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

Experimental evolution in maize with replicated divergent selection identifies two plant-height-associated regions

Experimental evolution studies are common in agricultural research, where they are often deemed "long-term selection." These are often used to perform selection mapping, which involves identifying markers that were putatively under selection based on finding signals of selection left in the genome. A challenge of previous selection mapping studies, especially in agricultural research, has been the specification of robust significance thresholds. This is in large part because long-term selection studies in crops have rarely included replication. Usually, significance thresholds in long-term selection experiments are based on outliers from an empirical distribution. This approach is prone to missing true positives or including false positives. Under laboratory conditions with model species, replicated selection has been shown to be a powerful tool, especially for the specification of significance thresholds. Another challenge is that commonly used single-marker-based statistics may identify neutral linked loci which have hitchhiked along with regions that are actually under selection. In this study, we conducted divergent, replicated selection for short and tall plant height in a random-mating maize population under real field conditions. Selection of the 5% tallest and shortest plants was conducted for 3 generations. Significance thresholds were specified using the false discovery rate for selection (FDRfS) based on a window-based statistic applied to a statistic leveraging replicated selection (FSTSum). Overall, we found 2 significant regions putatively under selection. One region was located on chromosome 3 close to the plant-height genes Dwarf1 and iAA8. We applied a haplotype block analysis to further dissect the pattern of selection in significant regions of the genome. We observed patterns of strong selection in the subpopulations selected for short plant height on chromosome 3.

Diverging cell wall strategies for drought adaptation in two maize inbreds with contrasting lodging resistance

The plant cell wall is a plastic structure of variable composition that constitutes the first line of defence against environmental challenges. Lodging and drought are two stressful conditions that severely impact maize yield. In a previous work, we characterised the cell walls of two maize inbreds, EA2024 (susceptible) and B73 (resistant) to stalk lodging. Here, we show that drought induces distinct phenotypical, physiological, cell wall, and transcriptional changes in the two inbreds, with B73 exhibiting lower tolerance to this stress than EA2024. In control conditions, EA2024 stalks had higher levels of cellulose, uronic acids and p-coumarate than B73. However, upon drought EA2024 displayed increased levels of arabinose-enriched polymers, such as pectin-arabinans and arabinogalactan proteins, and a decreased lignin content. By contrast, B73 displayed a deeper rearrangement of cell walls upon drought, including modifications in lignin composition (increased S subunits and S/G ratio; decreased H subunits) and an increase of uronic acids. Drought induced more substantial changes in gene expression in B73 compared to EA2024, particularly in cell wall-related genes, that were modulated in an inbred-specific manner. Transcription factor enrichment assays unveiled inbred-specific regulatory networks coordinating cell wall genes expression. Altogether, these findings reveal that B73 and EA2024 inbreds, with opposite stalk-lodging phenotypes, undertake different cell wall modification strategies in response to drought. We propose that the specific cell wall composition conferring lodging resistance to B73, compromises its cell wall plasticity, and renders this inbred more susceptible to drought.

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.

Deciphering transcriptional mechanisms of maize internodal elongation by regulatory network analysis

The lengths of the basal internodes is an important factor for lodging resistance of maize (Zea mays). In this study, foliar application of coronatine (COR) to 10 cultivars at the V8 growth stage had different suppression effects on the length of the eighth internode, with three being categorized as strong-inhibition cultivars (SC), five as moderate (MC), and two as weak (WC). RNA-sequencing of the eighth internode of the cultivars revealed a total of 7895 internode elongation-regulating genes, including 777 transcription factors (TFs). Genes related to the hormones cytokinin, gibberellin, auxin, and ethylene in the SC group were significantly down-regulated compared to WC, and more cell-cycle regulatory factors and cell wall-related genes showed significant changes, which severely inhibited internode elongation. In addition, we used EMSAs to explore the direct regulatory relationship between two important TFs, ZmABI7 and ZmMYB117, which regulate the cell cycle and cell wall modification by directly binding to the promoters of their target genes ZmCYC1, ZmCYC3, ZmCYC7, and ZmCPP1. The transcriptome reported in this study will provide a useful resource for studying maize internode development, with potential use for targeted genetic control of internode length to improve the lodging resistance of maize.

Experimental error analysis of biomechanical phenotyping for stalk lodging resistance in maize

Stalk lodging destroys between 5 and 25% of grain crops annually. Developing crop varieties with improved lodging resistance will reduce the yield gap. Field-phenotyping equipment is critical to develop lodging resistant crop varieties, but current equipment is hindered by measurement error. Relatively little research has been done to identify and rectify sources of measurement error in biomechanical phenotyping platforms. This study specifically investigated sources of error in bending stiffness and bending strength measurements of maize stalks acquired using an in-field phenotyping platform known as the DARLING. Three specific sources of error in bending stiffness and bending strength measurements were evaluated: horizontal device placement, vertical device placement and incorrect recordings of load cell height. Incorrect load cell heights introduced errors as large as 130% in bending stiffness and 50% in bending strength. Results indicated that errors on the order of 15-25% in bending stiffness and 1-10% in bending strength are common in field-based measurements. Improving the design of phenotyping devices and associated operating procedures can mitigate this error. Reducing measurement error in field-phenotyping equipment is crucial for advancing the development of improved, lodging-resistant crop varieties. Findings have important implications for reducing the yield gap.

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.

The Transcriptome and Metabolome Reveal the Potential Mechanism of Lodging Resistance in Intergeneric Hybrids between Brassica napus and Capsella bursa-pastoris

Lodging is one of the main reasons for the reduction in seed yield and is the limitation of mechanized harvesting in B. napus. The dissection of the regulatory mechanism of lodging resistance is an important goal in B. napus. In this study, the lodging resistant B. napus line, YG689, derived from the hybridization between B. napus cv. Zhongyou 821 (ZY821) and Capsella bursa-pastoris, was used to dissect the regulation mechanism of hard stem formation by integrating anatomical structure, transcriptome and metabolome analyses. It was shown that the lignocellulose content of YG689 is higher than that of ZY821, and some differentially expressed genes (DEGs) involved in the lignocellulose synthesis pathway were revealed by transcriptome analyses. Meanwhile, GC–TOF–MS and UPLC–QTOF–MS identified 40, 54, and 31 differential metabolites in the bolting stage, first flower stage, and the final flower stage. The differential accumulation of these metabolites might be associated with the lignocellulose biosynthesis in B. napus. Finally, some important genes that regulate the metabolic pathway of lignocellulose biosynthesis, such as BnaA02g18920D, BnaA10g15590D, BnaC05g48040D, and NewGene_216 were identified in B. napus through the combination of transcriptomics and metabolomics data. The present results explored the potential regulatory mechanism of lignocellulose biosynthesis, which provided a new clue for the breeding of B. napus with lodging resistance in the future.

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.

The Crop Clamp - A non-destructive electromechanical pinch test to evaluate stalk lodging resistance

Given the ever-increasing world population, maize plays a pivotal role in global food security. A major obstacle facing farmers is stalk lodging (the breakage of the stalk before harvest), which leads to substantial losses in annual yields. Weather, disease, and pest damage are major contributors to stalk lodging. Traditionally, evaluating a stalk's tendency to lodge was achieved with a 'pinch' test: pinching the stalk by hand to estimate its transverse stiffness. This test is inherently qualitative, and results vary from person to person. To combat these problems, a portable, battery-operated, non-destructive device for precisely measuring the transverse stiffness of maize stalks, known as the Crop Clamp, has been developed. The device is capable of recording over 100 measurements per hour and has been validated against laboratory tests.