We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

/pdf/a-reference-genome-for-pea-provides-insight-into-legume-4vzcjuqayo.pdf

A reference genome for pea provides insight into legume genome evolution

The study was aimed to investigate essential oil chemical composition (gas chromatography/flame ionization
detection [GC-FID] and gas chromatography/mass spectrometry [GC-MS]) and antioxidant (1,1-diphenyl-2-picrylhydrazyl free radical (DPPH) and 2,2’-azinobis--ethylbenzothiazoline-6-sulphonate [ABTS] assays) and antimicrobial (Gram-positive and Gram-negative bacteria, fungi, and yeast) activities of essential oils extracted from leaves of Mentha longifolia L. and Mentha viridis. GC-MS analysis revealed that M. longifolia was constituted by pulegone (54.41%) as a major component followed by isomenthone (12.02%), 1,8-cineole (7.41%), borneol (6.85%),and piperitenone oxide (3.19%). M. viridis was rich in carvone (50.47%), 1,8-cineole (9.14%), and limonene (4.87%).The antioxidant activity by ABTS assay showed IC50 values of 476.3 ± 11.7 and 195.1 ± 4.2 mg/L for M. longifolia and M. viridis, respectively, the DPPH assays have resulted in a moderate IC50 (>8000 mg/L and 3476.3 ± 133 mg/L for M. longifolia and M. viridis, respectively). Antimicrobial activity showed that Listeria monocytogenes and Klebsiella pneumoniae bacteria were more inhibited by the 2 essential oils tested. Escherichia coli was least susceptible. A strong activity was also observed on fungi and yeasts. Carvone, thymol, and piperitone oxide have not been detected in Tunisian M. longifolia. Camphor is reported for the 1st time for M. viridis. Antioxidant and antibacterial activities were correlated to chemical composition.

Chemical composition and antimicrobial and antioxidant activities of Mentha (longifolia L. and viridis) essential oils.

At 0.1 mg/mL, the ethyl acetate extract (EAE) of the crude 85% methanolic extract (CAE) of Stevia rebaudiana leaves exhibited preventive activity against DNA strand scission by *OH generated in Fenton's reaction on pBluescript II SK (-) DNA. Its efficacy is better than that of quercetin. The radical scavenging capacity of CAE was evaluated by the DPPH test (IC50=47.66+/-1.04 microg/mL). EAE was derived from CAE scavenged DPPH (IC50=9.26+/-0.04 microg/mL), ABTS+ (IC50=3.04+/-0.22 microg/mL) and *OH (IC50=3.08+/-0.19 microg/mL). Additionally, inhibition of lipid peroxidation induced with 25 mM FeSO 4 on rat liver homogenate as a lipid source was noted with CAE (IC50=2.1+/-1.07 mg/mL). The total polyphenols and total flavonoids of EAE were 0.86 mg gallic acid equivalents/mg and 0.83 mg of quercetin equivalents/mg, respectively. Flavonoids, isolated from EAE, were characterized as quercetin-3-O-arabinoside, quercitrin, apigenin, apigenin-4-O-glucoside, luteolin, and kaempferol-3-O-rhamnoside by LC-MS and NMR analysis. These results indicate that Stevia rebaudiana may be useful as a potential source of natural antioxidants.

Oxidative DNA Damage Preventive Activity and Antioxidant Potential of Stevia rebaudiana (Bertoni) Bertoni, a Natural Sweetener

Legumes play a vital role in ensuring global nutritional food security and improving soil quality through nitrogen fixation. Accelerated higher genetic gain is required to meet the demand of ever increasing global population. In recent years, speedy developments have been witnessed in legume genomics due to advancements in next-generation sequencing (NGS) and high-throughput genotyping technologies. Reference genome sequences for many legume crops have been reported in the last five years. The availability of draft genome sequences and re-sequencing of elite genotypes for several important legume crops have made it possible to identify structural variations at large scale. Availability of large-scale resources and low-cost and high-throughput genotyping technologies are enhancing the efficiency and resolution of genetic mapping and marker-trait association studies. Most importantly, deployment of molecular breeding approaches has resulted in development of improved lines in some legume crops such as chickpea and groundnut. In order to support genomics-driven crop improvement at a fast pace, the deployment of breeder-friendly genomics and decision support tools seem appear to be critical in breeding programs in developing countries. This review provides an overview of emerging genomics and informatics tools/approaches that will be the key driving force for accelerating genomics-assisted breeding and ultimately ensuring nutritional and food security in developing countries.

/pdf/emerging-genomic-tools-for-legume-breeding-current-status-43u7kn8nwt.pdf

Emerging Genomic Tools for Legume Breeding: Current Status and Future Prospects

In most crop breeding programs, the rate of yield increment is insufficient to cope with the increased food demand caused by a rapidly expanding global population. In plant breeding, the development of improved crop varieties is limited by the very long crop duration. Given the many phases of crossing, selection, and testing involved in the production of new plant varieties, it can take one or two decades to create a new cultivar. One possible way of alleviating food scarcity problems and increasing food security is to develop improved plant varieties rapidly. Traditional farming methods practiced since quite some time have decreased the genetic variability of crops. To improve agronomic traits associated with yield, quality, and resistance to biotic and abiotic stresses in crop plants, several conventional and molecular approaches have been used, including genetic selection, mutagenic breeding, somaclonal variations, whole-genome sequence-based approaches, physical maps, and functional genomic tools. However, recent advances in genome editing technology using programmable nucleases, clustered regularly interspaced short palindromic repeats (CRISPR), and CRISPR-associated (Cas) proteins have opened the door to a new plant breeding era. Therefore, to increase the efficiency of crop breeding, plant breeders and researchers around the world are using novel strategies such as speed breeding, genome editing tools, and high-throughput phenotyping. In this review, we summarize recent findings on several aspects of crop breeding to describe the evolution of plant breeding practices, from traditional to modern speed breeding combined with genome editing tools, which aim to produce crop generations with desired traits annually.

https://www.mdpi.com/1422-0067/21/7/2590/pdf

Conventional and Molecular Techniques from Simple Breeding to Speed Breeding in Crop Plants: Recent Advances and Future Outlook

Pigeonpea (Cajanus cajan) is an important grain legume of the Indian subcontinent, South-East Asia and East Africa. More than eighty five percent of the world pigeonpea is produced and consumed in India where it is a key crop for food and nutritional security of the people. Here we present the first draft of the genome sequence of a popular pigeonpea variety ‘Asha’. The genome was assembled using long sequence reads of 454 GS-FLX sequencing chemistry with mean read lengths of >550 bp and >10-fold genome coverage, resulting in 510,809,477 bp of high quality sequence. Total 47,004 protein coding genes and 12,511 transposable elements related genes were predicted. We identified 1,213 disease resistance/defense response genes and 152 abiotic stress tolerance genes in the pigeonpea genome that make it a hardy crop. In comparison to soybean, pigeonpea has relatively fewer number of genes for lipid biosynthesis and larger number of genes for cellulose synthesis. The sequence contigs were arranged in to 59,681 scaffolds, which were anchored to eleven chromosomes of pigeonpea with 347 genic-SNP markers of an intra-species reference genetic map. Eleven pigeonpea chromosomes showed low but significant synteny with the twenty chromosomes of soybean. The genome sequence was used to identify large number of hypervariable ‘Arhar’ simple sequence repeat (HASSR) markers, 437 of which were experimentally validated for PCR amplification and high rate of polymorphism among pigeonpea varieties. These markers will be useful for fingerprinting and diversity analysis of pigeonpea germplasm and molecular breeding applications. This is the first plant genome sequence completed entirely through a network of Indian institutions led by the Indian Council of Agricultural Research and provides a valuable resource for the pigeonpea variety improvement.

/pdf/the-first-draft-of-the-pigeonpea-genome-sequence-2tmjeufo6x.pdf

The first draft of the pigeonpea genome sequence

DNA damage protecting activity and antioxidant potential of pudina extract

Morphologically identical transgenic mint (Mentha arvensis L.) with bacterial glutathione synthetase gene has been developed. Transformed plants were obtained by co-cultivation of leaf disks with Agrobacterium tumefaciens strain LBA 4404 harbouring a binary vector pCAMBIA-CpGS that carried E. coli glutathione synthetase (GS), β-glucuronidase as reporter gene and nptII as selective marker gene for kanamycin resistance. Using a constitutive double CaMV 35S promoter and an rbcS transit peptide, we successfully addressed CpGS to the chloroplasts through pJIT 117 vector. Preculture and the presence of AS in the co-cultivation medium played a significant role in enhancing transformation frequency. The highest transformation frequency was achieved with MS selection medium supplemented with 25% coconut water, 1.12 mg l−1 BAP, 0.2 mg l−1 NAA, 50 mg l−1 kanamycin and 125 mg l−1 cefotaxime. Robust rooting of regenerated shoots was obtained in half-strength liquid MS medium containing 0.2 mg l−1 NAA and 50 mg l−1 kanamycin. The presence and expression of transgenes in transgenics (T0) was evidenced by GUS histoenzymatic assay, PCR and RT-PCR analysis of nptII and the gene of interest, i.e., GS of putative transgenic leaves. Chromosomal integration of GS gene was confirmed by Southern blot analysis. Transgenic plants were successfully acclimatized in the greenhouse. An overall transformation frequency of 15% was achieved in approximately 3 months of time period. These results are discussed in relation to heavy metal trafficking pathways in higher plants and to the interest of using plastid expression of PCS for biotechnological applications.

Agrobacterium-mediated genetic transformation of mint with E. coli glutathione synthetase gene

This invention relates to the leishmanicidal activity of night jasmine leaf extract, wherein the said method comprises the steps of, preparing the methanolic extract of night jasmine leaf, chromatographic purification of said extract to obtain bioactive fraction containing calceolarioside A, isolation and characterization of calceolarioside A, leishmanicidal activity of calceolarioside A against axenic promastigote culture of Leishmania donovani, treatment of L. donovani infected chronic golden hamster with bioactive fraction for a period of 21 days for detection of leishmanicidal activity in vivo, administering of PE in normal hamster to obtain non-toxic nature, combination therapy of bioactive fraction + SAG against said model for synergistic potentiation of antileishmanial activity and complete clearance of parasitemia from liver and spleen as reflected by LDU wherein comprising a potential medicament against kala-azar.

Akhilesh Kumar

Papers

The first draft of the pigeonpea genome sequence

DNA damage protecting activity and antioxidant potential of pudina extract

Agrobacterium-mediated genetic transformation of mint with E. coli glutathione synthetase gene

Extracts from nyctanthes arbortristis for the treatement of leishmaniasis