Single-molecule DNA sequencing technologies for future genomics research

During the current genomics revolution, the genomes of a large number of living organisms have been fully sequenced. However, with the advent of new sequencing technologies, genomics research is now at the threshold of a second revolution. Several second-generation sequencing platforms became available in 2007, but a further revolution in DNA resequencing technologies is being witnessed in 2008, with the launch of the first single-molecule DNA sequencer (Helicos Biosciences), which has already been used to resequence the genome of the M13 virus. This review discusses several single-molecule sequencing technologies that are expected to become available during the next few years and explains how they might impact on genomics research

Guest Editorial: Computational Biology

Computational biology has been used to help sequence the human genome, create accurate models of the human brain, and assist in modeling biological systems. With the availability of massive datasets, it has also become possible to study different systems in an organism in its entirety, thus aiding the sciences of systems biology and integrative biology

Abnormal meiosis in hexaploid Setaria verticillata

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Genetics and breeding for resistance against four leaf spot diseases in wheat (Triticum aestivum L.)

In wheat, major yield losses are caused by a variety of diseases including rusts, spike diseases, leaf spot and root diseases. The genetics of resistance against all these diseases have been studied in great detail and utilized for breeding resistant cultivars. The resistance against leaf spot diseases caused by each individual necrotroph/hemi-biotroph involves a complex system involving resistance (R) genes, sensitivity (S) genes, small secreted protein (SSP) genes and quantitative resistance loci (QRLs). This review deals with resistance for the following four-leaf spot diseases: (i) Septoria nodorum blotch (SNB) caused by Parastagonospora nodorum; (ii) Tan spot (TS) caused by Pyrenophora tritici-repentis; (iii) Spot blotch (SB) caused by Bipolaris sorokiniana and (iv) Septoria tritici blotch (STB) caused by Zymoseptoria tritici

Genetics of spot blotch resistance in bread wheat (Triticum aestivum L.) using five models for GWAS

Genetic architecture of resistance to spot blotch in wheat was examined using a Genome-Wide Association Study (GWAS) involving an association panel comprising 303 diverse genotypes. The association panel was evaluated at two different locations in India including Banaras Hindu University (BHU), Varanasi (Uttar Pradesh), and Borlaug Institute for South Asia (BISA), Pusa, Samastipur (Bihar) for two consecutive years (2017-2018 and 2018-2019), thus making four environments (E1, BHU 2017-18; E2, BHU 2018-19; E3, PUSA, 2017-18; E4, PUSA, 2018-19). The panel was genotyped for 12,196 SNPs based on DArT-seq (outsourced to DArT Ltd by CIMMYT); these SNPs included 5,400 SNPs, which could not be assigned to individual chromosomes and were therefore, described as unassigned by the vendor. Phenotypic data was recorded on the following three disease-related traits: (i) Area Under Disease Progress Curve (AUDPC), (ii) Incubation Period (IP), and (iii) Lesion Number (LN). GWAS was conducted using each of five different models, which included two single-locus models (CMLM and SUPER) and three multi-locus models (MLMM, FarmCPU, and BLINK). This exercise gave 306 MTAs, but only 89 MTAs (33 for AUDPC, 30 for IP and 26 for LN) including a solitary MTA detected using all the five models and 88 identified using four of the five models (barring SUPER) were considered to be important. These were used for further analysis, which included identification of candidate genes (CGs) and their annotation. A majority of these MTAs were novel. Only 70 of the 89 MTAs were assigned to individual chromosomes; the remaining 19 MTAs belonged to unassigned SNPs, for which chromosomes were not known. Seven MTAs were selected on the basis of minimum P value, number of models, number of environments and location on chromosomes with respect to QTLs reported earlier. These 7 MTAs, which included five main effect MTAs and two for epistatic interactions, were considered to be important for marker-assisted selection (MAS). The present study thus improved our understanding of the genetics of resistance against spot blotch in wheat and provided seven MTAs, which may be used for MAS after due validation

Physical mapping of wheat and rye expressed sequence tag-simple sequence repeats on wheat chromosomes

Six hundred and seventy two loci belonging to 275 expressed sequence tag-simple sequence repeats [EST-SSRs, including 93 wheat (Triticum aestivum L.) and 182 rye (Secale cereale L.) EST-SSRs] were physically mapped on 21 wheat chromosomes. The mapping involved two approaches, the wet-lab approach involving use of deletion stocks and the in silico approach involving matching with ESTs that were previously mapped. The number of loci per EST-SSR mapped using the in silico approach was almost double the number of loci mapped using the wet-lab approach (using deletion stocks). The distribution of loci on the three subgenomes, on the seven homoeologous groups and on the 21 individual chromosomes was nonrandom (P « 0.01). Long arms had disproportionately (relative to the difference in DNA content) higher number of loci, with more loci mapped to the distal regions of chromosome arms. A fairly high proportion of EST-SSRs had multiple loci, which were largely (81%) homoeoloci. Rye EST-SSRs showed a high level of transferability (≈77%) to the wheat genome. Putative functions were assigned to 216 SSR-containing ESTs through homology searches against the protein database. As many as 104 SSR-containing ESTs (a subset of the above ESTs) were also mapped to the 12 rice chromosomes, which corresponded with the known homology between wheat and rice chromosomes. These physical maps of EST-SSRs should prove useful for comparative genomics, gene tagging, fine mapping, and cloning of genes and QTLs. Dna-based molecular markers, particularly SSRs, have been developed and mapped on chromosomes in a variety of crop plants. In bread wheat, genetic and physical mapping of SSRs has been an ongoing exercise, and, to date, ≈2450 SSRs (1 SSR 1.63 cM-1) have been genetically mapped (for details see Torada et al., 2006) and ≈1320 SSRs (62 SSRs chromosome-1) have been physically mapped (for details see Goyal et al., 2005). With a genome size of ≈16 000 Mbp, it is evident that despite concerted efforts, the density of mapped SSRs in bread wheat remains relatively low and continued efforts are needed to increase the density of these SSRs on available genetic and physical maps. In recent years, emphasis has also shifted from genomic SSRs to EST-SSRs due to the availability of very large databases of ESTs from all of the cereals including bread wheat. Consequently, the number of EST-SSRs in cereals now includes 43 598 from bread wheat (Peng and Lapitan, 2005), 16 917 from rice and 184 from rye (La Rota et al., 2005; Hackauf and Wehling, 2002). The genetic mapping of these EST-SSRs is difficult due to a low level of polymorphism, as a result of their conserved nature. Physical mapping of these EST-SSRs in wheat is equally difficult due to the occurrence of homoeoloci exhibiting no polymorphism. This has discouraged wheat researchers from undertaking a large-scale project to genetically or physically map wheat EST-SSRs although genetic mapping of 325 EST-SSRs (Gao et al., 2004; Nicot et al., 2004; Yu et al., 2004) and physical mapping of 305 EST-SSRs was recently undertaken (Yu et al., 2004; Zhang et al., 2005; Peng and Lapitan, 2005). We previously reported genetic mapping of 58 and physical mapping of 270 genomic SSRs (Gupta et al., 2002; Goyal et al., 2005). The present study is an extension of our earlier studies on physical mapping of SSRs and involved both wet-lab and in silico approaches, leading to the successful mapping of as many as 672 loci. The in silico approach allowed mapping of twice the number of loci (per EST-SSR) mapped using wet-lab analysis

Dependence of Exchange Bias on Interparticle Interactions in Co/CoO Core/Shell Nanostructures

This article reports the dependence of exchange bias (EB) effect on interparticle interactions in nanocrystalline Co/CoO core/shell structures, synthesized using the conventional sol-gel technique. Analysis via powder X-Ray diffraction (PXRD) studies and transmission electron microscope (TEM) images confirm the presence of crystalline phases of core/shell Co/CoO with average particle size ≈ 18 nm. Volume fraction (φ) is varied (from 20% to 1%) by the introduction of a stoichiometric amount of non-magnetic amorphous silica matrix (SiO2) which leads to a change in interparticle interaction (separation). The influence of exchange and dipolar interactions on the EB effect, caused by the variation in interparticle interaction (separation) is studied for a series of Co/CoO core/shell nanoparticle systems. Studies of thermal variation of magnetization (M−T) and magnetic hysteresis loops (M−H) for the series point towards strong dependence of magnetic properties on dipolar interaction in concentrated assemblies whereas individual nanoparticle response is dominant in isolated nanoparticle systems. The analysis of the EB effect reveals a monotonic increase of coercivity (HC) and EB field (HE) with increasing volume fraction. When the nanoparticles are close enough and the interparticle interaction is significant, collective behavior leads to an increase in the effective antiferromagnetic (AFM) CoO shell thickness which results in high HC and HE. Moreover, in concentrated assemblies, the dipolar field superposes to the local exchange field and enhances the EB effect contributing as an additional source of unidirectional anisotropy