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Subject: search.filters.subject.Foxtail Millet

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    Genome-wide association study of major agronomic traits in foxtail millet (Setaria italica L.) using ddRAD sequencing
    (Springer Nature, 2019) Jaiswal, Vandana; Gupta, Sarika; Gahlaut, Vijay; Muthamilarasan, Mehanathan; Bandyopadhyay, Tirthankar; Ramchiary, Nirala; Prasad, Manoj
    Foxtail millet (Setaria italica), the second largest cultivated millet crop after pearl millet, is utilized for food and forage globally. Further, it is also considered as a model crop for studying agronomic, nutritional and biofuel traits. In the present study, a genome-wide association study (GWAS) was performed for ten important agronomic traits in 142 foxtail millet core eco-geographically diverse genotypes using 10 K SNPs developed through GBS-ddRAD approach. Number of SNPs on individual chromosome ranged from 844 (chromosome 5) to 2153 (chromosome 8) with an average SNP frequency of 25.9 per Mb. The pairwise linkage disequilibrium (LD) estimated using the squared-allele frequency correlations was found to decay rapidly with the genetic distance of 177 Kb. However, for individual chromosome, LD decay distance ranged from 76 Kb (chromosome 6) to 357 Kb (chromosome 4). GWAS identified 81 MTAs (marker-trait associations) for ten traits across the genome. High confidence MTAs for three important agronomic traits including FLW (flag leaf width), GY (grain yield) and TGW (thousand-grain weight) were identified. Significant pyramiding effect of identified MTAs further supplemented its importance in breeding programs. Desirable alleles and superior genotypes identified in the present study may prove valuable for foxtail millet improvement through marker-assisted selection.
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    Genome-wide association studies for improving agronomic traits in foxtail millet
    (Springer, 2017) Singh, Roshan Kumar; Prasad, Manoj
    With the immense advancements in sequencing and data mining approaches, identification of genome-wide genetic variants in a population has become very popular. The use of these resources in the development of a dense genetic map of genome variations and to identify associated quantitative traits has become widespread in crop genetics. In recent years, genome-wide association study (GWAS) has become a powerful tool in revealing the relationship between natural variation of complex genotype and genetic locus. A slight variation in the genetic architecture of an individual in a population results in contrasting agronomic traits compared to the other individuals. GWAS utilized high-throughput genotyping platform and extensively phenotyping data to detect the links between genetic variations that underlie variations in agronomic traits. These studies can accelerate the use of genomic selection in marker-assisted breeding for crop improvement. Here, a brief discussion of available genomic resources and their utilization, quantitative trait loci (QTL) underlying agronomic traits, GWAS in foxtail millet, and the prospects for this field in crop designing is given.
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    Foxtail millet: An introduction
    (Springer, 2017) Singh, Roshan Kumar; Muthamilarasan, Mehanathan; Prasad, Manoj
    Foxtail millet (Setaria italica L.) is a versatile crop known for being genetically closely related to biofuel grasses, for its C4 photosynthesis, and for its tolerance to abiotic stresses. These attributes have made this crop a model system and, in view of this, the genome of foxtail millet has been sequenced. Among millets, foxtail millet is the only crop possessing rich genetic and genomic resources, and globally it is the second most cultivated millet next to pearl millet. In the context of its importance in agronomic and research terms, the present chapter summarizes the origin, domestication, phylogeny, and agroeconomic importance of foxtail millet.
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    Foxtail millet genome sequencing, assembly, annotation, and application
    (Springer, 2017) Muthamilarasan, Mehanathan; Shweta, Shweta; Prasad, Manoj
    Among millets, foxtail millet (Setaria italica L.) is a well-studied crop, which is known for its genetic close-relatedness to biofuel grasses and cereals, C4 photosynthesis, and appreciable tolerance to broad-spectrum abiotic stresses. Foxtail millet, along with its wild ancestor, green foxtail (S. viridis L.), are accentuated as model crops for studying the aforementioned traits. In view of their importance, the genomes have been sequenced and released. The present chapter summarizes the sequencing efforts, the outcomes, and the application of sequence information in expediting genomics studies. In addition, the chapter also provides a snapshot of how the genome sequence information has been exploited to develop different genomic resources useful for crop improvement.
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    Nutrition potential of foxtail millet in comparison to other millets and major cereals
    (Springer, 2017) Bandyopadhyay, Tirthankar; Jaiswal, Vandana; Prasad, Manoj
    Global population is burgeoning at an alarming rate and is expected to reach 9.7 billion by 2050 and 11.2 billion by the end of this century. This has led to immense pressure on global agriculture, compounded by dwindling productivity of the existing systems and acreage because of climate change, resulting in ever-increasing input costs for the cultivation of most resource-intensive cereal crops such as rice, wheat, and maize. Ironically, the most affected populations are those with least resources to mitigate the problem—those belonging to Asian and Sub-Saharan Africa. It is against this backdrop that there is an ever-increasing need for adopting cereal crops that are easy to cultivate, less resource hungry, climate resilient, and importantly, that meet the major nutritional requirement of the feeding population. Foxtail millet is a perfect cereal crop in this light and stands to help significantly global endeavors toward food security and nutrition. The present chapter provides a comparative nutritional assessment of foxtail millet with other cereal crops, summarizes the major scientific approaches currently being undertaken for its biofortification and highlights potential avenues of crop improvement using conventional breeding, genomics, and other interdisciplinary “omic” tools.
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    FmMDb: A versatile database of foxtail millet markers for millets and bioenergy grasses research
    (PLOS, 2013) Suresh B, Venkata; Muthamilarasan, Mehanathan; Misra, Gopal; Prasad, Manoj
    The prominent attributes of foxtail millet (Setaria italica L.) including its small genome size, short life cycle, inbreeding nature, and phylogenetic proximity to various biofuel crops have made this crop an excellent model system to investigate various aspects of architectural, evolutionary and physiological significances in Panicoid bioenergy grasses. After release of its whole genome sequence, large-scale genomic resources in terms of molecular markers were generated for the improvement of both foxtail millet and its related species. Hence it is now essential to congregate, curate and make available these genomic resources for the benefit of researchers and breeders working towards crop improvement. In view of this, we have constructed the Foxtail millet Marker Database (FmMDb; http://www.nipgr.res.in/foxtail.html), a comprehensive online database for information retrieval, visualization and management of large-scale marker datasets with unrestricted public access. FmMDb is the first database which provides complete marker information to the plant science community attempting to produce elite cultivars of millet and bioenergy grass species, thus addressing global food insecurity.
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    Comprehensive genome-wide survey, genomic constitution and expression profiling of the NAC transcription factor family in foxtail millet (Setaria italica L.)
    (PLOS, 2013) Puranik, Swati; Sahu, Pranav Pankaj; Mandal, Sambhu Nath; Suresh B., Venkata; Parida, Swarup K.; Prasad, Manoj
    The NAC proteins represent a major plant-specific transcription factor family that has established enormously diverse roles in various plant processes. Aided by the availability of complete genomes, several members of this family have been identified in Arabidopsis, rice, soybean and poplar. However, no comprehensive investigation has been presented for the recently sequenced, naturally stress tolerant crop, Setaria italica (foxtail millet) that is famed as a model crop for bioenergy research. In this study, we identified 147 putative NAC domain-encoding genes from foxtail millet by systematic sequence analysis and physically mapped them onto nine chromosomes. Genomic organization suggested that inter-chromosomal duplications may have been responsible for expansion of this gene family in foxtail millet. Phylogenetically, they were arranged into 11 distinct sub-families (I-XI), with duplicated genes fitting into one cluster and possessing conserved motif compositions. Comparative mapping with other grass species revealed some orthologous relationships and chromosomal rearrangements including duplication, inversion and deletion of genes. The evolutionary significance as duplication and divergence of NAC genes based on their amino acid substitution rates was understood. Expression profiling against various stresses and phytohormones provides novel insights into specific and/or overlapping expression patterns of SiNAC genes, which may be responsible for functional divergence among individual members in this crop. Further, we performed structure modeling and molecular simulation of a stress-responsive protein, SiNAC128, proffering an initial framework for understanding its molecular function. Taken together, this genome-wide identification and expression profiling unlocks new avenues for systematic functional analysis of novel NAC gene family candidates which may be applied for improvising stress adaption in plants.