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The pod and seed counts are important yield-related traits in soybean. High-precision soybean breeders face the major challenge of accurately phenotyping the number of pods and seeds in a high-throughput manner. Recent advances in artificial intelligence, especially deep learning (DL) models, have provided new avenues for high-throughput phenotyping of crop traits with increased precision. However, the available DL models are less effective for phenotyping pods that are densely packed and overlap in in situ soybean plants; thus, accurate phenotyping of the number of pods and seeds in soybean plant is an important challenge. To address this challenge, the present study proposed a bottom-up model, DEKR-SPrior (disentangled keypoint regression with structural prior), for in situ soybean pod phenotyping, which considers soybean pods and seeds analogous to human people and joints, respectively. In particular, we designed a novel structural prior (SPrior) module that utilizes cosine similarity to improve feature discrimination, which is important for differentiating closely located seeds from highly similar seeds. To further enhance the accuracy of pod location, we cropped full-sized images into smaller and high-resolution subimages for analysis. The results on our image datasets revealed that DEKR-SPrior outperformed multiple bottom-up models, viz., Lightweight-OpenPose, OpenPose, HigherHRNet, and DEKR, reducing the mean absolute error from 25.81 (in the original DEKR) to 21.11 (in the DEKR-SPrior) in pod phenotyping. This paper demonstrated the great potential of DEKR-SPrior for plant phenotyping, and we hope that DEKR-SPrior will help future plant phenotyping.

Abstract Global climate change has threatened world crop production and food security. Decoding the adaptive genetic basis of wild relatives provides an invaluable genomic resource for climate‐smart crop breedinG. Here, we performed whole‐genome sequencing of 185 diverse wild soybean (Glycine soja) accessions collected from three major agro‐ecological zones in China to parse the genomic basis of local adaptation in wild soybean. The population genomic diversity pattern exhibited clear agro‐ecological zone‐based population structure, and multiple environmental factors were observed to contribute to the genetic divergence. Demographic analysis shows that wild soybeans from the three ecological zones diverged about 1 × 105 years ago, and then the effective population sizes have undergone different degrees of expansions. Genome‐environment association identified multiple genes involved in the local adaptation, such as flowering time and temperature‐related genes. A locus containing two adjacent MADS‐box transcription factors on chromosome 19 was identified for multiple environmental factors, and it experienced positive selection that enables the adaptation to high‐latitude environment. This study provides insights into the genetic mechanism of ecological adaptation in wild soybean that may facilitate climate‐resilient soybean breeding.

Salinity threatens soybean germination, growth and production. The germination stage is a key period in the life of soybean. Wild soybean contains many genes related to stress resistance that are valuable resources for the genetic improvement of soybean. To identify the genetic loci of wild soybean that are active during seed germination under salt stress, two populations, a soybean interspecific hybrid population comprising 142 lines and a natural population comprising 121 wild soybean accessions, were screened for three germination-related traits in this study. By using single-nucleotide polymorphism (SNP) markers with three salt tolerance indices, 25 quantitative trait loci (QTLs), 21 significant SNPs (–log10(P)≥4.0) and 24 potential SNPs (3.5

In this Review, Bhat et al. highlight ways to mine crop haplotypes and apply them for dissecting complex traits and genomics-assisted breeding (GAB) approaches. This Review presents new avenues to discover superior haplotypes and assemble them in targeted manner in crop breeding for faster delivery of high-yielding cultivars with better adaptation to future climates.

Most plant traits are governed by polygenes including both major and minor genes. Linkage mapping and positional cloning have contributed greatly to mapping genomic loci controlling important traits in crop species. However, they are low-throughput, time-consuming, and have low resolution due to which their efficiency in crop breeding is reduced. In this regard, the bulk segregant analysis sequencing (BSA-seq) and its related approaches, viz., quantitative trait locus (QTL)-seq, bulk segregant RNA-Seq (BSR)-seq, and MutMap, have emerged as efficient methods to identify the genomic loci/QTLs controlling specific traits at high resolution, accuracy, reduced time span, and in a high-throughput manner. These approaches combine BSA with next-generation sequencing (NGS) and enable the rapid identification of genetic loci for qualitative and quantitative assessments. Many previous studies have shown the successful identification of the genetic loci for different plant traits using BSA-seq and its related approaches, as discussed in the text with details. However, the efficiency and accuracy of the BSA-seq depend upon factors like sequencing depth and coverage, which enhance the sequencing cost. Recently, the rapid reduction in the cost of NGS together with the expected cost reduction of third-generation sequencing in the future has further increased the accuracy and commercial applicability of these approaches in crop improvement programs. This review article provides an overview of BSA-seq and its related approaches in crop breeding together with their merits and challenges in trait mapping.

Identifying the genetic components underlying yield-related traits in soybean is crucial for improving its production and productivity. Here, 211 soybean genotypes were evaluated across six environments for four yield-related traits, including seed yield per plant (SYP), number of pods per plant number of seeds per plant and 100-seed weight (HSW). Genome-wide association study (GWAS) and genomic prediction (GP) analyses were performed using 12,617 single nucleotide polymorphism markers from NJAU 355K SoySNP Array. A total of 57 SNPs were significantly associated with four traits across six environments and a combined environment using five Genome-wide association study models. Out of these, six significant SNPs were consistently identified in more than three environments using multiple GWAS models. The genomic regions (±670 kb) flanking these six consistent SNPs were considered stable QTL regions. Gene annotation and in silico expression analysis revealed 15 putative genes underlying the stable QTLs that might regulate soybean yield. Haplotype analysis using six significant SNPs revealed various allelic combinations regulating diverse phenotypes for the studied traits. Furthermore, the GP analysis revealed that accurate breeding values for the studied soybean traits is attainable at an earlier generation. Our study paved the way for increasing soybean yield performance within a short breeding cycle.

The novel coronavirus pandemic has led to morbidity and mortality throughout the world. Until now, it is a highly virulent contagion attacking the respiratory system in humans, especially people with chronic diseases and the elderly who are most vulnerable. A majority of afflicted are those suffering from cardiovascular and coronary diseases. In this review article, an attempt has been made to discuss and thoroughly review the mode of therapies that alleviate cardiac complications and complications due to hypercoagulation in patients infected with the SARS-CoV-2 virus. Presently a host of thrombolytic drugs are in use like Prourokinase, Retelapse, RhTNK-tPA and Urokinase. However, thrombolytic therapy, especially if given intravenously, is associated with a serious risk of intracranial haemorrhage, systemic haemorrhage, immunologic complications, hypotension and myocardial rupture. The effects of the SARS-CoV-2 virus upon the cardiovascular system and coagulation state of the body are being closely studied. In connection to the same, clinical prognosis and complications of thrombolytic therapy are being scrutinized. It is noteworthy to mention that myocardial oxygen supply/demand mismatch, direct myocardial cells injury and acute plaque rupture are the multiple mechanisms responsible for acute coronary syndrome and cardiac complications in Covid-19 infection. However, this review has limitations as data available in this context is limited, scattered and heterogenous that questions the reliability of the same. So, more multi-centric studies involving representative populations, carried out meticulously, could further assist in responding better to cardiac complications among Covid-19 patients.

Wheat is an important cereal crop species consumed globally. The growing global population demands a rapid and sustainable growth of agricultural systems. The development of genetically efficient wheat varieties has solved the global demand for wheat to a greater extent. The use of chemical substances for pathogen control and chemical fertilizers for enhanced agronomic traits also proved advantageous but at the cost of environmental health. An efficient alternative environment-friendly strategy would be the use of beneficial microorganisms growing on plants, which have the potential of controlling plant pathogens as well as enhancing the host plant’s water and mineral availability and absorption along with conferring tolerance to different stresses. Therefore, a thorough understanding of plant-microbe interaction, identification of beneficial microbes and their roles, and finally harnessing their beneficial functions to enhance sustainable agriculture without altering the environmental quality is appealing. The wheat microbiome shows prominent variations with the developmental stage, tissue type, environmental conditions, genotype, and age of the plant. A diverse array of bacterial and fungal classes, genera, and species was found to be associated with stems, leaves, roots, seeds, spikes, and rhizospheres, etc., which play a beneficial role in wheat. Harnessing the beneficial aspect of these microbes is a promising method for enhancing the performance of wheat under different environmental stresses. This review focuses on the microbiomes associated with wheat, their spatio-temporal dynamics, and their involvement in mitigating biotic and abiotic stresses.

The present study was carried out to explore the possible role of kinetin and gibberellic acid (GA3) on faba bean under chromium (Cr) stress. Cr treatment negatively affected growth and biomass production, reduced photosynthetic pigments, and inhibited photosynthesis, gas exchange parameters, antioxidant enzymes, and the glyoxylase cycle. Moreover, Cr stress enhanced the production of malondialdehyde (MDA, 216.11%) and hydrogen peroxide (H2O2, 230.16%), electrolyte leakage (EL, 293.30%), and the accumulation of proline and glycine betaine. Exogenous application of kinetin and GA3 increased growth and biomass, improved pigment contents and photosynthesis, as well as up-regulated the antioxidant system by improving the antioxidant enzyme activities and the content of nonenzymatic components, and the glyoxylase cycle. Additionally, kinetin and GA3 application displayed a considerable enhancement in proline (602.61%) and glycine betaine (423.72), which help the plants to maintain water balance under stress. Furthermore, a decline in Cr uptake was also observed due to kinetin and GA3 application. Exogenous application of kinetin and GA3 ameliorated the toxic effects of Cr in faba bean plants, up-shooting the tolerance mechanisms, including osmolyte metabolism and the antioxidant system.

Cadmium (Cd) is a trace element causing severe toxicity symptoms in plants, besides posing hazardous fitness issue due to its buildup in the human body through food chain. Nanoparticles (NPs) are recently employed as a novel strategy to directly ameliorate the Cd stress and acted as nano-fertilizers. The intend of the current study was to explore the effects of zinc oxide nanoparticles (ZnO-NPs; 50 mg/L) on plant growth, photosynthetic activity, elemental status and antioxidant activity in Oryza sativa (rice) under Cd (0.8 mM) stress. To this end, the rice plants are treated by Cd stress at 15 days after sowing (DAS), and the treatment was given directly into the soil. Supply of ZnO-NPs as foliar spray was given for five consecutive days from 30 to 35 DAS, and sampling was done at 45 DAS. However, rice plants supplemented with ZnO-NPs under the Cd toxicity revealed significantly increased shoot length (SL; 34.0%), root fresh weight (RFW; 30.0%), shoot dry weight (SDW; 23.07%), and root dry weight (RDW; 12.24%). Moreover, the ZnO-NPs supplement has also positive effects on photosynthesis related parameters, SPAD value (40%), chloroplast structure, and qualitatively high fluorescence observed by confocal microscopy even under Cd stress. ZnO-NPs also substantially prevented the increases of hydrogen peroxide (H2O2) and malondialdehyde (MDA) triggered by Cd. Physiological and biochemical analysis showed that ZnO-NPs increased enzymatic activities of superoxide dismutase (SOD; 59%), catalase (CAT; 52%), and proline (17%) that metabolize reactive oxygen species (ROS); these increases coincided with the changes observed in the H2O2 and MDA accumulation after ZnO-NPs application. In conclusion, ZnO-NPs application to foliage has great efficiency to improve biomass, photosynthesis, protein, antioxidant enzymes activity, mineral nutrient contents and reducing Cd levels in rice. This can be attributed mainly from reduced oxidative damage resulted due to the ZnO-NPs application.

Abstract Soybean is an important food crop that provides edible protein and oil for human and animal nutrition. Conventional phenotypic‐based breeding approaches have made significant contribution in the last century by developing many improved soybean varieties. However, due to the longer time taken to develop a variety, low genetic gain per unit time, and adverse environmental influence of phenotypic‐based selection, conventional approaches are not sufficient to maintain pace with growing population and climate change. In this context, the recent method of genotypic selection, that is, genomics‐assisted breeding (GAB) is considered a promising approach to address the challenges in soybean breeding. However, to harness the true potential of GAB in soybean improvement, the great coverage and precision in the genotyping and phenotyping are required. Previously, a huge gap was observed between the discovery and practical use of quantitative trait loci (QTLs) in soybean improvement. It has been suggested that low marker density and manually collected phenotypes are the major reasons for this failure. Hence, high‐throughput genotyping (HTG) providing higher genome‐wide marker density, as well as accurate and precise phenotyping using high‐throughput digital phenotyping (HTP) platforms, can significantly increase the success of QTL and candidate gene identification in soybean. These approaches can greatly increase the practical utility of GAB in soybean and also offer a faster characterization of germplasm and breeding materials. This review provides the detailed information on how the recent innovations in genomics and phenomics can assists in improving the efficiency and potential of GAB in soybean improvement.

Nanoparticles (NPs) have recently emerged as potential agents for plants to ameliorate abiotic stresses by acting as nano-fertilizers. In this regard, the influence of the zinc oxide nanoparticles (ZnO-NPs) on plant responses to copper (Cu) stress has been poorly understood. Hence, the present study was executed to explore the role of ZnO-NPs (foliar) and 24-epibrassinolide (EBL; root dipping) individually or in combined form in the resilience of tomato (Solanum lycopersicum) plant to Cu stress. Tomato seeds were sown to make the nursery; and at 20 days after sowing (DAS) the plantlets were submerged in 10−8 M of EBL solution for 2 h, and subsequently transplanted in the soil-filled earthen pots. Cu concentration (100 mg kg−1) was applied to the soil at 30 DAS, whereas at 35 DAS plants were sprinkled with double distilled water (DDW; control), 50 mg/L of Zinc (Zn) and 50 mg/L of ZnO-NPs; and plant performance were evaluated at 45 DAS. It was evident that Cu-stress reduced photosynthesis (17.3%), stomatal conductance (18.1%), plant height (19.7%), and nitrate reductase (NR) activity (19.2%), but increased malondialdehyde (MDA; 29.4%), superoxide radical (O2-; 22.3%) and hydrogen peroxide (H2O2; 26.2%) content in S. lycopersicum. Moreover, ZnO-NPs and/or EBL implemented via different modes improved photosynthetic activity, stomatal aperture, growth, cell viability and activity of antioxidant enzymes and proline that augmented resilience of tomato plants to Cu stress. These observations depicted that application of ZnO-NPs and EBL could be a useful approach to assist Cu confiscation and stress tolerance against Cu in tomato plants grown in Cu contaminated sites.

Abstract Background Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in seed aging, and enhancing seed storability is an imperative goal for soybean breeding. The aim of this study is to identify quantitative trait loci (QTLs) using high-density genetic linkage maps of soybean for seed storability. In this regard, two recombinant inbred line (RIL) populations derived from Zhengyanghuangdou × Meng 8206 (ZM6) and Linhefenqingdou × Meng 8206 (LM6) crosses were evaluated for three seed-germination related traits viz., germination rate (GR), normal seedling length (SL) and normal seedling fresh weight (FW) under natural and artificial aging conditions to map QTLs for seed storability. Results A total of 34 QTLs, including 13 QTLs for GR, 11 QTLs for SL and 10 QTLs for FW, were identified on 11 chromosomes with the phenotypic variation ranged from 7.30 to 23.16% under both aging conditions. All these QTLs were novel, and 21 of these QTLs were clustered in five QTL-rich regions on four different chromosomes viz., Chr3, Chr5, Chr17 &Chr18, among them the highest concentration of seven and six QTLs were found in “QTL hotspot A” (Chr17) and “QTL hotspot B” (Chr5), respectively. Furthermore, QTLs within all the five QTL clusters are linked to at least two studied traits, which is also supported by highly significant correlation between the three germination-related traits. QTLs for seed-germination related traits in “QTL hotspot B” were found in both RIL populations and aging conditions, and also QTLs underlying “QTL hotspot A” are identified in both RIL populations under artificial aging condition. These are the stable genomic regions governing the inheritance of seed storability in soybean, and will be the main focus for soybean breeders. Conclusion This study uncovers the genetic basis of seed storability in soybean. The newly identified QTLs provides valuable information, and will be main targets for fine mapping, candidate gene identification and marker-assisted breeding. Hence, the present study is the first report for the comprehensive and detailed investigation of genetic architecture of seed storability in soybean.

Chromium (Cr) phytotoxicity severely inhibits plant growth and development which makes it a prerequisite to developing techniques that prevent Cr accumulation in food chains. However, little is explored related to the protective role of brassinosteroids (BRs) against Cr-induced stress in soybean plants. Herein, the morpho-physiological, biochemical, and molecular responses of soybean cultivars with/without foliar application of BRs under Cr toxicity were intensely investigated. Our outcomes deliberated that BRs application noticeably reduced Cr-induced phytotoxicity by lowering Cr uptake (37.7/43.63%), accumulation (63.92/81.73%), and translocation (26.23/38.14%) in XD-18/HD-19, plant tissues, respectively; besides, improved seed germination ratio, photosynthetic attributes, plant growth, and biomass, as well as prevented nutrient uptake inhibition under Cr stress, especially in HD-19 cultivar. Furthermore, BRs stimulated antioxidative defense systems, both enzymatic and non-enzymatic, the compartmentalization of ion chelation, diminished extra production of reactive oxygen species (ROS), and electrolyte leakage in response to Cr-induced toxicity, specifically in HD-19. In addition, BRs improved Cr stress tolerance in soybean seedlings by regulating the expression of stress-related genes involved in Cr accumulation, and translocation. Inclusively, by considering the above-mentioned biomarkers, foliar spray of BRs might be considered an effective inhibitor of Cr-induced damages in soybean cultivars, even in Cr polluted soil.

Chromium (Cr) is an important environmental constraint effecting crop productivity. Spermine (SPM) is a polyamine compound regulating plant responses to abiotic stresses. However, SPM-mediated tolerance mechanisms against Cr stress are less commonly explored in plants. Thus, current research was conducted to explore the protective mechanisms of SPM (0.01 mM) against Cr (100 µM) toxicity in two rice cultivars, CY927 (sensitive) and YLY689 (tolerant) at the seedling stage. Our results revealed that, alone, Cr exposure significantly reduced seed germination, biomass and photosynthetic related parameters, caused nutrient and hormonal imbalance, desynchronized antioxidant enzymes, and triggered oxidative damage by over-accretion of reactive oxygen species (ROS), malondialdehyde (MDA) and electrolyte leakage in both rice varieties, with greater impairments in CY927 than YLY689. However, seed priming with SPM notably improved or reversed the above-mentioned parameters, especially in YLY689. Besides, SPM stimulated the stress-responsive genes of endogenous phytohormones, especially salicylic acid (SA), as confirmed by the pronounced transcript levels of SA-related genes (OsPR1, OsPR2 and OsNPR1). Our findings specified that SPM enhanced rice tolerance against Cr toxicity via decreasing accumulation of Cr and markers of oxidative damage (H2O2, O2•− and MDA), improving antioxidant defense enzymes, photosynthetic apparatus, nutrients and phytohormone balance.

Chitinases are enzymes catalyzing the hydrolysis of chitin that are present on the cell wall of fungal pathogens. Here, we identified and characterized the chitinase gene family in cultivated soybean (Glycine max L.) across the whole genome. A total of 38 chitinase genes were identified in the whole genome of soybean. Phylogenetic analysis of these chitinases classified them into five separate clusters, I–V. From a broader view, the I–V classes of chitinases are basically divided into two mega-groups (X and Y), and these two big groups have evolved independently. In addition, the chitinases were unevenly and randomly distributed in 17 of the total 20 chromosomes of soybean, and the majority of these chitinase genes contained few introns (≤2). Synteny and duplication analysis showed the major role of tandem duplication in the expansion of the chitinase gene family in soybean. Promoter analysis identified multiple cis-regulatory elements involved in the biotic and abiotic stress response in the upstream regions (1.5 kb) of chitinase genes. Furthermore, qRT-PCR analysis showed that pathogenic and drought stress treatment significantly induces the up-regulation of chitinase genes belonging to specific classes at different time intervals, which further verifies their function in the plant stress response. Hence, both in silico and qRT-PCR analysis revealed the important role of the chitinases in multiple plant defense responses. However, there is a need for extensive research efforts to elucidate the detailed function of chitinase in various plant stresses. In conclusion, our investigation is a detailed and systematic report of whole genome characterization of the chitinase family in soybean.

Plants coevolved with their antioxidant defense systems, which detoxify and adjust levels of reactive oxygen species (ROS) under multiple plant stresses. We performed whole-genome identification of ascorbate peroxidase (APX) and catalase (CAT) families in cultivated and wild soybeans. In cultivated and wild soybean genomes, we identified 11 and 10 APX genes, respectively, whereas the numbers of identified CAT genes were four in each species. Comparative phylogenetic analysis revealed more homology among cultivated and wild soybeans relative to other legumes. Exon/intron structure, motif and synteny blocks are conserved in cultivated and wild species. According to the Ka/Ks value, purifying selection is a major force for evolution of these gene families in wild soybean; however, the APX gene family was evolved by both positive and purifying selection in cultivated soybean. Segmental duplication was a major factor involved in the expansion of APX and CAT genes. Expression patterns revealed that APX and CAT genes are differentially expressed across fourteen different soybean tissues under water deficit (WD), heat stress (HS) and combined drought plus heat stress (WD + HS). Altogether, the current study provides broad insights into these gene families in soybeans. Our results indicate that APX and CAT gene families modulate multiple stress response in soybeans.

Plant stresses causing accumulation of reactive oxidative species (ROS) are scavenged by effective antioxidant defense systems. Therefore, the present study performed genome-wide identification of superoxide dismutase (SOD) and glutathione peroxidase (GPX) gene families in cultivated and wild soybeans, and 11 other legume species. We identified a total of 101 and 95 genes of SOD and GPX, respectively, across thirteen legume species. The highest numbers of SODs and GPXs were identified in cultivated (Glycine max) and wild (Glycine soja). A comparative phylogenetic study revealed highest homology among the SODs and GPXs of cultivated and wild soybeans relative to other legumes. The exon/intron structure, motif and synteny blocks were conserved in both soybean species. According to Ka/Ks, purifying the selection played the major evolutionary role in these gene families, and segmental duplication are major driving force for SODs and GPXs expansion. In addition, the qRT-PCR analysis of the G. max and G. soja SOD and GPX genes revealed significant differential expression of these genes in response to oxidative, drought and salinity stresses in root tissue. In conclusion, our study provides new insights for the evolution of SOD and GPX gene families in legumes, and provides resources for further functional characterization of these genes for multiple stresses.

Seed-weight is one of the most important traits determining soybean yield. Hence, it is prerequisite to have detailed understanding of the genetic basis regulating seed-weight for the development of improved cultivars. In this regard, the present study used high-density interspecific linkage map of NJIR4P recombinant inbred population evaluated in four different environments to detect stable Quantitative trait loci (QTLs) as well as mine candidate genes for 100-seed weight. In total, 19 QTLs distributed on 12 chromosomes were identified in all individual environments plus combined environment, out of which seven were novel and eight are stable identified in more than one environment. However, all the novel QTLs were minor (R2 < 10%). The remaining 12 QTLs detected in this study were co-localized with the earlier reported QTLs with narrow genomic regions, and out of these only 2 QTLs were major (R2 > 10%) viz., qSW-17-1 and qSW-17-4. Beneficial alleles of all identified QTLs were derived from cultivated soybean parent (Nannong493-1). Based on Protein ANalysis THrough Evolutionary Relationships, gene annotation information, and literature search, 29 genes within 5 stable QTLs were predicted to be possible candidate genes that might regulate seed-weight/size in soybean. However, it needs further validation to confirm their role in seed development. In conclusion, the present study provides better understanding of trait genetics and candidate gene information through the use high-density inter-specific bin map, and also revealed considerable scope for genetic improvement of 100-seed weight in soybean using marker-assisted breeding.

Short petiole is a valuable trait for the improvement of plant canopy of ideotypes with high yield. Here, we identified a soybean mutant line derived short petiole (dsp) with extremely short petiole in the field, which is obviously different from most short-petiole lines identified previously. Genetic analysis on 941 F2 individuals and subsequent segregation analysis of 184 F2:3 and 172 F3:4 families revealed that the dsp mutant was controlled by two recessive genes, named as dsp1 and dsp2. Map-based cloning showed that these two recessive genes were located on two nonhomologous regions of chromosome 07 and chromosome 11, of which the dsp1 locus was mapped at a physical interval of 550.5-Kb on chromosome 07 near to centromere with flanking markers as BARCSOYSSR_07_0787 and BARCSOYSSR_07_0808; whereas, the dsp2 locus was mapped to a 263.3-Kb region on chromosome 11 with BARCSOYSSR_11_0037 and BARCSOYSSR_11_0043 as flanking markers. A total of 36 and 33 gene models were located within the physical genomic interval of dsp1 and dsp2 loci, respectively. In conclusion, the present study identified markers linked with genomic regions responsible for short-petiole phenotype of soybean, which can be effectively used to develop ideal soybean cultivars through marker-assisted breeding.

Plant height (PH) is an important agronomic trait that is closely related to soybean yield and quality. However, it is a complex quantitative trait governed by multiple genes and is influenced by environment. Unraveling the genetic mechanism involved in PH, and developing soybean cultivars with desirable PH is an imperative goal for soybean breeding. In this regard, the present study used high-density linkage maps of two related recombinant inbred line (RIL) populations viz., MT and ZM evaluated in three different environments to detect additive and epistatic effect quantitative trait loci (QTLs) as well as their interaction with environments for PH in Chinese summer planting soybean. A total of eight and 12 QTLs were detected by combining the composite interval mapping (CIM) and mixed-model based composite interval mapping (MCIM) methods in MT and ZM populations, respectively. Among these QTLs, nine QTLs viz., QPH-2, qPH-6-2MT, QPH-6, qPH-9-1ZM, qPH-10-1ZM, qPH-13-1ZM, qPH-16-1MT, QPH-17 and QPH-19 were consistently identified in multiple environments or populations, hence were regarded as stable QTLs. Furthermore, Out of these QTLs, three QTLs viz., qPH-4-2ZM, qPH-15-1MT and QPH-17 were novel. In particular, QPH-17 could detect in both populations, which was also considered as a stable and major QTL in Chinese summer planting soybean. Moreover, eleven QTLs revealed significant additive effects in both populations, and out of them only six showed additive by environment interaction effects, and the environment-independent QTLs showed higher additive effects. Finally, six digenic epistatic QTLs pairs were identified and only four additive effect QTLs viz., qPH-6-2MT, qPH-19-1MT/QPH-19, qPH-5-1ZM and qPH-17-1ZM showed epistatic effects. These results indicate that environment and epistatic interaction effects have significant influence in determining genetic basis of PH in soybean. These results would not only increase our understanding of the genetic control of plant height in summer planting soybean but also provide support for implementing marker assisted selection (MAS) in developing cultivars with ideal plant height as well as gene cloning to elucidate the mechanisms of plant height.

Over the past few decades, heavy metal contamination in soil and water has increased due to anthropogenic activities. The higher exposure of crop plants to heavy metal stress reduces growth and yield, and affect the sustainability of agricultural production. In this regard, the use of silicon (Si) supplementation offers a promising prospect since numerous studies have reported the beneficial role of Si in mitigating stresses imposed by biotic as well as abiotic factors including heavy metal stress. The fundamental mechanisms involved in the Si-mediated heavy metal stress tolerance include reduction of metal ions in soil substrate, co-precipitation of toxic metals, metal-transport related gene regulation, chelation, stimulation of antioxidants, compartmentation of metal ions, and structural alterations in plants. Exogenous application of Si has been well documented to increase heavy metal tolerance in numerous plant species. The beneficial effects of Si are particularly evident in plants able to accumulate high levels of Si. Consequently, to enhance metal tolerance in plants, the inherent genetic potential for Si uptake should be improved. In the present review, we have discussed the potential role and mechanisms involved in the Si-mediated alleviation of metal toxicity as well as different approaches for enhancing Si-derived benefits in crop plants.

One hundred forty one basmati rice genotypes collected from different geographic regions of North Western Himalayas were characterized using 40 traits linked microsatellite markers. Number of alleles detected by the abovementioned primers were 112 with a maximum and minimum frequency of 5 and 2 alleles, respectively. The maximum and minimum polymorphic information content values were found to be 0.63 and 0.17 for the primers RM206 and RM213, respectively. The genetic similarity coefficient for the most number of pairs ranged between of 0.2-0.9 with the average value of 0.60 for all possible combinations, indicating moderate genetic diversity among the chosen genotypes. Phylogenetic cluster analysis of the SSR data based on distance divided all genotypes into four groups (I, II, III and IV), whereas model based clustering method divided these genotypes into five groups (A, B, C, D and E). However, the result from both the analysis are in well agreement with each other for clustering on the basis of place of collection and geographic region, except the local basmati genotypes which clustered into three subpopulations in structure analysis comparison to two clusters in distance based clustering. The diverse genotypes and polymorphic trait linked microsatellites markers in the present study will be used for the identification of quantitative trait loci/genes for different economically important traits to be utilized in molecular breeding programme of rice in the future.