Genetic analysis of popping quality traits and development of superior quality popcorn hybrids for a sustainable popcorn breeding program in India.

BACKGROUND: Popcorn is the most popular specialty maize and it makes a significant contribution to the Indian and global economies. Despite perfect exploration of heterosis in field corn, progress in popcorn breeding remains constrained due to its narrow genetic base, leading to a significant dependence on imports. In this study, 15 landrace- and population-derived inbreds from temperate and tropical germplasm were crossed with five testers, which are the parents of superior popcorn hybrids, in a line × tester mating design. RESULTS: Significant variation was observed in popping quality and agronomic traits among crosses evaluated across three locations representing diverse maize-based agro-climatic zones in India. Additive genetic variance governed the traits related to popping quality, whereas dominance variance was responsible for the agronomic traits. In addition to significant heterosis specific to certain traits, we identified promising crosses that exhibited superior performance in both popping quality and grain yield (GY). The genotype + genotype × environment (GGE) biplot methodology identified PMI-PC-104 and PMI-PC-101 as the best discriminating testers for popping quality traits and Dpcl-15-90 for GY. Lines PMI-PC-205, PMI-PC-207, and PMI-PC-209 were the best general combiners for popping quality traits and GY. The heterotic groups identified based on GGE-biplots and the magnitude, direction and stability of combining ability effects would serve in the development of competitive popcorn hybrids for a sustainable popcorn market. CONCLUSION: Using the additive nature of popping quality traits and the dominant nature of GY, recurrent intrapopulation selection can be employed to derive desirable popping quality inbreds with high GY for genetic enhancement. Desirable popping quality alleles from novel germplasm can thus be combined with high-yielding domestic elite inbreds to establish a sustainable popcorn breeding program. © 2024 Society of Chemical Industry.

Multilocus functional characterization of indigenous and exotic inbreds for dgat1-2, fatb, ge2 and wri1a genes affecting kernel oil and fatty acid profile in maize.

Demand for maize oil is progressively increasing due to its diverse industrial applications, aside from its primary role in human nutrition and animal feed. Oil content and composition are two crucial determinants of maize oil in the international market. As kernel oil in maize is a complex quantitative trait, improving this trait presents a challenge for plant breeders and biotechnologists. Here, we characterized a set of 292 diverse maize inbreds of both indigenous and exotic origin by exploiting functional polymorphism of the dgat1-2, fatb, ge2, and wri1a genes governing kernel oil in maize. Genotyping using gene-based functional markers revealed a lower frequencies of dgat1-2 (0.15) and fatb (0.12) mutant alleles and a higher frequencies of wild-type alleles (Dgat1-2: 0.85; fatB: 0.88). The favorable wri1a allele was conserved across genotypes, while its wild-type allele (WRI1a) was not detected. In contrast, none of the genotypes possessed the ge2 favorable allele. The frequency of favorable alleles of both dgat1-2 and fatb decreased to 0.03 when considered together. Furthermore, pairwise protein-protein interactions among target gene products were conducted to understand the effect of one protein on another and their responses to kernel oil through functional enrichments. Thus, the identified maize genotypes with dgat1-2, fatb, and wri1a favourable alleles, along with insights gained through the protein-protein association network, serve as prominent and unique genetic resources for high-oil maize breeding programs. This is the first comprehensive report on the functional characterization of diverse genotypes at the molecular and protein levels.

Metabolic stratification of human breast tumors reveal subtypes of clinical and therapeutic relevance.

Extensive metabolic heterogeneity in breast cancers has limited the deployment of metabolic therapies. To enable patient stratification, we studied the metabolic landscape in breast cancers (∼3000 patients combined) and identified three subtypes with increasing degrees of metabolic deregulation. Subtype M1 was found to be dependent on bile-acid biosynthesis, whereas M2 showed reliance on methionine pathway, and M3 engaged fatty-acid, nucleotide, and glucose metabolism. The extent of metabolic alterations correlated strongly with tumor aggressiveness and patient outcome. This pattern was reproducible in independent datasets and using in vivo tumor metabolite data. Using machine-learning, we identified robust and generalizable signatures of metabolic subtypes in tumors and cell lines. Experimental inhibition of metabolic pathways in cell lines representing metabolic subtypes revealed subtype-specific sensitivity, therapeutically relevant drugs, and promising combination therapies. Taken together, metabolic stratification of breast cancers can thus aid in predicting patient outcome and designing precision therapies.

Integrative multiomics and weighted network approach reveals the prognostic role of RPS7 in lung squamous cell carcinoma pathogenesis.

Lung cancer is one of the most commonly occurring malignant cancers with the highest rate of mortality globally. Difference between lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD) and their treatment strategies according to genetic markers may be helpful in reducing the cancer progression and increasing the overall survival (OS) in patients. LUSC is known for comparatively less typical onco-drivers, target therapy resistance, marked genomic complexity, and a reasonably higher mutation rate. The mRNA-seq data and clinical information of LUAD and LUSC cohorts from UCSC Xena comprising 437 and 379 patient samples were extracted. Differential expression and weighted network analyses revealed 47 and 18 hub differentially expressed genes (DEGs) corresponding to LUAD and LUSC cohorts. These hub DEGs were further subjected to protein-protein interaction network (PPIN) and OS analyses. Lower mRNA expression levels of both RPS15A and RPS7 worsened the OS of LUSC patients. Additionally, both these prognostic biomarkers were validated via external sources such as UALCAN, cBioPortal, TIMER, and HPA. RPS7 had higher mutation frequency compared to RPS15A and showed significant negative correlations with infiltrating levels of CD4+ T cells, CD8+ T cells, neutrophils, and macrophages. Our findings provided novel insights into biomarker discovery and the critical role of ribosomal biogenesis especially smaller ribosomal subunit in pathogenesis of LUSC.

CDH1 overexpression sensitizes TRAIL resistant breast cancer cells towards rhTRAIL induced apoptosis.

PURPOSE: Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) is well known for its unique ability to induce apoptosis in cancer cells but not normal cells. However, a subpopulation of cancer cells exist that does not respond to toxic doses of TRAIL. In this study, we aimed to identify key factors regulating TRAIL resistance in breast cancer. METHODS: rhTRAIL (recombinant human TRAIL) resistant cells (TR) isolated from TRAIL sensitive MDA-MB-231 parental cells (TS) were confirmed using trypan blue assay, cell viability assay and AO/EtBr (acridine orange/ethidium bromide) staining. Microarray was performed followed by analysis using DAVID and Cytoscape bioinformatics software to identify the candidate hub gene. Gene expression of the candidate gene was confirmed using real-time PCR and western blot. Candidate gene was overexpressed via transient transfection to identify its significance in the context of rhTRAIL. Breast cancer patient data was obtained from The Cancer Genome Atlas (TCGA) database. RESULTS: Whole transcriptome analysis identified 4907 differentially expressed genes (DEGs) between TS and TR cells. CDH1 was identified as the candidate hub gene, with 18-degree centrality. We further observed CDH1 protein to be downregulated, overexpression of which increased apoptosis in TR cells after rhTRAIL treatment. TCGA patient data analysis also showed CDH1 mRNA to be low in TRAIL resistant patient group compared to TRAIL sensitive group. CONCLUSION: CDH1 overexpression sensitizes TR cells towards rhTRAIL induced apoptosis. Therefore, we can hypothesize that CDH1 expression should be taken into account while performing TRAIL therapy in breast cancer.

Investigating the link between miR-34a-5p and TLR6 signaling in sepsis-induced ARDS.

Acute lung injury (ALI)/acute respiratory distress syndrome (ARDS) are lung complications diagnosed by impaired gaseous exchanges leading to mortality. From the diverse etiologies, sepsis is a prominent contributor to ALI/ARDS. In the present study, we retrieved sepsis-induced ARDS mRNA expression profile and identified 883 differentially expressed genes (DEGs). Next, we established an ARDS-specific weighted gene co-expression network (WGCN) and picked the blue module as our hub module based on highly correlated network properties. Later we subjected all hub module DEGs to form an ARDS-specific 3-node feed-forward loop (FFL) whose highest-order subnetwork motif revealed one TF (STAT6), one miRNA (miR-34a-5p), and one mRNA (TLR6). Thereafter, we screened a natural product library and identified three lead molecules that showed promising binding affinity against TLR6. We then performed molecular dynamics simulations to evaluate the stability and binding free energy of the TLR6-lead molecule complexes. Our results suggest these lead molecules may be potential therapeutic candidates for treating sepsis-induced ALI/ARDS. In-silico studies on clinical datasets for sepsis-induced ARDS indicate a possible positive interaction between miR-34a and TLR6 and an antagonizing effect on STAT6 to promote inflammation. Also, the translational study on septic mice lungs by IHC staining reveals a hike in the expression of TLR6. We report here that miR-34a actively augments the effect of sepsis on lung epithelial cell apoptosis. This study suggests that miR-34a promotes TLR6 to heighten inflammation in sepsis-induced ALI/ARDS. Supplementary Information: The online version contains supplementary material available at 10.1007/s13205-023-03700-1.

Morpho-physiological traits and SSR markers-based analysis of relationships and genetic diversity among fodder maize landraces in India.

BACKGROUND: Maize is an excellent fodder crop due to its high biomass, better palatability, succulency, and nutrition. Studies on morpho-physiological and biochemical characterization of fodder maize are limited. The present study aimed to explore the genetic variation in fodder maize landraces for various morpho-physiological traits and estimation of genetic relationship and population structure. METHODS AND RESULTS: The study on 47 fodder maize landraces revealed significant variation for all morpho-physiological traits except leaf-stem ratio. Plant height, stem girth, leaf-width and number of leaves showed positive correlation with green fodder yield. Morpho-physiological traits-based clustering grouped the landraces into three major clusters, whereas neighbour joining cluster and population structure analysis using 40 SSR markers revealed four and five major groups, respectively. Most landraces of Northern Himalaya-Kashmir and Ludhiana fall into a single group, whereas rest groups mainly had landraces from North-Eastern Himalaya. A total of 101 alleles were generated with mean polymorphic information content value of 0.36 and major allele frequency of 0.68. The pair wise genetic dissimilarity between genotypes ranged from 0.21 to 0.67. Mantel test revealed weak but significant correlation between morphological and molecular distance. Biochemical characterisation of superior landraces revealed significant variation for neutral detergent fibre, acid detergent fibre, cellulose and lignin content. CONCLUSION: Interestingly, significant, and positive correlation of SPAD with lignin content can be explored to bypass the costly affair of invitro quality assessment for digestibility parameters. The study identified superior landraces and demonstrated the use of molecular markers in genetic diversity assessment and grouping of genotypes for fodder maize improvement.

Brønsted acid catalyzed mechanochemical domino multicomponent reactions by employing liquid assisted grindstone chemistry.

Here, we have demonstrated a metal-free energy-efficient mechanochemical approach for expedient access to a diverse set of 2-amino-3-cyano-aryl/heteroaryl-4H-chromenes, tetrahydrospiro[chromene-3,4'-indoline], 2,2'-aryl/heteroarylmethylene-bis(3-hydroxy-5,5-dimethylcyclohex-2-enone) as well as tetrahydro-1H-xanthen-1-one by employing the reactivity of 5,5-dimethylcyclohexane-1,3-dione/cyclohexane-1,3-dione with TsOH⋅H2O as Brønsted acid catalyst under water-assisted grinding conditions at ambient temperature. The ability to accomplish multiple C-C, C=C, C-O, and C-N bonds from readily available starting materials via a domino multicomponent strategy in the absence of metal-catalyst as well as volatile organic solvents with an immediate reduction in the cost of the transformation without necessitates complex operational procedures, features the significant highlights of this approach. The excellent yield of the products, broad functional group tolerances, easy set-up, column-free, scalable synthesis with ultralow catalyst loading, short reaction time, waste-free, ligand-free, and toxic-free, are other notable advantages of this approach. The greenness and sustainability of the protocol were also established by demonstrating several green metrics parameters.

Direct Michael addition/decarboxylation reaction catalyzed by a composite of copper ferrite nanoparticles immobilized on microcrystalline cellulose: an eco-friendly approach for constructing 3,4-dihydrocoumarin frameworks.

A composite of copper ferrite oxide nanoparticles immobilized on microcrystalline cellulose (CuFe2O4@MCC) was synthesized. The synthesized composite was characterized by FESEM with EDS-Mapping, TEM, P-XRD, TEM, and BET analysis and investigated for its catalytic activity toward Tandem Michael addition and decarboxylation of coumarin-3-carboxylic acid with cyclic 1,3-diketones to obtain novel 3,4-dihydrocoumarin derivatives. This protocol was established with wide substrate scope and significant yield. The significant characteristics of this methodology are mild reaction conditions, easy setup procedure, non-toxic, and cost-effectiveness. A gram-scale synthesis with low catalyst loading was also demonstrated.

Deciphering the role of aberrant DNA methylation in NAFLD and NASH.

The global incidence of nonalcoholic fatty liver disease (NAFLD) is mounting incessantly, and it is emerging as the most frequent cause of chronic and end stage liver disorders. It is the starting point for a range of conditions from simple steatosis to more progressive nonalcoholic steatohepatitis (NASH) and associated hepatocellular carcinoma (HCC). Dysregulation of insulin secretion and dyslipidemia due to obesity and other lifestyle variables are the primary contributors to establishment of NAFLD. Onset and progression of NAFLD is orchestrated by an interplay of metabolic environment with genetic and epigenetic factors. An incompletely understood mechanism of NAFLD progression has greatly hampered the progress in identification of novel prognostic and therapeutic strategies. Emerging evidence suggests altered DNA methylation pattern as a key determinant of NAFLD pathogenesis. Environmental and lifestyle factors can manipulate DNA methylation patterns in a reversible manner, which manifests as changes in gene expression. In this review we attempt to highlight the importance of DNA methylation in establishment and progression of NAFLD. Development of novel diagnostic, prognostic and therapeutic strategies centered around DNA methylation signatures and modifiers has also been explored.

Leaf Damage Based Phenotyping Technique and Its Validation Against Fall Armyworm, Spodoptera frugiperda (J. E. Smith), in Maize.

Globally, maize is an important cereal food crop with the highest production and productivity. Among the biotic constraints that limit the productivity of maize, the recent invasion of fall armyworm (FAW) in India is a concern. The first line of strategy available for FAW management is to evaluate and exploit resistant genotypes for inclusion in an IPM schedule. Screening for resistant maize genotypes against FAW is in its infancy in India, considering its recent occurrence in the country. The present work attempts to optimize screening techniques suited to Indian conditions, which involve the description of leaf damage rating (LDR) by comparing injury levels among maize genotypes and to validate the result obtained from the optimized screening technique by identification of lines potentially resistant to FAW under artificial infestation. Exposure to 20 neonate FAW larvae at the V5 phenological stage coupled with the adoption of LDR on a 1-9 scale aided in preliminary characterize maize genotypes as potentially resistant, moderately resistant, and susceptible. The LDR varies with genotype, neonate counts, and days after infestation. The genotypes, viz., DMRE 63, DML-163-1, CML 71, CML 141, CML 337, CML 346, and wild ancestor Zea mays ssp. parviglumis recorded lower LDR ratings against FAW and can be exploited for resistance breeding in maize.

Contribution of organokines in the development of NAFLD/NASH associated hepatocellular carcinoma.

Globally the incidence of hepatocellular carcinoma (HCC) is on an upsurge. Evidence is accumulating that liver disorders like nonalcoholic fatty liver disease (NAFLD) and its more progressive form nonalcoholic steatohepatitis (NASH) are associated with increased risk of developing HCC. NAFLD has a prevalence of about 25% and 50%-90% in obese population. With the growing burden of obesity epidemic worldwide, HCC presents a major healthcare burden. While cirrhosis is one of the major risk factors of HCC, available literature suggests that NAFLD/NASH associated HCC also develops in minimum or noncirrhotic livers. Therefore, there is an urgent need to understand the pathogenesis and risk factors associated with NAFLD and NASH related HCC that would help in early diagnosis and favorable prognosis of HCC secondary to NAFLD. Adipokines, hepatokines and myokines are factors secreted by adipocytes, hepatocytes and myocytes, respectively, playing essential roles in cellular homeostasis, energy balance and metabolism with autocrine, paracrine and endocrine effects. In this review, we endeavor to focus on the role of these organokines in the pathogenesis of NAFLD/NASH and its progression to HCC to augment the understanding of the factors stimulating hepatocytes to acquire a malignant phenotype. This shall aid in the development of novel therapeutic strategies and tools for early diagnosis of NAFLD/NASH and HCC.

Narrowing down molecular targets for improving phosphorus-use efficiency in maize (Zea mays L.).

Conventional agricultural practices rely heavily on chemical fertilizers to boost production. Among the fertilizers, phosphatic fertilizers are copiously used to ameliorate low-phosphate availability in the soil. However, phosphorus-use efficiency (PUE) for major cereals, including maize, is less than 30%; resulting in more than half of the applied phosphate being lost to the environment. Rock phosphate reserves are finite and predicted to exhaust in near future with the current rate of consumption. Thus, the dependence of modern agriculture on phosphatic fertilizers poses major food security and sustainability challenges. Strategies to optimize and improve PUE, like genetic interventions to develop high PUE cultivars, could have a major impact in this area. Here, we present the current understanding and recent advances in the biological phenomenon of phosphate uptake, translocation, and adaptive responses of plants under phosphate deficiency, with special reference to maize. Maize is one of the most important cereal crops that is cultivated globally under diverse agro-climatic conditions. It is an industrial, feed and food crop with multifarious uses and a fast-rising global demand and consumption. The interesting aspects of diversity in the root system architecture traits, the interplay between signaling pathways contributing to PUE, and an in-depth discussion on promising candidate genes for improving PUE in maize are elaborated.

Population Structure Analysis and Association Mapping for Turcicum Leaf Blight Resistance in Tropical Maize Using SSR Markers.

Maize is an important cereal crop in the world for feed, food, fodder, and raw materials of industries. Turcicum leaf blight (TLB) is a major foliar disease that can cause more than 50% yield losses in maize. Considering this, the molecular diversity, population structure, and genome-wide association study (GWAS) for TLB resistance were studied in 288 diverse inbred lines genotyped using 89 polymorphic simple sequence repeats (SSR) markers. These lines werescreened for TLB disease at two hot-spot locations under artificially inoculated conditions. The average percent disease incidence (PDI) calculated for each genotype ranged from 17 (UMI 1201) to 78% (IML 12-22) with an overall mean of 40%. The numbers of alleles detected at a locus ranged from twoto nine, with a total of 388 alleles. The polymorphic information content (PIC) of each marker ranged between 0.04 and 0.86. Out of 89 markers, 47 markers were highly polymorphic (PIC ≥ 0.60). This indicated that the SSR markers used were very informative and suitable for genetic diversity, population structure, and marker-trait association studies.The overall observed homozygosity for highly polymorphic markers was 0.98, which indicated that lines used were genetically pure. Neighbor-joining clustering, factorial analysis, and population structure studies clustered the 288 lines into 3-5 groups. The patterns of grouping were in agreement with the origin and pedigree records of the genotypesto a greater extent.A total of 94.10% lines were successfully assigned to one or another group at a membership probability of ≥0.60. An analysis of molecular variance (AMOVA) revealed highly significant differences among populations and within individuals. Linkage disequilibrium for r2 and D' between loci ranged from 0 to 0.77 and 0 to 1, respectively. A marker trait association analysis carried out using a general linear model (GLM) and mixed linear model (MLM), identified 15 SSRs markers significantly associated with TLB resistance.These 15 markers were located on almost all chromosomes (Chr) except 7, 8, and 9. The phenotypic variation explained by these loci ranged from 6% (umc1367) to 26% (nc130, phi085). Maximum 7 associated markers were located together on Chr 2 and 5. The selected regions identified on Chr 2 and 5 corroborated the previous studies carried out in the Indian maize germplasm. Further, 11 candidate genes were identified to be associated with significant markers. The identified sources for TLB resistance and associated markers may be utilized in molecular breeding for the development of suitable genotypes.

Genetic Diversity, Population Structure and Linkage Disequilibrium Analyses in Tropical Maize Using Genotyping by Sequencing.

Several maize breeding programs in India have developed numerous inbred lines but the lines have not been characterized using high-density molecular markers. Here, we studied the molecular diversity, population structure, and linkage disequilibrium (LD) patterns in a panel of 314 tropical normal corn, two sweet corn, and six popcorn inbred lines developed by 17 research centers in India, and 62 normal corn from the International Maize and Wheat Improvement Center (CIMMYT). The 384 inbred lines were genotyped with 60,227 polymorphic single nucleotide polymorphisms (SNPs). Most of the pair-wise relative kinship coefficients (58.5%) were equal or close to 0, which suggests the lack of redundancy in the genomic composition in the majority of inbred lines. Genetic distance among most pairs of lines (98.3%) varied from 0.20 to 0.34 as compared with just 1.7% of the pairs of lines that differed by <0.20, which suggests greater genetic variation even among sister lines. The overall average of 17% heterogeneity was observed in the panel indicated the need for further inbreeding in the high heterogeneous genotypes. The mean nucleotide diversity and frequency of polymorphic sites observed in the panel were 0.28 and 0.02, respectively. The model-based population structure, principal component analysis, and phylogenetic analysis revealed three to six groups with no clear patterns of clustering by centers-wise breeding lines, types of corn, kernel characteristics, maturity, plant height, and ear placement. However, genotypes were grouped partially based on their source germplasm from where they derived.

Association of PARK-2 Non-synonyms Polymorphisms and Their In Silico Validation Among North Indian Colorectal Cancer Patients.

PURPOSE: PARK2 is a potential tumour suppressor gene and its genetic alterations (regionic loss) are common across many human cancers. The association of PARK2 germline variations (SNPs) with Parkinson's has been shown, but their association in development and progression of cancer remains elusive. The aim of this study was to identify association of PARK2 polymorphisms (rs1801474, rs1801334) with colorectal cancer in a case control study design. METHODS: This case control study included a total of 650 genetically unrelated subjects comprising 300 colorectal cancer cases and 350 healthy controls belonging to North Indian. Both SNPs were analyzed using the PCR-RFLP assay. Statistical analysis for describing risk and association was performed using SPSS-17 software. Structural deviations due to non- synonymous substitutions (S167N and D394N) were analyzed using MD simulations. RESULTS: The genotype distributions of both the SNPs were in Hardy-Weinberg equilibrium. For both the polymorphisms, the allelic model showed statistically significant risk with OR ~ 1.3. Many of the associations remained significant even after Bonferroni correction (P < 0.00125). The result suggested that both S167N and D394N were deviated from wild type and structures and were stable after 5 ns. The average value of RMSD for backbone atoms was calculated from 5 to 10 ns molecular dynamics simulation data. CONCLUSION: In conclusion, our study revealed a significant association of PARK2 SNPs with colorectal cancer as well as their relations with other clinical parameters highlighting their contribution towards colorectal cancer susceptibility in North Indian population.

FMD and CIMT: Surrogate Markers of Atherosclerosis in Subclinical and Overt Hypothyroidism in Sub Himalyan Region.

INTRODUCTION: Hypothyroidism increases the risk of atherosclerosis. Carotid intima-media thickness (CIMT) and flow-mediated dilation (FMD) have been used as a noninvasive method to detect atherosclerosis. But the literature is scarce on patients with subclinical hypothyroidism. Such a study was not done in our region, so we conducted this study at a tertiary care center to compare CIMT and FMD among subclinical and overt hypothyroid patients and to analyze the risk of atherosclerosis. METHODS: We evaluated 68 patients aged 18-50 years, with newly diagnosed hypothyroidism. We divided them into overt and subclinical hypothyroidism groups and compared the findings. All analyses were performed by the computerized SPSS 17.0. The results were noted as means ± SD and percentage. Student's t-test was used to compare continuous variables, and the Chi-square test was used to compare differences. RESULTS: The total number of patients with dyslipidemia in the subclinical hypothyroidism (SCH) group was 22 (45.83%) and in the overt hypothyroidism (OH) group was 26 (54.16%) with a P- value of 0.009. The mean FMD% in subclinical hypothyroidism patients was 6.9816 ± 3.4224 and in overt hypothyroidism patients was 5.3670 ± 2.7278 (P = 0.03). The mean CIMT was 0.5009 ± 0.0732, CIMT in the SCH group was 0.5082 ± 0.0672 and in the OH group was 0.5305 ± 0.0799 (P = 0.2). CONCLUSION: The outcome of this study specifies that hypothyroidism is associated with endothelial dysfunction as established by impaired FMD, and it may be the first marker of atherosclerosis appearing before any structural evidence like CIMT. We can speculate that there is a link between subclinical hypothyroidism and atherosclerosis, and thyroxine replacement in SCH may help to prevent the progression of atherosclerosis.

Skim sequencing: an advanced NGS technology for crop improvement.

High-throughput genotyping has become more convenient and cost-effective due to recent advancements in next-generation sequencing (NGS) techniques. Numerous approaches exploring sequencing advances for genotyping have been developed over the past decade, which includes different variants of genotyping-by-sequencing (GBS), and restriction-site associated DNA sequencing (RAD-seq). Most of these methods are based on the reduced representation of the genome, which ultimately reduces the cost of sequencing by many folds. However, continuously lowering the cost of sequencing makes it more convenient to use whole genome-based approaches. In this regard, skim sequencing, where low coverage whole-genome sequencing is used for the identification of large numbers of polymorphic markers cost-effectively. In the present review, we have discussed recent technological advancements, applicability, and challenges of skim sequencing-based genotypic approaches for crop improvement programmes. Skim sequencing is being extensively used for genotyping in diverse plant species and has a wide range of applications, particularly in quantitative trait loci (QTL) mapping, genomewide association studies (GWAS), fine genetic map construction, and identification of recombination and gene conversion events in various breeding programmes. The cost-effectiveness, simplicity, and genomewide coverage will increase the application of skims sequencing-based genotyping. The article summarizes the protocol, uses, bioinformatics tools, its application, and future prospects of skim sequencing in crop improvement.

Development of sub-tropically adapted diverse provitamin-A rich maize inbreds through marker-assisted pedigree selection, their characterization and utilization in hybrid breeding.

Malnutrition has emerged as one of the major health problems worldwide. Traditional yellow maize has low provitamin-A (proA) content and its genetic base in proA biofortification breeding program of subtropics is extremely narrow. To diversify the proA rich germplasm, 10 elite low proA inbreds were crossed with a proA rich donor (HP702-22) having mutant crtRB1 gene. The F2 populations derived from these crosses were genotyped using InDel marker specific to crtRB1. Severe marker segregation distortion was observed. Seventeen crtRB1 inbreds developed through marker-assisted pedigree breeding and seven inbreds generated using marker-assisted backcross breeding were characterized using 77 SSRs. Wide variation in gene diversity (0.08 to 0.79) and dissimilarity coefficient (0.28 to 0.84) was observed. The inbreds were grouped into three major clusters depicting the existing genetic diversity. The crtRB1-based inbreds possessed high ß-carotene (BC: 8.72µg/g), ß-cryptoxanthin (BCX: 4.58µg/g) and proA (11.01µg/g), while it was 2.35µg/g, 1.24µg/g and 2.97µg/g in checks, respectively. Based on their genetic relationships, 15 newly developed crtRB1-based inbreds were crossed with five testers (having crtRB1 gene) using line × tester mating design. 75 experimental hybrids with crtRB1 gene were evaluated over three locations. These experimental hybrids possessed higher BC (8.02µg/g), BCX (4.69µg/g), proA (10.37µg/g) compared to traditional hybrids used as check (BC: 2.36 µg/g, BCX: 1.53µg/g, proA: 3.13µg/g). Environment and genotypes × environment interaction had minor effects on proA content. Both additive and dominance gene action were significant for proA. The mean proportion of proA to total carotenoids (TC) was 44% among crtRB1-based hybrids, while 11% in traditional hybrids. BC was found to be positively correlated with BCX (r = 0.68) and proA (r = 0.98). However, no correlation was observed between proA and grain yield. Several hybrids with >10.0 t/ha grain yield with proA content >10.0 µg/g were identified. This is the first comprehensive study on development of diverse proA rich maize hybrids through marker-assisted pedigree breeding approach. The findings provides sustainable and cost-effective solution to alleviate vitamin-A deficiency.

Multiomics integrative analysis reveals antagonistic roles of CBX2 and CBX7 in metabolic reprogramming of breast cancer.

Striking similarity exists between metabolic changes associated with embryogenesis and tumorigenesis. Chromobox proteins-CBX2/4/6/7/8, core components of canonical polycomb repressor complex 1, play essential roles in embryonic development and aberrantly expressed in breast cancer. Understanding how altered CBX expression relates to metabolic reprogramming in breast cancer may reveal vulnerabilities of therapeutic pertinence. Using transcriptomic and metabolomic data from breast cancer patients (N > 3000 combined), we performed pathway-based analysis and identified outstanding roles of CBX2 and CBX7 in positive and negative regulation of glucose metabolism, respectively. Genetic ablation experiments validated the contrasting roles of two isoforms in cancer metabolism and cell growth. Furthermore, we provide evidence for the role of mammalian target of rapamycin complex 1 signaling in mediating contrary effects of CBX2 and CBX7 on breast cancer metabolism. Underpinning the biological significance of metabolic roles, CBX2 and CBX7 were found to be the most up- and downregulated isoforms, respectively, in breast tumors compared with normal tissues. Moreover, CBX2 and CBX7 expression (not other isoforms) correlated strongly, but oppositely, with breast tumor subtype aggressiveness and the proliferation markers. Consistently, genomic data also showed higher amplification frequency of CBX2, not CBX7, in breast tumors. Highlighting the clinical significance of findings, disease-specific survival and drug sensitivity analysis revealed that CBX2 and CBX7 predicted patient outcome and sensitivity to FDA-approved/investigational drugs. In summary, this work identifies novel cross talk between CBX2/7 and breast tumor metabolism, and the results presented may have implications in strategies targeting breast cancer.