Genetic analyses of morphological traits, and phenotypic screening of tossa jute germplasm grown under salinity stress

Corchorus olitorius L. jute is a natural fiber crop that is very susceptible to salinity stress. Salinity in soil is a serious threat to tossa jute cultivation in salt-prone regions of Bangladesh. Development of salinity stress tolerant tossa jute variety is a crying need in Bangladesh. Hence, 22 tossa jute genotypes were investigated in an augmented design against 7.86-7.93 dSm^-1 salinity stress at coastal regions of Bangladesh during 2017-2019. Salt-tolerant jute genotypes were phenotypically screened out based on survivability, vegetative growth, plant height, base diameter, and fiber yield capacity. Among all genotypes, Acc. 4160 and Acc. 2311 showed good fiber yield (18.0 and 13.8 g plant-1, respectively) with the lowest mortality rate (5.67 and 8.0%, respectively). Acc. 1381, Acc. 2307, Acc. 1334, Acc. 1381 and the pre-released varieties, namely O-9897, BJRI Tossa Pat 5, JRO-524 (Green) were also found good for the aforesaid traits. Among the studied characters, high heritability in a broad sense, genetic advance (%) of mean and significant associations were found which contribute to fiber yield significantly. According to the Clustering and principal component analyses, the relatively salt-tolerant genotypes of cluster II (Acc. 4160, Acc. 2311, Acc. 2307, JRO-524 (Green), Acc. 4327, BJRI Tossa Pat 5, Acc. 1334 & Acc. 1381) could be used as breeding materials and sources of salt-tolerant genes to develop salt-tolerant tossa jute variety.

Comparative transcriptomics of stem bark reveals genes associated with bast fiber development in Boehmeria nivea L. gaud (ramie)

BACKGROUND

Boehmeria nivea L. Gaud (Ramie) produces one of the longest natural fibers in nature. The bark of ramie mainly comprises of the phloem tissue of stem and is the raw material for fiber. Therefore, identifying the molecular regulation of phloem development is important for understanding of bast fiber biosynthesis and improvement of fiber quality in ramie.

RESULTS

In this study, we collected top bud (TB), bark from internode elongating region (ER) and bark from internode fully elongated region (FER) from the ramie variety Zhongzhu No. 1. Histological study indicated that these samples contain phloem tissues at different developmental and maturation stages, with a higher degree of maturation of phloem tissue in FER. RNA sequencing (RNA-seq) was performed and de novo transcriptome was assembled. Unigenes and differentially expressed genes (DEGs) in these three samples were identified. The analysis of DEGs by using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed clear differences in gene expression between ER and FER. Some unigenes involved in secondary cell wall biosynthesis were up-regulated in both ER and FER, while unigenes for some cell wall components or cell wall modifications showed differential expression between ER and FER. In addition, the ethylene respond factors (ERFs) in the ethylene signaling pathway were up-regulated in FER, and ent-kaurenoic acid oxidase (KAO) and GA 20-oxidase (GA20ox) for gibberellins biosynthesis were up-regulated while GA 2-oxidase (GA2ox) for gibberellin inactivation was down-regulated in FER.

CONCLUSIONS

Both morphological study and gene expression analysis supported a burst of phloem and vascular developmental processes during the fiber maturation in the ramie stem, and ethylene and gibberellin are likely to be involved in this process. Our findings provide novel insights into the phloem development and fiber maturation in ramie, which could be useful for fiber improvement in ramie and other fiber crops.

De novo transcriptome assembly of textile hemp from datasets on hypocotyls and adult plants

We here provide an updated de novo transcriptome of the hemp textile variety Santhica 27. The assembly was performed by merging the reads obtained previously on a time-series relative to the hypocotyl development and on bast fibers isolated from internodes of adult plants at different heights with those obtained from a newly performed transcriptome study on the hypocotyl in response to jasmonic acid treatment. More specifically, hypocotyls aged 15 days were treated with jasmonic acid and collected 3 and 5 days after the application of the plant growth regulator. RNA-Seq was then performed on the treated hypocotyls. The transcriptome reported here will be a useful resource for those scientists engaged in the study of bast fiber development, as well as cell wall biosynthesis in textile hemp. The transcriptome is also useful for molecular studies relative to the synthesis of secondary metabolites, such as phenolic compounds (e.g. flavonoids) and lignans/lignanamides.

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. Thirty-one polymorphic ReG-SSR primers, amplifying SSR loci length of at least 20 bp were chosen from 134 screened primers. This primer set was used to characterize a diversity panel of 93 flax accessions. The panel included 33 accessions from India, including released varieties, dual-purpose lines and landraces, and 60 fiber flax accessions from the global core collection. Thirty-one ReG-SSR markers generated 76 alleles, with an average of 2.5 alleles per primer and a mean allele frequency of 0.77. These markers recorded 0.32 average gene diversity, 0.26 polymorphism information content and 1.35% null alleles. All the 31 ReG-SSR loci were found selectively neutral and showed no evidence of population reduction. A model-based clustering analysis separated the flax accessions into two sub-populations-Indian and global, with some accessions showing admixtures. The distinct clustering pattern of the Indian accessions compared to the global accessions, conforms to the principal coordinate analysis, genetic dissimilarity-based unweighted neighbor-joining tree and analysis of molecular variance. Fourteen flax accessions with 99.3% allelic richness were found optimum to adopt in breeding programs. In summary, the genome-wide ReG-SSR markers will serve as a functional marker resource for genetic and phenotypic relationship studies, marker-assisted selections, and provide a basis for selection of accessions from the Indian and global gene pool in fiber flax breeding programs.

Digital gene expression profiling of flax (Linum usitatissimum L.) stem peel identifies genes enriched in fiber-bearing phloem tissue

To better understand the molecular mechanisms and gene expression characteristics associated with development of bast fiber cell within flax stem phloem, the gene expression profiling of flax stem peels and leaves were screened, using Illumina's Digital Gene Expression (DGE) analysis. Four DGE libraries (2 for stem peel and 2 for leaf), ranging from 6.7 to 9.2 million clean reads were obtained, which produced 7.0 million and 6.8 million mapped reads for flax stem peel and leave, respectively. By differential gene expression analysis, a total of 975 genes, of which 708 (73%) genes have protein-coding annotation, were identified as phloem enriched genes putatively involved in the processes of polysaccharide and cell wall metabolism. Differential expression genes (DEGs) was validated using quantitative RT-PCR, the expression pattern of all nine genes determined by qRT-PCR fitted in well with that obtained by sequencing analysis. Cluster and Gene Ontology (GO) analysis revealed that a large number of genes related to metabolic process, catalytic activity and binding category were expressed predominantly in the stem peels. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of the phloem enriched genes suggested approximately 111 biological pathways. The large number of genes and pathways produced from DGE sequencing will expand our understanding of the complex molecular and cellular events in flax bast fiber development and provide a foundation for future studies on fiber development in other bast fiber crops.