Umakanta Ngangkham

• PhD
• Scientist at ICAR Research Complex North East Hill Region, Manipur Centre

Breeding for aluminum (Al) tolerance in crops is crucial for improving agricultural productivity in acid soils, where Al toxicity hampers root development and nutrient uptake, ultimately affecting yields. In this study, a hydroponic screening system was used to evaluate Al tolerance in 161 rice bean (Vigna umbellate (Thunb.) Ohwi and Ohashi) genoty...

An essential element for healthy plant growth and development is phosphorus (P). Globally, lack of phosphorus (P) is a major factor affecting rice productivity. P insufficiency issues generally occur in iron-toxicity soils, soils with aluminium or manganese content, and acidic soils which accounts for over 80% of the area of land in North Eastern I...

An essential element for healthy plant growth and development is phosphorus (P). Globally, lack of phosphorus (P) is a major factor affecting rice productivity. P insufficiency issues generally occur in iron-toxicity soils, soils with aluminium or manganese content, and acidic soils which accounts for over 80% of the area of land in North Eastern I...

Early seedling vigour (ESV) is a key trait that enhances early establishment, stress tolerance, and grain yield in rice, especially in direct-seeded rice (DSR) systems. The aus varietal groups is known for its high seedling vigour. The screening of aus diversity panel for ESV traits and subsequent genome-wide association study (GWAS) can lead to th...

In Manipur, where Chak-hao is traditionally grown, there are two main variants: Chak-hao Poreiton (purple) and Chak-hao Amubi (red). This aromatic pigmented rice, known for its unique fragrance and nutty taste, has earned a Geographical Indication (GI) tag. It now faces a new and significant threat from the rice hopper complex. Recently, hopperburn...

The loss of rice's genetic diversity caused by the replacement of landraces with superior cultivars in modern agriculture highlights the importance of genetic diversity assessment. Therefore, a set of 96 rice genotypes collected from different parts of Manipur, India was used for genetic diversity assessment in the present investigation. Nine agron...

Global warming is causing increased temperatures that are affecting crop yield and sustainability. To harness the diversity present in rice germplasm, 1100 rice genotypes from the north-eastern Himalayan region (NEHR) were evaluated for high yield stability and marker-trait associations using SSR markers under ambient and elevated temperature condi...

Chickpea (Cicer arietinum L.) serves as a vital protein and mineral source in vegetarian diets worldwide. We assessed 96 diverse chickpea genotypes for seven yield and yield-related traits, and investigated genetic diversity, population structure, and marker-trait associations for yield-contributing traits using 21 gene-based SSR markers. The simpl...

Chakhao is a popular pigmented black rice variety with remarkably high anthocyanin content. Due to its susceptibility to various biotic and abiotic stresses, its production has remained low. Here, two genes, Pi54 blast-resistant and OsSPL14, high-yielding genes of rice, were pyramided in a Chakhao lan-drace by crossing with CR Dhan 307. From a tota...

Brown spot (BS) disease causes significant losses to rice productivity. In this study, a roving survey in the Karnataka state of India revealed a wider distribution of BS with a percent disease index range of 20.56-50.74. From the symptomatic geo-distinct samples, pure cultures of 63 isolates were obtained. Based on the conidial morphology, 63 isol...

Rice variety differentiation was based on morphological descriptors (DUS) before the advent of genomic and proteomic technology. DNA fingerprinting is becoming an important molecular marker approach because of its wide application in varietal protection, classification, and conflict settlement. In the present study, genetic diversity and variabilit...

Rice variety differentiation was based on morphological descriptors (DUS) before the advent of genomic and proteomic technology. DNA fingerprinting is becoming an important molecular marker approach because of its wide application in varietal protection, classification, and conflict settlement. In the present study, genetic diversity and variabilit...

The limited availability of Phosphorus (P) in the soil poses a significant challenge to of rice productivity in rainfed tropical regions. There has been a constant demand of diverse donors for enhancing tolerance to P‐deficient soils. In this study, we evaluated 181 aus rice accessions of the 3000 Rice Genome Project (3 K‐RGP) for grain yield and s...

The aus (Oryza sativa L.) varietal group comprises of aus, boro, ashina and rayada seasonal and/or field ecotypes, and exhibits unique stress tolerance traits, making it valuable for rice breeding. Despite its importance, the agro-morphological diversity and genetic control of yield traits in aus rice remain poorly understood. To address this knowl...

The evolutionary relationship between domesticated Oryza species and their wild relatives in North East India is not well understood. To improve the understanding of the evolutionary relationship, this study investigates the genetic diversity of 68 indigenous rice landraces from North East India, ten O. rufipogon genotypes, and nine O. nivara genot...

The North-Eastern region (NER) of India falls under the Eastern Himalayan region and it is a bio-diversity hub. Diverse maize landraces with wide adaptability to extreme climatic and soil scenario like heavy rainfall, drought and acidic soil conditions have been grown in NER since time immemorial. However, maize diversity in NER region has drastica...

In cereals and legumes, phytic acid (PA) is the principal phosphorus reserve that serves the biosynthetic and nutritional demands of growing tissues during germination. Because of strong antioxidant activity and ability to chelate mineral ions, it provides several health and physiological benefits. Phytic acid is widely regarded as an anti-nutritio...

The inheritance of the mitochondria genome and its diversity is unique for genetic and evolutionary studies relative to nuclear genomes. Northeast India and Himalayan regions are considered as one of the centres of indica rice origin. Also, rice diversity in northeast India is very distinct and highly suited for evolutionary studies. Although repor...

Magnaporthe oryzae, the rice blast fungus, is one of the most dangerous rice pathogens, causing considerable crop losses around the world. In order to explore the rice blast-resistant sources, initially performed a large-scale screening of 277 rice accessions. In parallel with field evaluations, fifty-two rice accessions were genotyped for 25 major...

Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the significant constraints for rice production. A study was carried out to analyze the virulence, genetic diversity, and population structure of Xoo isolates collected from different rice ecosystems of Karnataka, India. The taxonomic identity of all...

The present investigation was carried out to identify the potential donors of resistant gene(s)/the source of white rust disease in B. juncea using 30 genotypes, including locally adapted accessions and advanced breeding lines. Out of 30 genotypes, ten lines viz. Bio-YSR, CAULC-1, CAULC-2, CAULC-3, CAULC-4, CAURM-2, CAULR-7, CAURM-4, CAURM 4-1, and...

A study on stability analysis was carried out in 30 diverse genotypes of ricebean (Vigna umbellata Thunb.) in eastern hill region of India. Significant differences among the genotypes over the years were observed for all the three traits studied. The first two principal components axis (IPCA1, 90.4% and IPCA2, 9.6%) could explain 100% of the total...

Aims: To investigate the genetic diversity, population structure, and mating-type distribution among the eco-distinct isolates of Magnaporthe oryzae from Karnataka, India. Methods and results: A set of 38 isolates of M. oryzae associated with leaf blast disease of rice were collected from different rice ecosystems of Karnataka, India, and analyz...

North- Eastern parts of India fall under the Eastern Himalayan region and it is a diversity hotspot of many crops, including maize. Maize is an important traditional cereal crop grown in hill ecology of the region mainly for food, fodder and feed. To tap the potentiality of maize genetic resources in crop improvement programmes, assessment of genet...

North- Eastern parts of India fall under Eastern Himalayan region and it is a diversity hotspot of many crops including maize. Evaluation of genetic diversity is required to tape the potentiality of genetic resources in any crop improvement programmes. In the present study, genetic diversity at fifty two microsatellite markers were conducted in 30...

Aims: To investigate the diversity of eco-distinct isolates of Magnaporthe oryzae for their morphological, virulence and molecular diversity and relative distribution of five Avr genes. Methods and results: Fifty-two M. oryzae isolates were collected from different rice ecosystems of southern India. A majority of them (n = 28) formed a circular...

Seed germination is the most sensitive stage of rice for salinity stress. To map the genomic regions, a set of 117 doubled haploid (DH) lines derived from the F1s of salinity tolerant, Pokkali and susceptible, Savitri was used. Preliminary screening at 0, 4, 8, 12, 16 and 20 dsm-1 of NaCl solution, Pokkali and savitri showed significant variation o...

Phosphorus (P) flow in agricultural land depends on the P taken off from harvested product, its losses through runoff and fertilizer applied to balance the removed P. Phytic acid (PA), the major storage form of phosphorus (P) in cereal grains is a key anti-nutrient for human and non-ruminants leads to eutrophication of waterways. As the natural non...

The rise of the most appealing genome editing technology, i.e. CRISPR/Cas9 (clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9), had stimulated researchers to exploit it for its wide implementation in several eukaryotic organisms along with crop plants. The technology has proven to be economical, easy to use and hi...

Aims: To characterize the geo-distinct isolates of Ustilaginoidea virens for morpho-molecular and mating-type locus diversity METHODS AND RESULTS: Sixty-one isolates of U. virens collected from Southern India exhibited significant diversity in mycelial width (3.45-5.50 µm), colony color (yellow, pale yellow, and white), and growth pattern (thick l...

Rice varieties are generally bred for higher yield but may possess genomic regions conferring tolerance to abiotic stresses. Climate change driven heat stress during reproductive stage of the crop affects spikelet fertility and yield. Though genetic regions associated with heat stress tolerance have been identified in rice, but response of rice var...

Magnaporthe oryzae, a hemibiotrophic fungus, is one of the most destructive fungal pathogens causing potential threat to the production of rice and it can result in complete yield losses in major rice-growing areas. In the present study, seventy two M. oryzae isolates were collected from five major rice growing states of India. The blast isolates w...

A large diversity of Ricebean exists in northeast India. Ricebean is a hardy crop and rich in protein with added nutritional advantage. It has the potential to emerge as an important crop. Understanding and utilizing the available genetic resources that may harbor useful genes for yield and biotic and abiotic stress tolerance is pertinent to improv...

In the present study, we developed a set of 100 BC 2 F 4 mapping lines derived from the cross between the Oryza nivara (AC100476) and high yielding indica rice, Lalat. Out of 410 RM markers used for polymorphism survey between the parental lines, we identified around 113 (28.9%) polymorphic rice microsatellite (RM) markers between the parental line...

Commercial exploitation of rice hybrid for sustainable production and productivity largely depends on genetic purity of hybrid seed used. To detect genetic impurity in the hybrid seeds developed through the three-line system using wild abortive (WA) cytoplasmic-based male sterility, a multiplex PCR assay was designed . A total of six primers, namel...

RNA interference/RNAi is a promising natural mechanism for crop protection that permits knockdown of a gene (which may be a foreign gene, transposonsor a virus) by limiting its expression. Conventionally, RNAi is based on the use of transgenics that express double-stranded RNA (dsRNA) or artificially activated through the use of virus-induced gene...

Mango is the most popular fruits and is used from the immature stage to the ripe stage and processed products. The present experiment was conducted to understand the effects of sowing depth and gibberrellic acids (GA3) treatments on the seed percentage of mango. The experiment was carried out in the fruit nursery of the College of Horticulture and...

Rice exhibits relatively high glycemic index (GI) value compared to other carbohydrate rich foods. Eating rice as a staple food and leading sedentary life style may lead to obesity and type‐II diabetes. National Rice Research Institute (ICAR‐NRRI), Cuttack, India released varieties were analyzed for low GI and high resistant starch (RS) content. La...

RNA-Seq technology was used to analyze the transcriptome of two rice hybrids, Ajay (based on wild-abortive (WA)-cytoplasm) and Rajalaxmi (based on Kalinga-cytoplasm), and their respective parents at the panicle initiation (PI) and grain filling (GF) stages. Around 293 and 302 million high quality paired-end reads of Ajay and Rajalaxmi, respectively...

RNA editing changes the nucleotides at the transcript level of mitochondrial genes which results in synthesis of functional proteins. This study was designed to find the editing sites which could be implicated in male fertility restoration and to develop editing based markers for differentiation of cytoplasmic male sterility and maintainer lines fr...

Rice blast is one of the most serious diseases in the world. The use of resistant cultivars is the most preferred means to control this disease. Resistance often breaks down due to emergence of new races; hence identification of novel resistance donors is indispensable. In this study, a panel of 80 released varieties from National Rice Research Ins...

The main aim of this study is to assess the potentiality of SSR markers for the identification of the cross-species transferability frequency in a large set of the diverse genome types of wild relative rice along with cultivated rice. Here, we used 18 different rice genotypes representing nine different genome types with 70 SSR markers to investiga...

Low light intensity is a great limitation for grain yield and quality in rice. However, yield is not significantly reduced in low light tolerant rice varieties. The work therefore planned for comparative transcriptome profiling under low light stress to decipher the genes involved and molecular mechanism of low light tolerance in rice. At active ti...

[This corrects the article DOI: 10.1371/journal.pone.0211061.].

Lack of appropriate donors, non-utilization of high throughput phenotyping and genotyping platforms and high genotype × environment interaction restrained identification of robust QTLs for grain protein content (GPC) in rice. In the present investigation 190 BC F lines belonging to a mapping population derived from a cross between grain protein don...

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice in the world. The blast fungus shows a high degree of variability in the field and limited information is available on its genetic diversity and population structure in India. Twenty five polymorphic SSR markers were used to investigate the genetic diversity and...

Low light (LL) stress is an important abiotic stress of wet season which adversely affects starch biosynthesis and results in drastic reduction in rice grain yield. In general, the grain yield decreased together with reduction in the amylose (AC) and resistant starch (RS) contents while the glycemic index (GI) values increased in plants exposed to...

Rice blast caused by Magnaporthe oryzae is one of the most destructive diseases of rice in the world. The blast fungus shows a high degree of variability in the field and limited information is available on its genetic diversity and population structure in India. Twenty five polymorphic SSR markers were used to investigate the genetic diversity and...

Understanding of genetic diversity is important to explore existing gene in any crop breeding program. Most of the diversity preserved in the landraces which are well–known reservoirs of important traits for biotic and abiotic stresses. In the present study, the genetic diversity at twenty-four most significant blast resistance gene loci using twen...

Population assignment of landraces described by GenAlEx charts representing the log likelihood data of landrace using disease reaction: a) Moderately resistant and resistant and populations b) Susceptible and resistant populations c) Susceptible and moderately resistant populations. (TIF)

Details of landraces used in the current study. (XLSX)

Reaction of landraces to leaf blast disease in the uniform blast nursery. (TIF)

Genotyping of 161 landraces using markers associated with blast resistance genes, associated gene frequency and their phenotypic reaction to leaf blast in uniform blast nursery. (XLSX)

Population structure group of 161 landraces based on inferred ancestry values. (XLSX)

Rice blast disease caused by the fungus Magnaporthe oryzae is one of the most devastating disease causing huge losses worldwide. In the present study, mining of major blast resistance genes were investigated in landraces originated from Northeastern India. Based on phenotypic evaluation, two hundred eighty‐eight landraces were classified into three...

Rice blast disease is one of the most destructive disease causing enormous yield losses to rice in different rice growing regions of the world. The present study aims to identify and characterize the rice blast pathogen Magnaporthe oryzae from different rice growing regions of Odisha. Twenty isolates were collected and categorized into three groups...

Rice (Oryza sativa L.) is the major cereal crops providing staple food for more than half of the world population. Considering the rate of world population growth expansion, doubling the rice production is utmost necessary. Achieving of such production targets of rice will be successful only after trapping the heterosis process in rice. Adoption of...

Grain shape and size influence yield and consumer preferences in rice. In the present study, we characterized and mapped a short and bold grained mutant and named it as TEMS5032, as the mutant is a result of EMS-induced transition from C to T at the 5032nd bp of SRS3 gene, which is known to affect grain size in rice. The substitution led to creatio...

Grain shape and size influence yield and consumer preferences in rice. In the present study, we characterized and mapped a short and bold grained mutant and named it as TEMS5032, as the mutant is a result of EMS-induced transition from C to T at the 5032nd bp of SRS3 gene, which is known to affect grain size in rice. The substitution led to creatio...

Rice (Oryza sativa L.) is the major cereal crops providing staple food for more than half of the world population. Considering the rate of world population growth expansion, doubling the rice production is utmost necessary. Phosphorus is the second most important inorganic plant nutrient after nitrogen, but is also one of the least available nutrie...

Rice is generally considered a high glycemic index (GI) food. With diabetes rates increasing alarmingly in Asia, there is an urgent need to find methods of reducing the glycemic impact of rice. Rice genotypes varied widely with respect to GI (57.9 for PB177 to 75.9for O. ridleyi), resistant starch (RS) (0.4% for O. ridleyi to 2.7% for SS7) and amyl...

Biotechnological strategies such as in-vitro culture, transgenics and genome editing (CRISPR/Cas9) provide immense opportunities for rice improvement. These tools have been effectively utilized for development of new varieties, mapping of QTLs, characterization and functional validation of genes, development of novel variants etc. However, indica r...

Rice grain quality is a multifaceted trait and is the prime determinant of consumer choice and marketability of a variety. Thus, improving nutritional quality occupies an important position in rice improvement programs. Climate change and its associated consequences further emphasise upon development of nutrient packed rice grains to cater to the n...

The increased demand for rice will have to be met from less land, less water, less labour and fewer chemicals under changing climate. Can we meet the challenges to rice productivity, stability and nutritional quality improvement by strategic use of the available germplasm resources? Can India, having more than 106,000 germplasm accessions in the Na...

A breakthrough in yield ceiling in rice is warranted in view of increasing competition for resources. Ideotype/ New Plant Type/ New Generation Rice is one of the potential approach based on tailoring a plant architecture with incorporation of efficient traits for harnessing light and nutrients for optimum biomass (source) and grain yield (sink). In...

The grain size is one of the complex trait of rice yield controlled by a plethora of interaction of several genes in different pathways. The present study was undertaken to investigate the influence of seven known grain size regulating genes: DEP1, GS7, GS3, GW8, GL7, GS5 and GW2. A wide phenotypic variation for grain length, grain width and grain...

Phenotypic data of rice germplasm used in the present study. (DOCX)

Population structure groups of rice germplasm based on inferred ancestry values. (DOCX)

Rice blast, caused by the fungus Magnaporthe oryzae, is one of the most devastating diseases of rice (Oryza sativa L.), causing tremendous yield loss worldwide. In the present study, twenty isolates of M. oryzae were categorized into three groups based on colony colour i.e., greyish blackish, greyish and white, and in two group based on the texture...

World food security is becoming an ever more serious problem due to continuing population growth and increasing competition for arable land between food and energy crops. Considering the rate of world population growth expansion, doubling the rice production is utmost necessary. Achieving of such production targets of rice will be successful only a...

Rice (Oryza sativa L.) is consumed by more than half of the world's population for whom it is the main source of nutrients and carbohydrates. Rice starch is hydrolyzed by enzymes in the digestive tract and converted into glucose which is the main energy source for metabolic functions. After meeting the energy requirement of the body, the extra calo...

World food security is becoming an ever more serious problem due to continuing population growth and increasing competition for arable land between food and energy crops. In Asia, it serves as the major source of energy, protein, thiamine, riboflavin, niacin, iron (Fe), zinc (Zn) and calcium (Ca) in the diet. Nutritional quality of rice has receive...

Pigmented rice or coloured rice such as black, red and purple are well known for nutritional benefits as well as high antioxidant contents like anthocyanins and phenolic compounds. Anthocyanins are a subclass of water soluble flavonoids with potential benefits for preventing chronic and degenerative diseases, and possesses anticancer properties etc...

Rice plant architecture is one of the most important traits for grain yield. The ideal plant architecture (IPA) of rice displays low tiller numbers with few unproductive tillers, more grains per panicle, and thick and sturdy stems which substantially enhances rice grain yield. Recently, a QTL named as IPA1 (Ideal Plant Architecture 1) was cloned an...