Single seed-based high-throughput genotyping and rapid generation advancement for accelerated groundnut genetics and breeding research

The groundnut breeding program at International Crops Research Institute for the Semi-Arid Tropics routinely performs marker-based early generation selection (MEGS) in thousands of segregating populations. The existing MEGS includes planting of segregating populations in fields or glasshouses, label tagging, and sample collection using leaf-punch from 20–25 day old plants followed by genotyping with 10 single nucleotide polymorphisms based early generation selection marker panels in a high throughput genotyping (HTPG) platform. The entire process is laborious, time consuming, and costly. Therefore, in order to save the time of the breeder and to reduce the cost during MEGS, we optimized a single seed chipping (SSC) process based MEGS protocol and deployed on large scale by genotyping >3000 samples from ongoing groundnut breeding program. In SSC-based MEGS, we used a small portion of cotyledon by slicing-off the posterior end of the single seed and transferred to the 96-deep well plate for DNA isolation and genotyping at HTPG platform. The chipped seeds were placed in 96-well seed-box in the same order of 96-well DNA sampling plate to enable tracking back to the selected individual seed. A high germination rate of 95–99% from the chipped seeds indicated that slicing of seeds from posterior end does not significantly affect germination percentage. In addition, we could successfully advance 3.5 generations in a year using a low-cost rapid generation turnover glass-house facility as compared to routine practice of two generations in field conditions. The integration of SSC based genotyping and rapid generation advancement (RGA) could significantly reduce the operational requirement of person-hours and expenses, and save a period of 6–8 months in groundnut genetics and breeding research

Nutraceutical potential of Ficus roxburghii an underutilized fruit of Sikkim Himalayas

Ficus roxburghii, “Elephant ear fig “or wild fig is one of very popular fruits found growing wild in the hills of North Eastern and North Western Himalayan region. The fruit of wild fig has also been used as medicine by the tribal people of Sikkim and other states of India. Keeping this in view, the present study was conducted at Laboratory of Department of Horticulture, Sikkim University, Sikkim to access the different nutraceuticals properties as nutritional constituent like protein, fat, fibre, carbohydrate and energy value, mineral content viz.Ca, K, Mg, Na, Zn, Co, Mo, Fe, Mn and phytochemical content such as total phenols, flavonoid, ascorbic acid, anthocyanin and total carotenoids of F. roxburghii. The results of present study revealed that fruit of F. roxburghii contains significant amount of nutritional, mineral and phytochemical properties viz. protein (3.00±0.06%), fat (0.13±0.04%), fibre (3.06±0.02%), carbohydrate (90.81±0.44 %), energy value (376.45±1.44), Ca (23.69 ± 1.7), Mg  (73.09 ± 2.1), K (819.64 ± 12.54), Mo (0.58 ±  0.06), Na (6.73 ± 1.2), Zn (0.34 ± 0.10). Fe (26.55 ± 2.8), Cu (4.22 ± 0.20), Mn (7.11 ± 0.11), total phenols (4.13±0.52 mg GAE/ G), total flavonoid (3.10±0.09 mg GAE/ G), ascorbic acid (3.36±0.27 mg GAE/ G), anthocyanin (1.13±0.15 mg GAE/ G) and total carotenoids (0.68±0.10 mg GAE/ G). It may be concluded that the fruit of F. roxburghiiis rich in nutraceuticals and must be incorporated in our balanced diet

Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.)

Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes

Dimensional stabilization of wood by chemical modification using isopropenyl acetate

Chemical modification of wood with isopropenyl acetate (IPA) using iodine (I2) as catalyst has been carried out. Rubber wood (Hevea brasiliensis) specimens were reacted with IPA using iodine (I2) catalyst at 95°C up to 10 h under solvent free conditions. The effect of catalyst concentration and reaction time was studied. The extent of acetylation was measured by determining weight percent gain and the modified wood was characterized by FTIR-ATR and 13C NMR spectroscopy. It was found that IPA in the presence of iodine is an excellent acylating reagent for wood. Modified wood exhibited highdimensional stabilit

Genomic tools in groundnut breeding program: Status and perspectives

Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut

Comparative transcriptome analysis identified candidate genes for late leaf spot resistance and cause of defoliation in groundnut

Late leaf spot (LLS) caused by fungus Nothopassalora personata in groundnut is responsible for up to 50% yield loss. To dissect the complex nature of LLS resistance, comparative transcriptome analysis was performed using resistant (GPBD 4), susceptible (TAG 24) and a resistant introgression line (ICGV 13208) and identified a total of 12,164 and 9954 DEGs (differentially expressed genes) respectively in A- and B-subgenomes of tetraploid groundnut. There were 135 and 136 unique pathways triggered in A- and B-subgenomes, respectively, upon N. personata infection. Highly upregulated putative disease resistance genes, an RPP-13 like (Aradu.P20JR) and a NBS-LRR (Aradu.Z87JB) were identified on chromosome A02 and A03, respectively, for LLS resistance. Mildew resistance Locus (MLOs)-like proteins, heavy metal transport proteins, and ubiquitin protein ligase showed trend of upregulation in susceptible genotypes, while tetratricopeptide repeats (TPR), pentatricopeptide repeat (PPR), chitinases, glutathione S-transferases, purple acid phosphatases showed upregulation in resistant genotypes. However, the highly expressed ethylene responsive factor (ERF) and ethylene responsive nuclear protein (ERF2), and early responsive dehydration gene (ERD) might be related to the possible causes of defoliation in susceptible genotypes. The identified disease resistance genes can be deployed in genomics-assisted breeding for development of LLS resistant cultivars to reduce the yield loss in groundnut

Mitigating aflatoxin contamination in groundnut through a combination of genetic resistance and post-harvest management practices

Aflatoxin is considered a “hidden poison” due to its slow and adverse effect on various biological pathways in humans, particularly among children, in whom it leads to delayed development, stunted growth, liver damage, and liver cancer. Unfortunately, the unpredictable behavior of the fungus as well as climatic conditions pose serious challenges in precise phenotyping, genetic prediction and genetic improvement, leaving the complete onus of preventing aflatoxin contamination in crops on post-harvest management. Equipping popular crop varieties with genetic resistance to aflatoxin is key to effective lowering of infection in farmer’s fields. A combination of genetic resistance for in vitro seed colonization (IVSC), pre-harvest aflatoxin contamination (PAC) and aflatoxin production together with pre- and post-harvest management may provide a sustainable solution to aflatoxin contamination. In this context, modern “omics” approaches, including next-generation genomics technologies, can provide improved and decisive information and genetic solutions. Preventing contamination will not only drastically boost the consumption and trade of the crops and products across nations/regions, but more importantly, stave off deleterious health problems among consumers across the globe

Identification of two major quantitative trait locus for fresh seed dormancy using the diversity arrays technology and diversity arrays technology-seq based genetic map in Spanish-type peanuts

Seed quality for both germination in the next generation and for human consumption is adversely affected due to preharvest sprouting in peanut. It also makes seeds more vulnerable to infection by a number of pathogens. Therefore, it is desirable to have 2–3 weeks of fresh seed dormancy (FSD) in the peanut varieties. In this context, one F2 population was developed from a cross between non-dormant (ICGV 00350) and dormant (ICGV 97045) genotypes. Phenotyping of this population showed control of the trait by two recessive genes. In parallel, genotyping of the population with Diversity Arrays Technology (DArT) and DArT-seq markers provided a genetic map with 1152 loci covering a map distance of 2423.12 cM and map density of 2.96 cM/loci. Quantitative trait locus (QTL) analysis identified two major QTLs, namely qfsd-1 and qfsd-2 explaining 22.14% and 71.21% of phenotypic variation, respectively. These QTLs, after validation in different genetic backgrounds, may be useful for molecular breeding for FSD in peanut

Prototype tasks: Improving crowdsourcing results through rapid, iterative task design

Low-quality results have been a long-standing problem on microtask crowdsourcing platforms, driving away requesters and justifying low wages for workers. To date, workers have been blamed for low-quality results: they are said to make as little effort as possible, do not pay attention to detail, and lack expertise. In this paper, we hypothesize that requesters may also be responsible for low-quality work: they launch unclear task designs that confuse even earnest workers, under-specify edge cases, and neglect to include examples. We introduce prototype tasks, a crowdsourcing strategy requiring all new task designs to launch a small number of sample tasks. Workers attempt these tasks and leave feedback, enabling the requester to iterate on the design before publishing it. We report a field experiment in which tasks that underwent prototype task iteration produced higher-quality work results than the original task designs. With this research, we suggest that a simple and rapid iteration cycle can improve crowd work, and we provide empirical evidence that requester “quality” directly impacts result quality

An investigation of the potential application of chitosan/aloe-based membranes for regenerative medicine

A significant number of therapeutics derived from natural polymers and plants have been developed to replace or to be used in conjunction with existing dressing products. The use of the therapeutic properties of aloe vera could be very useful in the creation of active wound dressing materials. The present work was undertaken to examine issues concerning structural features, topography, enzymatic degradation behavior, antibacterial activity and cellular response of chitosan/aloe vera-based membranes. The chitosan/aloe vera-based membranes that were developed displayed satisfactory degradation, roughness, wettability and mechanical properties. A higher antibacterial potency was displayed by the blended membranes. Moreover, in vitro assays demonstrated that these blended membranes have good cell compatibility with primary human dermal fibroblasts. The chitosan/aloe vera-based membranes might be promising wound dressing materials.The authors acknowledge financial support from the Portuguese Foundation for Science and Technology (grants SFRH/BPD/45307/2008 and SFRH/BD/64601/2009), the "Fundo Social Europeu", and the "Programa Diferencial de Potencial Humano". This work was partially supported by the FEDER through POCTEP 0330_IBEROMARE_1_P