GBS-SNP and SSR based genetic mapping and QTL analysis for drought tolerance in upland cotton.

A recombinant inbred line mapping population of intra-species upland cotton was generated from a cross between the drought-tolerant female parent (AS2) and the susceptible male parent (MCU13). A linkage map was constructed deploying 1,116 GBS-based SNPs and public domain-based 782 SSRs spanning a total genetic distance of 28,083.03 cM with an average chromosomal span length of 1,080.12 cM with inter-marker distance of 10.19 cM.A total of 19 quantitative trait loci (QTLs) were identified in nine chromosomes for field drought tolerance traits. Chromosomes 3 and 8 harbored important drought tolerant QTLs for chlorophyll stability index trait while for relative water content trait, three QTLs on chromosome 8 and one QTL each on chromosome 4, 12 were identified. One QTL on each chromosome 8, 5, and 7, and two QTLs on chromosome 15 linking to proline content were identified. For the nitrate reductase activity trait, two QTLs were identified on chromosome 3 and one on each chromosome 8, 13, and 26. To complement our QTL study, a meta-analysis was conducted along with the public domain database and resulted in a consensus map for chromosome 8. Under field drought stress, chromosome 8 harbored a drought tolerance QTL hotspot with two in-house QTLs for chlorophyll stability index (qCSI01, qCSI02) and three public domain QTLs (qLP.FDT_1, qLP.FDT_2, qCC.ST_3). Identified QTL hotspot on chromosome 8 could play a crucial role in exploring abiotic stress-associated genes/alleles for drought trait improvement. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01041-y.

Assessment of bioactive compound variations and in-vitro and in-vivo antioxidant activity in edible fresh and processed Bambusa nutans shoot through FTIR, GC/MS and HPLC analyses.

This study explores the impact of processing techniques on the bioactive composition and antioxidant properties of Bambusa nutans shoots, an underutilized superfood. Boiling resulted in a significant reduction of total phenols (39.52%), flavonoid (8.07%), and tannin (27.77%). Conversely, fermentation increased total phenols (25.92%), tannin (34.72%), and phytosterol (75.39%). Antioxidant activities were notably higher in fermented-shoots, as indicated by DPPH and FRAP assays, and in-vivo experiments demonstrated increased GSH (31.85%) and decreased LPO levels (11.12%) post-administration of fermented-shoots extract. Spectral analysis revealed an increased diversity of compounds in fermented shoots, with GC/MS identifying hexadecane-1-ol in significantly higher proportions and 11 characteristic bands in FTIR spectra. HPLC analysis demonstrated changes in phenolic acids and flavonoid content, with fermentation enhancing 3,4,5-trihydroxybenzoic acid, 4'-hydroxycinnamic acid, benzene-1,2-diol, and luteolin contents. This study underscores the dynamic nature of B. nutans shoots, highlighting the potential for enhanced bioactivity and antioxidant properties through fermentation, offering promising avenues for culinary and pharmaceutical developments.

Comparative hepato-ameliorative effects of Bambusa nutans fresh and fermented shoot extracts on STZ induced diabetic LACA mice.

Bamboo shoots are nutritionally rich source of antioxidants and bioactive compounds with immense therapeutic potentials. The fresh shoot is acrid and needs to be processed to make it palatable. Fermentation is one the best processing methods for long term storage and make the shoot palatable and enhance taste. This study aims to assess the prophylactic hepatoprotective effects of fresh and fermented B. nutans shoot aqueous extract (200 mg/kg b.w.) in STZ induced diabetic LACA mice. Both extracts effectively improved body weight loss, hyperglycemia, and hepatomegaly. Fresh shoot reduced LDH activity and LPO level by 26.1% and 46.6%, while fermented shoot reduced them by 51.5% and 55.8%, respectively. The fermented shoot extract group demonstrated a noteworthy decrease in liver enzymes (SGPT, SGOT, ALP, and bilirubin levels) and an increase in albumin and A/G ratio, with more substantial improvements compared to the group treated with fresh extract. Additionally, the extracts enhanced antioxidant activities and showed histological improvements in hepatocytes and central vein structure. The findings indicate that both fresh and fermented B. nutans extracts are non-toxic and possess hepatoprotective potential in hyperglycaemic liver dysfunction, with fermented shoot extract exhibiting superior efficacy suggesting its potential as a therapeutic agent for hyperglycemic liver conditions.

Phytobial remediation advances and application of omics and artificial intelligence: a review.

Industrialization and urbanization increased the use of chemicals in agriculture, vehicular emissions, etc., and spoiled all environmental sectors. It causes various problems among living beings at multiple levels and concentrations. Phytoremediation and microbial association are emerging as a potential method for removing heavy metals and other contaminants from soil. The treatment uses plant physiology and metabolism to remove or clean up various soil contaminants efficiently. In recent years, omics and artificial intelligence have been seen as powerful techniques for phytobial remediation. Recently, AI and modeling are used to analyze large data generated by omics technologies. Machine learning algorithms can be used to develop predictive models that can help guide the selection of the most appropriate plant and plant growth-promoting rhizobacteria combination that is most effective at remediation. In this review, emphasis is given to the phytoremediation techniques being explored worldwide in soil contamination.

De Novo Hybrid Assembled Draft Genome of Commiphora wightii (Arnott) Bhandari Reveals Key Enzymes Involved in Phytosterol Biosynthesis.

Genome sequence and identification of specific genes involved in the targeted secondary metabolite biosynthesis are two essential requirements for the improvement of any medicinal plant. Commiphora wightii (Arnott) Bhandari (family: Burseraceae), a medicinal plant native to Western India, produces a phytosterol guggulsterone, which is useful for treating atherosclerosis, arthritis, high cholesterol, acne, and obesity. For enhanced guggulsterone yield, key genes involved in its biosynthesis pathway need to be predicted, for which the genome sequence of the species is a pre-requisite. Therefore, we assembled the first-ever hybrid draft genome of C. wightii with a genome size of 1.03 Gb and 107,221 contigs using Illumina and PacBio platforms. The N50 and L50 values in this assembled genome were ~74 Kb and 3486 bp, respectively with a guanine-cytosine (GC) content of 35.6% and 98.7%. The Benchmarking Universal Single Copy Ortholog (BUSCO) value indicated good integrity of assembly. Analysis predicted the presence of 31,187 genes and 342.35 Mb repeat elements in the genome. The comparative genome analysis of C. wightii with relevant orthogroups predicted a few key genes associated with phytosterol biosynthesis and secondary metabolism pathways. The assembled draft genome and the predicted genes should help the future variety development program with improved guggulsterone contents in C. wightii.

Genome-wide association study of fiber yield-related traits uncovers the novel genomic regions and candidate genes in Indian upland cotton (Gossypium hirsutum L.).

Upland cotton (Gossypium hirsutum L.) is a major fiber crop that is cultivated worldwide and has significant economic importance. India harbors the largest area for cotton cultivation, but its fiber yield is still compromised and ranks 22nd in terms of productivity. Genetic improvement of cotton fiber yield traits is one of the major goals of cotton breeding, but the understanding of the genetic architecture underlying cotton fiber yield traits remains limited and unclear. To better decipher the genetic variation associated with fiber yield traits, we conducted a comprehensive genome-wide association mapping study using 117 Indian cotton germplasm for six yield-related traits. To accomplish this, we generated 2,41,086 high-quality single nucleotide polymorphism (SNP) markers using genotyping-by-sequencing (GBS) methods. Population structure, PCA, kinship, and phylogenetic analyses divided the germplasm into two sub-populations, showing weak relatedness among the germplasms. Through association analysis, 205 SNPs and 134 QTLs were identified to be significantly associated with the six fiber yield traits. In total, 39 novel QTLs were identified in the current study, whereas 95 QTLs overlapped with existing public domain data in a comparative analysis. Eight QTLs, qGhBN_SCY_D6-1, qGhBN_SCY_D6-2, qGhBN_SCY_D6-3, qGhSI_LI_A5, qGhLI_SI_A13, qGhLI_SI_D9, qGhBW_SCY_A10, and qGhLP_BN_A8 were identified. Gene annotation of these fiber yield QTLs revealed 2,509 unique genes. These genes were predominantly enriched for different biological processes, such as plant cell wall synthesis, nutrient metabolism, and vegetative growth development in the gene ontology (GO) enrichment study. Furthermore, gene expression analysis using RNAseq data from 12 diverse cotton tissues identified 40 candidate genes (23 stable and 17 novel genes) to be transcriptionally active in different stages of fiber, ovule, and seed development. These findings have revealed a rich tapestry of genetic elements, including SNPs, QTLs, and candidate genes, and may have a high potential for improving fiber yield in future breeding programs for Indian cotton.

Chloroplast Genome of Lithocarpus dealbatus (Hook.f. & Thomson ex Miq.) Rehder Establishes Monophyletic Origin of the Species and Reveals Mutational Hotspots with Taxon Delimitation Potential

There is phylogenetic ambiguity in the genus Lithocarpus and subfamily Quercoideae (Family: Fagaceae). Lithocarpus dealbatus, an ecologically important tree, is the dominant species among the Quercoideae in India. Although several studies have been conducted on the species' regeneration and ecological and economic significance, limited information is available on its phylo-genomics. To resolve the phylogeny in Quercoideae, we sequenced and assembled the 161,476 bp chloroplast genome of L. dealbatus, which has a large single-copy section of 90,732 bp and a small single-copy region of 18,987 bp, separated by a pair of inverted repeat regions of 25,879 bp. The chloroplast genome contained 133 genes, of which 86 were protein-coding genes, 39 were transfer RNAs, and eight were ribosomal RNAs. Analysis of repeat elements and RNA editing sites revealed interspecific similarities within the Lithocarpus genus. DNA diversity analysis identified five highly diverged coding and noncoding hotspot regions in the four genera, which can be used as polymorphic markers for species/taxon delimitation across the four genera of Quercoideae viz., Lithocarpus, Quercus, Castanea, and Castanopsis. The chloroplast-based phylogenetic analysis among the Quercoideae established a monophyletic origin of Lithocarpus, and a closer evolutionary lineage with a few Quercus species. Besides providing insights into the chloroplast genome architecture of L. dealbatus, the study identified five mutational hotspots having high taxon-delimitation potential across four genera of Quercoideae.

Identification of Stable and Multiple Environment Interaction QTLs and Candidate Genes for Fiber Productive Traits Under Irrigated and Water Stress Conditions Using Intraspecific RILs of Gossypium hirsutum var. MCU5 X TCH1218.

Cotton productivity under water-stressed conditions is controlled by multiple quantitative trait loci (QTL). Enhancement of these productivity traits under water deficit stress is crucial for the genetic improvement of upland cotton, Gossypium hirsutum. In the present study, we constructed a genetic map with 504 single nucleotide polymorphisms (SNPs) covering a total span length of 4,416 cM with an average inter-marker distance of 8.76 cM. A total of 181 intra-specific recombinant inbred lines (RILs) were derived from a cross between G. hirsutum var. MCU5 and TCH1218 were used. Although 2,457 polymorphic SNPs were detected between the parents using the CottonSNP50K assay, only 504 SNPs were found to be useful for the construction of the genetic map. In the SNP genotyping, a large number of SNPs showed either >20% missing data, duplication, or segregation distortion. However, the mapped SNPs of this study showed collinearity with the physical map of the reference genome (G. hirsutum var.TM-1), indicating that there was no chromosomal rearrangement within the studied mapping population. RILs were evaluated under multi-environments and seasons for which the phenotypic data were acquired. A total of 53 QTL controlling plant height (PH), number of sympodial branches, boll number (BN), and boll weight (BW) were dissected by QTL analysis under irrigated and water stress conditions. Additionally, it was found that nine QTL hot spots not only co-localized for more than one investigated trait but were also stable with major QTL, i.e., with > 10% of phenotypic variation. One QTL hotspot on chromosome 22 flanked by AX-182254626-AX-182264770 with a span length of 89.4 cM co-localized with seven major and stable QTL linked to a number of sympodial branches both under irrigated and water stress conditions. In addition, putative candidate genes associated with water stress in the QTL hotspots were identified. Besides, few QTL from the hotspots were previously reported across various genetic architects in cotton validating the potential applications of these identified QTL for cotton breeding and improvement. Thus, the major and stable QTL identified in the present study would improve the cotton productivity under water-limited environments through marker-assisted selection.