Association mapping identifies stable loci containing novel genes for developmental and reproductive traits in sorghum.

Key message We mapped 11 sorghum traits, identified 33 candidate genes, and found a grain yield gene (GID1) that regulates seed development and a grass-specific tillering gene (DUF1618) transferred to Striga hermonthica.

Genome-wide assessment of population structure and association mapping for agronomic and grain nutritional traits in proso millet (Panicum miliaceum L.).

Proso millet is an important but under-researched and underutilized crop with the potential to become a future smart crop because of its climate-resilient features and high nutrient content. Assessing diversity and marker-trait associations are essential to support the genomics-assisted improvement of proso millet. This study aimed to assess the population structure and diversity of a proso millet diversity panel and identify marker-trait associations for agronomic and grain nutrient traits. In this study, genome-wide single nucleotide polymorphisms (SNPs) were identified by mapping raw genotyping-by-sequencing (GBS) data onto the proso millet genome, resulting in 5621 quality-filtered SNPs in 160 diverse accessions. The modified Roger's Distance assessment indicated an average distance of 0.268 among accessions, with the race miliaceum exhibiting the highest diversity and ovatum the lowest. Proso millet germplasm diversity was structured according to geographic centers of origin and domestication. Genome-wide association mapping identified 40 marker-trait associations (MTAs), including 34 MTAs for agronomic traits and 6 for grain nutrients; 20 of these MTAs were located within genes. Favourable alleles and phenotypic values were estimated for all MTAs. This study provides valuable insights into the population structure and diversity of proso millet, identified marker-trait associations, and reported favourable alleles and their phenotypic values for supporting genomics-assisted improvement efforts in proso millet.

Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.

Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.

Assessment of Understandability and Actionability of YouTube Videos on Hemolytic Disease of the Newborn.

Introduction With revolutions in Information Technology, information and misinformation are easier to be found online. YouTube is the largest and most commonly searched video content website in the world. It is assumed that, due to the coronavirus pandemic, most patients try to know about diseases through the internet and reduce the number of hospital exposures unless otherwise. In order to assess the understandability and actionability of such YouTube videos available freely online about the disease, Hemolytic disease of the newborn (HDN), this study was planned. Methods This is a cross-sectional study conducted with the first 160 videos available on May 14, 2021, with the search keyword "HDN" with a relevance filter and a duration of 4 to 20 minutes. The videos were further screened regarding the information content and language. These videos were assessed by three independent assessors using the patient educational materials assessment tool for audio-visual content. Results Out of the first 160 videos selected for screening, 58 videos were excluded due to a lack of content about the searched disease "HDN". Another 63 videos were excluded due to the language of instruction not being in English. Finally, 39 videos were assessed by three assessors. The understandability and actionability responses were checked for reliability and a Cronbach's alpha of 93.6% was found, indicating good data reliability. To reduce subjectivity, average scores of understandability and actionability were taken based on the scores of these three assessors. There were eight and 34 videos with average understandability and actionability scores of <70% respectively. The median average understandability and actionability scores were 84.4% and 50% respectively. There was a statistically significant difference between understandability and actionability scores with considerably lower actionability scores of YouTube videos on the disease, HDN (p<0.001). Conclusion There is a great need to include actionable information by content developers in videos. Most information available has adequate understandable content making it easier for the general public to know about the diseases. YouTube and similar social sites thus possibly are helping in the dissemination of information promoting awareness among the public in general and patients in particular.

A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea.

Identifying potential molecular tags for drought tolerance is essential for achieving higher crop productivity under drought stress. We employed an integrated genomics-assisted breeding and functional genomics strategy involving association mapping, fine mapping, map-based cloning, molecular haplotyping and transcript profiling in the introgression lines (ILs)- and near isogenic lines (NILs)-based association panel and mapping population of chickpea (Cicer arietinum). This combinatorial approach delineated a bHLH (basic helix-loop-helix) transcription factor, CabHLH10 (Cicer arietinum bHLH10) underlying a major QTL, along with its derived natural alleles/haplotypes governing yield traits under drought stress in chickpea. CabHLH10 binds to a cis-regulatory G-box promoter element to modulate the expression of RD22 (responsive to desiccation 22), a drought/abscisic acid (ABA)-responsive gene (via a trans-expression QTL), and two strong yield-enhancement photosynthetic efficiency (PE) genes. This, in turn, upregulates other downstream drought-responsive and ABA signaling genes, as well as yield-enhancing PE genes, thus increasing plant adaptation to drought with reduced yield penalty. We showed that a superior allele of CabHLH10 introgressed into the NILs improved root and shoot biomass and PE, thereby enhancing yield and productivity during drought without compromising agronomic performance. Furthermore, overexpression of CabHLH10 in chickpea and Arabidopsis (Arabidopsis thaliana) conferred enhanced drought tolerance by improving root and shoot agro-morphological traits. These findings facilitate translational genomics for crop improvement and the development of genetically tailored, climate-resilient, high-yielding chickpea cultivars.

Genome-wide association mapping identifies an SNF4 ortholog that impacts biomass and sugar yield in sorghum and sugarcane.

Sorghum is a feed/industrial crop in developed countries and a staple food elsewhere in the world. This study evaluated the sorghum mini core collection for days to 50% flowering (DF), biomass, plant height (PH), soluble solid content (SSC), and juice weight (JW), and the sorghum reference set for DF and PH, in 7-12 testing environments. We also performed genome-wide association mapping with 6 094 317 and 265 500 single nucleotide polymorphism markers in the mini core collection and the reference set, respectively. In the mini core panel we identified three quantitative trait loci for DF, two for JW, one for PH, and one for biomass. In the reference set panel we identified another quantitative trait locus for PH on chromosome 6 that was also associated with biomass, DF, JW, and SSC in the mini core panel. Transgenic studies of three genes selected from the locus revealed that Sobic.006G061100 (SbSNF4-2) increased biomass, SSC, JW, and PH when overexpressed in both sorghum and sugarcane, and delayed flowering in transgenic sorghum. SbSNF4-2 encodes a γ subunit of the evolutionarily conserved AMPK/SNF1/SnRK1 heterotrimeric complexes. SbSNF4-2 and its orthologs will be valuable in genetic enhancement of biomass and sugar yield in plants.

A chickpea genetic variation map based on the sequencing of 3,366 genomes.

Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources1. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level2. Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

Genome-Wide Association Mapping Identifies Novel Panicle Morphology Loci and Candidate Genes in Sorghum.

Panicle morphology is an important trait in racial classification and can determine grain yield and other agronomic traits in sorghum. In this study, we performed association mapping of panicle length, panicle width, panicle compactness, and peduncle recurving in the sorghum mini core panel measured in multiple environments with 6,094,317 single nucleotide polymorphism (SNP) markers. We mapped one locus each on chromosomes 7 and 9 to recurving peduncles and eight loci for panicle length, panicle width, and panicle compactness. Because panicle length was positively correlated with panicle width, all loci for panicle length and width were colocalized. Among the eight loci, two each were on chromosomes 1, 2, and 6, and one each on chromosomes 8 and 10. The two loci on chromosome 2, i.e., Pm 2-1 and Pm 2-2, were detected in 7 and 5 out of 11 testing environments, respectively. Pm 2-2 colocalized with panicle compactness. Candidate genes were identified from both loci. The rice Erect Panicle2 (EP2) ortholog was among the candidate genes in Pm 2-2. EP2 regulates panicle erectness and panicle length in rice and encodes a novel plant-specific protein with unknown functions. The results of this study may facilitate the molecular identification of panicle morphology-related genes and the enhancement of yield and adaptation in sorghum.

Variation for Photoperiod and Temperature Sensitivity in the Global Mini Core Collection of Sorghum.

Information on photoperiod and temperature sensitivity of sorghum germplasm is important to identify appropriate sources for developing cultivars with a broad adaptation. The sorghum mini core collection consisting of 242 accessions along with three control cultivars were evaluated for days to 50% flowering (DFL) and plant height in two long-day rainy and two short-day post-rainy seasons, and for grain yield and 100-seed weight in the two post-rainy seasons. Differences in DFL and cumulative growing degree days (CGDD) in the rainy and post-rainy seasons were used to classify the accessions for photoperiod and temperature sensitivity. Results revealed 18 mini core landraces as photoperiod and temperature insensitive (PTINS), 205 as photoperiod sensitive and temperature insensitive (PSTINS), and 19 as photoperiod and temperature-sensitive (PTS) sources. The 19 PTS sources and 80 PSTINS sources took less DFL in the long-day rainy seasons than in the short-day post-rainy season indicating their adaptation to the rainy season and a possible different mechanism than that trigger flowering in the short-day sorghums. In all three groups, several accessions with desirable combinations of agronomic traits were identified for use in the breeding programs to develop climate-resilient cultivars and for genomic studies to identify genes responsible for the photoperiod and temperature responses.

Exploring the genetic variability and diversity of pearl millet core collection germplasm for grain nutritional traits improvement.

Improving essential nutrient content in staple food crops through biofortification breeding can overcome the micronutrient malnutrition problem. Genetic improvement depends on the availability of genetic variability in the primary gene pool. This study was aimed to ascertain the magnitude of variability in a core germplasm collection of diverse origin and predict pearl millet biofortification prospects for essential micronutrients. Germplasm accessions were evaluated in field trials at ICRISAT, India. The accessions differed significantly for all micronutrients with over two-fold variation for Fe (34-90 mg kg-1), Zn (30-74 mg kg-1), and Ca (85-249 mg kg-1). High estimates of heritability (> 0.81) were observed for Fe, Zn, Ca, P, Mo, and Mg. The lower magnitude of genotype (G) × environment (E) interaction observed for most of the traits implies strong genetic control for grain nutrients. The top-10 accessions for each nutrient and 15 accessions, from five countries for multiple nutrients were identified. For Fe and Zn, 39 accessions, including 15 with multiple nutrients, exceeded the Indian cultivars and 17 of them exceeded the biofortification breeding target for Fe (72 mg kg-1). These 39 accessions were grouped into 5 clusters. Most of these nutrients were positively and significantly associated among themselves and with days to 50% flowering and 1000-grain weight (TGW) indicating the possibility of their simultaneous improvement in superior agronomic background. The identified core collection accessions rich in specific and multiple-nutrients would be useful as the key genetic resources for developing biofortified and agronomically superior cultivars.

A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction.

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage-only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57-.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection.

Phenotypic responses of foxtail millet (Setaria italica) genotypes to phosphate supply under greenhouse and natural field conditions.

Food insecurity is a looming threat for the burgeoning world population. Phosphorus (P), which is absorbed from soil as inorganic phosphate (Pi), is an essential macronutrient for the growth of all agricultural crops. This study reports phenotype analysis for P responses in natural field and greenhouse conditions, using 54 genotypes of foxtail millet (Setaria italica) representing wide geographic origins. The genotype responses were assessed in natural field conditions in two different seasons (monsoon and summer) under Pi-fertilized (P+) and unfertilized (P-) soil for eight above-ground traits. Enormous variations were seen among the genotypes in phenotypic responses for all the measured parameters under low P stress conditions. Variations were significant for plant height, leaf number and length, tillering ability and seed yield traits. Genotypes ISe 1234 and ISe 1541 were P+ responders, and the genotypes ISe 1181, ISe 1655, ISe 783 and ISe 1892 showed tolerance to low P for total seed yield. Genotypes that performed well under P- conditions were almost as productive as genotypes that performed well under P+ conditions suggesting some genotypes are well adapted to nutrient-poor soils. In the greenhouse, most of the genotypes produced changes in root architecture that are characteristic of P- stress, but to differing degrees. Significant variation was seen in root hair density and root hair number and in fresh and dry weight of shoot and root under P- stress. However, there was not much difference in the shoot and root total P and Pi levels of five selected high and low responding genotypes. We noticed contrasting responses in the greenhouse and natural field experiments for most of these genotypes. The leads from the study form the basis for breeding and improvement of foxtail millet for better Pi-use efficiency.

Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.).

Haplotype-based breeding, a recent promising breeding approach to develop tailor-made crop varieties, deals with identification of superior haplotypes and their deployment in breeding programmes. In this context, whole genome re-sequencing data of 292 genotypes from pigeonpea reference set were mined to identify the superior haplotypes for 10 drought-responsive candidate genes. A total of 83, 132 and 60 haplotypes were identified in breeding lines, landraces and wild species, respectively. Candidate gene-based association analysis of these 10 genes on a subset of 137 accessions of the pigeonpea reference set revealed 23 strong marker-trait associations (MTAs) in five genes influencing seven drought-responsive component traits. Haplo-pheno analysis for the strongly associated genes resulted in the identification of most promising haplotypes for three genes regulating five component drought traits. The haplotype C. cajan_23080-H2 for plant weight (PW), fresh weight (FW) and turgid weight (TW), the haplotype C. cajan_30211-H6 for PW, FW, TW and dry weight (DW), the haplotype C. cajan_26230-H11 for FW and DW and the haplotype C. cajan_26230-H5 for relative water content (RWC) were identified as superior haplotypes under drought stress condition. Furthermore, 17 accessions containing superior haplotypes for three drought-responsive genes were identified. The identified superior haplotypes and the accessions carrying these superior haplotypes will be very useful for deploying haplotype-based breeding to develop next-generation tailor-made better drought-responsive pigeonpea cultivars.

Thermotropic Liquid-Crystalline and Light-Emitting Properties of Bis(4-aalkoxyphenyl) Viologen Bis(triflimide) Salts.

A series of bis(4-alkoxyphenyl) viologen bis(triflimide) salts with alkoxy chains of different lengths were synthesized by the metathesis reaction of respective bis(4-alkoxyphenyl) viologen dichloride salts, which were in turn prepared from the reaction of Zincke salt with the corresponding 4-n-alkoxyanilines, with lithium triflimide in methanol. Their chemical structures were characterized by 1H and 13C nuclear magnetic resonance spectra and elemental analysis. Their thermotropic liquid-crystalline (LC) properties were examined by differential scanning calorimetry, polarizing optical microscopy, and variable temperature X-ray diffraction. Salts with short length alkoxy chains had crystal-to-liquid transitions. Salts of intermediate length alkoxy chains showed both crystal-to-smectic A (SmA) transitions, Tms, and SmA-to-isotropic transitions, Tis. Those with longer length of alkoxy chains had relatively low Tms at which they formed the SmA phases that persisted up to the decomposition at high temperatures. As expected, all of them had excellent thermal stabilities in the temperature range of 330-370 °C. Their light-emitting properties in methanol were also included.

Intranasal Lipid Particulate Drug Delivery Systems: An Update on Clinical Challenges and Biodistribution Studies of Cerebroactive Drugs in Alzheimer's disease.

BACKGROUND: Alzheimer's is the primary cause of death in the various countries that affect wide strata of the population. The treatment of it is restricted to a few conventional oral medications that act only superficially. It is evident that the delivery of a drug to the brain across the blood-brain barrier is challenging as the BBB is armed with several efflux transporters like the P-glycoprotein as well as nasal mucociliary clearance adds up leading to decreased concentration and reduced therapeutic efficacy. Considering these, the intranasal IN route of drug administration is emerging as an alternative route for the systemic delivery of a drug to the brain. The intranasal (IN) administration of lipid nanoparticles loaded with cerebroactive drugs showed promise in treating various neurodegenerative diseases, since the nasal route allows the direct nose to brain delivery by means of solid lipid nanoparticles (SLN's). The tailoring of intranasal lipid particulate drug delivery systems is a pleasing approach to facilitate uptake of therapeutic agents at the desired site of action, particularly when a free drug has poor pharmacokinetics/ biodistribution (PK/BD) or significant off-site toxicities. OBJECTIVES: 1) In this review, key challenges and physiological mechanisms regulating intranasal brain delivery in Alzheimer's disease, ex vivo studies, pharmacokinetics parameters including brain uptake and histopathological studies are thoroughly discussed. 2) A thorough understanding of the in vivo behaviour of the intranasal drug carriers will be the elusive goal. 3) The article emphasizes to drag the attention of the research community working in the intranasal field towards the challenges and hurdles of the practical applicability of intranasal delivery of cerebroactive drugs. METHOD: Various electronic databases, journals like nanotechnology and nanoscience, dove press are reviewed for the collection and compilation of data. RESULTS: From in vivo biodistribution studies, pharmacokinetics parameters, and gamma scintigraphy images of various drugs, it is speculated that intranasal lipid particulates drug delivery system shows better brain targeting efficiency for various CNS disorders in comparison to other routes. CONCLUSION: Various routes are explored for the delivery of drugs to increase bioavailability in the brain for CNS disorders but the intranasal route shows better results that pave the way for success in the future if properly explored.

Genomic signatures of seed mass adaptation to global precipitation gradients in sorghum.

Seed mass is a key component of adaptation in plants and a determinant of yield in crops. The climatic drivers and genomic basis of seed mass variation remain poorly understood. In the cereal crop Sorghum bicolor, globally-distributed landraces harbor abundant variation in seed mass, which is associated with precipitation in their agroclimatic zones of origin. This study aimed to test the hypothesis that diversifying selection across precipitation gradients, acting on ancestral cereal grain size regulators, underlies seed mass variation in global sorghum germplasm. We tested this hypothesis in a set of 1901 georeferenced and genotyped sorghum landraces, 100-seed mass from common gardens, and bioclimatic precipitation variables. As predicted, 100-seed mass in global germplasm varies significantly among botanical races and is correlated to proxies of the precipitation gradients. With general and mixed linear model genome-wide associations, we identified 29 and 56 of 100 a priori candidate seed size genes with polymorphisms in the top 1% of seed mass association, respectively. Eleven of these genes harbor polymorphisms associated with the precipitation gradient, including orthologs of genes that regulate seed size in other cereals. With FarmCPU, 13 significant SNPs were identified, including one at an a priori candidate gene. Finally, we identified eleven colocalized outlier SNPs associated with seed mass and precipitation that also carry signatures of selection based on FST scans and PCAdapt, which represents a significant enrichment. Our findings suggest that seed mass in sorghum was shaped by diversifying selection on drought stress, and can inform genomics-enabled breeding for climate-resilient cereals.

Hypoallergen Peanut Lines Identified Through Large-Scale Phenotyping of Global Diversity Panel: Providing Hope Toward Addressing One of the Major Global Food Safety Concerns.

Peanut allergy is one of the serious health concern and affects more than 1% of the world's population mainly in Americas, Australia, and Europe. Peanut allergy is sometimes life-threatening and adversely affect the life quality of allergic individuals and their families. Consumption of hypoallergen peanuts is the best solution, however, not much effort has been made in this direction for identifying or developing hypoallergen peanut varieties. A highly diverse peanut germplasm panel was phenotyped using a recently developed monoclonal antibody-based ELISA protocol to quantify five major allergens. Results revealed a wide phenotypic variation for all the five allergens studied i.e., Ara h 1 (4-36,833 µg/g), Ara h 2 (41-77,041 µg/g), Ara h 3 (22-106,765 µg/g), Ara h 6 (829-103,892 µg/g), and Ara h 8 (0.01-70.12 µg/g). The hypoallergen peanut genotypes with low levels of allergen proteins for Ara h 1 (4 µg/g), Ara h 2 (41 µg/g), Ara h 3 (22 µg/g), Ara h 6 (829 µg/g), and Ara h 8 (0.01 µg/g) have paved the way for their use in breeding and genomics studies. In addition, these hypoallergen peanut genotypes are available for use in cultivation and industry, thus opened up new vistas for fighting against peanut allergy problem across the world.