Preservation and storage of Lemon (Citrus Limon) Juice

Lemon fruits were sorted and washed before extraction of juice. Extracted juice of lemon fruits was treated with potassium metabisulphite, sodium benzoate and thermal processing. Treated and untreated samples of juice were stored at room and refrigeration temperature for 90 days and analyzed for chemical properties at 15 days of interval during storage. Total sugars, reducing sugars and browning of juice increased during storage. On the contrary, tannin content of juice decreased during storage. Storage at refrigeration temperature was found better effective in preservation and keeping quality of juice showing lesser changes in chemical properties of juice during storage than at room temperature. Results suggested that lemon juice after chemical and pasteurisation treatments can be stored safely at room and refrigeration temperature for 90 days

Amaranth Starch Isolation, Oxidation, Heat-Moisture Treatment and Application in Edible Film Formation

Starch was isolated from amaranth grains and subjected to modification treatments. Oxidation of isolated starch was done using sodium hypochlorite and heat-moisture treatment was done at 85°C for 6hr keeping the moisture content 30% during treatment. Native and modified starches of amaranth were used for preparation of edible films and different characteristics of films were evaluated. Both the modification treatments increased tensile strength of amaranth starch films. Heat moisture treatment increased water vapour permeability while oxidation had contrary effects on amaranth starch films. Water solubility of films of amaranth starches was reduced by modification treatments of starches. Heat moisture treatments increased yellowness of starch films

Genomic selection in aquaculture: application, limitations and opportunities with special reference to marine shrimp and pearl oysters

Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries

Genetic parameters of color phenotypes of black tiger shrimp (Penaeus monodon)

Black tiger shrimp (Penaeus monodon) is the second most important aquaculture species of shrimp in the world. In addition to growth traits, uncooked and cooked body color of shrimp are traits of significance for profitability and consumer acceptance. This study investigated for the first time, the phenotypic and genetic variances and relationships for body weight and body color traits, obtained from image analyses of 838 shrimp, representing the progeny from 55 sires and 52 dams. The color of uncooked shrimp was subjectively scored on a scale from 1 to 4, with “1” being the lightest/pale color and “4” being the darkest color. For cooked shrimp color, shrimp were graded firstly by subjective scoring using a commercial grading score card, where the score ranged from 1 to 12 representing light to deep coloration which was subsequently found to not be sufficiently reliable with poor repeatability of measurement (r = 0.68–0.78) Therefore, all images of cooked color were regraded on a three-point scale from brightest and lightest colored cooked shrimp, to darkest and most color-intense, with a high repeatability (r = 0.80–0.92). Objective color of both cooked and uncooked color was obtained by measurement of RGB intensities (values range from 0 to 255) for each pixel from each shrimp. Using the “convertColor” function in “R”, the RGB values were converted to L*a*b* (CIE Lab) systems of color properties. This system of color space was established in 1976, by the International Commission of Illumination (CIE) where “L*” represents the measure of degree of lightness, values range from 0 to 100, where 0 = pure black and 100 = pure white. The value “a*” represents red to green coloration, where a positive value represents the color progression towards red and a negative value towards green. The value “b*” represents blue to yellow coloration, where a positive value refers to more yellowish and negative towards the blue coloration. In total, eight color-related traits were investigated. An ordinal mixed (threshold) model was adopted for manually (subjectively) scored color phenotypes, whereas all other traits were analyzed by linear mixed models using ASReml software to derive variance components and estimated breeding values (EBVs). Moderate to low heritability estimates (0.05–0.35) were obtained for body color traits. For subjectively scored cooked and uncooked color, EBV-based selection would result in substantial genetic improvement in these traits. The genetic correlations among cooked, uncooked and body weight traits were high and ranged from −0.88 to 0.81. These suggest for the first time that 1) cooked color can be improved indirectly by genetic selection based on color of uncooked/live shrimp, and 2) intensity of coloration is positively correlated with body weight traits and hence selection for body weight will also improve color traits in this population

A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei

The Pacific whiteleg shrimp, Litopenaeus vannamei, is the most farmed aquaculture species worldwide with global production exceeding 3 million tonnes annually. Litopenaeus vannamei has been the focus of many selective breeding programs aiming to improve growth and disease resistance. However, these have been based primarily on phenotypic measurements and omit potential gains by integrating genetic selection into existing breeding programs. Such integration of genetic information has been hindered by the limited available genomic resources, background genetic parameters and knowledge on the genetic architecture of commercial traits for L. vannamei. This study describes the development of a comprehensive set of genomic gene-based resources including the identification and validation of 234,452 putative single nucleotide polymorphisms in-silico, of which 8,967 high value SNPs were incorporatedm into a commercially available Illumina Infinium ShrimpLD-24 v1.0 genotyping array. A framework genetic linkage map was constructed and combined with locus ordering by disequilibrium methodology to generate an integrated genetic map containing 4,817 SNPs, which spanned a total of 4552.5 cM and covered an estimated 98.12% of the genome. These gene-based genomic resources will not only be valuable for identifying regions underlying important L. vannamei traits, but also as a foundational resource in comparative and genome assembly activities

Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters

Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries

Agricultural and socioeconomic factors associated with farmer household dietary diversity in India: A comparative study of Visakhapatnam and Sonipat

This is the final version. Available from MDPI via the DOI in this record. Data Availability Statement: The datasets used and/or analyzed during the current study are available with CCDC, and can be obtained from Sailesh Mohan (co-author) on reasonable request.Using primary data from 479 farmer households, this study examined the associations between agricultural and socioeconomic factors and farmer household dietary diversity in Visakhapatnam and Sonipat. Cropping intensity was positively associated with farmers’ household dietary diversity score (HDDS), suggesting that higher cropping intensity may expand the gross cropped area and improve food security among subsistence farmers. Distance to food markets was also significantly associated with farmer HDDS, which suggests that market integration with rural households can improve farmer HDDS in Visakhapatnam. In Sonipat, wealth index had a positive association with farmer HDDS, targeting the income pathway by improving farmer HDDS in this region. Considering the relative contribution of these factors, distance to food markets, cropping intensity, and crop diversity were the three most important factors affecting farmer HDDS in Visakhapatnam, whereas wealth index, cropping intensity, and distance to food markets emerged as the top three important factors contributing to farmer HDDS in Sonipat. Our study concludes that the associations between agricultural and socioeconomic factors and farmer HDDS are complex but context- and location-specific; therefore, considering the site- and context-specific circumstances, different connections to HDDS in India can be found to better support policy priorities on the ground.Wellcome Trus

The combined effect of SNP-marker and phenotype attributes in genome-wide association studies

The last decade has seen rapid improvements in high-throughput single nucleotide polymorphism (SNP) genotyping technologies that have consequently made genome-wide association studies (GWAS) possible. With tens to hundreds of thousands of SNP markers being tested simultaneously in GWAS, it is imperative to appropriately pre-process, or filter out, those SNPs that may lead to false associations. This paper explores the relationships between various SNP genotype and phenotype attributes and their effects on false associations. We show that (i) uniformly distributed ordinal data as well as binary data are more easily influenced, though not necessarily negatively, by differences in various SNP attributes compared with normally distributed data; (ii) filtering SNPs on minor allele frequency (MAF) and extent of Hardy–Weinberg equilibrium (HWE) deviation has little effect on the overall false positive rate; (iii) in some cases, filtering on MAF only serves to exclude SNPs from the analysis without reduction of the overall proportion of false associations; and (iv) HWE, MAF and heterozygosity are all dependent on minor genotype frequency, a newly proposed measure for genotype integrity

Food insecurity and its determinants among adults in North and South India.

This is the final version. Available from BMC via the DOI in this record. Availability of data and materials: The datasets used and/or analysed during the current study are available from the corresponding author on reasonable request.BACKGROUND: Food insecurity is a major public health problem worldwide. In India, there are limited food insecurity assessment studies using a conventionally accepted method like the Food Insecurity Experience Scale (FIES), developed by the Food and Agricultural Organization (FAO). This study aims to measure food insecurity using the FIES and explore its determinants and association with body mass index (BMI) among Indian adults.  METHODS: In a cross-sectional study, we used FIES to measure food security in a sample of 9005 adults residing in North and South India. Using questionnaires, socio-demographic factors, dietary intake and food security data were collected. The dietary diversity scores (FAO-IDDS) and food insecurity scores (FAO-FIES) were calculated. Body size was measured and BMI was calculated.  RESULTS: The mean age of the study participants was 52.4 years (± 11.7); half were women and half resided in rural areas. Around 10% of the participants reported having experienced (mild or moderate or severe) food insecurity between October 2018 and February 2019. Dietary diversity (measured by FAO's Individual Dietary Diversity Scores, IDDS) was low and half of the participants consumed ≤ 3 food groups/day. The mean BMI was 24.7 kg/m2. In the multivariate analysis, a lower IDDS and BMI were associated with a higher FIES. The place of residence, gender and wealth index were important determinants of FIES, with those residing in South India, women and those belonging to the poorest wealth index reporting higher food insecurity. CONCLUSION: Food security is understudied in India. Our study adds important evidence to the literature. Despite having marginal food insecurity, high prevalence of low diet quality, especially among women, is disconcerting. Similar studies at the national level are warranted to determine the food insecurity situation comprehensively in India and plan appropriate policy actions to address it effectively, to attain the key Sustainable Development Goals (SDG).Wellcome TrustEli Lille

Genetic support for a quantitative trait nucleotide in the ABCG2 gene affecting milk composition of dairy cattle

<p>Abstract</p> <p>Background</p> <p>Our group has previously identified a quantitative trait locus (QTL) affecting fat and protein percentages on bovine chromosome 6, and refined the QTL position to a 420-kb interval containing six genes. Studies performed in other cattle populations have proposed polymorphisms in two different genes (<it>ABCG2 </it>and <it>OPN</it>) as the underlying functional QTL nucleotide. Due to these conflicting results, we have included these QTNs, together with a large collection of new SNPs produced from PCR sequencing, in a dense marker map spanning the QTL region, and reanalyzed the data using a combined linkage and linkage disequilibrium approach.</p> <p>Results</p> <p>Our results clearly exclude the <it>OPN </it>SNP (<it>OPN_3907</it>) as causal site for the QTL. Among 91 SNPs included in the study, the <it>ABCG2 </it>SNP (<it>ABCG2_49</it>) is clearly the best QTN candidate. The analyses revealed the presence of only one QTL for the percentage traits in the tested region. This QTL was completely removed by correcting the analysis for <it>ABCG2_49</it>. Concordance between the sires' marker genotypes and segregation status for the QTL was found for <it>ABCG2_49 </it>only. The C allele of <it>ABCG2_49 </it>is found in a marker haplotype that has an extremely negative effect on fat and protein percentages and positive effect on milk yield. Of the 91 SNPs, <it>ABCG2_49 </it>was the only marker in perfect linkage disequilibrium with the QTL.</p> <p>Conclusion</p> <p>Based on our results, OPN_3907 can be excluded as the polymorphism underlying the QTL. The results of this and other papers strongly suggest the [A/C] mutation in <it>ABCG2_49 </it>as the causal mutation, although the possibility that <it>ABCG2_49 </it>is only a marker in perfect LD with the true mutation can not be completely ruled out.</p