has a high positive correlation with the range between QTL genotypes for the sum of the additive, environment, and GxE interaction effects (0.76 to 0.96). The uncertainty about the magnitude and sign of the environment and GxE interaction effects makes QTL mapping in multi-environment trials unpredictable. Unfortunately, this uncertainty has no solution because the geneticist has no control over the magnitude and sign of the environment and GxE interaction effects. However, the single- and across-environment analyses are efficient even under a low correlation between QTL heritability and power.

Drought stress in maize: stress perception to molecular response and strategies for its improvement

Given the future demand for food crops, increasing crop productivity in drought-prone rainfed areas has become essential. Drought-tolerant varieties are warranted to solve this problem in major crops, with drought tolerance as a high-priority trait for future research. Maize is one such crop affected by drought stress, which limits production, resulting in substantial economic losses. It became a more serious issue due to global climate change. The most drought sensitive among all stages of maize is the reproductive stages and the most important for overall maize production. The exact molecular basis of reproductive drought sensitivity remains unclear due to genes' complex regulation of drought stress. Understanding the molecular biology and signaling of the unexplored area of reproductive drought tolerance will provide an opportunity to develop climate-smart drought-tolerant next-generation maize cultivars. In recent decades, significant progress has been made in maize to understand the drought tolerance mechanism. However, improving maize drought tolerance through breeding is ineffective due to the complex nature and multigenic control of drought traits. With the help of advanced breeding techniques, molecular genetics, and a precision genome editing approach like CRISPR-Cas, candidate genes for drought-tolerant maize can be identified and targeted. This review summarizes the effects of drought stress on each growth stage of maize, potential genes, and transcription factors that determine drought tolerance. In addition, we discussed drought stress sensing, its molecular mechanisms, different approaches to developing drought-resistant maize varieties, and how molecular breeding and genome editing will help with the current unpredictable climate change.

QTL mapping for flowering time in a maize-teosinte population under well-watered and water-stressed conditions

Maize grain yield can be greatly reduced when flowering time coincides with drought conditions, which delays silking and consequently increases the anthesis-silking interval. Although the genetic basis of delayed flowering time under water-stressed conditions has been elucidated in maize-maize populations, little is known in this regard about maize-teosinte populations. Here, 16 quantitative trait loci (QTL) for three flowering-time traits, namely days to anthesis, days to silk, and the anthesis-silking interval, were identified in a maize-teosinte introgression population under well-watered and water-stressed conditions; these QTL explained 3.98-32.61% of phenotypic variations. Six of these QTL were considered to be sensitive to drought stress, and the effect of any individual QTL was small, indicating the complex genetic nature of drought resistance in maize. To resolve which genes underlie the six QTL, 11 candidate genes were identified via colocalization analysis of known associations with flowering-time-related drought traits. Among the 11 candidate genes, five were found to be differentially expressed in response to drought stress or under selection during maize domestication, and thus represented the most likely candidates underlying the drought-sensitive QTL. The results lay a foundation for further studies of the genetic mechanisms of drought resistance and provide valuable information for improving drought resistance during maize breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01413-0.

Genomic insight into changes of root architecture under drought stress in maize

Drought stress is a central environmental factor that severely limits maize production worldwide. Root architecture plays an important role in drought tolerance and can be targeted in breeding programmes. Here, we conducted phenotyping of root architecture under different water treatments for 373 maize inbred lines, representative germplasm from both China and the United States in different breeding eras. We found that seminal root length in response to drought stress experienced convergent increase during breeding in both countries. Using a genome-wide association study, we identified a total of 221 associated loci underlying 13 root traits under well-watered and water-stressed conditions. These loci harboured many reported root- and abiotic stress-related genes. Furthermore, a total of 75 strong candidate genes were prioritised by integrating candidate genes associated with seminal root length and differentially expressed genes in seminal root. One of high-confidence candidate genes, ZmCIPK3 was functionally characterised and probably plays a role in enhancing drought tolerance through regulating seminal root growth. This study provides valuable information for genetic improvement of root architecture and drought tolerance in maize.

QTL and Candidate Genes: Techniques and Advancement in Abiotic Stress Resistance Breeding of Major Cereals

At least 75% of the world's grain production comes from the three most important cereal crops: rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays). However, abiotic stressors such as heavy metal toxicity, salinity, low temperatures, and drought are all significant hazards to the growth and development of these grains. Quantitative trait locus (QTL) discovery and mapping have enhanced agricultural production and output by enabling plant breeders to better comprehend abiotic stress tolerance processes in cereals. Molecular markers and stable QTL are important for molecular breeding and candidate gene discovery, which may be utilized in transgenic or molecular introgression. Researchers can now study synteny between rice, maize, and wheat to gain a better understanding of the relationships between the QTL or genes that are important for a particular stress adaptation and phenotypic improvement in these cereals from analyzing reports on QTL and candidate genes. An overview of constitutive QTL, adaptive QTL, and significant stable multi-environment and multi-trait QTL is provided in this article as a solid framework for use and knowledge in genetic enhancement. Several QTL, such as DRO1 and Saltol, and other significant success cases are discussed in this review. We have highlighted techniques and advancements for abiotic stress tolerance breeding programs in cereals, the challenges encountered in introgressing beneficial QTL using traditional breeding techniques such as mutation breeding and marker-assisted selection (MAS), and the in roads made by new breeding methods such as genome-wide association studies (GWASs), the clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 system, and meta-QTL (MQTL) analysis. A combination of these conventional and modern breeding approaches can be used to apply the QTL and candidate gene information in genetic improvement of cereals against abiotic stresses.

Modulating physiological and transcriptional regulatory mechanisms for enhanced climate resilience in cereal crops

Climate change adversely affects the yield and productivity of cereal crops, which consequently impacts food security. Therefore, studying stress acclimation, particularly transcriptional patterns and morpho-physiological responses of cereal crops to different stresses, will provide insights into the molecular determinants underlying climate resilience. The availability of advanced tools and approaches has enabled the characterization of plants at morphological, physiological, biochemical, and molecular levels, which will lead to the identification of genomic regions regulating the stress responses at these levels. This will further facilitate using transgenic, breeding, or genome editing approaches to manipulate the identified regions (genes, alleles, or QTLs) to enhance stress resilience. Next-generation sequencing approaches have advanced the identification of causal genes and markers in the genomes through forward or reverse genetics. In this context, the review enumerates the progress of dissecting the molecular mechanisms underlying transcriptional and physiological responses of major cereals to climate-induced stresses. The review systematically discusses different tools and approaches available to study the response of plants to various stresses and identify the molecular determinants regulating stress-resilience. Further, the application of genomics-assisted breeding, transgene-, and targeted editing-based approaches for modulating the genetic determinants for enhanced climate resilience has been elaborated.

Identification of Zinc Efficiency-Associated Loci (ZEALs) and Candidate Genes for Zn Deficiency Tolerance of Two Recombination Inbred Line Populations in Maize

Zinc (Zn) deficiency is one of the most common micronutrient disorders in cereal plants, greatly impairing crop productivity and nutritional quality. Identifying the genes associated with Zn deficiency tolerance is the basis for understanding the genetic mechanism conferring tolerance. In this study, the K22×BY815 and DAN340×K22 recombination inbred line (RIL) populations, which were derived from Zn-inefficient and Zn-efficient inbred lines, were utilized to detect the quantitative trait loci (QTLs) associated with Zn deficiency tolerance and to further identify candidate genes within these loci. The BLUP (Best Linear Unbiased Prediction) values under Zn-deficient condition (-Zn) and the ratios of the BLUP values under Zn deficient condition to the BLUP values under Zn-sufficient condition (-Zn/CK) were used to perform linkage mapping. In QTL analysis, 21 QTLs and 33 QTLs controlling the Zn score, plant height, shoot and root dry weight, and root-to-shoot ratio were detected in the K22×BY815 population and the DAN340×K22 population, explaining 5.5–16.6% and 4.2–23.3% of phenotypic variation, respectively. In addition, seventeen candidate genes associated with the mechanisms underlying Zn deficiency tolerance were identified in QTL colocalizations or the single loci, including the genes involved in the uptake, transport, and redistribution of Zn (ZmIRT1, ZmHMAs, ZmNRAMP6, ZmVIT, ZmNAS3, ZmDMAS1, ZmTOM3), and the genes participating in the auxin and ethylene signal pathways (ZmAFBs, ZmIAA17, ZmETR, ZmEIN2, ZmEIN3, ZmCTR3, ZmEBF1). Our findings will broaden the understanding of the genetic structure of the tolerance to Zn deficiency in maize.

Shaping the root system architecture in plants for adaptation to drought stress

Root system architecture plays an important role in plant adaptation to drought stress. The root system architecture (RSA) consists of several structural features, which includes number and length of main and lateral roots along with the density and length of root hairs. These features exhibit plasticity under water-limited environments and could be critical to developing crops with efficient root systems for adaptation under drought. Recent advances in the omics approaches have significantly improved our understanding of the regulatory mechanisms of RSA remodeling under drought and the identification of genes and other regulatory elements. Plant response to drought stress at physiological, morphological, biochemical, and molecular levels in root cells is regulated by various phytohormones and their crosstalk. Stress-induced reactive oxygen species play a significant role in regulating root growth and development under drought stress. Several transcription factors responsible for the regulation of RSA under drought have proven to be beneficial for developing drought tolerant crops. Molecular breeding programs for developing drought-tolerant crops have been greatly benefitted by the availability of quantitative trait loci (QTLs) associated with the RSA regulation. In the present review, we have discussed the role of various QTLs, signaling components, transcription factors, microRNAs and crosstalk among various phytohormones in shaping RSA and present future research directions to better understand various factors involved in RSA remodeling for adaptation to drought stress. We believe that the information provided herein may be helpful in devising strategies to develop crops with better RSA for efficient uptake and utilization of water and nutrients under drought conditions.

Plasticity of root anatomy during domestication of a maize-teosinte derived population

Maize (Zea mays L.) has undergone profound changes in root anatomy for environmental adaptation during domestication. However, the genetic mechanism of plasticity of maize root anatomy during the domestication process remains unclear. In this study, high-resolution mapping was performed for nine root anatomical traits using a maize-teosinte population (mexicana × Mo17) across three environments. Large genetic variations were detected for different root anatomical traits. The cortex, stele, aerenchyma areas, xylem vessel number, and cortical cell number had large variations across three environments, indicating high plasticity. Sixteen quantitative trait loci (QTL) were identified, including seven QTL with QTL × environment interaction (EIQTL) for high plasticity traits and nine QTL without QTL × environment interaction (SQTL). Most of the root loci were consistent with shoot QTL depicting domestication signals. Combining transcriptome and genome-wide association studies revealed that AUXIN EFFLUX CARRIER PIN-FORMED LIKE 4 (ZmPILS4) serves as a candidate gene underlying a major QTL of xylem traits. The near-isogenic lines (NILs) with lower expression of ZmPILS4 had 18-24% more auxin concentration in the root tips and 8-15% more xylem vessels. Nucleotide diversity values analysis in the promoter region suggested that ZmPILS4 was involved in maize domestication and adaptation. These results revealed the potential genetic basis of root anatomical plasticity during domestication.

QTL Map of Early- and Late-Stage Perennial Regrowth in Zea diploperennis

Numerous climate change threats will necessitate a shift toward more sustainable agricultural practices during the 21st century. Conversion of annual crops to perennials that are capable of regrowing over multiple yearly growth cycles could help to facilitate this transition. Perennials can capture greater amounts of carbon and access more water and soil nutrients compared to annuals. In principle it should be possible to identify genes that confer perenniality from wild relatives and transfer them into existing breeding lines to create novel perennial crops. Two major loci controlling perennial regrowth in the maize relative Zea diploperennis were previously mapped to chromosome 2 (reg1) and chromosome 7 (reg2). Here we extend this work by mapping perennial regrowth in segregating populations involving Z. diploperennis and the maize inbreds P39 and Hp301 using QTL-seq and traditional QTL mapping approaches. The results confirmed the existence of a major perennial regrowth QTL on chromosome 2 (reg1). Although we did not observe the reg2 QTL in these populations, we discovered a third QTL on chromosome 8 which we named regrowth3 (reg3). The reg3 locus exerts its strongest effect late in the regrowth cycle. Neither reg1 nor reg3 overlapped with tiller number QTL scored in the same population, suggesting specific roles in the perennial phenotype. Our data, along with prior work, indicate that perennial regrowth in maize is conferred by relatively few major QTL.

Exploiting natural variation in crown root traits via genome-wide association studies in maize

BACKGROUND

Root system architecture (RSA), which is determined by the crown root angle (CRA), crown root diameter (CRD), and crown root number (CRN), is an important factor affecting the ability of plants to obtain nutrients and water from the soil. However, the genetic mechanisms regulating crown root traits in the field remain unclear.

METHODS

In this study, the CRA, CRD, and CRN of 316 diverse maize inbred lines were analysed in three field trials. Substantial phenotypic variations were observed for the three crown root traits in all environments. A genome-wide association study was conducted using two single-locus methods (GLM and MLM) and three multi-locus methods (FarmCPU, FASTmrMLM, and FASTmrEMMA) with 140,421 SNP.

RESULTS

A total of 38 QTL including 126 SNPs were detected for CRA, CRD, and CRN. Additionally, 113 candidate genes within 50 kb of the significant SNPs were identified. Combining the gene annotation information and the expression profiles, 3 genes including GRMZM2G141205 (IAA), GRMZM2G138511 (HSP) and GRMZM2G175910 (cytokinin-O-glucosyltransferase) were selected as potentially candidate genes related to crown root development. Moreover, GRMZM2G141205, encoding an AUX/IAA transcriptional regulator, was resequenced in all tested lines. Five variants were identified as significantly associated with CRN in different environments. Four haplotypes were detected based on these significant variants, and Hap1 has more CRN.

CONCLUSIONS

These findings may be useful for clarifying the genetic basis of maize root system architecture. Furthermore, the identified candidate genes and variants may be relevant for breeding new maize varieties with root traits suitable for diverse environmental conditions.

Mapping and Validation of a Stable Quantitative Trait Locus Conferring Maize Resistance to Gibberella Ear Rot

Gibberella ear rot (GER), a prevalent disease caused by Fusarium graminearum, can result in significant yield loss and carcinogenic mycotoxin contamination in maize worldwide. However, only a few quantitative trait loci (QTLs) for GER resistance have been reported. In this study, we evaluated a Chinese recombinant inbred line (RIL) population comprising 204 lines, developed from a cross between a resistant parent DH4866 and a susceptible line T877, in three field trials under artificial inoculation with F. graminearum. The RIL population and their parents were genotyped with an Affymetrix microarray CGMB56K SNP Array. Based on the genetic linkage map constructed using 1,868 bins as markers, 11 QTLs, including five stable QTLs, were identified by individual environment analysis. Joint multiple environments analysis and epistatic interaction analysis revealed six additive and six epistatic (additive × additive) QTLs, respectively. None of the QTLs could explain more than 10% of phenotypic variation, suggesting that multiple minor-effect QTLs contributed to the genetic component of resistance to GER, and both additive and epistatic effects contributed to the genetic architecture of resistance to GER. A novel QTL, qGER4.09, with the largest effect, identified and validated using 588 F₂ individuals, was colocalized with genomic regions for Fusarium ear rot and Aspergillus ear rot, indicating that this genetic locus likely confers resistance to multiple pathogens and can potentially be utilized in breeding maize varieties aimed at improving the resistance not only to GER but also other ear rot diseases.

Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface

Maize illustrates one of the most complex cases of embryogenesis in higher plants that results in the development of early embryo with distinctive organs such as the mesocotyl, seminal and primary roots, coleoptile, and plumule. After seed germination, the elongation of root and mesocotyl follows opposite directions in response to specific tropisms (positive and negative gravitropism and hydrotropism). Tropisms represent the differential growth of an organ directed toward several stimuli. Although the life cycle of roots and mesocotyl takes place in darkness, their growth and functions are controlled by different mechanisms. Roots ramify through the soil following the direction of the gravity vector, spreading their tips into new territories looking for water; when water availability is low, the root hydrotropic response is triggered toward the zone with higher moisture. Nonetheless, there is a high range of hydrotropic curvatures (angles) in maize. The processes that control root hydrotropism and mesocotyl elongation remain unclear; however, they are influenced by genetic and environmental cues to guide their growth for optimizing early seedling vigor. Roots and mesocotyls are crucial for the establishment, growth, and development of the plant since both help to forage water in the soil. Mesocotyl elongation is associated with an ancient agriculture practice known as deep planting. This tradition takes advantage of residual soil humidity and continues to be used in semiarid regions of Mexico and USA. Due to the genetic diversity of maize, some lines have developed long mesocotyls capable of deep planting while others are unable to do it. Hence, the genetic and phenetic interaction of maize lines with a robust hydrotropic response and higher mesocotyl elongation in response to water scarcity in time of global heating might be used for developing more resilient maize plants.

Genetics and genomics of root system variation in adaptation to drought stress in cereal crops

Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.

Genetic dissection of maize drought tolerance for trait improvement

Maize is one of the most important crops, but its production is threatened by drought stress worldwide. Thus, increased drought tolerance has been a major goal of maize breeding. Conventional breeding strategies have led to significantly increase of maize yields; however, these strategies often fail to meet the need for drought stress tolerance enhancement. Here, we focus on progress related to the genetic dissection of drought tolerance in maize at different developmental stages achieved through linkage mapping and association mapping. Moreover, recent molecular breeding systems, including transgenic, genome-wide marker-assisted selection, and genome editing technologies, have provided a more direct, efficient, and accurate approach for trait improvement. We also provide perspectives on future directions regarding multi-omics studies and maize improvement. Overall, the application of acquired knowledge will facilitate maize breeding to meet the challenges.

Genetic regulation of root traits for soil flooding tolerance in genus Zea

Flooding stress caused by excessive precipitation and poor drainage threatens upland crop production and food sustainability, so new upland crop cultivars are needed with greater tolerance to soil flooding (waterlogging). So far, however, there have been no reports of highly flooding-tolerant upland crop cultivars, including maize, because of the lack of flooding-tolerant germplasm and the presence of a large number of traits affecting flooding tolerance. To achieve the goal of breeding flooding-tolerant maize cultivars by overcoming these difficulties, we chose highly flooding-tolerant teosinte germplasm. These flooding-tolerance-related traits were separately assessed by establishing a method for the accurate evaluation of each one, followed by performing quantitative trait locus (QTL) analyses for each trait using maize × teosinte mapping populations, developing introgression lines (ILs) or near-isogenic lines (NILs) containing QTLs and pyramiding useful traits. We have identified QTLs for flooding-tolerance-related root traits, including the capacity to form aerenchyma, formation of radial oxygen loss barriers, tolerance to flooded reducing soil conditions, flooding-induced adventitious root formation and shallow root angle. In addition, we have developed several ILs and NILs with flooding-tolerance-related QTLs and are currently developing pyramided lines. These lines should be valuable for practical maize breeding programs focused on flooding tolerance.

Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics?

Adventitious root (AR) formation is a complex developmental process controlled by a plethora of endogenous and environmental factors. Based on fossil evidence and genomic phylogeny, AR formation might be considered the default state of plant roots, which likely evolved independently several times. The application of next-generation sequencing techniques and bioinformatics analyses to non-model plants provide novel approaches to identify genes putatively involved in AR formation in multiple species. Recent results uncovered that the regulation of shoot-borne AR formation in monocots is an adaptive response to nutrient and water deficiency that enhances topsoil foraging and improves plant performance. A hierarchy of transcription factors required for AR initiation has been identified from genetic studies, and recent results highlighted the key involvement of additional regulation through microRNAs. Here, we discuss our current understanding of AR formation in response to specific environmental stresses, such as nutrient deficiency, drought or waterlogging, aimed at providing evidence for the integration of the hormone crosstalk required for the activation of root competent cells within adult tissues from which the ARs develop.

Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops

Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.

Transcriptome and GWAS analyses reveal candidate gene for seminal root length of maize seedlings under drought stress

Water deficits are a major constraint on maize growth and yield, and deep roots are one of the major mechanisms of drought tolerance. In this study, four root and shoot traits were evaluated within an association panel consisting of 209 diverse maize accessions under well-watered (WW) and water-stressed (WS) conditions. A significant positive correlation was observed between seminal root length (SRL) under WS treatment and the drought tolerance index (DI) of maize seedlings. The transcriptome profiles of maize seminal roots were compared between four drought-tolerant lines and four drought-sensitive lines under both water conditions to identify genes associated with the drought stress response. After drought stress, 343 and 177 common differentially expressed genes (DEGs) were identified in the drought-tolerant group and drought-sensitive group, respectively. In parallel, a coexpression network underlying SRL was constructed on the basis of transcriptome data, and 10 hub genes involved in two significant associated modules were identified. Additionally, a genome-wide association study (GWAS) of the SRL revealed 62 loci for the two water treatments. By integrating the results of the GWAS, the common DEGs and the coexpression network analysis, 7 promising candidate genes were prioritized for further research. Together, our results provide a foundation for the enhanced understanding of seminal root changes in response to drought stress in maize.

Identification of QTLs for resistance to maize rough dwarf disease using two connected RIL populations in maize

Maize rough dwarf disease (MRDD) is a significant viral disease caused by rice black-streaked dwarf virus (RBSDV) in China, which results in 30% yield losses in affected summer maize-growing areas. In this study, two connected recombinant inbred line (RIL) populations were constructed to elucidate the genetic basis of resistance during two crop seasons. Ten quantitative trait loci (QTLs) for resistance to MRDD were detected in the two RILs. Individual QTLs accounted for 4.97-23.37% of the phenotypic variance explained (PVE). The resistance QTL (qZD-MRDD8-1) with the largest effect was located in chromosome bin 8.03, representing 16.27-23.37% of the PVE across two environments. Interestingly, one pair of common significant QTLs was located in the similar region on chromosome 4 in both populations, accounting for 7.11-9.01% of the PVE in Zheng58×D863F (RIL-ZD) and 9.43-13.06% in Zheng58×ZS301 (RIL-ZZ). A total of five QTLs for MRDD resistance trait showed significant QTL-by-Environment interactions (QEI). Two candidate genes associated with resistance (GDSL-lipase and RPP13-like gene) which were higher expressed in resistant inbred line D863F than in susceptible inbred line Zheng58, were located in the physical intervals of the major QTLs on chromosomes 4 and 8, respectively. The identified QTLs will be studied further for application in marker-assisted breeding in maize genetic improvement of MRDD resistance.

Combined linkage and association mapping reveal candidate loci for kernel size and weight in maize

Yield improvement is a top priority for maize breeding. Kernel size and weight are important determinants of maize grain yield. In this study, a recombinant inbred line (RIL) population and an association panel were used to identify quantitative trait loci (QTLs) for four maize kernel-related traits: kernel length, width, thickness and 100-kernel weight. Twenty-seven QTLs were identified for kernel-related traits across three environments and the best linear unbiased predictions (BLUPs) of each trait by linkage analysis, and four QTLs were stably detected in more than two environments. Additionally, 29 single nucleotide polymorphisms (SNPs) were identified as significantly associated with the four kernel-related traits and BLUPs by genome-wide association study, and two loci could be stably detected in both environments. In total, four QTLs/SNPs were co-associated with various traits in both populations. Using combined-linkage analysis and association mapping, PZE-101066560 on chromosome 1, associated with kernel width and with 100-kernel weight in the association panel, was co-localized within the QTL interval of qKW1-3 for kernel width in the RILs. Two annotated genes in the candidate region were considered as potential candidate genes. The QTLs and candidate genes identified here will facilitate molecular breeding for grain yield improvement in maize.

Natural variation of ZmHKT1 affects root morphology in maize at the seedling stage

Eight variants in ZmHKT1 promoter were significantly associated with root diameter, four haplotypes based on these significant variants were found, and Hap2 has the largest root diameter. Roots play an important role in uptake of water, nutrients and plant anchorage. Identification of gene and corresponding SNPs associated with root traits would enable develop maize lines with better root traits that might help to improve capacity for absorbing nutrients and water acquisition. The genomic sequences of a salt tolerance gene ZmHKT1 was resequenced in 349 maize inbred lines, and the association between nucleotide polymorphisms and seedling root traits was detected. A total of 269 variants in ZmHKT1 were identified, including 226 single nucleotide polymorphisms and 43 insertions and deletions. The gene displayed high level of nucleotide diversity, especially in non-genic regions. A total of 19 variations in untranslated region of ZmHKT1 were found to be associated with six seedling traits. Eight variants in promoter region were significantly associated with average root diameter (ARD), four haplotypes were found based on these significant variants, and Hap2 has the largest ARD. Two SNPs in high-linkage disequilibrium (SNP-415 and SNP 2169) with pleiotropic effects were significantly associated with plant height, root surface area, root volume, and shoot dry weight. This result revealed that ZmHKT1 was an important contributor to the phenotypic variations of seedling root traits in maize, these significant variants could use to develop functional markers to improve root traits.

Multiple genomic regions influence root morphology and seedling growth in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited conditions

With climate change and an ever-increasing human population threatening food security, developing a better understanding of the genetic basis of crop performance under stressful conditions has become increasingly important. Here, we used genome-wide association studies to genetically dissect variation in seedling growth traits in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited (i.e., osmotic stress) conditions, with a particular focus on root morphology. Water limitation reduced seedling size and produced a shift toward deeper rooting. These effects varied across genotypes, and we identified 13 genomic regions that were associated with traits of interest across the two environments. These regions varied in size from a single marker to 186.2 Mbp and harbored numerous genes, some of which are known to be involved in the plant growth/development as well as the response to osmotic stress. In many cases, these associations corresponded to growth traits where the common allele outperformed the rare variant, suggesting that selection for increased vigor during the evolution of cultivated sunflower might be responsible for the relatively high frequency of these alleles. We also found evidence of pleiotropy across multiple traits, as well as numerous environmentally independent genetic effects. Overall, our results indicate the existence of genetic variation in root morphology and allocation and further suggest that the majority of alleles associated with these traits have consistent effects across environments.