A. Pattanayak

Genetic Diversity and Population Structure in Aromatic and Quality Rice (Oryza sativa L.) Landraces from North-Eastern India.

The North-eastern (NE) India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland, Sikkim and Tripura, possess diverse array of locally adapted non-Basmati aromatic germplasm. The germplasm collections from this region could serve as valuable resources in breeding for abiotic stress tolerance, grain yield and cooking/eating quality. To utilize such collections, however, breeders need information about the extent and distribution of genetic diversity present within collections. In this study, we report the result of population genetic analysis of 107 aromatic and quality rice accessions collected from different parts of NE India, as well as classified these accessions in the context of a set of structured global rice cultivars. A total of 322 alleles were amplified by 40 simple sequence repeat (SSR) markers with an average of 8.03 alleles per locus. Average gene diversity was 0.67. Population structure analysis revealed that NE Indian aromatic rice can be subdivided into three genetically distinct population clusters: P1, joha rice accessions from Assam, tai rices from Mizoram and those from Sikkim; P2, chakhao rice germplasm from Manipur; and P3, aromatic rice accessions from Nagaland. Pair-wise FST between three groups varied from 0.223 (P1 vs P2) to 0.453 (P2 vs P3). With reference to the global classification of rice cultivars, two major groups (Indica and Japonica) were identified in NE Indian germplasm. The aromatic accessions from Assam, Manipur and Sikkim were assigned to the Indica group, while the accessions from Nagaland exhibited close association with Japonica. The tai accessions of Mizoram along with few chakhao accessions collected from the hill districts of Manipur were identified as admixed. The results highlight the importance of regional genetic studies for understanding diversification of aromatic rice in India. The data also suggest that there is scope for exploiting the genetic diversity of aromatic and quality rice germplasm of NE India for rice improvement.

Advances in Maize Transformation Technologies and Development of Transgenic Maize

Maize is the principal grain crop of the world. It is also the crop where genetic engineering has been employed to a great extent to improve its various traits. The ability to transform maize is a crucial step for application of gene technology in maize improvement. There have been constant improvements in the maize transformation technologies over past several years. The choice of genotype and the explant material to initiate transformation and the different types of media to be used in various stages of tissue culture can have significant impact on the outcomes of the transformation efforts. Various methods of gene transfer, like the particle bombardment, protoplast transformation, Agrobacterium-mediated, in planta transformation, etc., have been tried and improved over years. Similarly, various selection systems for retrieval of the transformants have been attempted. The commercial success of maize transformation and transgenic development is unmatched by any other crop so far. Maize transformation with newer gene editing technologies is opening up a fresh dimension in transformation protocols and work-flows. This review captures the various past and recent facets in improvement in maize transformation technologies and attempts to present a comprehensive updated picture of the current state of the art in this area.

Stability Performance of Inductively Coupled Plasma Mass Spectrometry-Phenotyped Kernel Minerals Concentration and Grain Yield in Maize in Different Agro-Climatic Zones.

Deficiency of iron and zinc causes micronutrient malnutrition or hidden hunger, which severely affects ~25% of global population. Genetic biofortification of maize has emerged as cost effective and sustainable approach in addressing malnourishment of iron and zinc deficiency. Therefore, understanding the genetic variation and stability of kernel micronutrients and grain yield of the maize inbreds is a prerequisite in breeding micronutrient-rich high yielding hybrids to alleviate micronutrient malnutrition. We report here, the genetic variability and stability of the kernel micronutrients concentration and grain yield in a set of 50 maize inbred panel selected from the national and the international centres that were raised at six different maize growing regions of India. Phenotyping of kernels using inductively coupled plasma mass spectrometry (ICP-MS) revealed considerable variability for kernel minerals concentration (iron: 18.88 to 47.65 mg kg–1; zinc: 5.41 to 30.85 mg kg–1; manganese: 3.30 to17.73 mg kg–1; copper: 0.53 to 5.48 mg kg–1) and grain yield (826.6 to 5413 kg ha–1). Significant positive correlation was observed between kernel iron and zinc within (r = 0.37 to r = 0.52, p < 0.05) and across locations (r = 0.44, p < 0.01). Variance components of the additive main effects and multiplicative interactions (AMMI) model showed significant genotype and genotype × environment interaction for kernel minerals concentration and grain yield. Most of the variation was contributed by genotype main effect for kernel iron (39.6%), manganese (41.34%) and copper (41.12%), and environment main effects for both kernel zinc (40.5%) and grain yield (37.0%). Genotype main effect plus genotype-by-environment interaction (GGE) biplot identified several mega environments for kernel minerals and grain yield. Comparison of stability parameters revealed AMMI stability value (ASV) as the better representative of the AMMI stability parameters. Dynamic stability parameter GGE distance (GGED) showed strong and positive correlation with both mean kernel concentrations and grain yield. Inbreds (CM-501, SKV-775, HUZM-185) identified from the present investigation will be useful in developing micronutrient-rich as well as stable maize hybrids without compromising grain yield.

Agriculturally Important Microbes for Sustainable Agriculture

Microorganisms that sustain the fertility of soils, resulting in improved plant nutrition, have continued to magnetize attention because of the increasing cost of agricultural inputs and some of their negative impacts on environmental sustainability. The continuous increase in the world population at an alarming rate requires more food for nutritional security. A doubling in global food demand projected for the next 50 years poses huge challenges for agricultural sustainability. Nowadays, plant growth is enhanced by the increasing input of agrochemicals, which act as plant growth regulators (PGRs) and as nutrients. Excessive/injudicious use of chemicals increases the chances of deteriorating soil and environmental quality. Rhizospheric plant growth–promoting microorganisms (PGPMs) are increasingly and promisingly being distributed in world agriculture. Meanwhile, current use of these efficient PGPMs may offer agronomic, pathogenic, and environmental benefits for intensive agricultural production systems. PGPMs are exhibiting a gradual increase in demand on the world market as sustainable and eco-friendly tools. Possible mechanisms for the effectiveness of biofertilizers are mobilization of the scarcely available plant nutrients nitrogen (N), fixer phosphorus (P), potassium (K), and zinc (Zn) solubilizers; production of plant growth–promoting substances; enhanced and induced resistance to environmental multistress factors; and direct or indirect suppression of harmful microbes. Research activities are currently limited by the lack of standards for production and quality control of different commercially used biofertilizers.

From zero to hero: the past, present and future of grain amaranth breeding

Key messageGrain amaranth is an underutilized crop with high nutritional quality from the Americas. Emerging genomic and biotechnological tools are becoming available that allow the integration of novel breeding techniques for rapid improvement of amaranth and other underutilized crops.AbstractOut of thousands of edible plants, only three cereals—maize, wheat and rice—are the major food sources for a majority of people worldwide. While these crops provide high amounts of calories, they are low in protein and other essential nutrients. The dependence on only few crops, with often narrow genetic basis, leads to a high vulnerability of modern cropping systems to the predicted climate change and accompanying weather extremes. Broadening our food sources through the integration of so-called orphan crops can help to mitigate the effects of environmental change and improve qualitative food security. Thousands of traditional crops are known, but have received little attention in the last century and breeding efforts were limited. Amaranth is such an underutilized pseudocereal that is of particular interest because of its balanced amino acid and micronutrient profiles. Additionally, the C4 photosynthetic pathway and ability to withstand environmental stress make the crop a suitable choice for future agricultural systems. Despite the potential of amaranth, efforts of genetic improvement lag considerably behind those of major crops. The progress in novel breeding methods and molecular techniques developed in model plants and major crops allow a rapid improvement of underutilized crops. Here, we review the history of amaranth and recent advances in genomic tools and give a concrete perspective how novel breeding techniques can be implemented into breeding programs. Our perspectives are transferable to many underutilized crops. The implementation of these could improve the nutritional quality and climate resilience of future cropping systems.

Assessment of genotypic variation in soybean (Glycine max)

Forty-two soybean genotypes were evaluated for their agro-morphological traits and the extent of genetic variability. Analysis of variance and mean performance for yield and its components revealed significant differences among all the genotypes for all the characters. Correlation was also found significant with yield and its component traits. The path analysis indicated that number of clusters (0.402) and number of pods (0.313) had shown highest direct effect on grain yield and thus selection based on these traits will be quite fruitful. Cluster diagram based on agro-morphological traits proposed two major clusters. The experimental data revealed that 3 principal components having greater than one eigenvalues contributed 82.66% of the total variation. Number of pods (0.508), number of clusters (0.506), number of branches (0.367), plant height (0.33) and days to flowering (0.360) were major contributors to PC1. Yield per ha (0.733) and seed weight (0.403) had contributed more positively to PC2.

Mapping quantitative trait loci for important agronomic traits in finger millet (Eleusine coracana) mini core collection with genomic and genic SSR markers

Allele identification for agro-morphological traits and stress resistance is a major concern across the globe for improving productivity of finger millet. Here, we used 46 genomic and 58 genic simple sequence repeats (SSRs) markers in a set of 66 accessions used to constitute a global mini-core collection for analysing their genetic structure as a population and establishing association among markers and twenty morphological traits including resistance to finger blast. Phenotypic data revealed a wide range of variation for all traits except flag leaf width and flag leaf sheath width. We got amplification of 81 alleles by the 31 genomic SSRs at an average of 2.61 alleles per locus. Polymorphism information content (PIC) values varied from 0.21 to 0.75 and average gene diversity was 0.49. Structure analysis of the population using the genomic SSR data divided the accessions into two clusters where Indian and exotic accessions were grouped in separate clusters. Genic SSRs which were associated with blast resistance genes, amplified 36 alleles at an average of 2 alleles per locus. PIC values ranged from 0.32 to 0.37 and average gene diversity was 0.45. Population structure analysis using data from these SSRs grouped the accessions into three clusters, which broadly correspond to their reaction to blast disease. Twenty-two significant associations were found using the GLM approach for 20 agro-morphological traits both in 2012 and 2014, while, 7 and 5 significant marker-trait associations were identified using MLM in 2012 and 2014 respectively. The SSR markers FMBLEST35 and FMBLEST36 designed from the Pi21 gene sequence of rice were found to be associated with blast disease resistance in finger millet indicating that the gene homologues play a significant role in an important role for neck blast resistance.

Potassium solubilization: Strategies to mitigate potassium deficiency in agricultural soils

In soil system, 90%-98% K reserves are non-exchangeable mineral sources and potassium solubilizing microbes (KSMs) can effectively dissolve this mineral. Nowadays focused research on efficient KSMs was started. These microbes are able to enhanced their root colonization and improve plant growth and development. They solubilize K-minerals through different mechanisms including chelation, acidolysis, lowering of pH, exchange reaction, complexation, biofilm formation and secretion of organic acid and polysaccharides. Bio-priming of seed/root through efficient KSMs resulted higher crop productivity, potassium use efficiency (KUE) and mitigate the K-deficiency in soils. In this article we are trying to summarize the KSMs current state of knowledge in agricultural crops. We highlighted the knowledge gaps and suggest future prospective of research, with hope that the use of KSMs in agricultural soil improved soil sustainability.

Sustainable agroforestry systems and their structural components as livelihood options along elevation gradient in central Himalaya

Abstract Himalayan ecosystems are complex, with fragile environment, rugged terrain, unique topography and sensitive to regional and global changes. This region harbours a variety of agricultural practices out of which traditional agroforestry systems are of paramount importance with regard to sustainability and livelihood. In the central Himalayan region, four major traditional agroforestry systems were observed; agrisilviculture (AS), agrihorticulture (AH), agrihortisilviculture (AHS) and agrisilvihorticulture (ASH). System units in each system varied from 8 to 24 and they also differed along the elevation. Likewise, structural components varied in the systems as well as along the elevation. These systems have evolved over long periods of time as farmers have grown the trees and crop combinations for generations. These systems fulfill diverse needs for food, fodder, fruit and timber for the inhabitants of the mountains and provide a backbone to the hill economy and livelihood security for local people.

Cross-genera transferability of rice and finger millet genomic SSRs to barnyard millet (Echinochloa spp.)

Abstract Barnyard millet (Echinochloa spp.) is an important crop from nutritional point of view, nevertheless, the genetic information is very scarce. In the present investigation, rice and finger millet genomic SSRs were used for assessing cross transferability, identification of polymorphic markers, syntenic regions, genetic diversity and population structure analysis of barnyard millet genotypes. We observed 100% cross transferability for finger millet SSRs, of which 91% were polymorphic, while 71% of rice markers were cross transferable with 48% polymorphic out of them. Twenty-nine and sixteen highly polymorphic finger millet and rice SSRs yielded a mean of 4.3 and 3.38 alleles per locus in barnyard millet genotypes, respectively. The PIC values varied from 0.27 to 0.73 at an average of 0.54 for finger millet SSRs, whereas it was from 0.15 to 0.67 at an average of 0.44 for rice SSRs. High synteny was observed for markers related to panicle length, yield-related traits, spikelet fertility, plant height, root traits, leaf senescence, blast and brown plant hopper resistance. Although the rice SSRs located on chromosome 10 followed by chromosome 6 and 11 were found to be more transferable to barnyard millet, the finger millet SSRs were more polymorphic and transferable to barnyard millet genotypes. These SSR data of finger millet and rice individually as well as combined together grouped the 11 barnyard millet genotypes into 2 major clusters. The results of population structure analysis were similar to cluster analysis.