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Fresh cut fruits and vegetable have gained penetration and popularity since last few years. These fresh cut commodities are in great demand among the consumers as these are ready-to-eat fresh and provide all essential nutrients. The increasing trend in fresh cut produce tends to increase the investment in research and development to address various issues regarding the product supply, refrigeration, packaging technology, processing and shelf life extension. Cutting and peeling causes physical damage to the raw fruit and vegetable that make them more perishable. In these review latest developments that plays the key role in extending the shelf life of the fresh cut are discussed. These technologies help in reducing the microbial load over the fresh cut without much altering the physicochemical properties. Future researches should consider various combined technologies which allow better preservation as well as supplemented with nutritional factors.

Yeasts have been used for the heterologous production of a range of enzymes. However, α-L-rhamnosidase production in yeasts as well as its vast potential for biotechnological processes is less reported. α-L-Rhamnosidase is one of the important biotechnologically attractive enzymes in several industrial and biotechnological processes. In food and agriculture industries, the enzyme catalyzes the hydrolysis of hesperidin to release L-rhamnose and hesperidin glucoside, industrial removal of bitterness from citrus juices caused by naringin, and enhancing aroma in grape juices and derived beverages. In pharmaceutical and chemical industries, this enzyme is used in the structural determination of polysaccharides, glycosides and glycolipids, metabolism of gellan, conversion of chloropolysporin B to chloropolysporin C, and production of prunin. Rhamnosidases are extensively distributed in fungi and bacteria while their production from yeast sources is less reported. Yeast rhamnosidase is very important as it is produced in short-duration fermentation, with enhanced shelf life, high thermal stability, capable of retaining juice flavor, and is non-toxic for human consumption. In this review, an attempt has been made to fill up this gap by focusing on production, purification, characterization, structural and molecular biological studies of yeast rhamnosidase and its potential biotechnological applications. Keywords: Industrial applications, Naringin, Rhamnosidase, Yeast

Genome wide association studies allowed prediction of 17 candidate genes for association with nitrogen use efficiency. Novel information obtained may provide better understanding of genomic controls underlying germplasm variations for this trait in Indian mustard. Nitrogen use efficiency (NUE) of Indian mustard (Brassica juncea (L.) Czern & Coss.) is low and most breeding efforts to combine NUE with crop performance have not succeeded. Underlying genetics also remain unexplored. We tested 92 SNP-genotyped inbred lines for yield component traits, N uptake efficiency (NUPEFF), nitrogen utilization efficiency (NUTEFF), nitrogen harvest index (NHI) and NUE for two years at two nitrogen doses (No without added N and N100 added @100 kg/ha). Genotypes IC-2489-88, M-633, MCP-632, HUJM 1080, GR-325 and DJ-65 recorded high NUE at low N. These also showed improved crop performance under high N. One determinate mustard genotype DJ-113 DT-3 revealed maximum NUTEFF. Genome wide association studies (GWAS) facilitated recognition of 17 quantitative trait loci (QTLs). Environment specificity was high. B-genome chromosomes (B02, B03, B05, B07 and B08) harbored many useful loci. We also used regional association mapping (RAM) to supplement results from GWAS. Annotation of the genomic regions around peak SNPs helped to predict several gene candidates for root architecture, N uptake, assimilation and remobilization. CAT9 (At1g05940) was consistently envisaged for both NUE and NUPEFF. Major N transporter genes, NRT1.8 and NRT3.1 were predicted for explaining variation for NUTEFF and NUPEFF, respectively. Most significant amino acid transporter gene, AAP1 appeared associated with NUE under limited N conditions. All these candidates were predicted in the regions of high linkage disequilibrium. Sequence information of the predicted candidate genes will permit development of molecular markers to aid breeding for high NUE.

The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.

The development and utilization of molecular-markers play an important role in genomics-assisted breeding during pyramiding of valuable genes. The aim of present study was to develop and validate a novel core-set of KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving rice grain yield and adaptability under direct-seeded cultivation conditions. The 110 phenotypically validated KASP assays out of 171 designed KASP, include assays for biotic-resistance genes, anaerobic germination, root-traits, grain yield, lodging resistance and early-uniform emergence. The KASP assays were validated for their robustness and reliability at five different levels using diverse germplasm, segregating and advanced population, comparison with SSR markers and on F

Timely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.

Indian mustard (Brassica juncea) is a major source of vegetable oil in the Indian subcontinent. The seed cake left after the oil extraction is used as livestock feed. We examined the genetic architecture of oil, protein, and glucosinolates by conducting a genome-wide association study (GWAS), using an association panel comprising 92 diverse genotypes. We conducted trait phenotyping over 2 years at two levels of nitrogen (N) application. Genotyping by sequencing was used to identify 66,835 loci, covering 18 chromosomes. Genetic diversity and phenotypic variations were high for the studied traits. Trait performances were stable when averaged over years and N levels. However, individual performances differed. General and mixed linear models were used to estimate the association between the SNP markers and the seed quality traits. Population structure, principal components (PCs) analysis, and discriminant analysis of principal components (DAPCs) were included as covariates to overcome the bias due to the population stratification. We identified 16, 23, and 27 loci associated with oil, protein, and glucosinolates, respectively. We also established LD patterns and haplotype structures for the candidate genes. The average block sizes were larger on A-genome chromosomes as compared to the B- genome chromosomes. Genetic associations differed over N levels. However, meta-analysis of GWAS datasets not only improved the power to recognize associations but also helped to identify common SNPs for oil and protein contents. Annotation of the genomic region around the identified SNPs led to the prediction of 21 orthologs of the functional candidate genes related to the biosynthesis of oil, protein, and glucosinolates. Notable among these are: LACS5 (A09), FAD6 (B05), ASN1 (A06), GTR2 (A06), CYP81G1 (B06), and MYB44 (B06). The identified loci will be very useful for marker-aided breeding for seed quality modifications in B. juncea.

The escalating population has prompted the focus to meet the demand of food materials by increasing crop yield. Out of the total farm output, India is the second largest producer of agricultural crops. Consequently, the lack of congruence between crop production and the disposal of agricultural wastes is a matter of serious environmental concern. An opportunity, therefore, prevails to switch the view of these agricultural residues from microbial bioprocessing of waste to valuable products which can be a huge market.

Soil and plant root are known as the microbial reservoir, and these microbes are found broadly in the plant rhizosphere and tissues. Phytobiome generally exists as epiphytic, endophytic, and rhizospheric that undertakes a critical role in plant development. These microbiomes may shape networks, to stabilize the function among different kinds of plant-associated factors to propagate or transmit in a different part of the plant. Microbial networks linked with plant health give crucial beneficial insights to look upon. The present section covers the features of such microbial networks that build the phytobiome. The chapter highlights their ability to better uptake nutrients or plant growth regulators in a stressed environment and further extends an evolution of studies depicting the supporting components that shape the phylogenetic and plant-related networks. The chapter advocates the possibility to understand the techniques by which plants select and connect with their microbiomes and affect plant improvement and well-being, thereby laying the foundation of novel microbiome-driven systems to the advancement of sustainable agriculture. The microbiome is unpredictably engaged with plant well-being providing extra qualities to the plant. To understand the guideline of plant characteristic articulation, henceforth plant execution, and how this impacts the biological systemic network, it is required to get well versed with phytobiome and its usefulness. In the present section, the significance of the phytobiome to plant genomics is tended to describe the phytobiome in assembly to the environment of the outline with attention on natural surroundings happening subterranean at the plant-soil between face, where the center is around the job of exudates as currency in this framework.

Several microbes are found in the community of biofilm that is associated with adhering to the surface and embedding in the extracellular polymeric matrix. The functional assets of microbial cells constituting a biofilm are different in comparison to planktonic cells. The lifecycle of biofilms comprises numerous development stages such as early attachment, development, conservation, and dispersion controlled by quorum sensing. Inside the biofilms, microbes exist in high concentrations and in close proximity, facilitating their interactions and signaling to participate in many metabolic processes as a consortia. Microbial biofilms are beneficially exploited in the use of drinking water, the action of wastewater, purification of toxic and harmful wastes, N2 fixation, oil degradation, microbial fuel, biological restoration (biocementation) of brickwork, and biofilm defense against several contagious pathogens. A biofilm development takes benefit for enhancing the food additives by using the microorganisms’ properties. A number of innovative procedures have been newly created to notice and evaluate the bacteria attached to the surfaces using reverse transcription polymerase chain reaction, microarrays, and confocal laser scanning microscopy. Research regarding the construction, working and molecular signaling in biofilms can give information about bacterial existence, perseverance, and promulgation in several environments. In this chapter, we discuss the different biological approaches, particularly biofilm knowledge, including the development as well as the structure and function. The beneficial aspects of biofilms are well addressed and a chemical ecology strategy via management of cultural environments and bacterial signaling is encouraged to improve the beneficial aspects of biofilms.

Sclerotinia stem rot caused by Sclerotinia sclerotiorum is a major disease of crop brassicas, with inadequate variation for resistance in primary gene pools. We utilized a wild Brassicaceae species with excellent resistance against stem rot to develop a set of B. juncea - B. fruticulosa introgression lines (ILs). These were assessed for resistance using a highly reproducible stem inoculation technique against a virulent pathogen isolate. Over 40% of ILs showed higher levels of resistance. IL-43, IL-175, IL-215, IL-223 and IL-277 were most resistant ILs over three crop seasons. Sequence reads (21x) from the three most diverse ILs were then used to create B. juncea pseudomolecules, by replacing SNPs of reference B. juncea with those of re-sequenced ILs. Genotyping by sequencing (GBS) was also carried out for 88 ILs. Resultant sequence tags were then mapped on to the B. juncea pseudomolecules, and SNP genotypes prepared for each IL. Genome wide association studies helped to map resistance responses to stem rot. A total of 13 significant loci were identified on seven B. juncea chromosomes (A01, A03, A04, A05, A08, A09 and B05). Annotation of the genomic region around identified SNPs allowed identification of 20 candidate genes belonging to major disease resistance protein families, including TIR-NBS-LRR class, Chitinase, Malectin/receptor-like protein kinase, defensin-like (DEFL), desulfoglucosinolate sulfotransferase protein and lipoxygenase. A majority of the significant SNPs could be validated using whole genome sequences (21x) from five advanced generation lines being bred for Sclerotinia resistance as compared to three susceptible B. juncea germplasm lines. Our findings not only provide critical new understanding of the defensive pathway of B. fruticulosa resistance, but will also enable development of marker candidates for assisted transfer of introgressed resistant loci in to agronomically superior cultivars of crop Brassica.

A set of 96 Brassica juncea–Erucastrum cardaminoides introgression lines (ILs) were developed with genomic regions associated with Sclerotinia stem rot (Sclerotinia sclerotiorum) resistance from a wild Brassicaceous species E. cardaminoides. ILs were assessed for their resistance responses to stem inoculation with S. sclerotiorum, over three crop seasons (season I, 2011/2012; II, 2014/2015; III, 2016–2017). Initially, ILs were genotyped with transferable SSR markers and subsequently through genotyping by sequencing. SSR based association mapping identified six marker loci associated to resistance in both A and B genomes. Subsequent genome-wide association analysis (GWAS) of 84 ILs recognized a large number of SNPs associated to resistance, in chromosomes A03, A06, and B03. Chromosomes A03 and A06 harbored the maximum number of resistance related SNPs. Annotation of linked genomic regions highlighted an array of resistance mechanisms in terms of signal transduction pathways, hypersensitive responses and production of anti-fungal proteins and metabolites. Of major importance was the clustering of SNPs, encoding multiple resistance genes on small regions spanning approximately 885 kb region on chromosome A03 and 74 kb on B03. Five SNPs on chromosome A03 (6,390,210-381) were associated with LRR-RLK (receptor like kinases) genes that encode LRR-protein kinase family proteins. Genetic factors associated with pathogen-associated molecular patterns (PAMPs) and effector-triggered immunity (ETI) were predicted on chromosome A03, exhibiting 11 SNPs (6,274,763-994). These belonged to three R-Genes encoding TIR-NBS-LRR proteins. Marker trait associations (MTAs) identified will facilitate marker assisted introgression of these critical resistances, into new cultivars of B. juncea initially and, subsequently, into other crop Brassica species.

The industrialization of agriculture significantly increased the essential yield productivity, and worldwide population growth has led to the demand for a substantial increase in the quantity of food produced. However, farmers regularly apply the maximum amount of chemical fertilizers, which are costly and non-biodegradable. Consequently, the uneven and longtime practice of using more chemical fertilizer has reduced the soil fertility and yield and is also detrimental to the available microorganisms in the soil. Therefore, scientists are anticipated to present a new and updated agricultural practice that is a benefit to raising agriculture products. In rhizosphere soil and on plant root surfaces, a collection of different natural microbial flora exist that execute the beneficial role of the various plants for growth and progress, which are usually reflected as plant growth promoting rhizobacteria (PGPR), and they have potential to be a promising method for agriculture practice. Several reports are available on the application of PGPR in plant growth development and in different crops. Generally, PGPR is classified into two mechanisms, i.e., direct and indirect. The mechanisms of PGPR facilitating the improvement of plant development consist of nitrogen fixation, solubilization of phosphate and mineralization of additional nutrients, production of siderophores, phytohormones (auxin-indole acetic acid, abscisic acid, ethylene, gibberellic acid and cytokinin), ACC-deaminase activity to decrease the ethylene level in crop roots to enhance root length, antagonistic activity, hydrolytic enzymes (s-1-3-glucanase, chitinases, protease), antibiotics, hydrogen cyanide against several pathogens, etc. Apart from this, PGPR might show a crucial function in the improvement of numerous stresses in several plants by secreting exopolysaccharides, volatile compounds, inducing osmolytes production, antioxidants enzymes, and up or down-regulation of stress-responsive genes. These plant-beneficial rhizobacteria can also decrease the amount of hazardous agricultural chemicals used, which are universally responsible for disrupting the agro-ecological systems. In this chapter, efforts are made to discuss the main functions of PGPR in crop growth enhancement and progress along with their important mechanisms and significance in crop production on a sustainable basis.

A myriad of small RNAs (18–25 nt in length) undergo heterogeneous modifications to inflect RNA stability and other complex physiological processes like stress responses, metabolism, immunity, and epigenetic inheritance of environmentally acquired traits. Such small RNAs include microRNAs (miRNAs), PIWI-interacting RNAs (piRNAs), small interfering RNAs (siRNAs), and tRNA-derived small RNAs (tsRNAs). Worldwide crop production and human health are affected when plants are attacked by pathogens and pests. Therefore, a large collection of genes get up- or down regulated to mediate the defense responses in plants against pathogens (bacteria, fungi, oomycetes, and viruses). Host endogenous small RNAs, thus, come into play to counter biotic stress where RNA silencing machinery is utilized to facilitate pathogen-associated molecular pattern-triggered immunity and effector-triggered immunity. RNA interference (RNAi) pathways trigger gene silencing in interacting species from even different kingdoms (cross-kingdom RNAi). Diverse pathways are involved in regulating the defense mechanism including Dicer-like proteins (DCLs), double-stranded RNA (dsRNA) binding protein, RNA-dependent RNA polymerases (RDRs), RNA polymerase IV and V, small RNA methyltransferase HEN1, and Argonaute (AGO) proteins showcasing their functional specificities as well as verbosity. Transgenic plants are newly emerging players that help in solving the problem of pathogen attack in fields. In this chapter, the recent breakthrough on the function of sRNAs in response to biotic stress, mainly in plant-pathogen interaction, and its application in disease control is discussed.

A set of 96 Brassica juncea–Erucastrum cardaminoides introgression lines (ILs) were developed with genomic regions associated with Sclerotinia stem rot (Sclerotinia sclerotiorum) resistance from a wild Brassicaceous species E. cardaminoides. ILs were assessed for their resistance responses to stem inoculation with S. sclerotiorum, over three crop seasons (season I, 2011/2012; II, 2014/2015; III, 2016–2017). Initially, ILs were genotyped with transferable SSR markers and subsequently through genotyping by sequencing. SSR based association mapping identified six marker loci associated to resistance in both A and B genomes. Subsequent genome-wide association analysis (GWAS) of 84 ILs recognized a large number of SNPs associated to resistance, in chromosomes A03, A06, and B03. Chromosomes A03 and A06 harbored the maximum number of resistance related SNPs. Annotation of linked genomic regions highlighted an array of resistance mechanisms in terms of signal transduction pathways, hypersensitive responses and production of anti-fungal proteins and metabolites. Of major importance was the clustering of SNPs, encoding multiple resistance genes on small regions spanning approximately 885 kb region on chromosome A03 and 74 kb on B03. Five SNPs on chromosome A03 (6,390,210-381) were associated with LRR-RLK (receptor like kinases) genes that encode LRR-protein kinase family proteins. Genetic factors associated with pathogen-associated molecular patterns (PAMPs) and effector-triggered immunity (ETI) were predicted on chromosome A03, exhibiting 11 SNPs (6,274,763-994). These belonged to three R-Genes encoding TIR-NBS-LRR proteins. Marker trait associations (MTAs) identified will facilitate marker assisted introgression of these critical resistances, into new cultivars of B. juncea initially and, subsequently, into other crop Brassica species.