Precise control of water stress in the field reveals different response thresholds for forage yield and digestibility of maize hybrids.

Introduction: With dwindling global freshwater supplies and increasing water stress, agriculture is coming under increasing pressure to reduce water use. Plant breeding requires high analytical capabilities. For this reason, near-infrared spectroscopy (NIRS) has been used to develop prediction equations for whole-plant samples, particularly for predicting dry matter digestibility, which has a major impact on the energy value of forage maize hybrids and is required for inclusion in the official French catalogue. Although the historical NIRS equations have long been used routinely in seed company breeding programmes, they do not predict all variables with the same accuracy. In addition, little is known about how accurate their predictions are under different water stress-environments. Methods: Here, we examined the effects of water stress and stress intensity on agronomic, biochemical, and NIRS predictive values in a set of 13 modern S0-S1 forage maize hybrids under four different environmental conditions resulting from the combination of a northern and southern location and two monitored water stress levels in the south. Results: First, we compared the reliability of NIRS predictions for basic forage quality traits obtained using the historical NIRS predictive equations and the new equations we recently developed. We found that NIRS predicted values were affected to varying degrees by environmental conditions. We also showed that forage yield gradually decreased as a function of water stress, whereas both dry matter and cell wall digestibilities increased regardless of the intensity of water stress, with variability among the tested varieties decreasing under the most stressed conditions. Discussion: By combining forage yield and dry matter digestibility, we were able to quantify digestible yield and identify varieties with different strategies for coping with water stress, raising the exciting possibility that important potential selection targets still exist. Finally, from a farmer's perspective, we were able to show that late silage harvest has no effect on dry matter digestibility and that moderate water stress does not necessarily result in a loss of digestible yield.

Responses of Maize Internode to Water Deficit Are Different at the Biochemical and Histological Levels.

Maize feeding value is strongly linked to plant digestibility. Cell wall composition and structure can partly explain cell wall digestibility variations, and we recently showed that tissue lignification and lignin spatial distribution also contribute to cell wall digestibility variations. Although the genetic determinism of digestibility and cell wall composition has been studied for more than 20 years, little is available concerning that of tissue lignification. Moreover, maize yield is negatively impacted by water deficit, and we newly highlighted the impact of water deficit on cell wall digestibility and composition together with tissue lignification. Consequently, the aim of this study was to explore the genetic mechanisms of lignin distribution in link with cell wall composition and digestibility under contrasted water regimes. Maize internodes from a recombinant inbred line (RIL) population grown in field trials with contrasting irrigation scenarios were biochemically and histologically quantified. Results obtained showed that biochemical and histological traits have different response thresholds to water deficit. Histological profiles were therefore only modified under pronounced water deficit, while most of the biochemical traits responded whatever the strength of the water deficit. Three main clusters of quantitative trait locus (QTL) for histological traits were detected. Interestingly, overlap between the biochemical and histological clusters is rare, and one noted especially colocalizations between histological QTL/clusters and QTL for p-coumaric acid content. These findings reinforce the suspected role of tissue p-coumaroylation for both the agronomic properties of plants as well as their digestibility.

Dataset of organic sample near infrared spectra acquired on different spectrometers.

This dataset presents 127 raw near infrared spectra of different organic samples acquired on three different spectrometers in three different labs. An example of data processing is shown to create six spectra transfer models between the three spectrometers (two by two). In order to build and validate these transfer models, the dataset was split into two sets of spectra: a first set was used to compute six spectra transfer models thanks to the Piecewise Direct standardisation function (PDS). A second set of spectra, independent of the first one was used to validate transfer models. Spectrum treatments and models were created on ChemFlow (https://vm-chemflow-francegrille.eu/), a free online chemometric software that includes all the necessary functions.

Water Deficit-Responsive QTLs for Cell Wall Degradability and Composition in Maize at Silage Stage.

The use of lignocellulosic biomass for animal feed or biorefinery requires the optimization of its degradability. Moreover, biomass crops need to be better adapted to the changing climate and in particular to periods of drought. Although the negative impact of water deficit on biomass yield has often been mentioned, its impact on biomass quality has only been recently reported in a few species. In the present study, we combined the mapping power of a maize recombinant inbred line population with robust near infrared spectroscopy predictive equations to track the response to water deficit of traits associated with biomass quality. The population was cultivated under two contrasted water regimes over 3 consecutive years in the south of France and harvested at silage stage. We showed that cell wall degradability and ß-O-4-linked H lignin subunits were increased in response to water deficit, while lignin and p-coumaric acid contents were reduced. A mixed linear model was fitted to map quantitative trait loci (QTLs) for agronomical and cell wall-related traits. These QTLs were categorized as "constitutive" (QTL with an effect whatever the irrigation condition) or "responsive" (QTL involved in the response to water deficit) QTLs. Fifteen clusters of QTLs encompassed more than two third of the 213 constitutive QTLs and 13 clusters encompassed more than 60% of the 149 responsive QTLs. Interestingly, we showed that only half of the responsive QTLs co-localized with constitutive and yield QTLs, suggesting that specific genetic factors support biomass quality response to water deficit. Overall, our results demonstrate that water deficit favors cell wall degradability and that breeding of varieties that reconcile improved drought-tolerance and biomass degradability is possible.

A systems biology approach uncovers a gene co-expression network associated with cell wall degradability in maize.

Understanding the mechanisms triggering variation of cell wall degradability is a prerequisite to improving the energy value of lignocellulosic biomass for animal feed or biorefinery. Here, we implemented a multiscale systems approach to shed light on the genetic basis of cell wall degradability in maize. We demonstrated that allele replacement in two pairs of near-isogenic lines at a region encompassing a major quantitative trait locus (QTL) for cell wall degradability led to phenotypic variation of a similar magnitude and sign to that expected from a QTL analysis of cell wall degradability in the F271 × F288 recombinant inbred line progeny. Using DNA sequences within the QTL interval of both F271 and F288 inbred lines and Illumina RNA sequencing datasets from internodes of the selected near-isogenic lines, we annotated the genes present in the QTL interval and provided evidence that allelic variation at the introgressed QTL region gives rise to coordinated changes in gene expression. The identification of a gene co-expression network associated with cell wall-related trait variation revealed that the favorable F288 alleles exploit biological processes related to oxidation-reduction, regulation of hydrogen peroxide metabolism, protein folding and hormone responses. Nested in modules of co-expressed genes, potential new cell-wall regulators were identified, including two transcription factors of the group VII ethylene response factor family, that could be exploited to fine-tune cell wall degradability. Overall, these findings provide new insights into the regulatory mechanisms by which a major locus influences cell wall degradability, paving the way for its map-based cloning in maize.