Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects

The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability

Preparation of low-cost magnetic nitrocellulose microbeads

In this work, new magnetic particles were prepared in uniform and spherical form for the range 125 mu m < D-p < 250 mu m from nitrocellulose and magnetite through a modified solvent evaporation technique. The most appropriate solvent, dispersion medium, stabilization and surface active agents and stirring rate were determined as acetone and 1,2-dichloroethane mixture, glycerol, SDS and pluronic F68 together with PVA and 700 rev./min, respectively. The magnet abundant in nature, magnetite (D-p < 40 mu m), was successfully embedded in the particle structure during polymerization by an elaborated technique. Fine spherical particles with high magnetic quality (similar to 4.8 emu/g microbead at 6 kG magnetic field intensity) were produced for magnetically fluidized bed or magnetic filtration applications. Hydroxyl groups on the particle surface were activated with glutaraldehyde for the immobilization of a saccarifying enzyme, glucoamylase. (C) 2000 Elsevier Science B.V. All rights reserved

A low cost porous polyvinylbutyral membrane for BSA adsorption

In this work, a feasible membrane was prepared in uniform thickness for the range 120-145 mum from a commercial resin, Mowital(R) B30HH (polyvinylbutyral) using phase inversion technique. For the production of the membrane, the most appropriate solvent, polymer concentration, temperature and the composition of casting solution were investigated. Macroporous membranes were produced with 6-20% (w/v) polymer concentration using N,N-dimethylacedamid and water as the solvent and casting solution, respectively, at 20degreesC, determined to be the optimum chemicals and conditions. It was found that pore size, pore density, water permeation rate, water content, and elongation of the membranes decreased while breakpoint stress increased with the increase of polymer concentration. FT-IR studies proved the abundance of hydroxyl groups on the membrane surface, which were activated later by glutaraldehyde for bovine serum albumin (BSA) separation. Preliminary adsorption runs were conducted at pH 5.0, determined to be the optimum for BSA adsorption, with the membrane prepared at 9% polymer concentration in a batch reactor. For 10 mg/ml initial BSA concentration, the adsorbed BSA was calculated as 427 mug/cm(2) (35.44 mg/ml membrane) denoting a remarkable capacity for BSA adsorption compare to those of other membranes in literature. (C) 2004 Elsevier B.V. All rights reserved

A hybrid epithelial-mesenchymal transition program enables basal epithelial cells to bypass stress-induced stasis and contributes to a metaplastic breast cancer progenitor state

Abstract Background Human mammary epithelial cell (HMEC) cultures encounter a stress-associated barrier termed stasis, during which most cells adopt a senescence-like phenotype. From these cultures, rare variants emerge from the basal epithelial population, re-initiating growth. Variants exhibit pre-malignant properties, including an aberrant epigenetic program that enables continued proliferation and acquisition of genetic changes. Following oncogenic transformation, variants produce tumors that recapitulate the histopathological characteristics of metaplastic breast cancer (MBC), a rare and aggressive subtype marked by the differentiation of neoplastic epithelium into squamous and mesenchymal elements. Methods Using a serum-free HMEC culture system, we probed the capacity for phenotypic plasticity inherent to basal epithelial cell populations from human breast tissue as they navigated stasis and emerged as variant populations. Results We observed robust activation of a TGF-β-dependent epithelial-mesenchymal transition (EMT) program in basal epithelial cells during stasis, followed by subsequent attenuation of this program in emerging variants. Inhibition of the TGF-β pathway or depleting the EMT regulators Snail or Slug allowed basal epithelial cells to collectively bypass stasis, demonstrating that cellular dysfunction and arrest resulting from TGF-β and EMT activation are central to this in vitro barrier. The spontaneous emergence of variants from stasis cultures was associated with a restricted EMT trajectory, characterized by the stabilization of hybrid EMT states associated with greater proliferative capacity, rather than progressing to a complete mesenchymal state characterized by irreversible growth arrest. Epigenetic mechanisms, which contributed to the dysregulated growth control characteristic of the variant phenotype, also contributed to the stability of the hybrid EMT program in variants. By overcoming the cellular dysfunction and growth arrest resulting from TGF-β and complete EMT, variants exhibited a higher oncogenic transformation efficiency compared to pre-stasis basal epithelial cells. Inhibiting the TGF-β pathway prior to stasis significantly reduced EMT in the basal epithelial population, alleviated selective pressure driving variant emergence, and also enhanced oncogenic transformation efficiency, resulting in tumors with markedly diminished metaplastic differentiation. Conclusions This study reveals how an epigenetic program governs basal epithelial cell fate decisions and contributes to the development of MBC progenitors by restricting access to terminal mesenchymal states that induce growth arrest and, instead, favoring hybrid EMT states with enhanced tumorigenic potential

SOX2, OCT3/4 and NANOG expression and cellular plasticity in rare human somatic cells requires CD73.

Endogenous Plastic Somatic (ePS) cells isolated from adult human tissues exhibit extensive lineage plasticity in vitro and in vivo. Here we visualize these rare ePS cells in a latent state, i.e. lacking SOX2, OCT3/4 and NANOG (SON) expression, in non-diseased breast specimens through immunohistochemical analysis of previously identified ePS-specific biomarkers (CD73+, EpCAM+ and CD90-). We also report a novel mechanism by which these latent ePS cells acquire SON expression and plasticity in vitro. Four extracellular factors are necessary for the acquisition of SON expression and lineage plasticity in ePS cells: adenosine (which is produced by the 5' ecto-nucleotidase CD73 and activates in turn the PKA-dependent IL6/STAT3 pathway through the adenosine receptor ADORA2b), IL6, FGF2 and ACTIVIN A. Blocking any pathway component renders ePS cells incapable of SON expression and lineage plasticity. Notably, hESCs do not use adenosine or IL6 nor they express CD73 or ADORA2b and inhibition of adenosine signaling does not ablate their plasticity. Therefore, the data presented here delineate novel circuitry and physiological signals for accessing SON expression in rare, undifferentiated human cells

Identification of markers associated with traits for use in marker-assisted selection in saffron

Odredivanje veze izmedu molekularnih markera i agronomskih osobina predstavlja odlican alat za selekciju pomo u markera. U ovoj studiji, multivarijantna stepenasta regresiona analiza korišcena je za procenu veze izmedu SSR markera i nekih agronomskih osobina u ekotipovima šafrana. a analize asocijacija koriš ene su dvogodišnje prosecne vrednosti za izmerene osobine. Rezultati postupne analize regresije otkrili su znacajnu asocijaciju izmedu osobina i proucavanih lokusa. Identifikovano je ukupno 25 SSR markera. Markeri SCA382, SCA15 i SCD219 bili su povezani sa ve inom osobina, i mogu se koristiti kao kandidat markeri u selekciji pomo u molekularnih markera. © 2018, Serbian Genetics Society.Determination of association between molecular markers and agronomic traits provides an excellent tool for marker-assisted selection. In this study, multivariate stepwise regression analysis was used to estimate associations between SSR markers and some agronomic traits in saffron ecotypes. Two-year average values for the measured traits were used for association analyses. The results of stepwise regression analysis revealed significant associations between the traits and some of the studied loci. More than one informative marker was detected for most of the traits. Totally 25 informative SSR markers were identified in two years. Markers SCA382, SCA15 and SCD219 were associated with most traits under both years. These markers are considered to be relatively more reliable. Among the SSR primers, special attention should be drawn to primers SCA382, SCA15, and SCD219, which had the highest associated fragments with most traits in two years and could be considered for use as candidate markers in marker-assisted selection. © 2018, Serbian Genetics Society

Candidate gene analysis of organ pigmentation loci in the Solanaceae

Ten structural genes from the Capsicum (pepper) carotenoid biosynthetic pathway have been localized on a ( Capsicum annuum × Capsicum chinense )F 2 genetic map anchored in Lycopersicon (tomato). The positions of these genes were compared with positions of the same genes in tomato when known, and with loci from pepper, potato, and tomato that affect carotenoid levels in different tissues. C2, one of three phenotypically defined loci determining pepper fruit color, cosegregated with phytoene synthase. The capsanthin–capsorubin synthase ( Ccs ) locus, shown previously to cosegregate with Y, another pepper fruit color locus, mapped to pepper chromosome 6. Other structural genes in pepper corresponded to loci affecting carotenoid production as follows: Ccs in pepper and the B locus for hyperaccumulation of β-carotene in tomato fruit mapped to homeologous regions; the position of the lycopene β-cyclase gene in pepper may correspond to the lutescent-2 mutation in tomato; and the lycopene ɛ-cyclase locus in pepper corresponded to the lycopene ɛ-cyclase locus/ Del mutation for hyperaccumulation of δ-carotene in tomato fruit. Additional associations were seen between the structural genes and previously mapped loci controlling quantitative variation in pepper and tomato fruit color. These results demonstrate that comparative analyses using candidate genes may be used to link specific metabolic phenotypes and loci that affect these phenotypes in related species. </jats:p