Genome-wide association analysis for maize stem Cell Wall-bound Hydroxycinnamates

Genome-Wide Association Study and Genomic Predictions for Hydroxycinnamate Concentrations in Maize Stover

Hydroxycinnamates, like ferulate (FA) and p-coumarate (pCA), are important components of maize cell walls, which influence pest resistance, ruminal digestibility, and biofuel production. Increasing their concentration has been linked to increased pest resistance, but also may lead to a decrease in nutritional value or bioethanol production efficiency. Therefore, improving forage quality or biofuel production without compromising plant resistance and a thorough understanding of the biosynthesis and deposition of these compounds is necessary, especially in stover, which is the feedstock for second-generation biofuel production and determines animal forage quality. This study aimed to identify genomic regions associated with hydroxycinnamates and to develop genomic prediction models to determine the best selection approach to modify hydroxycinnamate content. Although heritability estimates for hydroxycinnamates were moderate, direct phenotypic selection is discouraged because hydroxycinnamate quantification is laborious and time-consuming. Negative genotypic correlations were observed between animal digestibility and pCA content and positive with diferulates content, suggesting differing effects compared to previous studies on maize pith. However, no colocalizations with digestibility QTLs were found, highlighting the need for further research. Given the moderate predictive capacity of GBLUP prediction models, genotypic selection is proposed as the most promising alternative for modifying hydroxycinnamate content.

Assessing the success of breeding maize inbred lines with contrasting diferulate concentrations

BACKGROUND

The crosslinking of maize cell wall components, particularly mediated by the formation of ferulic acid dimers or diferulates, has been associated with important crop valorization traits such as increased pest resistance, lower forage digestibility, or reduced bioethanol production. However, these relationships were based on studies performed using diverse unrelated inbred lines and/or populations, so genetic background could interfere on these associations.

RESULTS

In the present research, the success of a pedigree selection program aimed to obtain inbred lines from a common antecessor with contrasting diferulate concentration was evaluated. From the 10 inbreds lines developed we could validate the success of the breeding program, obtaining 4 inbred lines with significant contrating values of total diferulate content in the pith tissues (two of each group): high (X̅= 0.69 mg/g of DW) and low (X̅= 0.35 mg/g). Ferulate changes in the same way were also observed: high (X̅= 3.09 mg/g of DW) and low (X̅= 1.62 mg/g). On the other hand, we found strong and positive correlations between DFAT and individual dimers, and moderate negative correlations between total DFAT and a main cell wall component such as cellulose. However, we did not find a significant effect of DFAT on maize valorization traits, except of a negative effect of DFAT on the concentration of sugars released after the enzimatic hydrolysis of the pith tissues. Interestingly, increasing DFAT in the pith does not seem to affect the digestibility of the forage or the saccharification of the stover residue, highlighting that changes in a specific tissue do not encompass correlated changes in other resources.

CONCLUSIONS

Overall, we have obtained contrasting inbred lines with diferulates concentration, which could be uselful in further studies focussing in the identification of regions/genes predominantly involved in the hydroxycinnamate biosynthesis pathway and cell wall crosslinking network.

Synthetic-biology approach for plant lignocellulose engineering

Plant biomass is an abundant, renewable resource that offers multiple advantages for the production of green chemicals and recombinant proteins. However, the adoption of plant-based systems by industry is hindered because mammalian and other cell cultures are well-established and better characterized in an industrial setting, and thus it is difficult for plant-based processes to gain a foothold in the marketplace. Therefore, additional benefits of plant-based systems may be essential to tip the balance in favor of sustainable plant-derived products. A crucial factor in biomass valorization is to design mid- to high-value co-products that can be derived cost-effectively from the residual lignocellulose (LC). However, the utility of LC remains limited because LCs are, in general, too recalcitrant for industries to utilize their components (lignin, cellulose, and hemicelluloses). To overcome this issue, in planta engineering to reduce LC recalcitrance has been ongoing in recent decades, with essential input from synthetic biology owing to the complexity of LC pathways and the massive number of genes involved. In this review, we describe recent advances in LC manipulation and eight strategies for redesigning the pathways for lignin and structural glycans to reduce LC recalcitrance while mitigating against the growth penalty associated with yield loss.

Breeding for improved digestibility and processing of lignocellulosic biomass in Zea mays

Forage maize is a versatile crop extensively utilized for animal nutrition in agriculture and holds promise as a valuable resource for the production of fermentable sugars in the biorefinery sector. Within this context, the carbohydrate fraction of the lignocellulosic biomass undergoes deconstruction during ruminal digestion and the saccharification process. However, the cell wall's natural resistance towards enzymatic degradation poses a significant challenge during both processes. This so-called biomass recalcitrance is primarily attributed to the presence of lignin and ferulates in the cell walls. Consequently, maize varieties with a reduced lignin or ferulate content or an altered lignin composition can have important beneficial effects on cell wall digestibility. Considerable efforts in genetic improvement have been dedicated towards enhancing cell wall digestibility, benefiting agriculture, the biorefinery sector and the environment. In part I of this paper, we review conventional and advanced breeding methods used in the genetic improvement of maize germplasm. In part II, we zoom in on maize mutants with altered lignin for improved digestibility and biomass processing.

Silage maize as a potent candidate for sustainable animal husbandry development-perspectives and strategies for genetic enhancement

Maize is recognized as the queen of cereals, with an ability to adapt to diverse agroecologies (from 58^oN to 55^oS latitude) and the highest genetic yield potential among cereals. Under contemporary conditions of global climate change, C₄ maize crops offer resilience and sustainability to ensure food, nutritional security, and farmer livelihood. In the northwestern plains of India, maize is an important alternative to paddy for crop diversification in the wake of depleting water resources, reduced farm diversity, nutrient mining, and environmental pollution due to paddy straw burning. Owing to its quick growth, high biomass, good palatability, and absence of anti-nutritional components, maize is also one of the most nutritious non-legume green fodders. It is a high-energy, low-protein forage commonly used for dairy animals like cows and buffalos, often in combination with a complementary high-protein forage such as alfalfa. Maize is also preferred for silage over other fodders due to its softness, high starch content, and sufficient soluble sugars required for proper ensiling. With a rapid population increase in developing countries like China and India, there is an upsurge in meat consumption and, hence, the requirement for animal feed, which entails high usage of maize. The global maize silage market is projected to grow at a compound annual growth rate of 7.84% from 2021 to 2030. Factors such as increasing demand for sustainable and environment-friendly food sources coupled with rising health awareness are fueling this growth. With the dairy sector growing at about 4%-5% and the increasing shortage faced for fodder, demand for silage maize is expected to increase worldwide. The progress in improved mechanization for the provision of silage maize, reduced labor demand, lack of moisture-related marketing issues as associated with grain maize, early vacancy of farms for next crops, and easy and economical form of feed to sustain household dairy sector make maize silage a profitable venture. However, sustaining the profitability of this enterprise requires the development of hybrids specific for silage production. Little attention has yet been paid to breeding for a plant ideotype for silage with specific consideration of traits such as dry matter yield, nutrient yield, energy in organic matter, genetic architecture of cell wall components determining their digestibility, stalk standability, maturity span, and losses during ensiling. This review explores the available information on the underlying genetic mechanisms and gene/gene families impacting silage yield and quality. The trade-offs between yield and nutritive value in relation to crop duration are also discussed. Based on available genetic information on inheritance and molecular aspects, breeding strategies are proposed to develop maize ideotypes for silage for the development of sustainable animal husbandry.

β-Xylosidase SRBX1 Activity from Sporisorium reilianum and Its Synergism with Xylanase SRXL1 in Xylose Release from Corn Hemicellulose

Sposisorium reilianum is the causal agent of corn ear smut disease. Eleven genes have been identified in its genome that code for enzymes that could constitute its hemicellulosic system, three of which have been associated with two Endo-β-1,4-xylanases and one with α-L-arabinofuranosidase activity. In this study, the native protein extracellular with β-xylosidase activity, called SRBX1, produced by this basidiomycete was analyzed by performing production kinetics and its subsequent purification by gel filtration. The enzyme was characterized biochemically and sequenced. Finally, its synergism with Xylanase SRXL1 was determined. Its activity was higher in a medium with corn hemicellulose and glucose as carbon sources. The purified protein was a monomer associated with the sr16700 gene, with a molecular weight of 117 kDa and optimal activity at 60 °C in a pH range of 4-7, which had the ability to hydrolyze the ρ-nitrophenyl β-D-xylanopyranoside and ρ-Nitrophenyl α-L-arabinofuranoside substrates. Its activity was strongly inhibited by silver ions and presented Km and Vmax values of 2.5 mM and 0.2 μmol/min/mg, respectively, using ρ-nitrophenyl β-D-xylanopyranoside as a substrate. The enzyme degrades corn hemicellulose and birch xylan in combination and in sequential synergism with the xylanase SRXL1.

Identification of single nucleotide polymorphisms (SNPs) for maize cell wall hydroxycinnamates using a multi-parent advanced generation intercross (MAGIC) population

Higher hydroxycinnamate content makes maize tissues more recalcitrant to damage by insects, less digestible by ruminants, and less suitable for biofuel production. In a Genome Wide Association Analysis (GWAS) study carried out in a maize MAGIC population, we identified 24 SNPs associated with esterified cell wall-bound hydroxycinnamates, that represented 15 Quantitative Traic Loci (QTL). We identified new genomic regions associated to cell wall bound hydroxycinnamates in maize stover that could have an impact on their content across different genetic backgrounds. The high resolution QTL described in this study could be valuable for addressing positional mapping of genes involved in hydroxycinnamate biosynthesis and could uncover genes implicated in the esterification of hydroxycinnamic acids to the arabinoxylan chains that are poorly understood. However, we found that genetic correlation coefficients between hydroxycinnamate content and economical important traits such as saccharification efficiency, animal digestibility andi pest resistance were low to moderate, so modify specific hydroxycinnamates to indirectly improve cultivar performance will be unsuitable.

In Planta Cell Wall Engineering: From Mutants to Artificial Cell Walls

To mitigate the effects of global warming and to preserve the limited fossil fuel resources, an increased exploitation of plant-based materials and fuels is required, which would be one of the most important innovations related to sustainable development. Cell walls account for the majority of plant dry biomass and so is the target of such innovations. In this review, we discuss recent advances in in planta cell wall engineering through genetic manipulations, with a focus on wild-type-based and mutant-based approaches. The long history of using a wild-type-based approach has resulted in the development of many strategies for manipulating lignin, hemicellulose and pectin to decrease cell wall recalcitrance. In addition to enzyme-encoding genes, many transcription factor genes important for changing relevant cell wall characteristics have been identified. Although mutant-based cell wall engineering is relatively new, it has become feasible due to the rapid development of genome-editing technologies and systems biology-related research; we will soon enter an age of designed artificial wood production via complex genetic manipulations of many industrially important trees and crops.

The utility of metabolomics as a tool to inform maize biology

With the rise of high-throughput omics tools and the importance of maize and its products as food and bioethanol, maize metabolism has been extensively explored. Modern maize is still rich in genetic and phenotypic variation, yielding a wide range of structurally and functionally diverse metabolites. The maize metabolome is also incredibly dynamic in terms of topology and subcellular compartmentalization. In this review, we examine a broad range of studies that cover recent developments in maize metabolism. Particular attention is given to current methodologies and to the use of metabolomics as a tool to define biosynthetic pathways and address biological questions. We also touch upon the use of metabolomics to understand maize natural variation and evolution, with a special focus on research that has used metabolite-based genome-wide association studies (mGWASs).

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.

Association mapping for maize stover yield and saccharification efficiency using a multiparent advanced generation intercross (MAGIC) population

Cellulosic ethanol derived from fast growing C4 grasses could become an alternative to finite fossil fuels. With the potential to generate a major source of lignocellulosic biomass, maize has gained importance as an outstanding model plant for studying the complex cell wall network and also to optimize crop breeding strategies in bioenergy grasses. A genome-wide association study (GWAS) was conducted using a subset of 408 Recombinant Inbred Lines (RILs) from a Multi-Parent Advanced Generation Intercross (MAGIC) Population in order to identify single nucleotide polymorphisms (SNPs) associated with yield and saccharification efficiency of maize stover. We identified 13 SNPs significantly associated with increased stover yield that corresponded to 13 QTL, and 2 SNPs significantly associated with improved saccharification efficiency, that could be clustered into 2 QTL. We have pointed out the most interesting SNPs to be implemented in breeding programs based on results from analyses of averaged and yearly data. Association mapping in this MAGIC population highlight genomic regions directly linked to traits that influence the final use of maize. Markers linked to these QTL could be used in genomic or marker-assisted selection programs to improve biomass quality for ethanol production. This study opens a possible optimisation path for improving the viability of second-generation biofuels.