Association mapping for root system architecture traits under two nitrogen conditions in germplasm enhancement of maize doubled haploid lines

Phenotypic and genome-wide association analyses for nitrogen use efficiency related traits in maize (Zea mays L.) exotic introgression lines

Nitrogen (N) limits crop production, yet more than half of N fertilizer inputs are lost to the environment. Developing maize hybrids with improved N use efficiency can help minimize N losses and in turn reduce adverse ecological, economical, and health consequences. This study aimed to identify single nucleotide polymorphisms (SNPs) associated with agronomic traits (plant height, grain yield, and anthesis to silking interval) under high and low N conditions. A genome-wide association study (GWAS) was conducted using 181 doubled haploid (DH) lines derived from crosses between landraces from the Germplasm Enhancement of Maize (BGEM lines) project and two inbreds, PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers. The same lines from the per se trials were used as parental lines for the testcross field trials. Plant height, anthesis to silking interval, and grain yield were collected from high and low N conditions in three environments for both per se and testcross trials. We used three GWAS models, namely, general linear model (GLM), mixed linear model (MLM), and Fixed and Random model Circulating Probability Unification (FarmCPU) model. We observed significant genetic variation among the DH lines and their derived testcrosses. Interestingly, some testcrosses of exotic introgression lines were superior under high and low N conditions compared to the check hybrid, PHB47/PHZ51. We detected multiple SNPs associated with agronomic traits under high and low N, some of which co-localized with gene models associated with stress response and N metabolism. The BGEM panel is, thus, a promising source of allelic diversity for genes controlling agronomic traits under different N conditions.

Hybrid performance evaluation and genome-wide association analysis of root system architecture in a maize association population

KEY MESSAGE

The genetic architecture of RSA traits was dissected by GWAS and coexpression networks analysis in a maize association population. Root system architecture (RSA) is a crucial determinant of water and nutrient uptake efficiency in crops. However, the maize genetic architecture of RSA is still poorly understood due to the challenges in quantifying root traits and the lack of dense molecular markers. Here, an association mapping panel including 356 inbred lines were crossed with a common tester, Zheng58, and the test crosses were phenotyped for 12 RSA traits in three locations. We observed a 1.3 ~ sixfold phenotypic variation for measured RSA in the association panel. The association panel consisted of four subpopulations, non-stiff stalk (NSS) lines, stiff stalk (SS), tropical/subtropical (TST), and mixed. Zheng58 × TST has a 2.1% higher crown root number (CRN) and 8.6% less brace root number (BRN) than Zheng58 × NSS and Zheng58 × SS, respectively. Using a genome-wide association study (GWAS) with 1.25 million SNPs and correction for population structure, 191 significant SNPs were identified for root traits. Ninety (47%) of the significant SNPs showed positive allelic effects, and 101 (53%) showed negative effects. Each locus could explain 0.39% to 11.8% of phenotypic variation. By integrating GWAS results and comparing coexpression networks, 26 high-priority candidate genes were identified. Gene GRMZM2G377215, which belongs to the COBRA-like gene family, affected root growth and development. Gene GRMZM2G468657 encodes the aspartic proteinase nepenthesin-1, related to root development and N-deficient response. Collectively, our research provides progress in the genetic dissection of root system architecture. These findings present the further possibility for the genetic improvement of root traits in maize.

Molecular dissection of heterosis in cereal roots and their rhizosphere

Heterosis is already manifested early in root development. Consistent with the dominance model of heterosis, gene expression complementation is a general mechanism that contributes to phenotypic heterosis in maize hybrids. Highly heterozygous F1-hybrids outperform their parental inbred lines, a phenomenon known as heterosis. Utilization of heterosis is of paramount agricultural importance and has been widely applied to increase yield in many crop cultivars. Plant roots display heterosis for many traits and are an important target for further crop improvement. To explain the molecular basis of heterosis, several genetic hypotheses have been proposed. In recent years, high-throughput gene expression profiling techniques have been applied to investigate hybrid vigor. Consistent with the classical genetic dominance model, gene expression complementation has been demonstrated to be a general mechanism to contribute to phenotypic heterosis in diverse maize hybrids. Functional classification of these genes supported the notion that gene expression complementation can dynamically promote hybrid vigor under fluctuating environmental conditions. Hybrids tend to respond differently to available nutrients in the soil. It was hypothesized that hybrid vigor is promoted through a higher nutrient use efficiency which is linked to an improved root system performance of hybrids in comparison to their inbred parents. Recently, the interaction between soil microbes and their plant host was added as further dimension to disentangle heterosis in the belowground part of plants. Soil microbes influenced the performance of maize hybrids as illustrated in comparisons of sterile soil and soil inhabited by beneficial microorganisms.

Genome-Wide Meta-Analysis of QTLs Associated with Root Traits and Implications for Maize Breeding

Root system architecture (RSA), also known as root morphology, is critical in plant acquisition of soil resources, plant growth, and yield formation. Many QTLs associated with RSA or root traits in maize have been identified using several bi-parental populations, particularly in response to various environmental factors. In the present study, a meta-analysis of QTLs associated with root traits was performed in maize using 917 QTLs retrieved from 43 mapping studies published from 1998 to 2020. A total of 631 QTLs were projected onto a consensus map involving 19,714 markers, which led to the prediction of 68 meta-QTLs (MQTLs). Among these 68 MQTLs, 36 MQTLs were validated with the marker-trait associations available from previous genome-wide association studies for root traits. The use of comparative genomics approaches revealed several gene models conserved among the maize, sorghum, and rice genomes. Among the conserved genomic regions, the ortho-MQTL analysis uncovered 20 maize MQTLs syntenic to 27 rice MQTLs for root traits. Functional analysis of some high-confidence MQTL regions revealed 442 gene models, which were then subjected to in silico expression analysis, yielding 235 gene models with significant expression in various tissues. Furthermore, 16 known genes viz., DXS2, PHT, RTP1, TUA4, YUC3, YUC6, RTCS1, NSA1, EIN2, NHX1, CPPS4, BIGE1, RCP1, SKUS13, YUC5, and AW330564 associated with various root traits were present within or near the MQTL regions. These results could aid in QTL cloning and pyramiding in developing new maize varieties with specific root architecture for proper plant growth and development under optimum and abiotic stress conditions.

Crop germplasm: Current challenges, physiological-molecular perspective, and advance strategies towards development of climate-resilient crops

Germplasm is a long-term resource management mission and investment for civilization. An estimated ∼7.4 million accessions are held in 1750 plant germplasm centres around the world; yet, only 2% of these assets have been utilized as plant genetic resources (PGRs). According to recent studies, the current food yield trajectory will be insufficient to feed the world's population in 2050. Additionally, possible negative effects in terms of crop failure because of climate change are already being experienced across the world. Therefore, it is necessary to reconciliation of research advancement and innovation of practices for further exploration of the potential of crop germplasm especially for the complex traits associated with yield such as water- and nitrogen use efficiency. In this review, we tried to address current challenges, research gaps, physiological and molecular aspects of two broad spectrum complex traits such as water- and nitrogen-use efficiency, and advanced integrated strategies that could provide a platform for combined stress management for climate-smart crop development. Additionally, recent development in technologies that are directly related to germplasm characterization was highlighted for further molecular utilization towards the development of elite varieties.

Combining datasets for maize root seedling traits increases the power of GWAS and genomic prediction accuracies

The identification of genomic regions associated with root traits and the genomic prediction of untested genotypes can increase the rate of genetic gain in maize breeding programs targeting roots traits. Here, we combined two maize association panels with different genetic backgrounds to identify single nucleotide polymorphisms (SNPs) associated with root traits, and used a genome-wide association study (GWAS) and to assess the potential of genomic prediction for these traits in maize. For this, we evaluated 377 lines from the Ames panel and 302 from the Backcrossed Germplasm Enhancement of Maize (BGEM) panel in a combined panel of 679 lines. The lines were genotyped with 232 460 SNPs, and four root traits were collected from 14-day-old seedlings. We identified 30 SNPs significantly associated with root traits in the combined panel, whereas only two and six SNPs were detected in the Ames and BGEM panels, respectively. Those 38 SNPs were in linkage disequilibrium with 35 candidate genes. In addition, we found higher prediction accuracy in the combined panel than in the Ames or BGEM panel. We conclude that combining association panels appears to be a useful strategy to identify candidate genes associated with root traits in maize and improve the efficiency of genomic prediction.

GWAS and RNA-seq analysis uncover candidate genes associated with alkaline stress tolerance in maize (Zea mays L.) seedlings

Soil salt-alkalization is a common yet critical environmental stress factor for plant growth and development. Discovering and exploiting genes associated with alkaline tolerance in maize (Zea mays L.) is helpful for improving alkaline resistance. Here, an association panel consisting of 200 maize lines was used to identify the genetic loci responsible for alkaline tolerance-related traits in maize seedlings. A total of nine single-nucleotide polymorphisms (SNPs) and their associated candidate genes were found to be significantly associated with alkaline tolerance using a genome-wide association study (GWAS). An additional 200 genes were identified when the screen was extended to include a linkage disequilibrium (LD) decay distance of r² ≥ 0.2 from the SNPs. RNA-sequencing (RNA-seq) analysis was then conducted to confirm the linkage between the candidate genes and alkali tolerance. From these data, a total of five differentially expressed genes (DEGs; |log2FC| ≥ 0.585, p < 0.05) were verified as the hub genes involved in alkaline tolerance. Subsequently, two candidate genes, Zm00001d038250 and Zm00001d001960, were verified to affect the alkaline tolerance of maize seedlings by qRT-PCR analysis. These genes were putatively involved protein binding and "flavonoid biosynthesis process," respectively, based on Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) enrichment analyses. Gene promoter region contains elements related to stress and metabolism. The results of this study will help further elucidate the mechanisms of alkaline tolerance in maize, which will provide the groundwork for future breeding projects.

Effects of ZmHIPP on lead tolerance in maize seedlings: Novel ideas for soil bioremediation

Extensive lead (Pb) absorption by plants affects their growth and development and causes damage to the human body by entering the food chain. In this study, we cloned ZmHIPP, a gene associated with Pb tolerance and accumulation in maize, using combined linkage mapping and weighted gene co-expression network analysis. We show that ZmHIPP, which encodes a heavy metal-associated isoprenylated plant protein, positively modulated Pb tolerance and accumulation in maize seedlings, Arabidopsis, and yeast. The genetic variation locus (A/G) in the promoter of ZmHIPP contributed to the phenotypic disparity in Pb tolerance among different maize inbred lines by altering the expression abundance of ZmHIPP. Knockdown of ZmHIPP significantly inhibited growth and decreased Pb accumulation in maize seedlings under Pb stress. ZmHIPP facilitated Pb deposition in the cell wall and prevented it from entering the intracellular organelles, thereby alleviating Pb toxicity in maize seedlings. Compared to that in the mutant zmhipp, the accumulated Pb in the wild-type line mainly consisted of the low-toxicity forms of Pb. Our study increases the understanding of the mechanism underlying Pb tolerance in maize and provides new insights into the bioremediation of Pb-polluted soil.

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

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

Joint GWAS and WGCNA uncover the genetic control of calcium accumulation under salt treatment in maize seedlings

Soil salinization is an important factor threatening the yield and quality of maize. Ca²⁺ plays a considerable role in regulating plant growth under salt stress. Herein, we examined the shoot Ca²⁺ concentrations, root Ca²⁺ concentrations, and transport coefficients of seedlings in an association panel composed of 305 maize inbred lines under normal and salt conditions. A genome-wide association study was conducted by using the investigated phenotypes and 46,408 single-nucleotide polymorphisms of the panel. As a result, 53 significant SNPs were specifically detected under salt treatment, and 544 genes were identified in the linkage disequilibrium regions of these SNPs. According to the expression data of the 544 genes, we carried out a weighted coexpression network analysis. Combining the enrichment analyses and functional annotations, four hub genes (GRMZM2G051032, GRMZM2G004314, GRMZM2G421669, and GRMZM2G123314) were finally determined, which were then used to evaluate the genetic variation effects by gene-based association analysis. Only GRMZM2G123314, which encodes a pentatricopeptide repeat protein, was significantly associated with Ca²⁺ transport and the haplotype G-CT was identified as the superior haplotype. Our study brings novel insights into the genetic and molecular mechanisms of salt stress response and contributes to the development of salt-tolerant varieties in maize.

Phenotyping seedlings for selection of root system architecture in alfalfa (Medicago sativa L.)

BACKGROUND

The root system architecture (RSA) of alfalfa (Medicago sativa L.) affects biomass production by influencing water and nutrient uptake, including nitrogen fixation. Further, roots are important for storing carbohydrates that are needed for regrowth in spring and after each harvest. Previous selection for a greater number of branched and fibrous roots significantly increased alfalfa biomass yield. However, phenotyping root systems of mature alfalfa plant is labor-intensive, time-consuming, and subject to environmental variability and human error. High-throughput and detailed phenotyping methods are needed to accelerate the development of alfalfa germplasm with distinct RSAs adapted to specific environmental conditions and for enhancing productivity in elite germplasm. In this study methods were developed for phenotyping 14-day-old alfalfa seedlings to identify measurable root traits that are highly heritable and can differentiate plants with either a branched or a tap rooted phenotype. Plants were grown in a soil-free mixture under controlled conditions, then the root systems were imaged with a flatbed scanner and measured using WinRhizo software.

RESULTS

The branched root plants had a significantly greater number of tertiary roots and significantly longer tertiary roots relative to the tap rooted plants. Additionally, the branch rooted population had significantly more secondary roots > 2.5 cm relative to the tap rooted population. These two parameters distinguishing phenotypes were confirmed using two machine learning algorithms, Random Forest and Gradient Boosting Machines. Plants selected as seedlings for the branch rooted or tap rooted phenotypes were used in crossing blocks that resulted in a genetic gain of 10%, consistent with the previous selection strategy that utilized manual root scoring to phenotype 22-week-old-plants. Heritability analysis of various root architecture parameters from selected seedlings showed tertiary root length and number are highly heritable with values of 0.74 and 0.79, respectively.

CONCLUSIONS

The results show that seedling root phenotyping is a reliable tool that can be used for alfalfa germplasm selection and breeding. Phenotypic selection of RSA in seedlings reduced time for selection by 20 weeks, significantly accelerating the breeding cycle.

Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use

Plant genebanks provide genetic resources for breeding and research programs worldwide. These programs benefit from having access to high-quality, standardized phenotypic and genotypic data. Technological advances have made it possible to collect phenomic and genomic data for genebank collections, which, with the appropriate analytical tools, can directly inform breeding programs. We discuss the importance of considering genebank accession homogeneity and heterogeneity in data collection and documentation. Citing specific examples, we describe how well-documented genomic and phenomic data have met or could meet the needs of plant genetic resource managers and users. We explore future opportunities that may emerge from improved documentation and data integration among plant genetic resource information systems.

GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings

KEYMESSAGE

Two hub genes GRMZM2G075104 and GRMZM2G333183 involved in salt tolerance were identified by GWAS and WGCNA. Furthermore, they were verified to affect salt tolerance by candidate gene association analysis. Salt stress influences maize growth and development. To decode the genetic basis and hub genes controlling salt tolerance is a meaningful exploration for cultivating salt-tolerant maize varieties. Herein, we used an association panel consisting of 305 lines to identify the genetic loci responsible for Na+- and K+-related traits in maize seedlings. Under the salt stress, seven significant single nucleotide polymorphisms were identified using a genome-wide association study, and 120 genes were obtained by scanning the linkage disequilibrium regions of these loci. According to the transcriptome data of the above 120 genes under salinity treatment, we conducted a weighted gene co-expression network analysis. Combined the gene annotations, two SNaC/SKC (shoot Na+ content/shoot K+ content)-associated genes GRMZM2G075104 and GRMZM2G333183 were finally identified as the hub genes involved in salt tolerance. Subsequently, these two genes were verified to affect salt tolerance of maize seedlings by candidate gene association analysis. Haplotypes TTGTCCG-CT and CTT were determined as favorable/salt-tolerance haplotypes for GRMZM2G075104 and GRMZM2G333183, respectively. These findings provide novel insights into genetic architectures underlying maize salt tolerance and contribute to the cultivation of salt-tolerant varieties in maize.

Identification and characterization of circRNAs in maize seedlings under deficient nitrogen

Here, deep sequencing results of the maize transcriptome in leaves and roots were compared under high-nitrogen (HN) and low-nitrogen (LN) conditions to identify differentially expressed circRNAs (DECs). Circular RNAs (circRNAs) are covalently closed non-coding RNA with widely regulatory potency that has been identified in animals and plants. However, the understanding of circRNAs involved in responsive nitrogen deficiency remains to be elucidated. A total of 24 and 22 DECs were obtained from the leaves and roots, respectively. Ten circRNAs were validated by divergent and convergent primers, and 6 DECs showed the same expression tendency validated by reverse transcriptase-quantitative PCR. Integrating the identified differentially expressed miRNAs, 34 circRNAs could act as miRNA decoys, which might play important roles in multiple biological processes, including organonitrogen compound biosynthesis and regulation of the metabolic process. A total of 51 circRNA-parent genes located in the genome-wide association study identified loci were assessed between HN and LN conditions and were associated with root growth and development. In summary, our results provide valuable information regarding further study of maize circRNAs under nitrogen deficiency and provide new insights into screening of candidate genes as well as the improvement of maize regarding nitrogen deficiency resistance. CircRNA-miRNA-mRNA co-expression networks were constructed to explore the circRNAs that participated in biological development and nitrogen metabolism.

GWAS with a PCA uncovers candidate genes for accumulations of microelements in maize seedlings

Microelements are necessary for plant growth and development, they control key processes of physiological metabolism. Herein, we evaluated three accumulation-related performances for each of the four microelements (Fe, Zn, Cu, and Mn) among 305 inbred maize lines. Quantification of these microelements in maize roots and shoots revealed abundant phenotypic variations in the association panel, with the variation coefficients ranging from 0.31 to 0.76. Principal component analysis (PCA) of the three related traits (concentration in root, concentration in shoot, and transport coefficient) showed that PC1 and PC2 explained >95% of phenotypic variations for each element. The scores of PC1 and PC2 were thereby used for a genome-wide association study by combining 44,134 SNPs of this panel. A total of 27, 1, 5, and 3 SNPs were significantly (P < .05) associated with Zn-PC1, Zn-PC2, Cu-PC1, and Mn-PC2, respectively, with 11 genes closely linked (r²  > 0.8) to these SNPs. Of them, GRMZM2G142870, GRMZM2G045531, and GRMZM2G143512 were individually annotated as ABC transporter C family member 14, zinc transporter 3, and heavy metal ATPase10. A candidate gene association analysis further verified that GRMZM2G142870 and GRMZM2G045531 affect Zn and Mn accumulations, respectively. Evaluation of contrasting allele ratios in elite lines indicated that the majority of the alleles correlating with higher Zn or Cu had not been utilized in maize breeding. Integration of more "higher-accumulation" alleles in the elite lines will be practical for improving Zn and Cu accumulations in maize. Our findings contribute to genetic revelation and molecular marker-assisted selection of microelement accumulations in maize.

Genetic dissection of maize seedling traits in an IBM Syn10 DH population under the combined stress of lead and cadmium

The heavy metals lead and cadmium have become important pollutants in the environment, which exert negative effects on plant morphology, growth and photosynthesis. It is particularly significant to uncover the genetic loci and the causal genes for lead and cadmium tolerance in plants. This study used an IBM Syn10 DH population to identify the quantitative trait loci (QTL) controlling maize seedling tolerance to lead and cadmium by linkage mapping. The broad-sense heritability of these seedling traits ranged from 65.8-97.3% and 32.0-98.8% under control (CK) and treatment (T) conditions, respectively. A total of 53 and 64 QTL were detected under CK and T conditions, respectively. Moreover, 42 QTL were identified using lead and cadmium tolerance coefficient (LCTC). Among these QTL, five and two major QTL that explained > 10% of phenotypic variation were identified under T condition and using LCTC, respectively. Furthermore, eight QTL were simultaneously identified by T and LCTC, explaining 5.23% to 9.21% of the phenotypic variations. Within these major and common QTL responsible for the combined heavy metal tolerance, four candidate genes (Zm00001d048759, Zm00001d004689, Zm00001d004843, Zm00001d033527) were previously reported to correlate with heavy metal transport and tolerance. These findings will contribute to functional gene identification and molecular marker-assisted breeding for improving heavy metal tolerance in maize.