The genetic architecture of maize stalk strength

The effect of testing rate on biomechanical measurements related to stalk lodging

BACKGROUND

Stalk lodging (the premature breaking of plant stalks or stems prior to harvest) is a persistent agricultural problem that causes billions of dollars in lost yield every year. Three-point bending tests, and rind puncture tests are common biomechanical measurements utilized to investigate crops susceptibility to lodging. However, the effect of testing rate on these biomechanical measurements is not well understood. In general, biological specimens (including plant stems) are well known to exhibit viscoelastic mechanical properties, thus their mechanical response is dependent upon the rate at which they are deflected. However, there is very little information in the literature regarding the effect of testing rate (aka displacement rate) on flexural stiffness, bending strength and rind puncture measurements of plant stems.

RESULTS

Fully mature and senesced maize stems and wheat stems were tested in three-point bending at various rates. Maize stems were also subjected to rind penetration tests at various rates. Testing rate had a small effect on flexural stiffness and bending strength calculations obtained from three-point bending tests. Rind puncture measurements exhibited strong rate dependent effects. As puncture rate increased, puncture force decreased. This was unexpected as viscoelastic materials typically show an increase in resistive force when rate is increased.

CONCLUSIONS

Testing rate influenced three-point bending test results and rind puncture measurements of fully mature and dry plant stems. In green stems these effects are expected to be even larger. When conducting biomechanical tests of plant stems it is important to utilize consistent span lengths and displacement rates within a study. Ideally samples should be tested at a rate similar to what they would experience in-vivo.

Genetic basis of maize stalk strength decoded via linkage and association mapping

Stalk lodging is a severe problem that limits maize production worldwide, although little attention has been given to its genetic basis. Here we measured rind penetrometer resistance (RPR), an effective index for stalk lodging, in a multi-parent population of 1948 recombinant inbred lines (RILs) and an association population of 508 inbred lines (AMP508). Linkage and association mapping identified 53 and 29 single quantitative trait loci (QTLs) and 50 and 19 pairs of epistatic interactions for RPR in the multi-parent population and AMP508 population, respectively. Phenotypic variation explained by all identified epistatic QTLs (up to ~5%) was much less than that explained by all single additive QTLs (up to ~33% in the multi-parent population and ~ 60% in the AMP508 population). Among all detected QTLs, only eight single QTLs explained >10% of phenotypic variation in single RIL populations. Alleles that increased RPR were enriched in tropical/subtropical (TST) groups from the AMP508 population. Based on genome-wide association studies in both populations, we identified 137 candidate genes affecting RPR, which were assigned to multiple biological processes, such as the biosynthesis of cell wall components. Sixty-six candidate genes were cross-validated by multiple methods or populations. Most importantly, 23 candidate genes were upregulated or downregulated in high-RPR lines relative to low-RPR lines, supporting the associations between candidate genes and RPR. These findings reveal the complex nature of the genetic basis underlying RPR and provide loci or candidate genes for developing elite varieties that are resistant to stalk lodging via molecular breeding.

Genome-Wide Association Study for Maize Hybrid Performance in a Typical Breeder Population

Maize is one of the major crops that has demonstrated success in the utilization of heterosis. Developing high-yield hybrids is a crucial part of plant breeding to secure global food demand. In this study, we conducted a genome-wide association study (GWAS) for 10 agronomic traits using a typical breeder population comprised 442 single-cross hybrids by evaluating additive, dominance, and epistatic effects. A total of 49 significant single nucleotide polymorphisms (SNPs) and 69 significant pairs of epistasis were identified, explaining 26.2% to 64.3% of the phenotypic variation across the 10 traits. The enrichment of favorable genotypes is significantly correlated to the corresponding phenotype. In the confident region of the associated site, 532 protein-coding genes were discovered. Among these genes, the Zm00001d044211 candidate gene was found to negatively regulate starch synthesis and potentially impact yield. This typical breeding population provided a valuable resource for dissecting the genetic architecture of yield-related traits. We proposed a novel mating strategy to increase the GWAS efficiency without utilizing more resources. Finally, we analyzed the enrichment of favorable alleles in the Shaan A and Shaan B groups, as well as in each inbred line. Our breeding practice led to consistent results. Not only does this study demonstrate the feasibility of GWAS in F1 hybrid populations, it also provides a valuable basis for further molecular biology and breeding research.

The 2020 derecho revealed limited overlap between maize genes associated with root lodging and root system architecture

Roots anchor plants in soil, and the failure of anchorage (i.e., root lodging) is a major cause of crop yield loss. Anchorage is often assumed to be driven by root system architecture. We made use of a natural experiment to measure the overlap between the genetic regulation of root system architecture and anchorage. After one of the most devastating derechos ever recorded in August 2020, we phenotyped root lodging in a maize (Zea mays) diversity panel consisting of 369 genotypes grown in six environments affected by the derecho. Genome-wide association studies and transcriptome-wide association studies identified 118 candidate genes associated with root lodging. Thirty-four percent (40/118) of these were homologs of genes from Arabidopsis (Arabidopsis thaliana) that affect traits such as root morphology and lignin content, expected to affect root lodging. Finally, Gene Ontology enrichment analysis of the candidate genes and their predicted interaction partners at the transcriptional and translational levels revealed the complex regulatory networks of physiological and biochemical pathways underlying root lodging in maize. Limited overlap between genes associated with lodging resistance and root system architecture in this diversity panel suggests that anchorage depends in part on factors other than gross characteristics of root system architecture.

Brown midrib mutant and genome-wide association analysis uncover lignin genes for disease resistance in maize

Brown midrib (BMR) maize (Zea mays L.) harbors mutations that result in lower lignin levels and higher feed digestibility, making it a desirable silage market class for ruminant nutrition. Northern leaf blight (NLB) epidemics in upstate New York highlighted the disease susceptibility of commercially grown BMR maize hybrids. We found the bm1, bm2, bm3, and bm4 mutants in a W64A genetic background to be more susceptible to foliar fungal (NLB, gray leaf spot [GLS], and anthracnose leaf blight [ALB]) and bacterial (Stewart's wilt) diseases. The bm1, bm2, and bm3 mutants showed enhanced susceptibility to anthracnose stalk rot (ASR), and the bm1 and bm3 mutants were more susceptible to Gibberella ear rot (GER). Colocalization of quantitative trait loci (QTL) and correlations between stalk strength and disease traits in recombinant inbred line families suggest possible pleiotropies. The role of lignin in plant defense was explored using high-resolution, genome-wide association analysis for resistance to NLB in the Goodman diversity panel. Association analysis identified 100 single and clustered single-nucleotide polymorphism (SNP) associations for resistance to NLB but did not implicate natural functional variation at bm1-bm5. Strong associations implicated a suite of diverse candidate genes including lignin-related genes such as a β-glucosidase gene cluster, hct11, knox1, knox2, zim36, lbd35, CASP-like protein 8, and xat3. The candidate genes are targets for breeding quantitative resistance to NLB in maize for use in silage and nonsilage purposes.

Elucidating the patterns of pleiotropy and its biological relevance in maize

Pleiotropy-when a single gene controls two or more seemingly unrelated traits-has been shown to impact genes with effects on flowering time, leaf architecture, and inflorescence morphology in maize. However, the genome-wide impact of biological pleiotropy across all maize phenotypes is largely unknown. Here, we investigate the extent to which biological pleiotropy impacts phenotypes within maize using GWAS summary statistics reanalyzed from previously published metabolite, field, and expression phenotypes across the Nested Association Mapping population and Goodman Association Panel. Through phenotypic saturation of 120,597 traits, we obtain over 480 million significant quantitative trait nucleotides. We estimate that only 1.56-32.3% of intervals show some degree of pleiotropy. We then assess the relationship between pleiotropy and various biological features such as gene expression, chromatin accessibility, sequence conservation, and enrichment for gene ontology terms. We find very little relationship between pleiotropy and these variables when compared to permuted pleiotropy. We hypothesize that biological pleiotropy of common alleles is not widespread in maize and is highly impacted by nuisance terms such as population structure and linkage disequilibrium. Natural selection on large standing natural variation in maize populations may target wide and large effect variants, leaving the prevalence of detectable pleiotropy relatively low.

Genetic architecture of protein and oil content in soybean seed and meal

Soybean is grown primarily for the protein and oil extracted from its seed and its value is influenced by these components. The objective of this study was to map marker-trait associations (MTAs) for the concentration of seed protein, oil, and meal protein using the soybean nested association mapping (SoyNAM) population. The composition traits were evaluated on seed harvested from over 5000 inbred lines of the SoyNAM population grown in 10 field locations across 3 years. Estimated heritabilities were at least 0.85 for all three traits. The genotyping of lines with single nucleotide polymorphism markers resulted in the identification of 107 MTAs for the three traits. When MTAs for the three traits that mapped within 5 cM intervals were binned together, the MTAs were mapped to 64 intervals on 19 of the 20 soybean chromosomes. The majority of the MTA effects were small and of the 107 MTAs, 37 were for protein content, 39 for meal protein, and 31 for oil content. For cases where a protein and oil MTAs mapped to the same interval, most (94%) significant effects were opposite for the two traits, consistent with the negative correlation between these traits. A coexpression analysis identified candidate genes linked to MTAs and 18 candidate genes were identified. The large number of small effect MTAs for the composition traits suggest that genomic prediction would be more effective in improving these traits than marker-assisted selection.

A simple method for lodging resistance evaluation of maize in the field

The increase of planting density is a dominant approach for the higher yield of maize. However, the stalks of some varieties are prone to lodging under high density conditions. Much research has been done on the evaluation of maize lodging resistance. But there are few comprehensive reports on the determination of maize lodging resistance in situ without injury under field conditions. This study introduces a non-destructive in situ tester to determine the lodging resistance of the different maize varieties in the field. The force value can be obtained by pulling the stalk to different angles with this instrument, which is used to evaluate the lodging resistance of maize varieties. From 2018 to 2020, a total of 1,172 sample plants from 113 maize varieties were tested for the lodging resistance of plants. The statistical results show that the values of force on maize plants at 45° inclination angles (F₄₅) are appropriate to characterize maize lodging resistance in situ by nondestructive testing in the field. According to the F₄₅ value, the maximum lodging resistance F_max can be inferred. The formula is: F_max =1.1354 F₄₅ - 0.3358. The evaluation results of lodging resistance of different varieties of this study are basically consistent with the test results of three-point bending method, moving wind tunnel and other methods. Therefore, the F₄₅ value is the optimal index for nondestructive evaluation of maize stalk-lodging resistance under the field-planting conditions.

Genetic structure and molecular mechanism underlying the stalk lodging traits in maize (Zea mays L.)

Stalk lodging seriously affects yield and quality of crops, and it can be caused by several factors, such as environments, developmental stages, and internal chemical components of plant stalks. Breeding of stalk lodging-resistant varieties is thus an important task for maize breeders. To better understand the genetic basis underlying stalk lodging resistance, several methods such as quantitative trait locus (QTL) mapping and genome-wide association study (GWAS) have been used to mine potential gene resources. Based on different types of genetic populations and mapping methods, many significant loci associated with stalk lodging resistance have been identified so far. However, few work has been performed to compare and integrate these reported genetic loci. In this study, we first collected hundreds of QTLs and quantitative trait nucleotides (QTNs) related to stalk lodging traits in maize. Then we mapped and integrated the QTLs and QTNs in maize genome to identify overlapped hotspot regions. Based on the genomic confidence intervals harboring these overlapped hotspot regions, we predicted candidate genes related to stalk lodging traits. Meanwhile, we mapped reported genes to these hotspot regions. Finally, we constructed molecular regulatory networks underlying stalk lodging resistance in maize. Collectively, this study provides not only useful genetic loci for deeply exploring molecular mechanisms of stalk lodging resistance traits, but also potential candidate genes and targeted strategies for improving stalk lodging resistance to increase crop yields in future.

A spatiotemporal transcriptomic network dynamically modulates stalk development in maize

Maize (Zea mays) is an important cereal crop with suitable stalk formation which is beneficial for acquiring an ideal agronomic trait to resist lodging and higher planting density. The elongation pattern of stalks arises from the variable growth of individual internodes driven by cell division and cell expansion comprising the maize stalk. However, the spatiotemporal dynamics and regulatory network of the maize stalk development and differentiation process remain unclear. Here, we report spatiotemporally resolved transcriptomes using all internodes of the whole stalks from developing maize at the elongation and maturation stages. We identified four distinct groups corresponding to four developmental zones and nine specific clusters with diverse spatiotemporal expression patterns among individual internodes of the stalk. Through weighted gene coexpression network analysis, we constructed transcriptional regulatory networks at a fine spatiotemporal resolution and uncovered key modules and candidate genes involved in internode maintenance, elongation, and division that determine stalk length and thickness in maize. Further CRISPR/Cas9-mediated knockout validated the function of a cytochrome P450 gene, ZmD1, in the regulation of stalk length and thickness as predicted by the WGCN. Collectively, these results provide insights into the high genetic complexity of stalk development and the potentially valuable resources with ideal stalk lengths and widths for genetic improvements in maize.

Identification of quantitative trait loci for related traits of stalk lodging resistance using genome-wide association studies in maize (Zea mays L.)

BACKGROUND

Stalk lodging is one of the main factors affecting maize (Zea mays L.) yield and limiting mechanized harvesting. Developing maize varieties with high stalk lodging resistance requires exploring the genetic basis of lodging resistance-associated agronomic traits. Stalk strength is an important indicator to evaluate maize lodging and can be evaluated by measuring stalk rind penetrometer resistance (RPR) and stalk buckling strength (SBS). Along with morphological traits of the stalk for the third internodes length (TIL), fourth internode length (FIL), third internode diameter (TID), and the fourth internode diameter (FID) traits are associated with stalk lodging resistance.

RESULTS

In this study, a natural population containing 248 diverse maize inbred lines genotyped with 83,057 single nucleotide polymorphism (SNP) markers was used for genome-wide association study (GWAS) for six stalk lodging resistance-related traits. The heritability of all traits ranged from 0.59 to 0.72 in the association mapping panel. A total of 85 significant SNPs were identified for the association mapping panel using best linear unbiased prediction (BLUP) values of all traits. Additionally, five candidate genes were associated with stalk strength traits, which were either directly or indirectly associated with cell wall components.

CONCLUSIONS

These findings contribute to our understanding of the genetic basis of maize stalk lodging and provide valuable theoretical guidance for lodging resistance in maize breeding in the future.

Characterization and Fine Mapping of qRPR1-3 and qRPR3-1, Two Major QTLs for Rind Penetrometer Resistance in Maize

Stalk strength is one of the most important traits in maize, which affects stalk lodging resistance and, consequently, maize harvestable yield. Rind penetrometer resistance (RPR) as an effective and reliable measurement for evaluating maize stalk strength is positively correlated with stalk lodging resistance. In this study, one F₂ and three F_2:3 populations derived from the cross of inbred lines 3705I (the low RPR line) and LH277 (the high RPR line) were constructed for mapping quantitative trait loci (QTL), conferring RPR in maize. Fourteen RPR QTLs were identified in four environments and explained the phenotypic variation of RPR from 4.14 to 15.89%. By using a sequential fine-mapping strategy based on the progeny test, two major QTLs, qRPR1-3 and qRPR3-1, were narrowed down to 4-Mb and 550-kb genomic interval, respectively. The quantitative real-time PCR (qRT-PCR) assay was adopted to identify 12 candidate genes responsible for QTL qRPR3-1. These findings should facilitate the identification of the polymorphism loci underlying QTL qRPR3-1 and molecular breeding for RPR in maize.

COMPILE: a GWAS computational pipeline for gene discovery in complex genomes

BACKGROUND

Genome-Wide Association Studies (GWAS) are used to identify genes and alleles that contribute to quantitative traits in large and genetically diverse populations. However, traits with complex genetic architectures create an enormous computational load for discovery of candidate genes with acceptable statistical certainty. We developed a streamlined computational pipeline for GWAS (COMPILE) to accelerate identification and annotation of candidate maize genes associated with a quantitative trait, and then matches maize genes to their closest rice and Arabidopsis homologs by sequence similarity.

RESULTS

COMPILE executed GWAS using a Mixed Linear Model that incorporated, without compression, recent advancements in population structure control, then linked significant Quantitative Trait Loci (QTL) to candidate genes and RNA regulatory elements contained in any genome. COMPILE was validated using published data to identify QTL associated with the traits of α-tocopherol biosynthesis and flowering time, and identified published candidate genes as well as additional genes and non-coding RNAs. We then applied COMPILE to 274 genotypes of the maize Goodman Association Panel to identify candidate loci contributing to resistance of maize stems to penetration by larvae of the European Corn Borer (Ostrinia nubilalis). Candidate genes included those that encode a gene of unknown function, WRKY and MYB-like transcriptional factors, receptor-kinase signaling, riboflavin synthesis, nucleotide-sugar interconversion, and prolyl hydroxylation. Expression of the gene of unknown function has been associated with pathogen stress in maize and in rice homologs closest in sequence identity.

CONCLUSIONS

The relative speed of data analysis using COMPILE allowed comparison of population size and compression. Limitations in population size and diversity are major constraints for a trait and are not overcome by increasing marker density. COMPILE is customizable and is readily adaptable for application to species with robust genomic and proteome databases.

Genetic Architecture of Maize Stalk Diameter and Rind Penetrometer Resistance in a Recombinant Inbred Line Population

Stalk lodging presents a major constraint on maize (Zea mays L.) quantity and quality and hampers mechanized grain harvesting. Stalk diameter (SD) and rind penetrometer resistance (RPR) are crucial indicators of stalk lodging. To dissect the genetic architecture of these indicators, we constructed a recombinant inbred line (RIL) population derived from a cross between maize inbred lines LDC-1 and YS501 to identify quantitative trait loci (QTLs) controlling SD and RPR. Corresponding phenotypes of basal second, third, and fourth internodes in four environments were determined. By integrating QTL mapping results based on individual environments and best linear unbiased prediction (BLUP) values, we identified 12, 12, and 13 QTLs associated with SD and 17, 14, and 17 associated with RPR. Each QTL accounted for 3.83–21.72% of phenotypic variation. For SD-related QTLs, 30 of 37 were enriched in 12 QTL clusters; similarly, RPR-related QTLs had 38 of 48 enriched in 12 QTL clusters. The stable QTL qSD9-2 for SD on chromosome 9 was validated and delimited within a physical region of 9.97 Mb. Confidence intervals of RPR-related QTLs contained 169 genes involved in lignin and polysaccharide biosynthesis, with 12 of these less than 500 kb from the peak of the corresponding QTL. Our results deepen our understanding of the genetic mechanism of maize stalk strength and provide a basis for breeding lodging resistance.

Asian corn borer damage is affected by rind penetration strength of corn stalks in a spatiotemporally dependent manner

Asian corn borer, Ostrinia furnacalis (Guenée), is an important insect pest of maize throughout most of Asia. The rind of a maize stalk is a key barrier against corn borer larvae boring into the plant. There is a need to better understand the relationship between stalk strength and O. furnacalis larval injury, particularly for elite maize genotypes. To determine whether stalk strength is involved in maize resistance to O. furnacalis larval injury, 39 maize lines were evaluated in 2012 and 2013. Rind penetration strength (RPS) was measured at tassel (VT) and milk (R3) stages as a possible stalk resistance trait for O. furnacalis. RPS of primary ear internode at VT and R3 accounted for 37 and 38% of the variance in O. furnacalis injury (measured as number of holes) for simulated (artificially infested) first and second generation O. furnacalis, respectively. Relationships between stalk RPS values and tunnel length were weak. Results suggest that harder stalks have enhanced resistance to stalk boring but not to pith feeding or tunneling of O. furnacalis larvae. The RPS measures could provide classical maize breeders an important tool for evaluating stalk strength and corn borer resistance in maize. The assessments should focus on the internodes primary ear or above/below primary ear during both VT stage for first generation and R3 stage for second generation O. furnacalis resistance.

QTL Identification for Stem Fiber, Strength and Rot Resistance in a DH Population from an Alien Introgression of Brassica napus

Stem fiber, stem strength and stem-rot resistance are important agronomic traits in Brassica napus. To understand the molecular mechanism that controls the stem-related traits, we investigated the stem lignin (ADL), cellulose (Cel), hemicellulose (Hem) content, S/G monolignol ratio (SG), stem breaking force (BF), breaking strength (F) and Sclerotinia sclerotiorum resistance (SSR). Each trait was significantly positively or negatively correlated with more than three of the other six traits. QTL mapping for ADL, Cel, Hem, SG, BF, F and SSR were performed using a doubled haploid population derived from an intertribal B. napus introgression line 'Y689' crossed with B. napus cv. 'Westar'. A total of 67 additive QTL were identified and integrated into 55 consensus QTL by meta-analysis. Among the 55 consensus QTL, 23 (41.8%) QTL were co-located and were integrated into 11 unique QTL. The QTL by environment (Q × E) interactions were analyzed and 22 combined QTL were identified. In addition, candidate genes within the QTL intervals were proposed based on the known function of Arabidopsis orthologs. These results provided valuable information for improving lodging resistance, S. sclerotiorum resistance and mechanized harvesting of B. napus.

Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize

Efficiently exploiting natural genetic diversity captured by accessions stored in genebanks is crucial to genetic improvement of major crops. Selecting accessions of interest from genebanks has traditionally required information from extensive and expensive evaluation; however, low-cost genotyping combined with genomic prediction have enabled us to generate predicted genetic merits for the entire set with targeted phenotypic evaluation of representative subsets. To explore this general approach, analytical assessment and empirical validation of the maize (Zea mays L.) association population (MAP) as a training population were conducted in the present study. Cross-validation within the MAP revealed mostly modest to strong predictive ability for 36 traits, generally in parallel with the square root of heritability. The MAP was then used to train the prediction models to generate genomic estimated breeding values (GEBVs) for the Ames Diversity Panel. Empirical validation conducted for nine traits across two validation populations confirmed the accuracy level indicated by the cross-validation of the training population. An upper bound for reliability (U value) was calculated for the accessions in the prediction population using genotypic data. The group of accessions with high U values generally had high predictive ability, even though the range of observed trait values was similar to the group of accessions with low U values. Our comprehensive analysis validated the general approach of turbocharging genebanks with genomics and genomic prediction. In addition, breeders and researchers can consider both GEBVs and U values to balance the needs of improving specific traits and broadening genetic diversity when selecting accessions from genebanks.

Genetic Architecture of Maize Rind Strength Revealed by the Analysis of Divergently Selected Populations

The strength of the stalk rind, measured as rind penetrometer resistance (RPR), is an important contributor to stalk lodging resistance. To enhance the genetic architecture of RPR, we combined selection mapping on populations developed by 15 cycles of divergent selection for high and low RPR with time-course transcriptomic and metabolic analyses of the stalks. Divergent selection significantly altered allele frequencies of 3,656 and 3,412 single- nucleotide polymorphisms (SNPs) in the high and low RPR populations, respectively. Surprisingly, only 110 (1.56%) SNPs under selection were common in both populations, while the majority (98.4%) were unique to each population. This result indicated that high and low RPR phenotypes are produced by biologically distinct mechanisms. Remarkably, regions harboring lignin and polysaccharide genes were preferentially selected in high and low RPR populations, respectively. The preferential selection was manifested as higher lignification and increased saccharification of the high and low RPR stalks, respectively. The evolution of distinct gene classes according to the direction of selection was unexpected in the context of parallel evolution and demonstrated that selection for a trait, albeit in different directions, does not necessarily act on the same genes. Tricin, a grass-specific monolignol that initiates the incorporation of lignin in the cell walls, emerged as a key determinant of RPR. Integration of selection mapping and transcriptomic analyses with published genetic studies of RPR identified several candidate genes including ZmMYB31, ZmNAC25, ZmMADS1, ZmEXPA2, ZmIAA41 and hk5. These findings provide a foundation for an enhanced understanding of RPR and the improvement of stalk lodging resistance.

Developmental genetics of maize vegetative shoot architecture

More than 1.1 billion tonnes of maize grain were harvested across 197 million hectares in 2019 (FAOSTAT 2020). The vast global productivity of maize is largely driven by denser planting practices, higher yield potential per area of land, and increased yield potential per plant. Shoot architecture, the three-dimensional structural arrangement of the above-ground plant body, is critical to maize grain yield and biomass. Structure of the shoot is integral to all aspects of modern agronomic practices. Here, the developmental genetics of the maize vegetative shoot is reviewed. Plant architecture is ultimately determined by meristem activity, developmental patterning, and growth. The following topics are discussed: shoot apical meristem, leaf architecture, axillary meristem and shoot branching, and intercalary meristem and stem activity. Where possible, classical and current studies in maize developmental genetics, as well as recent advances leveraged by "-omics" analyses, are highlighted within these sections.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01208-1.

A Multi-Locus Association Model Framework for Nested Association Mapping With Discriminating QTL Effects in Various Subpopulations

Nested association mapping (NAM) has been an invaluable approach for plant genetics community and can dissect the genetic architecture of complex traits. As the most popular NAM analysis strategy, joint multifamily mapping can combine all information from diverse genetic backgrounds and increase population size. However, it is influenced by the genetic heterogeneity of quantitative trait locus (QTL) across various subpopulations. Multi-locus association mapping has been proven to be powerful in many cases of QTL mapping and genome-wide association studies. Therefore, we developed a multi-locus association model of multiple families in the NAM population, which could discriminate the effects of QTLs in all subpopulations. A series of simulations with a real maize NAM genomic data were implemented. The results demonstrated that the new method improves the statistical power in QTL detection and the accuracy in QTL effect estimation. The new approach, along with single-family linkage mapping, was used to identify QTLs for three flowering time traits in the maize NAM population. As a result, most QTLs detected in single family linkage mapping were identified by the new method. In addition, the new method also mapped some new QTLs with small effects, although their functions need to be identified in the future.

Factors Influencing Genomic Prediction Accuracies of Tropical Maize Resistance to Fall Armyworm and Weevils

Genomic selection (GS) can accelerate variety improvement when training set (TS) size and its relationship with the breeding set (BS) are optimized for prediction accuracies (PAs) of genomic prediction (GP) models. Sixteen GP algorithms were run on phenotypic best linear unbiased predictors (BLUPs) and estimators (BLUEs) of resistance to both fall armyworm (FAW) and maize weevil (MW) in a tropical maize panel. For MW resistance, 37% of the panel was the TS, and the BS was the remainder, whilst for FAW, random-based training sets (RBTS) and pedigree-based training sets (PBTSs) were designed. PAs achieved with BLUPs varied from 0.66 to 0.82 for MW-resistance traits, and for FAW resistance, 0.694 to 0.714 for RBTS of 37%, and 0.843 to 0.844 for RBTS of 85%, and these were at least two-fold those from BLUEs. For PBTS, FAW resistance PAs were generally higher than those for RBTS, except for one dataset. GP models generally showed similar PAs across individual traits whilst the TS designation was determinant, since a positive correlation (R = 0.92***) between TS size and PAs was observed for RBTS, and for the PBTS, it was negative (R = 0.44**). This study pioneered the use of GS for maize resistance to insect pests in sub-Saharan Africa.

Maize Introgression Library Provides Evidence for the Involvement of liguleless1 in Resistance to Northern Leaf Blight

Plant disease resistance is largely governed by complex genetic architecture. In maize, few disease resistance loci have been characterized. Near-isogenic lines are a powerful genetic tool to dissect quantitative trait loci. We analyzed an introgression library of maize (Zea mays) near-isogenic lines, termed a nested near-isogenic line library for resistance to northern leaf blight caused by the fungal pathogen Setosphaeria turcica The population was comprised of 412 BC₅F₄ near-isogenic lines that originated from 18 diverse donor parents and a common recurrent parent, B73. Single nucleotide polymorphisms identified through genotyping by sequencing were used to define introgressions and for association analysis. Near-isogenic lines that conferred resistance and susceptibility to northern leaf blight were comprised of introgressions that overlapped known northern leaf blight quantitative trait loci. Genome-wide association analysis and stepwise regression further resolved five quantitative trait loci regions, and implicated several candidate genes, including Liguleless1, a key determinant of leaf architecture in cereals. Two independently-derived mutant alleles of liguleless1 inoculated with S. turcica showed enhanced susceptibility to northern leaf blight. In the maize nested association mapping population, leaf angle was positively correlated with resistance to northern leaf blight in five recombinant inbred line populations, and negatively correlated with northern leaf blight in four recombinant inbred line populations. This study demonstrates the power of an introgression library combined with high density marker coverage to resolve quantitative trait loci. Furthermore, the role of liguleless1 in leaf architecture and in resistance to northern leaf blight has important applications in crop improvement.

Genome-wide association studies and QTL mapping uncover the genetic architecture of ear tip-barrenness in maize

Ear tip-barrenness (ETB) phenotype threatens crop yield, because it reduces the kernel number per ear. The genetic basis of ETB in maize remains largely unknown. Herein, a genome-wide association study (GWAS) and quantitative trait loci (QTL) mapping were jointly applied to identify the significant genetic loci interrelated with ETB. Six significant SNPs were detected at a stringent P-value threshold (1.95 × 10^-6 ). Additionally, four environment-stable SNPs were co-detected across a single environment and best linear unbiased prediction (BLUP) model at a less stringent P-value threshold (1 × 10^-4 ). The above 10 SNPs were closely linked to 6 candidate genes, which mainly involved seed development, photosynthesis and ethylene response. Moreover, the ratio of superior allele at each significant SNP ranged from 0 to 83.33% in 30 investigated maize elite lines. QTL mapping identified 14 QTL with phenotypic variation explained (PVE) ranging from 3.64 to 7.09%, of which one QTL (qETB2-1) was repeatedly identified in two environments. Combined analysis of GWAS and QTL mapping showed that one SNP (PZE-102175229, chromosome 2: 217 66 Mb) was located in the QTL (qETB2-2, chromosome 2: 215 90-217 82 Mb). Eighteen gene models situated in the linkage disequilibrium (LD) region of the co-localized SNP were further used to evaluate their correlation with ETB by candidate gene association analysis. Two superior haplotypes and two superior alleles were detected among 74 lines for Zm00001d007195, Zm00001d007197 and Zm00001d007201. These results provide more information for clarifying the molecular mechanism of ETB and for speeding up the genetic improvement of maize varieties.

Field-based mechanical phenotyping of cereal crops to assess lodging resistance

Plant mechanical failure, also known as lodging, is the cause of significant and unpredictable yield losses in cereal crops. Lodging occurs in two distinct failure modes-stalk lodging and root lodging. Despite the prevalence and detrimental impact of lodging on crop yields, there is little consensus on how to phenotype plants in the field for lodging resistance and thus breed for mechanically resilient plants. This review provides an overview of field-based mechanical testing approaches to assess stalk and root lodging resistance. These approaches are placed in the context of future perspectives. Best practices and recommendations for acquiring field-based mechanical phenotypes of plants are also presented.

Breeding Maize Maternal Haploid Inducers

Maize doubled haploid (DH) lines are usually created in vivo, through crosses with maternal haploid inducers. These inducers have the inherent ability of generating seeds with haploid embryos when used to pollinate other genotypes. The resulting haploid plants are treated with a doubling agent and self-pollinated, producing completely homozygous seeds. This rapid method of inbred line production reduces the length of breeding cycles and, consequently, increases genetic gain. Such advantages explain the wide adoption of this technique by large, well-established maize breeding programs. However, a slower rate of adoption was observed in medium to small-scale breeding programs. The high price and/or lack of environmental adaptation of inducers available for licensing, or the poor performance of those free of cost, might explain why smaller operations did not take full advantage of this technique. The lack of adapted inducers is especially felt in tropical countries, where inducer breeding efforts are more recent. Therefore, defining optimal breeding approaches for inducer development could benefit many breeding programs which are in the process of adopting the DH technique. In this manuscript, we review traits important to maize maternal haploid inducers, explain their genetic basis, listing known genes and quantitative trait loci (QTL), and discuss different breeding approaches for inducer development. The performance of haploid inducers has an important impact on the cost of DH line production.

Genetic mapping and genomic selection for maize stalk strength

BACKGROUND

Maize is one of the most important staple crops and is widely grown throughout the world. Stalk lodging can cause enormous yield losses in maize production. However, rind penetrometer resistance (RPR), which is recognized as a reliable measurement to evaluate stalk strength, has been shown to be efficient and useful for improving stalk lodging-resistance. Linkage mapping is an acknowledged approach for exploring the genetic architecture of target traits. In addition, genomic selection (GS) using whole genome markers enhances selection efficiency for genetically complex traits. In the present study, two recombinant inbred line (RIL) populations were utilized to dissect the genetic basis of RPR, which was evaluated in seven growth stages.

RESULTS

The optimal stages to measure stalk strength are the silking phase and stages after silking. A total of 66 and 45 quantitative trait loci (QTL) were identified in each RIL population. Several potential candidate genes were predicted according to the maize gene annotation database and were closely associated with the biosynthesis of cell wall components. Moreover, analysis of gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway further indicated that genes related to cell wall formation were involved in the determination of RPR. In addition, a multivariate model of genomic selection efficiently improved the prediction accuracy relative to a univariate model and a model considering RPR-relevant loci as fixed effects.

CONCLUSIONS

The genetic architecture of RPR is highly genetically complex. Multiple minor effect QTL are jointly involved in controlling phenotypic variation in RPR. Several pleiotropic QTL identified in multiple stages may contain reliable genes and can be used to develop functional markers for improving the selection efficiency of stalk strength. The application of genomic selection to RPR may be a promising approach to accelerate breeding process for improving stalk strength and enhancing lodging-resistance.

Time-dependent mechanical behavior of sweet sorghum stems

Grasses represent the most productive and widely grown crop family across the globe but are susceptible to structural failure (lodging) during growth (e.g., from wind). The mechanisms that contribute to structural failure in grass stems are poorly understood due to a lack of systematic studies of their biomechanical behavior. To this end, this study examines the biomechanical properties of sweet sorghum (Sorghum bicolor (L.) Moench), focusing on the time-dependent behavior of the stems. Specifically, we conducted uniaxial compression tests under ramp and creep loading on pith and stem specimens of the sorghum cultivar Della. The tests demonstrated significantly nonlinear and time-dependent stress-strain behavior in all samples. We surmise that this behavior arises from a combination of poroelasticity due to migration of water through the plant and viscoelasticity due to rearrangement of macromolecular networks, such as cellulose microfibrils and lignin matrices. Overall, our measurements demonstrate that sorghum is not a simple reversible elastic material. As such, a complete understanding of the conditions that lead to stem lodging will require knowledge of sorghum's time-dependent biomechanical properties. Of practical importance, the time-dependent biomechanical properties of the stem influence its mechanical stability under various loading conditions during growth in the field (e.g., different wind speeds).

A Large Transposon Insertion in the stiff1 Promoter Increases Stalk Strength in Maize

Stalk lodging, which is generally determined by stalk strength, results in considerable yield loss and has become a primary threat to maize (Zea mays) yield under high-density planting. However, the molecular genetic basis of maize stalk strength remains unclear, and improvement methods remain inefficient. Here, we combined map-based cloning and association mapping and identified the gene stiff1 underlying a major quantitative trait locus for stalk strength in maize. A 27.2-kb transposable element insertion was present in the promoter of the stiff1 gene, which encodes an F-box domain protein. This transposable element insertion repressed the transcription of stiff1, leading to the increased cellulose and lignin contents in the cell wall and consequently greater stalk strength. Furthermore, a precisely edited allele of stiff1 generated through the CRISPR/Cas9 system resulted in plants with a stronger stalk than the unedited control. Nucleotide diversity analysis revealed that the promoter of stiff1 was under strong selection in the maize stiff-stalk group. Our cloning of stiff1 reveals a case in which a transposable element played an important role in maize improvement. The identification of stiff1 and our edited stiff1 allele pave the way for efficient improvement of maize stalk strength.

Ethephon-regulated maize internode elongation associated with modulating auxin and gibberellin signal to alter cell wall biosynthesis and modification

Ethephon efficiently regulates plant growth to modulate the maize (Zea mays L.) stalk strength and yield potential, yet there is little information on how ethylene governs a specific cellular response for altering internode elongation. Here, the internode elongation kinetics, cell morphological and physiological properties and transcript expression patterns were investigated in the ethephon-treated elongating internode. Ethephon decreased the internode elongation rate, shortened the effective elongation duration, and advanced the growth process. Ethephon regulated the expression patterns of expansin and secondary cell wall-associated cellulose synthase genes to alter cell size. Moreover, ethephon increased the activities and transcripts level of phenylalanine ammonia-lyase and peroxidase, which contributed to lignin accumulation. Otherwise, ethephon-boosted ethylene evolution activated ethylene signal and increased ZmGA2ox3 and ZmGA2ox10 transcript levels while down-regulating ZmPIN1a, ZmPIN4 and ZmGA3ox1 transcript levels, which led to lower accumulation of gibberellins and auxin. In addition, transcriptome profiles confirmed previous results and identified several transcription factors that are involved in the ethephon-modulated transcriptional regulation of cell wall biosynthesis and modification and responses to ethylene, gibberellins and auxin. These results indicated that ethylene-modulated auxin and gibberellins signaling mediated the transcriptional operation of cell wall modification to regulate cell elongation in the ethephon-treated maize internode.

Single-plant GWAS coupled with bulk segregant analysis allows rapid identification and corroboration of plant-height candidate SNPs

BACKGROUND

Genome wide association studies (GWAS) are a powerful tool for identifying quantitative trait loci (QTL) and causal single nucleotide polymorphisms (SNPs)/genes associated with various important traits in crop species. Typically, GWAS in crops are performed using a panel of inbred lines, where multiple replicates of the same inbred are measured and the average phenotype is taken as the response variable. Here we describe and evaluate single plant GWAS (sp-GWAS) for performing a GWAS on individual plants, which does not require an association panel of inbreds. Instead sp-GWAS relies on the phenotypes and genotypes from individual plants sampled from a randomly mating population. Importantly, we demonstrate how sp-GWAS can be efficiently combined with a bulk segregant analysis (BSA) experiment to rapidly corroborate evidence for significant SNPs.

RESULTS

In this study we used the Shoepeg maize landrace, collected as an open pollinating variety from a farm in Southern Missouri in the 1960's, to evaluate whether sp-GWAS coupled with BSA can efficiently and powerfully used to detect significant association of SNPs for plant height (PH). Plant were grown in 8 locations across two years and in total 768 individuals were genotyped and phenotyped for sp-GWAS. A total of 306 k polymorphic markers in 768 individuals evaluated via association analysis detected 25 significant SNPs (P ≤ 0.00001) for PH. The results from our single-plant GWAS were further validated by bulk segregant analysis (BSA) for PH. BSA sequencing was performed on the same population by selecting tall and short plants as separate bulks. This approach identified 37 genomic regions for plant height. Of the 25 significant SNPs from GWAS, the three most significant SNPs co-localize with regions identified by BSA.

CONCLUSION

Overall, this study demonstrates that sp-GWAS coupled with BSA can be a useful tool for detecting significant SNPs and identifying candidate genes. This result is particularly useful for species/populations where association panels are not readily available.

QTL mapping and genome-wide prediction of heat tolerance in multiple connected populations of temperate maize

Climate change will lead to increasing heat stress in the temperate regions of the world. The objectives of this study were the following: (I) to assess the phenotypic and genotypic diversity of traits related to heat tolerance of maize seedlings and dissect their genetic architecture by quantitative trait locus (QTL) mapping, (II) to compare the prediction ability of genome-wide prediction models using various numbers of KASP (Kompetitive Allele Specific PCR genotyping) single nucleotide polymorphisms (SNPs) and RAD (restriction site-associated DNA sequencing) SNPs, and (III) to examine the prediction ability of intra-, inter-, and mixed-pool calibrations. For the heat susceptibility index of five of the nine studied traits, we identified a total of six QTL, each explaining individually between 7 and 9% of the phenotypic variance. The prediction abilities observed for the genome-wide prediction models were high, especially for the within-population calibrations, and thus, the use of such approaches to select for heat tolerance at seedling stage is recommended. Furthermore, we have shown that for the traits examined in our study, populations created from inter-pool crosses are suitable training sets to predict populations derived from intra-pool crosses.

Genetic dissection of stalk lodging-related traits using an IBM Syn10 DH population in maize across three environments (Zea mays L.)

Stalk lodging severely limits the grain yield of maize (Zea mays L.). Mechanical stalk strength can be reflected by the traits of stalk diameter (SD), stalk bending strength (SBS), and lodging rind penetrometer resistance (RPR). To determine the genetic basis of maize stalk lodging, quantitative trait loci (QTLs) were mapped for these three traits using the IBM Syn10 DH population in three environments. The results indicated that there were strong genetic correlations among the three traits, and the analyses of phenotypic variations for SD, SBS, and RPR across the three environments showed high broad-sense heritability (0.6843, 0.5175, and 0.7379, respectively). In total, 44 significant QTLs were identified control the above traits across the 3 environments. A total of 14, 14, and 16 QTLs were identified for SD, SBS, and RPR across single-environment mapping, respectively. Notably, ten QTLs were stably expressed across multiple-environments, including two QTLs for SD, three for SBS, and five for RPR. Three major QTLs each accounting for over 10% of the phenotypic variation were qSD6-2 (10.03%), qSD8-2 (13.73%), and qSBS1-2 (11.89%). Comprehensive analysis of all QTLs in this study revealed that 5 QTL clusters including 12 QTLs were located on chromosomes 1, 3, 7, and 8, respectively. Among these 44 QTLs, 9 harbored 13 stalk lodging-associated SNPs that were detected by our recently published work, with 1 SNP successfully validated in the IBM Syn10 DH population. These chromosomal regions will be useful for marker-assisted selection and fine mapping of stalk lodging-related traits in maize.

Ethephon Improved Stalk Strength of Maize (Zea Mays L.) Mainly through Altering Internode Morphological Traits to Modulate Mechanical Properties under Field Conditions

Stalk strength is critical for reducing maize stalk lodging and maintaining grain yield. Ethephon has been widely applied to molding compact plant-type to reduce the lodging risk in maize production. However, there is little information on how ethephon regulates internode mechanical properties to improve maize stalk strength. Multiyear field experiments (2013–2017) were conducted to determine the effects of foliar-applied ethephon on summer maize internode morphological, chemical and mechanical characteristics. The hypothetical structural equation model was used to analyze the contribution of ethephon-induced changes of internode morphological and chemical traits to stalk mechanical strength. Ethephon significantly reduced the basal internode length, while increasing internode diameters and breaking resistance. Meanwhile, ethephon significantly increased the ratio of structural dry matter to total dry matter and the amount of structural dry matter per unit length and volume. Mechanical assays suggested that ethephon significantly altered geometric properties and increased the maximum bending moment, maximum failure force, while depressing the material properties. Furthermore, correlation and path analyses revealed strong correlations and significant contribution of internode morphological properties to stalk mechanical strength, respectively. These results support the conclusion that ethephon-induced morphology alteration played a major role in improving maize internode strength.

Classification of Corn Stalk Lodging Resistance Using Equivalent Forces Combined with SVD Algorithm

Corn stalk lodging, which involves the breakage of the stalk below the ear following either bad weather, insect infestation or stormy rain, usually leads to harvest loss, increased harvesting time and higher drying costs. The objective of this study was to develop a method that can classify corn stalk lodging resistance. This method, which employed the maximum equivalent force exerted on a corn stalk, corresponding stalk agronomic traits, and the singular value decomposition (SVD) algorithm, showed that the five corn varieties with different stalk lodging resistance from two planting densities of 60,000 plants/ha and 75,000 plants/ha can be effectively classified. A customized device was designed to measure the equivalent forces. Three factors, including the planting density, the stalk diameter, and the maximum equivalent force with comprehensive contributions of −0.4603, 0.4196 and 0.4068, which are related to principal components, play an important role in the classification of corn stalk lodging resistance. The results showed that the corn stalk lodging resistance decreased with increase in planting density; however, with the increase in stalk diameter and maximum equivalent force, the lodging resistance significantly increased. Corn breeders can develop higher lodging resistance-based corn varieties by using this approach.

DARLING: a device for assessing resistance to lodging in grain crops

BACKGROUND

Stalk lodging (breakage of plant stems prior to harvest) is a major problem for both farmers and plant breeders. A limiting factor in addressing this problem is the lack of a reliable method for phenotyping stalk strength. Previous methods of phenotyping stalk strength induce failure patterns different from those observed in natural lodging events. This paper describes a new device for field-based phenotyping of stalk strength called "DARLING" (device for assessing resistance to lodging in grains). The DARLING apparatus consists of a vertical arm which is connected to a horizontal footplate by a hinge. The operator places the device next to a stalk, aligns the stalk with a force sensor, steps on the footplate, and then pushes the vertical arm forward until the stalk breaks. Force and rotation are continuously recorded during the test and these quantities are used to calculate two quantities: stalk flexural stiffness and stalk bending strength.

RESULTS

Field testing of DARLING was performed at multiple sites. Validation was based upon several factors. First, the device induces the characteristic "crease" or Brazier buckling failure patterns observed in naturally lodged stalks. Second, in agreement with prior research, flexural rigidity values attained using the DARLING apparatus are strongly correlated with bending strength measurements. Third, flexural stiffness and bending strength values obtained with DARLING are in agreement with laboratory-based stiffness and strength values for corn stalks. Finally, a paired specimen experimental design was used to determine that the flexural data obtained with DARLING is in agreement with laboratory-based flexural testing results of the same specimens. DARLING was also deployed in the field to assess phenotyping throughput (# of stalks phenotyped per hour). Over approximately 5000 tests, the average testing rate was found to be 210 stalks/h.

CONCLUSIONS

The DARLING apparatus provides a quantitative assessment of stalk strength in a field setting. It induces the same failure patterns observed in natural lodging events. DARLING can also be used to perform non-destructive flexural tests. This technology has many applications, including breeding, genetic studies on stalk strength, longitudinal studies of stalk flexural stiffness, and risk assessment of lodging propensity.

In situ evaluation of stalk lodging resistance for different maize (Zea mays L.) cultivars using a mobile wind machine

BACKGROUND

Stalk lodging is an impediment to improving profitability and production efficiency in maize. Lodging resistance, a comprehensive indicator to appraise genotypes, requires both characterization of mechanical properties in laboratory and investigation of lodging percentage in field. However, in situ characterization of maize lodging resistance still remains poor. The aim of this study was to develop an indicator, named cumulative lodging index (CLI), based on lodging percentages at different wind speeds for evaluating lodging resistance for different maize cultivars, and to evaluate the accuracy and reliability of this method.

RESULTS

Different cultivars showed different patterns of lodging percentage along with wind speeds. The failure wind speed (FWS) for maize ranged between 16 and 30 m s^-1 across cultivars. The CLI differed between maize cultivars and showed favorable reliability (i.e. nRMSE of 5.38%). Mechanical properties of the third internode did not vary significantly between cultivars. Significant differences in the reduction index (RI) of wind speed sheltered by maize canopy were found between cultivars.

CONCLUSION

Our findings implied that mobile wind machine is powerful in reproducing wind disaster that induce crop lodging. The newly-built CLI was demonstrated to be a more robust indicator than mechanical properties, FWS, and RI when evaluating lodging resistance in terms of both reliability and resolution. This study offers a new perspective for evaluating in situ lodging resistance of crops, and provides technical support for accurate identification of lodging-resistant phenotypic traits.

An assessment of the performance of the logistic mixed model for analyzing binary traits in maize and sorghum diversity panels

The logistic mixed model (LMM) is well-suited for the genome-wide association study (GWAS) of binary agronomic traits because it can include fixed and random effects that account for spurious associations. The recent implementation of a computationally efficient model fitting and testing approach now makes it practical to use the LMM to search for markers associated with such binary traits on a genome-wide scale. Therefore, the purpose of this work was to assess the applicability of the LMM for GWAS in crop diversity panels. We dichotomized three publicly available quantitative traits in a maize diversity panel and two quantitative traits in a sorghum diversity panel, and them performed a GWAS using both the LMM and the unified mixed linear model (MLM) on these dichotomized traits. Our results suggest that the LMM is capable of identifying statistically significant marker-trait associations in the same genomic regions highlighted in previous studies, and this ability is consistent across both diversity panels. We also show how subpopulation structure in the maize diversity panel can underscore the LMM’s superior control for spurious associations compared to the unified MLM. These results suggest that the LMM is a viable model to use for the GWAS of binary traits in crop diversity panels and we therefore encourage its broader implementation in the agronomic research community.

Genetic Architecture of Soybean Yield and Agronomic Traits

Soybean is the world's leading source of vegetable protein and demand for its seed continues to grow. Breeders have successfully increased soybean yield, but the genetic architecture of yield and key agronomic traits is poorly understood. We developed a 40-mating soybean nested association mapping (NAM) population of 5,600 inbred lines that were characterized by single nucleotide polymorphism (SNP) markers and six agronomic traits in field trials in 22 environments. Analysis of the yield, agronomic, and SNP data revealed 23 significant marker-trait associations for yield, 19 for maturity, 15 for plant height, 17 for plant lodging, and 29 for seed mass. A higher frequency of estimated positive yield alleles was evident from elite founder parents than from exotic founders, although unique desirable alleles from the exotic group were identified, demonstrating the value of expanding the genetic base of US soybean breeding.

Quantitative Identification of Maize Lodging-Causing Feature Factors Using Unmanned Aerial Vehicle Images and a Nomogram Computation

Maize (zee mays L.) is one of the most important grain crops in China. Lodging is a natural disaster that can cause significant yield losses and threaten food security. Lodging identification and analysis contributes to evaluate disaster losses and cultivates lodging-resistant maize varieties. In this study, we collected visible and multispectral images with an unmanned aerial vehicle (UAV), and introduce a comprehensive methodology and workflow to extract lodging features from UAV imagery. We use statistical methods to screen several potential feature factors (e.g., texture, canopy structure, spectral characteristics, and terrain), and construct two nomograms (i.e., Model-1 and Model-2) with better validation performance based on selected feature factors. Model-2 was superior to Model-1 in term of its discrimination ability, but had an over-fitting phenomenon when the predicted probability of lodging went from 0.2 to 0.4. The results show that the nomogram could not only predict the occurrence probability of lodging, but also explore the underlying association between maize lodging and the selected feature factors. Compared with spectral features, terrain features, texture features, canopy cover, and genetic background, canopy structural features were more conclusive in discriminating whether maize lodging occurs at the plot scale. Using nomogram analysis, we identified protective factors (i.e., normalized difference vegetation index, NDVI and canopy elevation relief ratio, CRR) and risk factors (i.e., Hcv1) related to maize lodging, and also found a problem of terrain spatial variability that is easily overlooked in lodging-resistant breeding trials.

A sorghum NAC gene is associated with variation in biomass properties and yield potential

Sorghum bicolor is a C4 grass widely cultivated for grain, forage, sugar, and biomass. The sorghum Dry Stalk (D) locus controls a qualitative difference between juicy green (dd) and dry white (D-) stalks and midribs, and co-localizes with a quantitative trait locus for sugar yield. Here, we apply fine-mapping and genome-wide association study (GWAS) to identify a candidate gene underlying D, and use nearly isogenic lines (NILs) to characterize the transcriptional, compositional, and agronomic effects of variation at the D locus. The D locus was fine-mapped to a 36 kb interval containing four genes. One of these genes is a NAC transcription factor that contains a stop codon in the NAC domain in the recessive (dd) parent. Allelic variation at D affects grain yield, sugar yield, and biomass composition in NILs. Green midrib (dd) NILs show reductions in lignin in stalk tissue and produce higher sugar and grain yields under well-watered field conditions. Increased yield potential in dd NILs is associated with increased stalk mass and moisture, higher biomass digestibility, and an extended period of grain filling. Transcriptome profiling of midrib tissue at the 4-6 leaf stages, when NILs first become phenotypically distinct, reveals that dd NILs have increased expression of a miniature zinc finger (MIF) gene. MIF genes dimerize with and suppress zinc finger homeodomain (ZF-HD) transcription factors, and a ZF-HD gene is associated with midrib color variation in a GWAS analysis across 1,694 diverse sorghum inbreds. A premature stop codon in a NAC gene is the most likely candidate polymorphism underlying the sorghum D locus. More detailed understanding of the sorghum D locus could help improve agronomic potential in cereals.

Analysis of the genetic basis of plant height-related traits in response to ethylene by QTL mapping in maize (Zea mays L.)

Ethylene (ET) is critical importance in the growth, development, and stress responses of plants. Plant hormonal stress responses have been extensively studied, however, the role of ET in plant growth, especially plant height (PH) remains unclear. Understanding the genetic control for PH in response to ET will provide insights into the regulation of maize development. To clarify the genetic basis of PH-related traits of maize in response to ET, we mapped QTLs for PH, ear height (EH), and internode length above the uppermost ear (ILAU) in two recombinant inbred line (RIL) populations of Zea mays after ET treatment and in an untreated control (CK) group. Sixty QTLs for the three traits were identified. Twenty-two QTLs were simultaneously detected under both ET treatment and untreated control, and five QTLs were detected at two geographic locations under ET treatment only. Individual QTL can be explained 3.87-17.71% of the phenotypic variance. One QTL (q2PH9-1, q1PH9, q1EH9/q1ILAU9-1, q2ILAU9, and q2EH9) for the measured traits (PH, EH, ILAU) was consistent across both populations. Two QTLs (q2PH2-5, q2ILAU2-2, q1PH2-2, and q1ILAU2-2; q1PH8-1, q1EH8-1, q2PH8-1) were identified for up to two traits in both locations and populations under both ET treatment and untreated control. These consistent and stable regions are important QTLs of potential hot spots for PH, ear height (EH), and internode length above the uppermost ear (ILAU) response to ET in maize; therefore, QTL fine-mapping and putative candidate genes validation should enable the cloning of PH, EH, and ILAU related genes to ET response. These results will be valuable for further fine-mapping and quantitative trait nucleotides (QTNs) determination, and elucidate the underlying molecular mechanisms of ET responses in maize.

Identification of QTL conferring resistance to stripe rust (Puccinia striiformis f. sp. hordei) and leaf rust (Puccinia hordei) in barley using nested association mapping (NAM)

The biotrophic rust fungi Puccinia hordei and Puccinia striiformis are important barley pathogens with the potential to cause high yield losses through an epidemic spread. The identification of QTL conferring resistance to these pathogens is the basis for targeted breeding approaches aiming to improve stripe rust and leaf rust resistance of modern cultivars. Exploiting the allelic richness of wild barley accessions proved to be a valuable tool to broaden the genetic base of resistance of barley cultivars. In this study, SNP-based nested association mapping (NAM) was performed to map stripe rust and leaf rust resistance QTL in the barley NAM population HEB-25, comprising 1,420 lines derived from BC₁S₃ generation. By scoring the percentage of infected leaf area, followed by calculation of the area under the disease progress curve and the average ordinate during a two-year field trial, a large variability of resistance across and within HEB-25 families was observed. NAM based on 5,715 informative SNPs resulted in the identification of twelve and eleven robust QTL for resistance against stripe rust and leaf rust, respectively. Out of these, eight QTL for stripe rust and two QTL for leaf rust are considered novel showing no overlap with previously reported resistance QTL. Overall, resistance to both pathogens in HEB-25 is most likely due to the accumulation of numerous small effect loci. In addition, the NAM results indicate that the 25 wild donor QTL alleles present in HEB-25 strongly differ in regard to their individual effect on rust resistance. In future, the NAM concept will allow to select and combine individual wild barley alleles from different HEB parents to increase rust resistance in barley. The HEB-25 results will support to unravel the genetic basis of rust resistance in barley, and to improve resistance against stripe rust and leaf rust of modern barley cultivars.

Genetic Mapping Populations for Conducting High-Resolution Trait Mapping in Plants

Fine mapping of quantitative trait loci (QTL) is the route to more detailed molecular characterization and functional studies of the relationship between polymorphism and trait variation. It is also of direct relevance to breeding since it makes QTL more easily integrated into marker-assisted breeding and into genomic selection. Fine mapping requires that marker-trait associations are tested in populations in which large numbers of recombinations have occurred. This can be achieved by increasing the size of mapping populations or by increasing the number of generations of crossing required to create the population. We review the factors affecting the precision and power of fine mapping experiments and describe some contemporary experimental approaches, focusing on the use of multi-parental or multi-founder populations such as the multi-parent advanced generation intercross (MAGIC) and nested association mapping (NAM). We favor approaches such as MAGIC since these focus explicitly on increasing the amount of recombination that occurs within the population. Whatever approaches are used, we believe the days of mapping QTL in small populations must come to an end. In our own work in MAGIC wheat populations, we started with a target of developing 1,000 lines per population: that number now looks to be on the low side. Graphical Abstract.

Genetic Properties of a Nested Association Mapping Population Constructed With Semi-Winter and Spring Oilseed Rapes

Nested association mapping (NAM) populations have been widely applied to dissect the genetic basis of complex quantitative traits in a variety of crops. In this study, we developed a Brassica napus NAM (BN-NAM) population consisting of 15 recombination inbred line (RIL) families with 2,425 immortal genotypes. Fifteen high-density genetic linkage maps were constructed by genotyping by sequencing (GBS) based on all RIL families, with further integration into a joint linkage map (JLM) having 30,209 unique markers in common with multiple linkage maps. Furthermore, an ultra-density whole-genome variation map was constructed by projecting 4,444,309 high-quality variants onto the JLM. The NAM population captured a total of 88,542 recombination events (REs). The uneven distribution of recombination rate along chromosomes is positively correlated with the densities of genes and markers, but negatively correlated with the density of transposable elements and linkage disequilibrium (LD). Analyses of population structure and principal components revealed that the BN-NAM population could be divided into three groups with weak stratification. The LD decay distance across genome varied between 170 and 2,400 Kb, with LD decay more rapid in the A than in the C sub-genome. The pericentromeric regions contained large LD blocks, especially in the C sub-genome. This NAM population provides a valuable resource for dissecting the genetic basis of important traits in rapeseed, especially in semi-winter oilseed rape.

An Integration of Genome-Wide Association Study and Gene Co-expression Network Analysis Identifies Candidate Genes of Stem Lodging-Related Traits in Brassica napus

Lodging is a persistent problem which severely reduce yield and impair seed quality in rapeseed (Brassica napus L.). Enhancing stem strength (SS) has proven to be an effective approach to decrease lodging risk. In the present study, four interrelated stem lodging-related traits, including stem breaking resistance (SBR), stem diameter (SD), SS, and lodging coefficient (LC), were investigated among 472 rapeseed accessions. A genome-wide association study (GWAS) using Brassica 60K SNP array for stem lodging-related traits identified 67 significantly associated quantitative trait loci (QTLs) and 71 candidate genes. In parallel, a gene co-expression network based on transcriptome sequencing was constructed. The module associated with cellulose biosynthesis was highlighted. By integrating GWAS and gene co-expression network analysis, some promising candidate genes, such as ESKIMO1 (ESK1, BnaC08g26920D), CELLULOSE SYNTHASE 6 (CESA6, BnaA09g06990D), and FRAGILE FIBER 8 (FRA8, BnaC04g39510D), were prioritized for further research. These findings revealed the genetic basis underlying stem lodging and provided worthwhile QTLs and genes information for genetic improvement of stem lodging resistance in B. napus.

A nested association mapping population identifies multiple small effect QTL conferring resistance against net blotch (Pyrenophora teres f. teres) in wild barley

The net form of net blotch caused by the necrotrophic fungus Pyrenophora teres f. teres is a major disease of barley, causing high yield losses and reduced malting and feed quality. Exploiting the allelic richness of wild barley proved to be a valuable tool to broaden the genetic base of resistance of modern elite cultivars. In this study, a SNP-based nested association mapping (NAM) study was conducted to map QTL for P. teres resistance in the barley population HEB-25 comprising 1,420 lines derived from BC1S3 generation. By scoring the percentage of infected leaf area followed by calculation of the average ordinate (AO) and scoring of the reaction type (RT) in two-year field trials a large variability of net blotch resistance across and within families of HEB-25 was observed. Genotype response to net blotch infection showed a range of 48.2% for AO (0.9-49.1%) and 6.4 for RT (2.2-8.6). NAM based on 5,715 informative SNPs resulted in the identification of 24 QTL for resistance against net blotch. Out of these, six QTL are considered novel showing no correspondence to previously reported QTL for net blotch resistance. Overall, variation of net blotch resistance in HEB-25 turned out to be controlled by small effect QTL. Results indicate the presence of alleles in HEB-25 differing in their effect on net blotch resistance. Results provide valuable information regarding the genetic architecture of the complex barley-P. teres f. teres interaction as well as for the improvement of net blotch resistance of elite barley cultivars.

Genetic and transcriptomic analyses of lignin- and lodging-related traits in Brassica napus

Candidate genes associated with lignin and lodging traits were identified by combining phenotypic, genotypic, and gene expression data in B. napus. Brassica napus is one of the world's most important oilseed crops, but its yield can be dramatically reduced by lodging, bending, and falling of its vertical stems. Lignin has been shown to contribute to stem mechanical strength. In this study, we found that the syringyl/guaiacyl (S/G) monolignol ratio exhibits a significant negative correlation with disease and lodging resistance. A total of 92 and 50 SNP and SSR loci, respectively, were found to be significantly associated with five traits, breaking force, breaking strength, lodging coefficient, acid detergent lignin content, and the S/G monolignol ratio using GWAS. To identify novel genes involved in lignin biosynthesis, transcriptome sequencing of high- (H) and low (L)-ADL content accessions was performed. The up-regulated genes were mainly involved in glycoside catabolic processes (especially glucosinolate catabolism) and cell wall biogenesis, while down-regulated genes were involved in glucosinolate biosynthesis, indicating that crosstalk exists between glucosinolate metabolic processes and lignin biosynthesis. Integrating this differential expression with the GWAS analysis, we identified four candidate genes regulating lignin, including glycosyl hydrolase (BnaA01g00480D), CYT1 (BnaA04g22820D), and two encoding transcription factors, SHINE1 (ERF family) and DAR6 (LIM family). This study provides insight into the genetic control of lodging and lignin in B. napus.

Quantitative trait loci from identification to exploitation for crop improvement

Advancement in the field of genetics and genomics after the discovery of Mendel's laws of inheritance has led to map the genes controlling qualitative and quantitative traits in crop plant species. Mapping of genomic regions controlling the variation of quantitatively inherited traits has become routine after the advent of different types of molecular markers. Recently, the next generation sequencing methods have accelerated the research on QTL analysis. These efforts have led to the identification of more closely linked molecular markers with gene/QTLs and also identified markers even within gene/QTL controlling the trait of interest. Efforts have also been made towards cloning gene/QTLs or identification of potential candidate genes responsible for a trait. Further new concepts like crop QTLome and QTL prioritization have accelerated precise application of QTLs for genetic improvement of complex traits. In the past years, efforts have also been made in exploitation of a number of QTL for improving grain yield or other agronomic traits in various crops through markers assisted selection leading to cultivation of these improved varieties at farmers' field. In present article, we reviewed QTLs from their identification to exploitation in plant breeding programs and also reviewed that how improved cultivars developed through introgression of QTLs have improved the yield productivity in many crops.

Development of a phenotyping platform for high throughput screening of nodal root angle in sorghum

BACKGROUND

In sorghum, the growth angle of nodal roots is a major component of root system architecture. It strongly influences the spatial distribution of roots of mature plants in the soil profile, which can impact drought adaptation. However, selection for nodal root angle in sorghum breeding programs has been restricted by the absence of a suitable high throughput phenotyping platform. The aim of this study was to develop a phenotyping platform for the rapid, non-destructive and digital measurement of nodal root angle of sorghum at the seedling stage.

RESULTS

The phenotyping platform comprises of 500 soil filled root chambers (50 × 45 × 0.3 cm in size), made of transparent perspex sheets that were placed in metal tubs and covered with polycarbonate sheets. Around 3 weeks after sowing, once the first flush of nodal roots was visible, roots were imaged in situ using an imaging box that included two digital cameras that were remotely controlled by two android tablets. Free software (openGelPhoto.tcl) allowed precise measurement of nodal root angle from the digital images. The reliability and efficiency of the platform was evaluated by screening a large nested association mapping population of sorghum and a set of hybrids in six independent experimental runs that included up to 500 plants each. The platform revealed extensive genetic variation and high heritability (repeatability) for nodal root angle. High genetic correlations and consistent ranking of genotypes across experimental runs confirmed the reproducibility of the platform.

CONCLUSION

This low cost, high throughput root phenotyping platform requires no sophisticated equipment, is adaptable to most glasshouse environments and is well suited to dissect the genetic control of nodal root angle of sorghum. The platform is suitable for use in sorghum breeding programs aiming to improve drought adaptation through root system architecture manipulation.

Genetic Characterization of the Soybean Nested Association Mapping Population

A set of nested association mapping (NAM) families was developed by crossing 40 diverse soybean [ (L.) Merr.] genotypes to the common cultivar. The 41 parents were deeply sequenced for SNP discovery. Based on the polymorphism of the single-nucleotide polymorphisms (SNPs) and other selection criteria, a set of SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 RILs from the 40 families. Analysis of the SNP profiles of the RILs showed a low average recombination rate. We constructed genetic linkage maps for each family and a composite linkage map based on recombinant inbred lines (RILs) across the families and identified and annotated 525,772 high confidence SNPs that were used to impute the SNP alleles in the RILs. The segregation distortion in most families significantly favored the alleles from the female parent, and there was no significant difference of residual heterozygosity in the euchromatic vs. heterochromatic regions. The genotypic datasets for the RILs and parents are publicly available and are anticipated to be useful to map quantitative trait loci (QTL) controlling important traits in soybean.