A genomic resource derived from the integration of genome sequences, expressed transcripts and genetic markers in ramie

Abstract

Background The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber crop. Results We obtained a high-quality transcriptome consisting of 30,591 non-redundant transcripts using single-molecule long-read sequencing and proposed it as a universal ramie transcriptome. Additionally, 55,882 single nucleotide polymorphisms (SNPs) were identified and a high-density genetic map was developed. Based on this genetic map, 181.7 Mb ramie genome sequences were assembled into 14 chromosomes. For the convenient use of these resources, 29,286 (~ 95.7%) of the transcripts and all 55,882 SNPs, along with 1827 previously reported sequence repeat markers (SSRs), were mapped into the ramie genome, and 22,343 (~ 73.0%) transcripts, 50,154 (~ 89.7%) SNPs, and 1466 (~ 80.3%) SSRs were assigned to a specific location in the corresponding chromosome. Conclusion This is the first study to characterize the ramie transcriptome by long-read sequencing, and the substantial number of transcripts of significant length obtained will accelerate our understanding of ramie growth and development. This integration of genome sequences, expressed transcripts, and genetic markers will provide an extremely useful resource for genetic, molecular, and breeding studies of ramie. Electronic supplementary material The online version of this article (10.1186/s12864-019-5878-8) contains supplementary material, which is available to authorized users.

Integration of Quantitative Trait Loci Mapping and Expression Profiling Analysis to Identify Genes Potentially Involved in Ramie Fiber Lignin Biosynthesis

“…Using genotype data of the population [16], the QTLs for the trait of fiber lignin content was detected. The LOD thresholds (1000 permutations) were estimated for the investigated traits in the two environments, and the values were 3.25 and 2.98, respectively.…”

“…We cultivated the ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT) according to the method described by Wang et al [16]. All the F 2 progeny and the two parents were reproduced by cutting propagation and generating an agamous line, which had an identical genotype to the corresponding F 2 individual.…”

“…A high-density genetic map with 1085 markers has been developed and reported previously, spanning a total length of 2118.8 cM [16]. The QTLs of the lignin content trait were detected in two environments using a composite interval mapping with the software MapQTL [17].…”

“…To obtain the DEGs located in a QTL region, the genes in the QTL region needed to be identified first. The flanking markers of each QTL were assigned to the ramie genome [16,24,25]. In case of a wave in the QTL location by statistical mapping, the genomic region of each QTL was enlarged by outer extending 300 kb from the two flanking markers.…”

“…Recently, a high-density genetic map with 1085 markers spanning 2118.8 cM was constructed using an F 2 agamous line population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT) [16]. Additionally, our previous study characterized the phloem-development-related expression profiling of the stem barks in ramie to identify the differentially expressed genes (unpublished data; sequence reads have been deposited in the SRA database).…”