Sorghum as a novel biomass for the sustainable production of cellulose nanofibers

Genomic footprints of sorghum domestication and breeding selection for multiple end uses.

Sorghum (Sorghum bicolor L. Moench) is one of the world's most cultivated cereal crops. Biotechnology approaches have great potential to complement traditional crop improvement. Earlier studies in rice and maize revealed that LIGULELESS-1 (LG1) is responsible for formation of the ligule and auricle, which determine the leaf inclination angle. However, generation and analysis of lg1 mutants in sorghum has so far not been described. Here, we describe CRISPR/Cas9 mediated targeted mutagenesis of LG1 in sorghum and phenotypic changes in mono- and bi-allelic lg1 mutants. Genome editing reagents were co-delivered to sorghum (var. Tx430) with the nptII selectable marker via particle bombardment of immature embryos followed by regeneration of transgenic plants. Sanger sequencing confirmed a single nucleotide insertion in the sgRNA LG1 target site. Monoallelic edited plantlets displayed more upright leaves in tissue culture and after transfer to soil when compared to wild type. T1 progeny plants with biallelic lg1 mutation lacked ligules entirely and displayed a more severe reduction in leaf inclination angle than monoallelic mutants. Transgene-free lg1 mutants devoid of the genome editing vector were also recovered in the segregating T1 generation. Targeted mutagenesis of LG1 provides a rapidly scorable phenotype in tissue culture and will facilitate optimization of genome editing protocols. Altering leaf inclination angle also has the potential to elevate yield in high-density plantings.

CRISPR/Cas9 mediated targeted mutagenesis of LIGULELESS-1 in sorghum provides a rapidly scorable phenotype by altering leaf inclination angle.

Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case "redomestication." Feral crops are plants which have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e., neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.

Prospects of Feral Crop De Novo Re-Domestication.

Leaf senescence is the last stage of leaf development, manifested by leaf yellowing due to the loss of chlorophyll, along with the degradation of macromolecules and facilitates nutrient translocation from the sink to the source tissues, which is essential for the plants' fitness. Leaf senescence is controlled by a sophisticated genetic network that has been revealed through the study of the molecular mechanisms of hundreds of senescence-associated genes (SAGs), which are involved in multiple layers of regulation. Leaf senescence is primarily regulated by plant age, but also influenced by a variety of factors, including phytohormones and environmental stimuli. Phytohormones, as important signaling molecules in plant, contribute to the onset and progression of leaf senescence. Recently, peptide hormones have been reported to be involved in the regulation of leaf senescence, enriching the significance of signaling molecules in controlling leaf senescence. This review summarizes recent advances in the regulation of leaf senescence by classical and peptide hormones, aiming to better understand the coordinated network of different pathways during leaf senescence.

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New Advances in the Regulation of Leaf Senescence by Classical and Peptide Hormones

The importance and potential of the multi-purpose crop sorghum in global food security have not yet been fully exploited, and the integration of the state-of-art genomics and high-throughput technologies into breeding practice is required. Sorghum, a historically vital staple food source and currently the fifth most important major cereal, is emerging as a crop with diverse end-uses as food, feed, fuel and forage and a model for functional genetics and genomics of tropical grasses. Rapid development in high-throughput experimental and data processing technologies has significantly speeded up sorghum genomic researches in the past few years. The genomes of three sorghum lines are available, thousands of genetic stocks accessible and various genetic populations, including NAM, MAGIC, and mutagenised populations released. Functional and comparative genomics have elucidated key genetic loci and genes controlling agronomical and adaptive traits. However, the knowledge gained has far away from being translated into real breeding practices. We argue that the way forward is to take a genome-based approach for tailored designing of sorghum as a multi-functional crop combining excellent agricultural traits for various end uses. In this review, we update the new concepts and innovation systems in crop breeding and summarise recent advances in sorghum genomic researches, especially the genome-wide dissection of variations in genes and alleles for agronomically important traits. Future directions and opportunities for sorghum breeding are highlighted to stimulate discussion amongst sorghum academic and industrial communities.

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Sorghum breeding in the genomic era: opportunities and challenges

Leaf senescence is important for crop yield as delaying it can increase the average yield. In this study, population genetics and transcriptomic profiling were combined to dissect its genetic basis in maize. To do this, the progenies of an elite maize hybrid Jidan27 and its parental lines Si-287 (early senescence) and Si-144 (stay-green), as well as 173 maize inbred lines were used. We identified two novel loci and their candidate genes, Stg3 (ZmATG18b) and Stg7 (ZmGH3.8), which are predicted to be members of autophagy and auxin pathways, respectively. Genomic variations in the promoter regions of these two genes were detected, and four allelic combinations existed in the examined maize inbred lines. The Stg3Si-144/Stg7Si-144 allelic combination with lower ZmATG18b expression and higher ZmGH3.8 expression could distinctively delay leaf senescence, increase ear weight and the improved hybrid of NIL-Stg3Si-144/Stg7Si-144 × Si-144 significantly reduced ear weight loss under drought stress, while opposite effects were observed in the Stg3Si-287/Stg7Si-287 combination with a higher ZmATG18b expression and lower ZmGH3.8 expression. Thus, we identify a potential interaction between autophagy and auxin which could modulate the timing of maize leaf senescence.

Potential interaction between autophagy and auxin during maize leaf senescence

Twelve QTL for flowering and leaf number were detected. The ZmWRKY14Hap4 could increase leaf number, flowering time and biomass yield which are promising for silage maize breeding. Silage maize, one of the most important feedstock for ruminants, is widely grown from temperate regions to the tropics. Flowering time and leaf number are two significantly correlated traits and important for the quality, adaptation and biomass yield of silage maize. In this study, a recombinant inbred line population consisting of 215 individuals and an association panel of 369 inbred lines were analysed in field conditions in three locations for 2 consecutive years, and five, four and three quantitative trait loci for the total leaf number, days to anthesis (DTA) and silking (DTS) were detected, which could explain 48.55, 35.37 and 34.22% of total phenotypic variation, respectively. Association analysis of qLN10 on chromosome 10 found that ZmWRKY14 was the candidate gene for leaf number, whose expression level was negatively correlated with the leaf number. There are five haplotypes for ZmWRKY14, and haplotype 4 could significantly increase flowering time, leaf number and biomass yield, but has no obvious influence on ear weight. The optimal allelic combination of ZmWRKY14 and ZCN8 could further increase leaf number and biomass yield. The results will provide important genetic information for silage maize breeding.

Zhigang Li

Papers

Sorghum breeding in the genomic era: opportunities and challenges

Potential interaction between autophagy and auxin during maize leaf senescence

Combined QTL mapping and association study reveals candidate genes for leaf number and flowering time in maize