The genetic architecture of nodal root number in maize

Breeding maize of ideal plant architecture for high-density planting tolerance through modulating shade avoidance response and beyond

Maize is a major staple crop widely used as food, animal feed, and raw materials in industrial production. High-density planting is a major factor contributing to the continuous increase of maize yield. However, high planting density usually triggers a shade avoidance response and causes increased plant height and ear height, resulting in lodging and yield loss. Reduced plant height and ear height, more erect leaf angle, reduced tassel branch number, earlier flowering, and strong root system architecture are five key morphological traits required for maize adaption to high-density planting. In this review, we summarize recent advances in deciphering the genetic and molecular mechanisms of maize involved in response to high-density planting. We also discuss some strategies for breeding advanced maize cultivars with superior performance under high-density planting conditions.

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.

Effects of different fertilization practices on maize yield, soil nutrients, soil moisture, and water use efficiency in northern China based on a meta-analysis

The application of fertilizer to ensure the steady improvement of crop yield has become the main means of agricultural production. However, it remains to be determined whether fertilization practices with different combinations of nitrogen (N), phosphorus (P), potassium (K), and organic (O) fertilizers play a positive role in the sustainability of maize yield and the soil in which it is grown. Therefore,this meta-analysis extracted 2663 data points from 76 studies to systematically analyze and explore the effects of different fertilization measures on maize yield, soil nutrients, water content and water use efficiency (WUE) in northern China. Articles addressing this topic showed that fertilization effectively increased the soil nutrient content and maize yield. The soil organic matter (SOM) increased by 2.36 (N)-55.38% (NPO), total nitrogen content increased by 6.10 (N)-56.39% (NPO), available phosphorus content increased by 17.12 (N)-474.74% (NPO), and available potassium content changed by - 2.90 (NP)-64.40% (NPO). Soil moisture increased by 3.59% under a single organic fertilizer application and decreased by 4.27-13.40% under the other treatments. Compared with no fertilization, the yield increase of fertilized maize reached 11.65-220.42%. NP, NPK and NPKO contributed the most to increased yield in lithological, black and fluvo-aquic soils, respectively. The effects of different fertilization practices on maize yield varied in response to the same meteorological factors. The WUE increased from 9.51 to 160.72%. In conclusion, rational fertilization can improve the soil nutrient content and increase maize yield. The combined application of chemical and organic fertilizer showed the greatest increase in yield and WUE. Organic fertilizer application alone increased soil moisture. Our results provide a theoretical basis for fertilizer application and for improving the soil structure for maize cultivation in northern China.

Identification of genetic and environmental factors influencing aerial root traits that support biological nitrogen fixation in sorghum

Plant breeding and genetics play a major role in the adaptation of plants to meet human needs. The current requirement to make agriculture more sustainable can be partly met by a greater reliance on biological nitrogen fixation by symbiotic diazotrophic microorganisms that provide crop plants with ammonium. Select accessions of the cereal crop sorghum (Sorghum bicolor (L.) Moench) form mucilage-producing aerial roots that harbor nitrogen-fixing bacteria. Breeding programs aimed at developing sorghum varieties that support diazotrophs will benefit from a detailed understanding of the genetic and environmental factors contributing to aerial root formation. A genome-wide association study of the sorghum minicore, a collection of 242 landraces, and 30 accessions from the sorghum association panel was conducted in Florida and Wisconsin and under 2 fertilizer treatments to identify loci associated with the number of nodes with aerial roots and aerial root diameter. Sequence variation in genes encoding transcription factors that control phytohormone signaling and root system architecture showed significant associations with these traits. In addition, the location had a significant effect on the phenotypes. Concurrently, we developed F2 populations from crosses between bioenergy sorghums and a landrace that produced extensive aerial roots to evaluate the mode of inheritance of the loci identified by the genome-wide association study. Furthermore, the mucilage collected from aerial roots contained polysaccharides rich in galactose, arabinose, and fucose, whose composition displayed minimal variation among 10 genotypes and 2 fertilizer treatments. These combined results support the development of sorghums with the ability to acquire nitrogen via biological nitrogen fixation.

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.

Identifying yield-related genes in maize based on ear trait plasticity

BACKGROUND

Phenotypic plasticity is defined as the phenotypic variation of a trait when an organism is exposed to different environments, and it is closely related to genotype. Exploring the genetic basis behind the phenotypic plasticity of ear traits in maize is critical to achieve climate-stable yields, particularly given the unpredictable effects of climate change. Performing genetic field studies in maize requires development of a fast, reliable, and automated system for phenotyping large numbers of samples.

RESULTS

Here, we develop MAIZTRO as an automated maize ear phenotyping platform for high-throughput measurements in the field. Using this platform, we analyze 15 common ear phenotypes and their phenotypic plasticity variation in 3819 transgenic maize inbred lines targeting 717 genes, along with the wild type lines of the same genetic background, in multiple field environments in two consecutive years. Kernel number is chosen as the primary target phenotype because it is a key trait for improving the grain yield and ensuring yield stability. We analyze the phenotypic plasticity of the transgenic lines in different environments and identify 34 candidate genes that may regulate the phenotypic plasticity of kernel number.

CONCLUSIONS

Our results suggest that as an integrated and efficient phenotyping platform for measuring maize ear traits, MAIZTRO can help to explore new traits that are important for improving and stabilizing the yield. This study indicates that genes and alleles related with ear trait plasticity can be identified using transgenic maize inbred populations.

Genetic and Hormonal Blueprint of Shoot-Borne Adventitious Root Development in Rice and Maize

The evolution of root architecture in plants was a prerequisite for the absorption of water and minerals from the soil, and thus a major determinant of terrestrial plant colonization. Cereals have a remarkably complex root system consisting of embryonic primary roots and post-embryonic lateral roots and shoot-borne adventitious roots. Among grass species, rice adventitious roots (also called crown roots) are developed from compressed nodes at the stem base, whereas in maize, besides crown roots, several aboveground brace roots are also formed, thus adventitious root types display species-specific diversity. Despite being the backbone for the adult root system in monocots, adventitious roots are the least studied of all the plant organs. In recent times, molecular genetics, genomics and proteomics-based approaches have been utilized to dissect the mechanism of post-embryonic meristem formation and tissue patterning. Adventitious root development is a cumulative effect of the actions and interactions of crucial genetic and hormonal regulators. In this review, we provide a comprehensive view of the key regulators involved during the different stages of adventitious root development in two important crop plants, rice and maize. We have reviewed the roles of major phytohormones, microRNAs and transcription factors and their crosstalk during adventitious root development in these cereal crops.

ZmCCT10-relayed photoperiod sensitivity regulates natural variation in the arithmetical formation of male germinal cells in maize

Extensive mutational screening studies have documented genes regulating anther and pollen development. Knowledge concerning how formation of male germinal cell is arithmetically controlled in natural populations, under different environmental conditions, is lacking. We counted pollen number within a single anther and a maize-teosinte BC₂ S₃ recombinant inbred line population to identify ZmCCT10 as a major determinant of pollen number variation. ZmCCT10 was originally identified as a photoperiod-sensitive negative regulator of flowering. ZmCCT10 inactivation, after transposon insertion within its promoter, is proposed to have accelerated maize spread toward higher latitudes, thus allowing temperate maize to flower under long-day conditions. We showed that the active ZmCCT10 allele decreased pollen formation. As different active and inactive ZmCCT10 alleles have been found in natural maize populations, this represents the first report of a gene controlling pollen number in a crop natural population. These findings suggest that higher pollen number, which provides a competitive advantage in open-pollinated populations, may have been one of the major driving forces for the selection of an inactive ZmCCT10 allele during tropical maize domestication. We provide evidence that ZmCCT10 has opposite effects on cell proliferation of archesporial and tapetum cells and it modulates expression of key regulators during early anther development.

Exogenous brassinosteroids promotes root growth, enhances stress tolerance, and increases yield in maize

Brassinosteroids (BRs) regulate of maize (Zea mays L.) growth, but the underlying molecular mechanism remains unclear. In this study, we used a multi-disciplinary approach to determine how BRs regulate maize morphology and physiology during development. Treatment with the BRs promoted primary root the elongation and growth during germination, and the early development of lateral roots. BRs treatment during the middle growth stage increased the levels of various stress resistance factors, and enhanced resistance to lodging, likely by protecting the plant against stem rot and sheath rot. BRs had no significant effect on plant height during late growth, but it increased leaf angle and photosynthetic efficiency, as well as yield and quality traits. Our findings increase our understanding of the regulatory effects of BR on maize root growth and development and the mechanism by which BR improves disease resistance, which could further the potential for using BR to improve maize yield.

QTL analyses of soybean root system architecture revealed genetic relationships with shoot-related traits

The genetic basis of soybean root system architecture (RSA) and the genetic relationship between shoot and RSA were revealed by integrating data from recombinant inbred population grafting and QTL mapping. Variations in root system architecture (RSA) affect the functions of roots and thus play vital roles in plant adaptations and agricultural productivity. The aim of this study was to unravel the genetic relationship between RSA traits and shoot-related traits in soybean. This study characterized RSA variability at seedling stage in a recombinant inbred population, derived from a cross between cultivated soybean C08 and wild soybean W05, and performed high-resolution quantitative trait locus (QTL) mapping. In total, 34 and 41 QTLs were detected for RSA-related and shoot-related traits, respectively, constituting eight QTL clusters. Significant QTL correspondence was found between shoot biomass and RSA-related traits, consistent with significant correlations between these phenotypes. RSA-related QTLs also overlapped with selection regions in the genome, suggesting the cultivar RSA could be a partial consequence of domestication. Using reciprocal grafting, we confirmed that shoot-derived signals affected root development and the effects were controlled by multiple loci. Meanwhile, RSA-related QTLs were found to co-localize with four soybean flowering-time loci. Consistent with the phenotypes of the parental lines of our RI population, diminishing the function of flowering controlling E1 family through RNA interference (RNAi) led to reduced root growth. This implies that the flowering time-related genes within the RSA-related QTLs are actually contributing to RSA. To conclude, this study identified the QTLs that determine RSA through controlling root growth indirectly via regulating shoot functions, and discovered superior alleles from wild soybean that could be used to improve the root structure in existing soybean cultivars.

Integrating advancements in root phenotyping and genome-wide association studies to open the root genetics gateway

Plant adaptation to challenging environmental conditions around the world has made root growth and development an important research area for plant breeders and scientists. Targeted manipulation of root system architecture (RSA) to increase water and nutrient use efficiency can minimize the adverse effects of climate change on crop production. However, phenotyping of RSA is a major bottleneck since the roots are hidden in the soil. Recently the development of 2- and 3D root imaging techniques combined with the genome-wide association studies (GWASs) have opened up new research tools to identify the genetic basis of RSA. These approaches provide a comprehensive understanding of the RSA, by accelerating the identification and characterization of genes involved in root growth and development. This review summarizes the latest developments in phenotyping techniques and GWAS for RSA, which are used to map important genes regulating various aspects of RSA under varying environmental conditions. Furthermore, we discussed about the state-of-the-art image analysis tools integrated with various phenotyping platforms for investigating and quantifying root traits with the highest phenotypic plasticity in both artificial and natural environments which were used for large scale association mapping studies, leading to the identification of RSA phenotypes and their underlying genetics with the greatest potential for RSA improvement. In addition, challenges in root phenotyping and GWAS are also highlighted, along with future research directions employing machine learning and pan-genomics approaches.

Genome-wide association study reveals the genetic basis of brace root angle and diameter in maize

Brace roots are the main organ to support the above-ground part of maize plant. It involves in plant growth and development by water absorption and lodging resistance. The bracing root angle (BRA) and diameter (BRD) are important components of brace root traits. Illuminating the genetic basis of BRA and BRD will contribute the improvement for mechanized harvest and increasing production. A GWAS of BRA and BRD was conducted using an associated panel composed of 508 inbred lines of maize. The broad-sense heritability of BRA and BRD was estimated to be respectively 71% ± 0.19 and 52% ± 0.14. The phenotypic variation of BRA and BRD in the non-stiff stalk subgroup (NSS) and the stiff stalk subgroup (SS) subgroups are significantly higher than that in the tropical/subtropical subgroup (TST) subgroups. In addition, BRA and BRD are significantly positive with plant height (PH), ear length (EL), and kernel number per row (KNPR). GWAS revealed 27 candidate genes within the threshold of p < 1.84 × 10⁻⁶ by both MLM and BLINK models. Among them, three genes, GRMZM2G174736, GRMZM2G445169 and GRMZM2G479243 were involved in cell wall function, and GRMZM2G038073 encoded the NAC transcription factor family proteins. These results provide theoretical support for clarifying the genetic basis of brace roots traits.

Teosinte confers specific alleles and yield potential to maize improvement

Teosinte improves maize grain yield and broadens the maize germplasm. Seventy-one quantitative trait loci associated with 24 differential traits between maize and teosinte were identified. Maize is a major cereal crop with a narrow germplasm that has limited its production and breeding progress. Teosinte, an ancestor of maize, provides valuable genetic resources for maize breeding. To identify the favorable alien alleles in teosinte and its yield potential for maize breeding, 4 backcrossed maize-teosinte recombinant inbred line (RIL) populations were cultivated under five conditions. A North Carolina mating design II experiment was conducted on inbred lines with B73 and Mo17 pedigree backgrounds to analyze their combining ability. Abundant phenotypic variation on 26 traits of four RIL populations were found, of which barren tip length, kernel height, and test weight showed positive genetic improvement potential. The hybrid FM132 (BD138/MP116) showed a superior grain yield to that of the check, with an average yield gain of 4.86%. Moreover, inbred lines BD138 and MP048 showed a higher general grain yield combining ability than those of their corresponding checks. We screened 4,964,439 high-quality single-nucleotide polymorphisms in the BD (B73/Zea diploperennis) RIL population for bin construction and used 2322 bin markers for genetic map construction and quantitative trait loci (QTL) mapping. Via inclusive composite interval mapping, 71 QTL associated with 24 differential traits were identified. Gene annotation and transcriptional expression suggested that Zm00001eb352570 and Zm00001eb352580, both annotated as ethylene-responsive transcription factors, were key candidate genes that regulate ear height and the ratio of ear to plant height. Our results indicate that teosinte could broaden the narrow maize germplasm, improve yield potential, and provide desirable alleles for maize breeding.

Root system architecture for abiotic stress tolerance in potato: Lessons from plants

The root is an important plant organ, which uptakes nutrients and water from the soil, and provides anchorage for the plant. Abiotic stresses like heat, drought, nutrients, salinity, and cold are the major problems of potato cultivation. Substantial research advances have been achieved in cereals and model plants on root system architecture (RSA), and so root ideotype (e.g., maize) have been developed for efficient nutrient capture to enhance nutrient use efficiency along with genes regulating root architecture in plants. However, limited work is available on potatoes, with a few illustrations on root morphology in drought and nitrogen stress. The role of root architecture in potatoes has been investigated to some extent under heat, drought, and nitrogen stresses. Hence, this mini-review aims to update knowledge and prospects of strengthening RSA research by applying multi-disciplinary physiological, biochemical, and molecular approaches to abiotic stress tolerance to potatoes with lessons learned from model plants, cereals, and other plants.

ZmCCT haplotype H5 improves yield, stalk-rot resistance, and drought tolerance in maize

The ZmCCT locus underlies both stalk-rot resistance and photoperiod sensitivity in maize (Zea mays L.). We previously introduced nine resistant ZmCCT haplotypes into seven elite but susceptible maize inbred lines (containing the haplotype H1) to generate 63 backcross families. Here, we continued backcrossing, followed by selfing, to develop 63 near-isogenic lines (NILs). We evaluated 22 of these NILs for stalk-rot resistance and flowering time under long-day conditions. Lines harboring the haplotype H5 outperformed the others, steadily reducing disease severity, while showing less photoperiod sensitivity. To demonstrate the value of haplotype H5 for maize production, we selected two pairs of NILs, 83B28 ^H1 /83B28 ^H5 and A5302 ^H1 /A5302 ^H5 , and generated F₁ hybrids with the same genetic backgrounds but different ZmCCT alleles: 83B28 ^H1 × A5302 ^H1 , 83B28 ^H1 × A5302 ^H5 , 83B28 ^H5 × A5302 ^H1 , and 83B28 ^H5 × A5302 ^H5 . We performed field trials to investigate yield/yield-related traits, stalk-rot resistance, flowering time, and drought/salt tolerance in these four hybrids. 83B28 ^H5 × A5302 ^H1 performed the best, with significantly improved yield, stalk-rot resistance, and drought tolerance compared to the control (83B28 ^H1 × A5302 ^H1 ). Therefore, the ZmCCT haplotype H5 has great value for breeding maize varieties with high yield potential, stalk-rot resistance, and drought tolerance.

A Genome-Wide Association Study Dissects the Genetic Architecture of the Metaxylem Vessel Number in Maize Brace Roots

Metaxylem vessels in maize brace roots are key tissue, and their number (MVN) affects plant water and inorganic salt transportation and lodging resistance. Dissecting the genetic basis of MVN in maize brace roots can help guide the genetic improvement of maize drought resistance and lodging resistance during late developmental stages. In this study, we used 508 inbred lines with tropical, subtropical, and temperate backgrounds to analyze the genetic architecture of MVN in maize brace roots. The phenotypic variation in MVN in brace roots was evaluated in three environments, which revealed broad natural variation and relative low levels of heritability (h ² = 0.42). Stiff-stalk lines with a temperate background tended to have higher MVNs than plants in other genetic backgrounds. MVN was significantly positively correlated with plant height, tassel maximum axis length, ear length, and kernel number per row, which indicates that MVN may affect plant morphological development and yield. In addition, MVN was extremely significantly negatively correlated with brace root radius, but significantly positively correlated with brace root angle (BRA), diameter, and number, thus suggesting that the morphological function of some brace root traits may be essentially determined by MVN. Association analysis of MVN in brace roots combined 1,253,814 single nucleotide polymorphisms (SNPs) using FarmCPU revealed a total of nine SNPs significantly associated with MVN at P < 7.96 × 10^-7. Five candidate genes for MVN that may participate in secondary wall formation (GRMZM2G168365, GRMZM2G470499, and GRMZM2G028982) and regulate flowering time (GRMZM2G381691 and GRMZM2G449165). These results provide useful information for understanding the genetic basis of MVN in brace root development. Further functional studies of identified candidate genes should help elucidate the molecular pathways that regulate MVN in maize brace roots.

Deconstructing the root system of grasses through an exploration of development, anatomy and function

Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.

A gene regulatory network for tiller development mediated by Tin8 in maize

The complex gene regulatory network underlying tiller development in maize remains largely unknown. Here we identified two major quantitative trait loci for tiller number, Tin8 on chromosome 8 and the previously known Tb1 on chromosome 1, in a population derived from a teosinte-maize cross. Map-based cloning and association mapping revealed that Tin8, corresponding to Zcn8 encoding a phosphatidylethanolamine-binding-related kinase, is down-regulated in transcription, which results in decreased tiller number. A strong interaction between Tin8 and the key gen Tb1 was detected for tiller number. Further RNA-seq analysis showed that the expression of 13 genes related to tiller development was controlled by Tin8. Our results support the existence of a complex gene regulatory network for the outgrowth of the tiller bud in maize, in which Zcn8 controls 13 tiller-related genes, including four genes for hormonal responses. In particular, Zcn8 represses Gt1, D14, and Tru1 through the interaction with Tb1.

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.

Analyses of open-access multi-omics data sets reveal genetic and expression characteristics of maize ZmCCT family genes

Flowering in maize (Zea mays) is influenced by photoperiod. The CO, CO-like/COL and TOC1 (CCT) domain protein-encoding genes in maize, ZmCCTs, are particularly important for photoperiod sensitivity. However, little is known about CCT protein-encoding gene number across plant species or among maize inbred lines. Therefore, we analysed CCT protein-encoding gene number across plant species, and characterized ZmCCTs in different inbred lines, including structural variations (SVs), copy number variations (CNVs), expression under stresses, dark-dark (DD) and dark-light (DL) cycles, interaction network and associations with maize quantitative trait loci (QTLs) by referring to the latest v4 genome data of B73. Gene number varied greatly across plant species, more in polyploids than in diploids. The numbers of ZmCCTs identified were 58 in B73, 59 in W22, 48 in Mo17, and 57 in Huangzao4 for temperate maize inbred lines, and 68 in tropical maize inbred line SK. Some ZmCCTs underwent duplications and presented chromosome collinearity. Structural variations and CNVs were found but they had no germplasm specificity. Forty-two ZmCCTs responded to stresses. Expression of 37 ZmCCTs in embryonic leaves during seed germination of maize under DD and DL cycles was roughly divided into five patterns of uphill pattern, downhill-pattern, zigzag-pattern, └-pattern and ⅃-pattern, indicating some of them have a potential to perceive dark and/or dark-light transition. Thirty-three ZmCCTs were co-expressed with 218 other maize genes; and 24 ZmCCTs were associated with known QTLs. The data presented in this study will help inform further functions of ZmCCTs.

Opposite response of maize ZmCCT to photoperiod due to transposon jumping

The new 4.2-kb transposable insertion in the intron of ZmCCT reversely responded relative to the known 5.1-kb transposable insertion to photoperiods between low- and high-latitude regions. Flowering time is a key trait for cereal adaptation that is controlled by a complex genetic background in maize. The effect of multiple alleles from a quantitative trait locus (QTL) on flowering time remains largely unknown. Here, we fine-mapped a major QTL for flowering time on maize chromosome 10 corresponding to ZmCCT, where a new allele with a 4.2-kilobase (kb) transposable insertion was present in the intron. The known allele with a 5.1-kb transposon insertion in the promoter of ZmCCT enhances flowering in high-latitude regions, but has no effect on flowering time in low-latitude regions in comparison with the null allele lacking this insertion. However, our new allele with a 4.2-kb insertion reduced flowering in the low-latitude region, but produced unchanged flowering time in the high-latitude region relative to the 5.1-kb transposable insertion. Transcription analysis revealed that the new allele with 4.2-kb insertion versus the 5.1-kb insertion repressed and unchanged the transcription of ZmCCT in the low- and high-latitude regions, respectively. Thus, the allele with the 4.2-kb transposable insertion showed a completely opposite response to photoperiods between these two regions. Phylogenetic analysis revealed that the 4.2-kb transposable insertion in the two Northern flint corns originated from tropical maize. RNA-seq analysis and dual-luciferase transient expression assays further identified a conserved gene regulation network of ZmCCT between maize and rice, in which ZmCCT directly repressed the transcription of the florigen gene ZCN8 via ZmEhd1. Our results suggest that transposable elements play an important role in maize adaptation.

Use of Transcriptomic Analyses to Elucidate the Mechanism Governing Nodal Root Development in Eremochloa ophiuroides (Munro) Hack

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] is a perennial warm-season grass that originated in China, and its speed of nodal rooting is important for lawn establishment. In our study, centipedegrass nodal rooting ability was limited by node aging. Transcriptome sequencing of nodal roots after 0, 2, 4, and 8 days of water culture was performed to investigate the molecular mechanisms of root development. GO enrichment and KEGG pathway analyses of DEGs indicated that plant hormone signal transduction and transcription factors might play important roles in centipedegrass nodal root growth. Among them, E3 ubiquitin-protein ligases participated in multiple hormone signal transduction pathways and interacted with transcription factors. Furthermore, an E3 ubiquitin protein ligase EoSINAT5 overexpressed in rice resulted in longer roots and more numerous root tips, while knockout of LOC_Os07g46560 (the homologous gene of EoSINAT5 in rice) resulted in shorter roots and fewer root tips. These results indicated that EoSINAT5 and its homologous gene are able to promote nodal root development. This research presents the transcriptomic analyses of centipedegrass nodal roots, and may contribute to elucidating the mechanism governing the development of nodal roots and facilitates the use of molecular breeding in improving rooting ability.

Genome-wide identification and function characterization of GATA transcription factors during development and in response to abiotic stresses and hormone treatments in pepper

Pepper (Capsicum annuum L.) is an economically important vegetable crop whose production and quality are severely reduced under adverse environmental stress conditions. The GATA transcription factors belonging to type IV zinc-finger proteins, play a significant role in regulating light morphogenesis, nitrate assimilation, and organ development in plants. However, the functional characteristics of GATA gene family during development and in response to environmental stresses have not yet been investigated in pepper. In this study, a total of 28 pepper GATA (CaGATA) genes were identified. To gain an overview of the CaGATAs, we analyzed their chromosomal distribution, gene structure, conservative domains, cis-elements, phylogeny, and evolutionary relationship. We divided 28 CaGATAs into four groups distributed on 10 chromosomes, and identified 7 paralogs in CaGATA family of pepper and 35 orthologous gene pairs between CaGATAs and Arabidopsis GATAs (AtGATAs). The results of promoter cis-element analysis and the quantitative real-time PCR (qRT-PCR) analysis revealed that CaGATA genes were involved in regulating the plant growth and development and the responses to various abiotic stresses and hormone treatments in pepper. Tissue-specific expression analysis showed that most CaGATA genes were preferentially expressed in flower buds, flowers, and leaves. Several CaGATA genes, especially CaGATA14, were significantly regulated under multiple abiotic stresses, and CaGATA21 and CaGATA27 were highly responsive to phytohormone treatments. Taken together, our results lay a foundation for the biological function analysis of GATA gene family in pepper.

Bracing for sustainable agriculture: the development and function of brace roots in members of Poaceae

Optimization of crop production requires root systems to function in water uptake, nutrient use, and anchorage. In maize, two types of nodal roots-subterranean crown and aerial brace roots function in anchorage and water uptake and preferentially express multiple water and nutrient transporters. Brace root development shares genetic control with juvenile-to-adult phase change and flowering time. We present a comprehensive list of the genes known to alter brace roots and explore these as candidates for QTL studies in maize and sorghum. Brace root development and function may be conserved in other members of Poaceae, however research is limited. This work highlights the critical knowledge gap of aerial nodal root development and function and suggests new focus areas for breeding resilient crops.

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.

Gravity Reduced Nitrogen Uptake via the Regulation of Brace Unilateral Root Growth in Maize Intercropping

Water, nutrient, light, and interspecific facilitation regulation of soil physicochemical properties and root morphology modulate nitrogen (N) uptake in cereal and legume intercropping systems. However, maize root morphological plasticity and N uptake capability response to gravity in the intercropping system remains to be determined. In this study, maize was grown under 20 cm (I₂₀), 40 cm (I₄₀), and 60 cm (I₆₀) of narrow row spacing in an intercropping system (maize-soybean strip relay intercropping) and equal row spacing of monoculture (M) in a 2-year field experiment. As a supplementary for the field experiment, maize root barrier and plant inclination experiments were conducted. Plant inclination, brace root morphology, N uptake, indole-3-acetic acid (IAA) level, IAA synthesis genes, and grain yield were assessed. The result showed that the plant inclination increased with decreasing narrow row spacing in intercropping system. Also, the brace unilateral root growth ratio (BURR) increased with increasing plant inclination in intercropping treatments. The plant inclination experiment showed the BURR achieved 94% after inclination at 45°. BURR tended to be positively correlated (p = 0.00) with plant inclination. Thus, gravity (plant inclination) causes brace unilateral root growth. The IAA concentration of stem nodes in the wide row increased with increasing plant inclination, while the IAA accumulation decreased in the narrow row. The Zmvt2 and ZM2G141383 genes (associated with IAA biosynthesis) were highly expressed in a wide row. There was a strong correlation (p = 0.03) between the IAA concentration of wide row and the BURR. Therefore, gravity regulates the IAA level, which affects BURR. In addition, the brace root number, volume, and surface area were decreased when BURR was increased. Subsequently, the leaf N, cob N, and kernel N accumulation were reduced. These organs N and grain yield in I₆₀ were not significantly different as compared to the control treatment. The excessive brace unilateral root growth was not conducive to N uptake and increased yield. Our results suggest that gravity is essential in regulating root morphology plasticity by regulating IAA levels and decreasing N uptake capacity. Furthermore, these results indicate that plant inclination can regulate root phenotype and N uptake of maize and by adjusting the spacing of narrow maize row, we can improve the N uptake and yield of the maize-soybean strip relay-intercropping system.

Maize brace roots provide stalk anchorage

Mechanical failure, known as lodging, negatively impacts yield and grain quality in crops. Limiting crop loss from lodging requires an understanding of the plant traits that contribute to lodging-resistance. In maize, specialized aerial brace roots are reported to reduce root lodging. However, their direct contribution to plant biomechanics has not been measured. In this manuscript, we use a non-destructive field-based mechanical test on plants before and after the removal of brace roots. This precisely determines the contribution of brace roots to establish a rigid base (i.e. stalk anchorage) that limits plant deflection in maize. These measurements demonstrate that the more brace root whorls that contact the soil, the greater their overall contribution to anchorage, but that the contributions of each whorl to anchorage were not equal. Previous studies demonstrated that the number of nodes that produce brace roots is correlated with flowering time in maize. To determine if flowering time selection alters the brace root contribution to anchorage, a subset of the Hallauer's Tusón tropical population was analyzed. Despite significant variation in flowering time and anchorage, selection neither altered the number of brace root whorls in the soil nor the overall contribution of brace roots to anchorage. These results demonstrate that brace roots provide a rigid base in maize and that the contribution of brace roots to anchorage was not linearly related to flowering time.

A combination of linkage mapping and GWAS brings new elements on the genetic basis of yield-related traits in maize across multiple environments

Using GWAS and QTL mapping identified 100 QTL and 138 SNPs, which control yield-related traits in maize. The candidate gene GRMZM2G098557 was further validated to regulate ear row number by using a segregation population. Understanding the genetic basis of yield-related traits contributes to the improvement of grain yield in maize. This study used an inter-mated B73 × Mo17 (IBM) Syn10 doubled-haploid (DH) population and an association panel to identify the genetic loci responsible for nine yield-related traits in maize. Using quantitative trait loci (QTL) mapping, 100 QTL influencing these traits were detected across different environments in the IBM Syn10 DH population, with 25 co-detected in multiple environments. Using a genome-wide association study (GWAS), 138 single-nucleotide polymorphisms (SNPs) were identified as correlated with these traits (P < 2.04E-06) in the association panel. Twenty-one pleiotropic QTL/SNPs were identified to control different traits in both populations. A combination of QTL mapping and GWAS uncovered eight significant SNPs (PZE-101097575, PZE-103169263, ZM011204-0763, PZE-104044017, PZE-104123110, SYN8062, PZE-108060911, and PZE-102043341) that were co-located within seven QTL confidence intervals. According to the eight co-localized SNPs by the two populations, 52 candidate genes were identified, among which the ear row number (ERN)-associated SNP SYN8062 was closely linked to SBP-transcription factor 7 (GRMZM2G098557). Several SBP-transcription factors were previously demonstrated to modulate maize ERN. We then validated the phenotypic effects of SYN8062 in the IBM Syn10 DH population, indicating that the ERN of the lines with the A-allele in SYN8062 was significantly (P < 0.05) larger than that of the lines with the G-allele in SYN8062 in each environment. These findings provide valuable information for understanding the genetic mechanisms of maize grain yield formation and for improving molecular marker-assisted selection for the high-yield breeding of maize.

Genome-wide sRNA and mRNA transcriptomic profiling insights into dynamic regulation of taproot thickening in radish (Raphanus sativus L.)

BACKGROUND

Taproot is the main edible organ and ultimately determines radish yield and quality. However, the precise molecular mechanism underlying taproot thickening awaits further investigation in radish. Here, RNA-seq was performed to identify critical genes involved in radish taproot thickening from three advanced inbred lines with different root size.

RESULTS

A total of 2606 differentially expressed genes (DEGs) were shared between 'NAU-DY' (large acicular) and 'NAU-YB' (medium obovate), which were significantly enriched in 'phenylpropanoid biosynthesis', 'glucosinolate biosynthesis', and 'starch and sucrose metabolism' pathway. Meanwhile, a total of 16 differentially expressed miRNAs (DEMs) were shared between 'NAU-DY' and 'NAU-YH' (small circular), whereas 12 miRNAs exhibited specific differential expression in 'NAU-DY'. Association analysis indicated that miR393a-bHLH77, miR167c-ARF8, and miR5658-APL might be key factors to biological phenomenon of taproot type variation, and a putative regulatory model of taproot thickening and development was proposed. Furthermore, several critical genes including SUS1, EXPB3, and CDC5 were characterized and profiled by RT-qPCR analysis.

CONCLUSION

This integrated study on the transcriptional and post-transcriptional profiles could provide new insights into comprehensive understanding of the molecular regulatory mechanism underlying taproot thickening in root vegetable crops.

CCT domain-containing genes in cereal crops: flowering time and beyond

The review summarizes the functions of the plant special transcription factors CCT family genes in multiple traits and discusses the molecular breeding strategies with CCT family genes in the future. Plants integrate circadian clock and external signals such as temperature and photoperiod to synchronize flowering with seasonal environmental changes. This process makes cereal crops including short-day crops, such as rice and maize, and long-day crops, such as wheat and barley, better adapt to varied growth zones from temperate to tropical regions. CCT family genes involve circadian clock and photoperiodic flowering pathways and help plants set a suitable flowering time to produce offspring. Beyond the flowering time, CCT family genes in cereal crops are associated with biomass and grain yield. Moreover, recent studies showed that they also associate with photosynthesis, nutrition use efficiency and stress tolerance. Here, we systematically review the progress in functional characterization of CCT family genes in flowering, geographical adaptation and grain yield formation, raise the core questions related to their molecular mechanisms and discuss how to practice them in genetic improvement in cereal crops by combining gene diagnosis and top-level design.

TeoNAM: A Nested Association Mapping Population for Domestication and Agronomic Trait Analysis in Maize

Recombinant inbred lines (RILs) are an important resource for mapping genes controlling complex traits in many species. While RIL populations have been developed for maize, a maize RIL population with multiple teosinte inbred lines as parents has been lacking. Here, we report a teosinte nested association mapping (TeoNAM) population, derived from crossing five teosinte inbreds to the maize inbred line W22. The resulting 1257 BC1S4 RILs were genotyped with 51,544 SNPs, providing a high-density genetic map with a length of 1540 cM. On average, each RIL is 15% homozygous teosinte and 8% heterozygous. We performed joint linkage mapping (JLM) and a genome-wide association study (GWAS) for 22 domestication and agronomic traits. A total of 255 QTL from JLM were identified, with many of these mapping near known genes or novel candidate genes. TeoNAM is a useful resource for QTL mapping for the discovery of novel allelic variation from teosinte. TeoNAM provides the first report that PROSTRATE GROWTH1, a rice domestication gene, is also a QTL associated with tillering in teosinte and maize. We detected multiple QTL for flowering time and other traits for which the teosinte allele contributes to a more maize-like phenotype. Such QTL could be valuable in maize improvement.

Maize with fewer nodal roots allocates mass to more lateral and deep roots that improve nitrogen uptake and shoot growth

Simulations indicated that reduced nodal root (NR) number (NRN) was promising for maize breeding, and were partially confirmed by relying on variation in NRN among inbreds. Using maize inbred line B73, experiments were conducted in hydroponics and tall mesocosms containing solid media with treatments involving no NR excision (0% NRE) or excising either 33% or 67% of the NRs as they emerged under high or low levels of nitrogen (N). Reduced NRN was hypothesized to increase elongation of all remaining root classes, N acquisition under low N, and shoot mass. Plants with 67% NRE had 12% and 19% less root mass fraction, 61% and 91% greater lateral to axial root length ratio regardless of N levels, and 61% and 182% greater biomass of embryonic roots under low N, compared with 0% NRE for hydroponics and mesocosms studies, respectively. Under low N in mesocosms, plants with 67% NRE had 52% greater shoot biomass, 450% greater root length at depth, and 232% greater deep-injected 15N content in the shoot relative to 0% NRE. These results reveal the mechanism by which plants with fewer NRs increase N capture and shoot mass by reallocation of biomass to lateral roots, embryonic roots, and first whorl NRs that increases foraging efficiency in solid media.

Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage

Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize.

Genetic Dissection of Root System Architectural Traits in Spring Barley

Breeding new crop cultivars with efficient root systems carries great potential to enhance resource use efficiency and plant adaptation to unstable climates. Here, we evaluated the natural variation of root system architectural traits in a diverse spring barley association panel and conducted genome-wide association mapping to identify genomic regions associated with root traits. For six studied traits, root system depth, root spreading angle, seminal root number, total seminal root length, and average seminal root length 1.9- to 4.2-fold variations were recorded. Using a mixed linear model, 55 QTLs were identified cumulatively explaining between 12.1% of the phenotypic variance for seminal root number to 48.1% of the variance for root system depth. Three major QTLs controlling root system depth, root spreading angle and total seminal root length were found on Chr 2H (56.52 cM), Chr 3H (67.92 cM), and Chr 2H (76.20 cM) and explained 12.4%, 18.4%, and 22.2% of the phenotypic variation, respectively. Meta-analysis and allele combination analysis indicated that root system depth and root spreading angle are valuable candidate traits for improving grain yield by pyramiding of favorable alleles.

ZmRAP2.7, an AP2 Transcription Factor, Is Involved in Maize Brace Roots Development

In maize, shoot-borne roots dominate the whole root system and play essential roles in water and nutrient acquisition and lodging tolerance. Shoot-borne roots initiate at shoot nodes, including crown roots from the belowground nodes and brace roots from aboveground nodes. In contrast to crown roots, few genes for brace roots development have been identified. Here, we characterized a maize AP2/ERF transcription factor, ZmRAP2.7, to be involved in brace roots development. ZmRAP2.7 expressed in all types of roots, and the encoded protein localized in the nucleus with transcriptional activation activity. A maize transposon insert mutant RAP2.7-Mu defective in ZmRAP2.7 expression revealed a decreased number of brace roots but not crown roots. Maize Corngrass1 mutant, which showed an elevated expression of ZmRAP2.7, however, revealed an increased number of brace roots. The ZmRAP2.7-based association analysis in a maize panel further identified a SNP marker at the fifth exon of gene to be associated with number of brace roots. These results uncovered a function of ZmRAP2.7 in brace roots development and provided the valuable gene and allele for genetic improvement of maize root systems.

Designer Roots for Future Crops

Despite the importance of roots, they have largely been ignored by modern crop research and breeding. We discuss important progress in crop root research and highlight how the context-dependent optimisation of below- and above-ground plant components provides opportunities to improve future crops in the face of increasing environmental fluctuations.

The Quantitative Genetic Control of Root Architecture in Maize

Roots remain an underexplored frontier in plant genetics despite their well-known influence on plant development, agricultural performance and competition in the wild. Visualizing and measuring root structures and their growth is vastly more difficult than characterizing aboveground parts of the plant and is often simply avoided. The majority of research on maize root systems has focused on their anatomy, physiology, development and soil interaction, but much less is known about the genetics that control quantitative traits. In maize, seven root development genes have been cloned using mutagenesis, but no genes underlying the many root-related quantitative trait loci (QTLs) have been identified. In this review, we discuss whether the maize mutants known to control root development may also influence quantitative aspects of root architecture, including the extent to which they overlap with the most recent maize root trait QTLs. We highlight specific challenges and anticipate the impacts that emerging technologies, especially computational approaches, may have toward the identification of genes controlling root quantitative traits.