Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

Abstract

BackgroundRamie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known.ResultsA genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170–64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170–64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie.ConclusionsThe identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1573-1) contains supplementary material, which is available to authorized users.

Comparative Transcriptome Analysis Provides New Insights into the Molecular Regulatory Mechanism of Adventitious Root Formation in Ramie (Boehmeria nivea L.)

“…Briefly, 0.5 μg total RNA was used to synthesize cDNA with oligo (dT) using a PrimeScript RT perfect real-time reagent kit (Takara, Japan), and then the cDNA was diluted four times. The qPCR analysis was performed using a CFX96 Real-Time System (Bio-Rad) with the special primers showed in Additional file 1: sheet1 , according to the method of Chen et al [ 23 ]. Briefly, the reaction systems contained 10 μL 2 × T5 Fast qPCR Mix (SYBR Green I, TSINGKE Biological Technology, Beijing, China), 0.4 μmol/L of each of the forward and reverse primers, 2 μL diluted cDNA, and an appropriate amount of sterile double-distilled water.…”

Comparative transcriptome analysis provides new insights into the molecular regulatory mechanism of adventitious root formation in ramie (Boehmeria nivea L.)

“…Total RNA was reverse transcribed using a PrimeScript RT perfect real-time reagent kit (Takara, Japan), and then the cDNA was diluted four times. The qPCR analysis was performed using the special primers showed in Additional le 1: sheet1, according to the method of Chen et al [23]. 18S rRNA gene was used as the internal control to normalize q-PCR data.…”

Genome-wide association analysis of fiber fineness and yield in ramie (Boehmeria nivea) using SLAF-seq

“…Using the genotyping-by-sequencing technique, Liu et al [21] and Chen et al [22] discovered numerous SNPs and detected QTLs associated with ramie fiber yield. However, the QTLs of Liu et al [21] were based on the F2 agamous line population of the varieties Qingdaye and Zhongzhu 1.…”

“…However, the QTLs of Liu et al [21] were based on the F2 agamous line population of the varieties Qingdaye and Zhongzhu 1. Chen et al [22] focused only on the ramet number and made no reference to the ramie genome. There are still lack studies assess the genetic variation and GWAS for fiber yield and fineness in natural ramie population.…”