Consensus genetic linkage map and QTL mapping allow to capture the genomic regions associated with agronomic traits in pearl millet.

MAIN CONCLUSION: A genetic linkage map representing the pearl millet genome was constructed with SNP markers. Major and stable QTL associated with flowering, number of productive tillers, ear head length, and test weight were mapped on chromosomes 1 and 3. Pearl millet (Pennisetum glaucum) is a major cereal and fodder crop in arid and semi-arid regions of Asia and Africa. Agronomic traits are important traits in pearl millet breeding and genetic and environmental factors highly influence them. In the present study, an F9 recombinant inbred line (RIL) population derived from a cross between PT6029 and PT6129 was evaluated for agronomic traits in three environments. Utilizing a genotyping by sequencing approach, a dense genetic map with 993 single nucleotide polymorphism markers covering a total genetic distance of 1035.4 cM was constructed. The average interval between the markers was 1.04 cM, and the seven chromosomes varied from 115.39 to 206.72 cM. Quantitative trait loci (QTL) mapping revealed 35 QTL for seven agronomic traits, and they were distributed on all pearl millet chromosomes. These QTL individually explained 11.35 to 26.71% of the phenotypic variation, with LOD values ranging from 2.74 to 5.80. Notably, four QTL (qDFF1.1, qNPT3.1, qEHL3.1, and qTW1.1) associated with days to fifty percent flowering, the number of productive tillers, ear head length, and test weight were found to be major and stable QTL located on chromosomes 1 and 3. Collectively, our results provide an important base for understanding the genetic architecture of agronomic traits in pearl millet, which is useful for accelerating the genetic gain toward crop improvement.

GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.).

Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi , threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%-18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs.

Volatiles of antagonistic soil yeasts inhibit growth and aflatoxin production of Aspergillus flavus.

Minimizing Aspergillus flavus growth is an effective strategy to mitigate aflatoxin contamination in food and agricultural products. In the present investigation, we attempted to utilize soil-associated yeasts from the Western and Eastern Ghats of India against A. flavus to reduce aflatoxin contamination. Forty-five yeast isolates were screened against A. flavus using overlay and dual plate assays. Among them, 12 isolates effectively inhibited the growth of A. flavus. The 18S rDNA gene sequence analysis identified the twelve antagonistic isolates as belonging to Saccharomyces cerevisiae, Suhomyces xylopsoci, Pichia kudriavzevii, and Candida tropicalis. From the isolated yeasts, S. cerevisiae strains were selected for further evaluation based on the potential antagonistic activity. Volatiles of S. cerevisiae effectively suppressed the mycelial growth of A. flavus (P < 0.05) up to 92.1 % at 7 DAI. Scanning electron microscopic images of the fungus exposed to volatiles showed hyphal deformity and mycelial damage. Aflatoxin B1 (AFB1) production was drastically reduced up to 99.0 % in the volatile-exposed fungus compared to the control. The yeast strain YKK1 showed consistent Aspergillus flavus growth inhibition (80.7 %) and AFB1 production (98.1 %) for 14 days. Gas chromatography-mass spectrophotometry analysis of the yeast volatiles revealed the presence of antimicrobial compounds, including 1-pentanol, 1-propanol, ethyl hexanol, ethanol, 2-methyl-1-butanol, ethyl acetate, dimethyl trisulfide, p-xylene, styrene, and 1,4-pentadiene. The evaluated compounds of yeast volatiles, including ethyl acetate, hexanal, 1-propanol, 1-heptanol, 1-butanol, and benzothiazole, inhibited the fungal growth and AFB1 production of Aspergillus flavus when applied as pure chemicals. Benzothiazole at 5 mM was responsible for a high level of growth inhibition (23.6 %) and reduction of AFB1 synthesis (93.5 %). Hence, volatile compounds produced by soil yeast strains could be a potential biocontrol mechanism against aflatoxin contamination.

Dynamic Transcriptome Profiling of Mungbean Genotypes Unveil the Genes Respond to the Infection of Mungbean Yellow Mosaic Virus.

Yellow mosaic disease (YMD), incited by mungbean yellow mosaic virus (MYMV), is a primary viral disease that reduces mungbean production in South Asia, especially in India. There is no detailed knowledge regarding the genes and molecular mechanisms conferring resistance of mungbean to MYMV. Therefore, disclosing the genetic and molecular bases related to MYMV resistance helps to develop the mungbean genotypes with MYMV resistance. In this study, transcriptomes of mungbean genotypes, VGGRU-1 (resistant) and VRM (Gg) 1 (susceptible) infected with MYMV were compared to those of uninfected controls. The number of differentially expressed genes (DEGs) in the resistant and susceptible genotypes was 896 and 506, respectively. Among them, 275 DEGs were common between the resistant and susceptible genotypes. Functional annotation of DEGs revealed that the DEGs belonged to the following categories defense and pathogenesis, receptor-like kinases; serine/threonine protein kinases, hormone signaling, transcription factors, and chaperons, and secondary metabolites. Further, we have confirmed the expression pattern of several DEGs by quantitative real-time PCR (qRT-PCR) analysis. Collectively, the information obtained in this study unveils the new insights into characterizing the MYMV resistance and paved the way for breeding MYMV resistant mungbean in the future.

Interaction of water activity and temperature on growth, gene expression, and aflatoxin B1 production in Aspergillus flavus on Indian senna (Cassia angustifolia Vahl.).

Senna (Cassia angustifolia Vahl.) is a medicinal crop with laxative properties, and it has significant demand in the global pharmaceutical market. Senna pods are highly susceptible to aflatoxin contamination, and the successful export of pods is hindered due to the regulatory limits of importing countries. The senna pod water activity (aw) from harvest to storage is the key factor determining AFB1 accumulation. The temperature conditions from field to warehouse also interact with pod aw, which influences fungal growth and AFB1 production. The determination of an ideal combination of aw and temperature led to the assessment of the critical control point for AFB1 synthesis in senna. Hence, this study aimed to evaluate the influence of aw (0.99, 0.96, 0.93, 0.90, and 0.87 aw) and temperature (20, 28, and 37 °C) on fungal growth, gene expression (aflR and aflS), and AFB1 production by A. flavus in senna agar medium. The fungus showed the longest lag time (7.7 days) at 20 °C with 0.87 aw. We observed that 0.96 aw (P < 0.01) was optimum for the diametric growth rate at 28 and 37 °C. However, the peak expression of regulatory genes (aflR and aflS) and the maximum AFB1 production were observed only at 28 °C (0.96 aw). The highest growth rate occurred at 37 °C, which did not favor the expression of genes and AFB1 production. However, at 28 °C, it positively correlated with gene expression and AFB1 production. The suppressed expression of regulatory genes and a trace amount of aflatoxin B1 were found at 20 °C with all the tested aw. In our experiments, the low aw (0.87 and 0.90 aw) suppressed the fungal growth, gene expression, and AFB1 production of A. flavus at all of the tested temperatures (20, 28, and 37 °C). The rapid drying of senna pods with a low water activity (≤0.87 aw) and storage at low temperature (20 °C) are ideal conditions to avoid AFB1 and ensure the quality of produce for export.

Nanocurcumin: A Promising Candidate for Therapeutic Applications.

Curcuma longa is an important medicinal plant and a spice in Asia. Curcumin (diferuloylmethane) is a hydrophobic bioactive ingredient found in a rhizome of the C. longa. It has drawn immense attention in recent years for its variety of biological and pharmacological action. However, its low water solubility, poor bioavailability, and rapid metabolism represent major drawbacks for its successful therapeutic applications. Hence, researchers have attempted to enhance the biological and pharmacological activity of curcumin and overcome its drawbacks by efficient delivery systems, particularly nanoencapsulation. Research efforts so far and data from the available literature have shown a satisfactory potential of nanorange formulations of curcumin (Nanocurcumin), it increases all the biological and pharmacological benefits of curcumin, which was not significantly possible earlier. For the synthesis of nanocurcumin, an array of techniques has been developed and each technique has its own advantages and individual characteristics. The two most popular and effective techniques are ionic gelation and antisolvent precipitation. So far, many curcumin nanoformulations have been developed to enhance curcumin delivery, thereby overcoming the low therapeutic effects. However, most of the nanoformulation of curcumin remained at the concept level evidence, thus, several questions and challenges still exist to recommend the nanocurcumin as a promising candidate for therapeutic applications. In this review, we discuss the different curcumin nanoformulation and nanocurcumin implications for different therapeutic applications as well as the status of ongoing clinical trials and patents. We also discuss the research gap and future research directions needed to propose curcumin as a promising therapeutic candidate.

Domesticating Vigna Stipulacea: A Potential Legume Crop With Broad Resistance to Biotic Stresses.

Though crossing wild relatives to modern cultivars is a usual means to introduce alleles of stress tolerance, an alternative is de novo domesticating wild species that are already tolerant to various kinds of stresses. As a test case, we chose Vigna stipulacea Kuntze, which has fast growth, short vegetative stage, and broad resistance to pests and diseases. We developed an ethyl methanesulfonate-mutagenized population and obtained three mutants with reduced seed dormancy and one with reduced pod shattering. We crossed one of the mutants of less seed dormancy to the wild type and confirmed that the phenotype was inherited in a Mendelian manner. De novo assembly of V. stipulacea genome, and the following resequencing of the F2 progenies successfully identified a Single Nucleotide Polymorphism (SNP) associated with seed dormancy. By crossing and pyramiding the mutant phenotypes, we will be able to turn V. stipulacea into a crop which is yet primitive but can be cultivated without pesticides.

Detection of QTLs associated with mungbean yellow mosaic virus (MYMV) resistance using the interspecific cross of Vigna radiata × Vigna umbellata.

Mungbean (Vigna radiata) and ricebean (V. umbellata) were utilized to obtain an inter-specific recombinant inbred line (RIL) population with the objective of detecting quantitative trait loci (QTL) associated with mungbean yellow mosaic virus (MYMV) resistance. To precisely map QTLs, accurate genetic linkage maps are essential. In the present study, genotyping-by-sequencing (GBS) platform was utilized to develop the genetic linkage map. The map contained 538 single nucleotide polymorphism (SNP) markers, consisted of 11 linkage groups and spanned for 1291.7 cM with an average marker distance of 2.40 cM. The individual linkage group ranged from 90.2 to 149.1 cM in length, and the SNP markers were evenly distributed in the genetic linkage map, with 30-79 SNP markers per chromosome. The QTL analysis using the genetic map and 2 years (2015 and 2016) of phenotyping data identified five QTLs with phenotypic variation explained (PVE) from 10.11 to 20.04%. Of these, a QTL on chromosome 4, designated as qMYMV4-1, was major and stably detected in the same marker interval in both years. This QTL region harbours possible candidate genes for controlling MYMV resistance. The linkage map and QTL/gene (s) for MYMV resistance identified in this study should be useful for QTL fine mapping and cloning for further studies.

Evolution of the Grain Dispersal System in Barley.

About 12,000 years ago in the Near East, humans began the transition from hunter-gathering to agriculture-based societies. Barley was a founder crop in this process, and the most important steps in its domestication were mutations in two adjacent, dominant, and complementary genes, through which grains were retained on the inflorescence at maturity, enabling effective harvesting. Independent recessive mutations in each of these genes caused cell wall thickening in a highly specific grain "disarticulation zone," converting the brittle floral axis (the rachis) of the wild-type into a tough, non-brittle form that promoted grain retention. By tracing the evolutionary history of allelic variation in both genes, we conclude that spatially and temporally independent selections of germplasm with a non-brittle rachis were made during the domestication of barley by farmers in the southern and northern regions of the Levant, actions that made a major contribution to the emergence of early agrarian societies.

Genetic susceptibility of lumbar degenerative disc disease in young Indian adults.

PURPOSE: Although the exact mechanisms that lead to degenerative disc disease (DDD) are not well understood, a significant genetic influence has been found. Focusing on DDD that occurs in young adults can be valuable in determining the exact role of genetic predisposition to DDD. METHODS: Patients (<40 years) with lumbar disc degeneration were evaluated with MRI imaging (1.5 Tesla) and genetic association analysis for 58 single nucleotide polymorphism (SNP) of 35 candidate genes was performed. Disc degeneration of individual discs of lumbar spine from L1 to S1 was graded by Pfirrmann's grading. The subjects were stratified into two groups based on Total Disc Degenerative Score (TDDS). Based on TDDS, the severity of DDD was classified as mild (Group A: TDDS <10) and severe (Group B: TDDS >10). RESULTS: 695 Indian subjects including 308 with mild TDDS and 387 with severe TDDS were studied. The mean age of the patients was 29.6 ± 6.9 years in group A and 31.7 ± 6.1 in group B (p < 0.05). Five of the 35 candidate genes viz., rs1337185 of COL11A (p = 0.02), rs5275 (p = 0.03) and rs5277 (p = 0.05) of COX2, rs7575934 of IL1F5 (p = 0.04), rs3213718 of CALM1 (p = 0.04) and rs162509 of ADAMTS5 (p = 0.04) were found to be significantly associated with severe TDDS. CONCLUSION: The study identifies specific SNP associations of five genes in young adults with severe lumbar disc degeneration. These five genes (COL11A1, ADAMTS5, CALM1, IL1F5 and COX2) have different functions in the matrix metabolism, intracellular signalling and inflammatory cascade. This shows that disc degeneration is a complex disease with an intricate interplay of multiple genetic polymorphisms.

BrassicaTED - a public database for utilization of miniature transposable elements in Brassica species.

BACKGROUND: MITE, TRIM and SINEs are miniature form transposable elements (mTEs) that are ubiquitous and dispersed throughout entire plant genomes. Tens of thousands of members cause insertion polymorphism at both the inter- and intra- species level. Therefore, mTEs are valuable targets and resources for development of markers that can be utilized for breeding, genetic diversity and genome evolution studies. Taking advantage of the completely sequenced genomes of Brassica rapa and B. oleracea, characterization of mTEs and building a curated database are prerequisite to extending their utilization for genomics and applied fields in Brassica crops. FINDINGS: We have developed BrassicaTED as a unique web portal containing detailed characterization information for mTEs of Brassica species. At present, BrassicaTED has datasets for 41 mTE families, including 5894 and 6026 members from 20 MITE families, 1393 and 1639 members from 5 TRIM families, 1270 and 2364 members from 16 SINE families in B. rapa and B. oleracea, respectively. BrassicaTED offers different sections to browse structural and positional characteristics for every mTE family. In addition, we have added data on 289 MITE insertion polymorphisms from a survey of seven Brassica relatives. Genes with internal mTE insertions are shown with detailed gene annotation and microarray-based comparative gene expression data in comparison with their paralogs in the triplicated B. rapa genome. This database also includes a novel tool, K BLAST (Karyotype BLAST), for clear visualization of the locations for each member in the B. rapa and B. oleracea pseudo-genome sequences. CONCLUSIONS: BrassicaTED is a newly developed database of information regarding the characteristics and potential utility of mTEs including MITE, TRIM and SINEs in B. rapa and B. oleracea. The database will promote the development of desirable mTE-based markers, which can be utilized for genomics and breeding in Brassica species. BrassicaTED will be a valuable repository for scientists and breeders, promoting efficient research on Brassica species. BrassicaTED can be accessed at http://im-crop.snu.ac.kr/BrassicaTED/index.php.

Phenotype variations affect genetic association studies of degenerative disc disease: conclusions of analysis of genetic association of 58 single nucleotide polymorphisms with highly specific phenotypes for disc degeneration in 332 subjects.

BACKGROUND CONTEXT: Although the influence of genetics on the process of disc degeneration is well recognized, in recently published studies, there is a wide variation in the race and selection criteria for such study populations. More importantly, the radiographic features of disc degeneration that are selected to represent the disc degeneration phenotype are variable in these studies. The study presented here evaluates the association between single nucleotide polymorphisms (SNPs) of candidate genes and three distinct radiographic features that can be defined as the degenerative disc disease (DDD) phenotype. PURPOSE: The study objectives were to examine the allelic diversity of 58 SNPs related to 35 candidate genes related to lumbar DDD, to evaluate the association in a hitherto unevaluated ethnic Indian population that represents more than one-sixth of the world population, and to analyze how genetic associations can vary in the same study subjects with the choice of phenotype. STUDY DESIGN: A cross-sectional, case-control study of an ethnic Indian population was carried out. METHODS: Fifty-eight SNPs in 35 potential candidate genes were evaluated in 342 subjects and the associations were analyzed against three highly specific markers for DDD, namely disc degeneration by Pfirrmann grading, end-plate damage evaluated by total end-plate damage score, and annular tears evaluated by disc herniations and hyperintense zones. Genotyping of cases and controls was performed on a genome-wide SNP array to identify potential associated disease loci. The results from the genome-wide SNP array were then used to facilitate SNP selection and genotype validation was conducted using Sequenom-based genotyping. RESULTS: Eleven of the 58 SNPs provided evidence of association with one of the phenotypes. For annular tears, rs1042631 SNP of AGC1 and rs467691 SNP of ADAMTS5 were highly significantly associated (p<.01) and SNPs in NGFB, IL1B, IL18RAP, and MMP10 were also significantly associated (p<.05). The rs4076018 SNP of NGFB was highly significant (p<.01) and rs2292657 SNP of GLI1 was significantly (p<.05) correlated to disc degeneration. For end-plate damage, the rs2252070 SNP of MMP 13 showed a significant association (p<.05). Previously associated genes such as COL 9, SKT, CHST 3, CILP, IGFR, SOXp, BMP, MMP 2-12, ADH2, IL1RN, and COX2 were not significantly associated and new associations (NGFB and GLI1) were identified. The validity of all the associations was found to be phenotype dependent. CONCLUSIONS: For the first time, genetic associations with DDD have been performed in an Indian population. Apart from identifying new associations, the highlight of the study was that in the same study population with DDD, SNP associations completely changed when different radiographic features were used to define the DDD phenotype. Our study results therefore indicate that standardization of the phenotypes chosen to study the genetics of disc degeneration is essential and should be strongly considered before planning genetic association studies.