Extraordinary high allelic diversity in a groundnut (Arachis hypogaea L.) germplasm collection assayed by robust and informative SSR markers

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CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea

Molecular markers are valuable tools for breeders to help accelerate crop improvement. High throughput sequencing technologies facilitate the discovery of large-scale variations such as single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs). Sequencing of chickpea genome along with re-sequencing of several chickpea lines has enabled the discovery of 4.4 million variations including SNPs and InDels. Here we report a repository of 1.9 million variations (SNPs and InDels) anchored on eight pseudomolecules in a custom database, referred as CicArVarDB that can be accessed at http://cicarvardb.icrisat.org/. It includes an easy interface for users to select variations around specific regions associated with quantitative trait loci, with embedded webBLAST search and JBrowse visualisation. We hope that this database will be immensely useful for the chickpea research community for both advancing genetics research as well as breeding applications for crop improvement

Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)

Physical map of chickpea was developed for the reference chickpea genotype (ICC 4958) using bacterial artificial chromosome (BAC) libraries targeting 71,094 clones (~12× coverage). High information content fingerprinting (HICF) of these clones gave high-quality fingerprinting data for 67,483 clones, and 1,174 contigs comprising 46,112 clones and 3,256 singletons were defined. In brief, 574 Mb genome size was assembled in 1,174 contigs with an average of 0.49 Mb per contig and 3,256 singletons represent 407 Mb genome. The physical map was linked with two genetic maps with the help of 245 BAC-end sequence (BES)-derived simple sequence repeat (SSR) markers. This allowed locating some of the BACs in the vicinity of some important quantitative trait loci (QTLs) for drought tolerance and reistance to Fusarium wilt and Ascochyta blight. In addition, fingerprinted contig (FPC) assembly was also integrated with the draft genome sequence of chickpea. As a result, ~965 BACs including 163 minimum tilling path (MTP) clones could be mapped on eight pseudo-molecules of chickpea forming 491 hypothetical contigs representing 54,013,992 bp (~54 Mb) of the draft genome. Comprehensive analysis of markers in abiotic and biotic stress tolerance QTL regions led to identification of 654, 306 and 23 genes in drought tolerance “QTL-hotspot” region, Ascochyta blight resistance QTL region and Fusarium wilt resistance QTL region, respectively. Integrated physical, genetic and genome map should provide a foundation for cloning and isolation of QTLs/genes for molecular dissection of traits as well as markers for molecular breeding for chickpea improvement

[Cu]-catalyzed direct coupling of dibromoalkenes: Synthesis of symmetrical 1,3-diynes and triazoles

An efficient [Cu]-catalyzed homocoupling of 1,1-dibromoalk-1-enes is described for the synthesis of symmetrical 1,3-diyines. The method showed good substrate scope and amenable to aryl and heteroaryl systems. Significantly, the strategy was also successfully applied to the sequential one-pot synthesis of triazoles

Bifunctional nanocrystalline MgO for chiral epoxy ketones via claisen-schmidt condensation-asymmetric epoxidation reactions

Design and development of a truly nanobifunctional heterogeneous catalyst for the Claisen-Schmidt condensation (CSC) of benzaldehydes with acetophenones to yield chalcones quantitatively followed by asymmetric epoxidation (AE) to afford chiral epoxy ketones with moderate to good yields and impressive ee's is described. The nanomagnesium oxide (aerogel prepared) NAP-MgO was found to be superior over the NA-MgO and CM-MgO in terms of activity and enantioselectivity as applicable in these reactions. An elegant strategy for heterogenization of homogeneous catalysts is presented here to evolve single-site chiral catalysts for AE by a successful transfer of molecular chemistry to surface metal-organic chemistry with the retention of activity, selectivity/enantioselectivity. Bronsted hydroxyls are established as sole contributors for the epoxidation reaction, while they add on to the CSC, which is largely driven by Lewis basic O<SUP>2-</SUP>sites. Strong hydrogen-bond interactions between the surface -OH on MgO and -OH groups of diethyl tartrate are found inducing enantioselectivity in the AE reaction. Thus, the nanocrystalline NAP-MgO with its defined shape, size, and accessible OH groups allows the chemisorption of TBHP, DET, and olefin on its surface to accomplish single-site chiral catalysts to provide optimum ee's in AE reactions

The one-pot wittig reaction: a facile synthesis of α,β-unsaturated esters and nitriles by using nanocrystalline magnesium oxide

Nanocrystalline magnesium oxide was found to be an effective heterogeneous, solid base catalyst for the one-pot Wittig reaction to afford α,β-unsaturated esters and nitriles in excellent yields with high E-stereoselectivity in the presence of triphenylphosphine under mild conditions

Asymmetric Michael addition of malonates to enones catalyzed by nanocrystalline MgO

Highly enantioselective Michael addition of malonates to cyclic and acyclic enones has been achieved by using nanocrystalline magnesium oxide at -20 °C

Flowchart of NGS-QCbox pipeline illustrating the two modes of usage namely <i>quick</i> and <i>complete</i>.

<p>NGS-QCbox comprises of two workflow modes namely <i>quick</i> and <i>complete</i>. In <i>quick</i> mode, read/base level metrics are computed in parallel using Raspberry, an in-house tool, both before and after quality trimming. On the other hand, <i>complete</i> mode is full-fledged quality control and variant calling pipeline that integrates quick mode and additionally generates genome coverage information in parallel. Quality of the data generated could be assessed using this information.</p