Detection of stable QTLs for grain protein content in rice (Oryza sativa L.) employing high throughput phenotyping and genotyping platforms.

Lack of appropriate donors, non-utilization of high throughput phenotyping and genotyping platforms with high genotype × environment interaction restrained identification of robust QTLs for grain protein content (GPC) in rice. In the present investigation a  BCF mapping population was developed using grain protein donor, ARC10075 and high-yielding cultivar Naveen and 190 lines were genotyped using 40 K Affimetrix custom SNP array with the objective to identify stable QTLs for protein content. Three of the identified QTLs, one for GPC (qGPC1.

Pollution tolerance assessment of temperate woody vegetation growing along the National Highway-5 in Himachal Pradesh, India.

Industrialization and globalization have resulted in pollution of all the three ecosystems, including soil, water, and air. Among these, air pollution has generated much interest, since it has a major influence on the transboundary dispersion of pollutants globally. Air pollution tolerance index (APTI) value represents tolerance level of plants which help in selecting the most suitable plant species for plantation in/around affected areas.

Resolving population structure and genetic differentiation associated with RAD-SNP loci under selection in tossa jute (Corchorus olitorius L.).

The genetic basis of selection for geographic adaptation and how it has contributed to population structure are unknown in tossa jute (Corchorus olitorius), an important bast fibre crop. We performed restriction site-associated DNA (RAD) sequencing-based (1115 RAD-SNPs) population genomic analyses to investigate genetic differentiation and population structure within a collection of 221 fibre-type lines from across nine geographic regions of the world. Indian populations, with relatively higher overall diversity, were significantly differentiated (based on F and PCA) from the African and the other Asian populations.

Genome-wide regulatory gene-derived SSRs reveal genetic differentiation and population structure in fiber flax genotypes.

We designed a set of 580 simple sequence repeat markers; 506 from transcription factor-coding genes, and 74 from long non-coding RNAs and designated them as regulatory gene-derived simple sequence repeat (ReG-SSR) markers. From this set, we could anchor 559 ReG-SSR markers on 15 flax chromosomes with an average marker distance of 0.56 Mb.

Detection of Mesta yellow vein mosaic virus (MeYVMV) in field samples by a loop-mediated isothermal amplification reaction.

A loop-mediated isothermal amplification (LAMP) assay was optimized for the detection of Mesta yellow vein mosaic virus (MeYVMV) in diseased plants of mesta (Hibiscus sabdariffa L.& H. cannabinus L.

Transcriptome profiling uncovers β-galactosidases of diverse domain classes influencing hypocotyl development in jute (Corchorus capsularis L.).

Enzyme β-galactosidase (EC 3.2.1.

UGbS-Flex, a novel bioinformatics pipeline for imputation-free SNP discovery in polyploids without a reference genome: finger millet as a case study.

Background: Research on orphan crops is often hindered by a lack of genomic resources. With the advent of affordable sequencing technologies, genotyping an entire genome or, for large-genome species, a representative fraction of the genome has become feasible for any crop. Nevertheless, most genotyping-by-sequencing (GBS) methods are geared towards obtaining large numbers of markers at low sequence depth, which excludes their application in heterozygous individuals.

The draft genome of cv. JRO-524 (Navin).

Here, we present the draft genome (377.3 Mbp) of cv. JRO-524 (Navin), which is a leading dark jute variety developed from a cross between African (cv.

Morphological, Histobiochemical and Molecular Characterisation of Low Lignin Phloem Fibre (llpf) Mutant of Dark Jute (Corchorus olitorius L.).

Lignin is a versatile plant metabolite challenging high-end industrial applications of several plant products including jute. Application of developmental mutant in regulation of lignification in jute may open up door for much awaited jute based diversified products. In the present study, a novel dark jute (Corchorus olitorius L.

SSR and morphological trait based population structure analysis of 130 diverse flax (Linum usitatissimum L.) accessions.

A total of 130 flax accessions of diverse morphotypes and worldwide origin were assessed for genetic diversity and population structure using 11 morphological traits and microsatellite markers (15 gSSRs and 7 EST-SSRs). Analysis performed after classifying these accessions on the basis of plant height, branching pattern, seed size, Indian/foreign origin into six categories called sub-populations viz. fibre type exotic, fibre type indigenous, intermediate type exotic, intermediate type indigenous, linseed type exotic and linseed type indigenous.

Start codon targeted (SCoT) polymorphism reveals genetic diversity in wild and domesticated populations of ramie (Boehmeria nivea L. Gaudich.), a premium textile fiber producing species.

Twenty-four start codon targeted (SCoT) markers were used to assess genetic diversity and population structure of indigenous, introduced and domesticated ramie (Boehmeria nivea L. Gaudich.).

Pathways associated with lignin biosynthesis in lignomaniac jute fibres.

We generated the bast transcriptomes of a deficient lignified phloem fibre mutant and its wild-type jute (Corchorus capsularis) using Illumina paired-end sequencing. A total of 34,163 wild-type and 29,463 mutant unigenes, with average lengths of 1442 and 1136 bp, respectively, were assembled de novo, ~77-79 % of which were functionally annotated. These annotated unigenes were assigned to COG (~37-40 %) and GO (~22-28 %) classifications and mapped to 189 KEGG pathways (~19-21 %).