Pearl millet [Pennisetum glaucum (L.) R. Br., syn. Cenchrus americanus (L.) Morrone], is a staple food for over 90 million poor farmers in arid and semi-arid regions of sub-Saharan Africa and South Asia. We report the ~1.79 Gb genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. Resequencing analysis of 994 (963 inbreds of the highly cross-pollinated cultigen, and 31 wild accessions) provides insights into population structure, genetic diversity, evolution and domestication history. In addition we demonstrated the use of re-sequence data for establishing marker trait associations, genomic selection and prediction of hybrid performance and defining heterotic pools. The genome wide variations and abiotic stress proteome data are useful resources for pearl millet improvement through deploying modern breeding tools for accelerating genetic gains in pearl millet.publishersversionPeer reviewe

Tomato is a globally important crop grown and consumed worldwide. Its reproductive activity is highly sensitive to environmental fluctuations, for instance temperature and drought. Here, pollen development is one of the most decisive processes. The present study aims for the identification of cell-specific proteins during pollen developmental stages of tomato. We have setup a protocol for stage-specific pollen isolation including microsporocytes (pollen mother cells), tetrads, microspores, polarized microspores, and mature pollen. Proteins were extracted using phenol and prefractionated using SDS-PAGE followed by protein digestion, peptide extraction, and desalting. Identification and quantification of proteins were performed using nanoHPLC coupled to LTQ-Orbitrap-MS. In total, 1821 proteins were identified. Most of these proteins were classified based on their homology and designated functions of orthologs. Cluster and principal components analysis revealed stage-specific proteins and demonstrated that pollen development of tomato is a highly controlled sequential process at the proteome level. Intermediate stages such as tetrad and polarized microspore are clearly distinguished by different functionality compared to other stages. From the predicted functions, energy-related proteins are increased during the later stages of development, which indicates that pollen germination depends upon presynthesized proteins in mature pollen. In contrast, heat stress-related proteins are highly abundant in very early developmental stages, suggesting a dominant role in stress protection. Taken together, the data provide a first cell-specific protein reference set for tomato pollen development from pollen mother cells to the mature pollen and give evidence for developmentally controlled processes that might help to prepare the cells for specific developmental programs and environmental stresses.

Sustainable crop production is the major challenge in the current global climate change scenario. Drought stress is one of the most critical abiotic factors which negatively impact crop productivity. In recent years, knowledge about molecular regulation has been generated to understand drought stress responses. For example, information obtained by transcriptome analysis has enhanced our knowledge and facilitated the identification of candidate genes which can be utilized for plant breeding. On the other hand, it becomes more and more evident that the translational and post-translational machinery plays a major role in stress adaptation, especially for immediate molecular processes during stress adaptation. Therefore, it is essential to measure protein levels and post-translational protein modifications to reveal information about stress inducible signal perception and transduction, translational activity and induced protein levels. This information cannot be revealed by genomic or transcriptomic analysis. Eventually, these processes will provide more direct insight into stress perception then genetic markers and might build a complementary basis for future marker-assisted selection of drought resistance. In this review, we survey the role of proteomic studies to illustrate their applications in crop stress adaptation analysis with respect to productivity. Cereal crops such as wheat, rice, maize, barley, sorghum and pearl millet are discussed in detail. We provide a comprehensive and comparative overview of all detected protein changes involved in drought stress in these crops and have summarized existing knowledge into a proposed scheme of drought response. Based on a recent proteome study of pearl millet under drought stress we compare our findings with wheat proteomes and another recent study which defined genetic marker in pearl millet.

Summary Genotyping‐by‐sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post‐transcriptional, translational, post‐translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment‐dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost‐effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment‐dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker‐dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large‐scale functional validation of trait‐specific precision breeding.

Being rooted in place, plants are faced with the challenge of responding to unfavourable local conditions. One such condition, heat stress, contributes massively to crop losses globally. Heatwaves are predicted to increase, and it is of vital importance to generate crops that are tolerant to not only heat stress but also to several other abiotic stresses (e.g. drought stress, salinity stress) to ensure that global food security is protected. A better understanding of the molecular mechanisms that underlie the temperature stress response in pollen will be a significant step towards developing effective breeding strategies for high and stable production in crop plants. While most studies have focused on the vegetative phase of plant growth to understand heat stress tolerance, it is the reproductive phase that requires more attention as it is more sensitive to elevated temperatures. Every phase of reproductive development is affected by environmental challenges, including pollen and ovule development, pollen tube growth, male-female cross-talk, fertilization, and embryo development. In this review we summarize how pollen is affected by heat stress and the molecular mechanisms employed during the stress period, as revealed by classical and -omics experiments.

Metabolomics is an essential technology for functional genomics and systems biology. It plays a key role in functional annotation of genes and understanding towards cellular and molecular, biotic and abiotic stress responses. Different analytical techniques are used to extend the coverage of a full metabolome. The commonly used techniques are NMR, CE-MS, LC-MS, and GC-MS. The choice of a suitable technique depends on the speed, sensitivity, and accuracy. This chapter provides insight into plant metabolomic techniques, databases used in the analysis, data mining and processing, compound identification, and limitations in metabolomics. It also describes the workflow of measuring metabolites in plants. Metabolomic studies in plant responses to stress are a key research topic in many laboratories worldwide. We summarize different approaches and provide a generic overview of stress responsive metabolite markers and processes compiled from a broad range of different studies. Graphical Abstract.

Chemical composition, antioxidant potential and corresponding lipid preoxidation of Indian commercial beers were evaluated. The presence of polyphenolic compounds such as tannic acid, gallic acid, catechol, vanillin, caffeic acid, quercetin, p-coumaric acid and rutin was quantified using LC-MS while the organic acids including tartaric, malic, acetic, citric and succinic acids were analysed using HPLC. Beer sample B8 had the greatest concentration of phenolic and flavonoid components (0.620 ± 0.084 mg/mL and 0.379 ± 0.020 mg/mL respectively) among the beer samples studied. The DPPH radical scavenging activity was observed in the range of 68.34 ± 0.85 % to 89.90 ± 0.71 % and ABTS radical cation scavenging activity was in the range of 59.75 ± 0.20 % to 76.22 ± 0.50 %. Percent protection in lipid peroxidation was quantified to be maximum (54.45 ± 3.39 %) in sample B5. Total phenolic content positively correlates with antioxidant assays, DPPH and ABTS (r = 0.35 and r = 0.58 respectively) with p < 0.001 and also with lipid peroxidation (r = 0.04) with p < 0.001. Negative correlation was observed between total flavonoid content with ABTS and lipid peroxidation (r = -0.1 and r = -0.05) respectively. The process of brewing warrants additional research to determine how the concentration of selected phenolic compounds can be increased.

The adaptive radiation of Bromeliaceae (pineapple family) is one of the most diverse among Neotropical flowering plants. Diversification in this group was facilitated by shifts in several adaptive traits or "key innovations" including the transition from C 3 to CAM photosynthesis associated with xeric (heat/drought) adaptation. We used phylogenomic approaches, complemented by differential gene expression (RNA-seq) and targeted metabolite profiling, to address the mechanisms of C 3 /CAM evolution in the extremely species-rich bromeliad genus, Tillandsia, and related taxa. Evolutionary analyses of whole-genome sequencing and RNA-seq data suggest that evolution of CAM is associated with coincident changes to different pathways mediating xeric adaptation in this group. At the molecular level, C 3 /CAM shifts were accompanied by gene expansion of XAP5 CIRCADIAN TIMEKEEPER homologs, a regulator involved in sugar-and light-dependent regulation of growth and development. Our analyses also support the reprogramming of abscisic acid-related gene expression via differential expression of ABF2/ABF3 transcription factor homologs, and adaptive sequence evolution of an ENO2/LOS2 enolase homolog, effectively tying carbohydrate flux to abscisic acid-mediated abiotic stress response. By pinpointing different regulators of overlapping molecular responses, our results suggest plausible mechanistic explanations for the repeated evolution of correlated adaptive traits seen in a textbook example of an adaptive radiation.