Institutional Publications

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    Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement
    (Oxford University Press, 2017) Gupta, Sonal; Nawaz, Kashif; Parween, Sabiha; Roy, Riti; Sahu, Kamlesh; Pole, Anil Kumar; Khandal, Hitaishi; Srivastava, Rishi; Parida, Swarup K.; Chattopadhyay, Debasis
    Cicer reticulatum L. is the wild progenitor of the fourth most important legume crop chickpea (C. arietinum L.). We assembled short-read sequences into 416 Mb draft genome of C. reticulatum and anchored 78% (327 Mb) of this assembly to eight linkage groups. Genome annotation predicted 25,680 protein-coding genes covering more than 90% of predicted gene space. The genome assembly shared a substantial synteny and conservation of gene orders with the genome of the model legume Medicago truncatula. Resistance gene homologs of wild and domesticated chickpeas showed high sequence homology and conserved synteny. Comparison of gene sequences and nucleotide diversity using 66 wild and domesticated chickpea accessions suggested that the desi type chickpea was genetically closer to the wild species than the kabuli type. Comparative analyses predicted gene flow between the wild and the cultivated species during domestication. Molecular diversity and population genetic structure determination using 15,096 genome-wide single nucleotide polymorphisms revealed an admixed domestication pattern among cultivated (desi and kabuli) and wild chickpea accessions belonging to three population groups reflecting significant influence of parentage or geographical origin for their cultivar-specific population classification. The assembly and the polymorphic sequence resources presented here would facilitate the study of chickpea domestication and targeted use of wild Cicer germplasms for agronomic trait improvement in chickpea.
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    Millets: genetic and genomic resources
    (John Wiley & Sons, 2011) Dwivedi, Sangam; Upadhyaya, Hari; Senthilvel, Senapathy; Hash, Charles; Fukunaga, Kenji; Diao, Xiamin; Santra, Dipak; Baltensperger, David; Prasad, Manoj
    all-grained millets, comprising ten annual grasses from the family Poaceae and grown for grain, contribute $13% of annual global cereal production. Some are widely grown, while cultivation of others is restricted. They differ in ploidy, genome size, and breeding system, but their grains are all highly nutritious. Their most common nonfood uses are in brewing and as livestock feeds. Millets are C4 plants adapted to marginal lands in hot, drought-prone arid and semiarid regions. Selection for plant phenology and architecture, panicle shape, spikelet structure and reduced shattering, seed dormancy, and seed coat hardness contributed to their domestication. Approximately 161,708 millet accessions are preserved in gene banks globally. These show exceptional diver- sity associated for phenology, photoperiod sensitivity, tolerance to abiotic stresses, resistance to biotic stresses, seed storability and shelf life, and specific grain characteristics associated with end user preferences. Contributions from wild relatives’ toward enhancing cultivated gene pools have been limited to pearl millet and foxtail millet. Core or minicore/reference collections have been used to identify new sources of biotic stress resistances and abiotic stress tolerances. Waxy mutants have been selected in barnyard millet, foxtail millet, and proso millet for specific food uses. Pearl millet hybrids and open pollinated varieties (OPVs) with high iron and zinc grain densities will soon be available in India. While no transgenic work has reached field level, DNA markers are routinely used to assess millets’ population structure and genetic diversity. Genetic maps of varying density are reported in finger millet, foxtail millet, pearl millet, proso millet, and tef. Major quantitative trait loci associated with resis- tance to downy mildew, rust, and blast and tolerance to terminal drought stress have been backcrossed into elite inbred pearl millet hybrid parents. Marker- assisted backcrossing has been used to improve downy mildew resistance in pearl millet. Cytoplasmic-genetic male sterility (CMS)–based hybrids of pearl millet are extensively cultivated, and CMS systems for foxtail millet are under development. An aligned genome sequence of foxtail millet will be released in the near future as this millet is closely related to several polyploid bioenergy grasses. This foxtail millet genome sequence is highly syntenic with those of rice, sorghum, and maize, which should allow comprehensive surveys of genetic diversity for identifying and conserving diversity in grass germplasm with bioenergy crop potential.