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

Abstract

Background Ramie is a major natural fiber crop cultivated in East Asia. The improvement of its fiber yield and fineness are important breeding goals. Fiber yield is a complex quantitative trait comprising ramet number, stem diameter, plant height, skin thickness, and fiber percentage. The fiber fineness is a crucial trait for ramie fiber quality. However, there are few association studies for fiber yield traits and fiber fineness on ramie, and lack high-density SNP maps in natural ramie population. Results Here, a panel of 112 core ramie germplasms were genotyped by 215,376 consistent singlenucleotide polymorphisms (SNPs) from specific-locus amplified-fragment sequencing (SLAF-seq), and used for genome-wide association study of fiber fineness and yield. Subsequently, the genetic diversity, linkage disequilibrium (LD), and population structure was conducted based on 215,376 SNPs. Population cluster analysis disclosed five subpopulations. Neighbor-joining (NJ) analysis revealed three major clusters. No obvious relationships were identified between them and their

Genetic insights into the crude protein and fiber content of ramie leaves

“…KAN2 plays a crucial role in vascular tissue formation, and its loss-of-function mutants cause ectopic xylem and fiber differentiation in amphivasal vascular tissue ( Ilegems et al, 2010 ). Recently, Genome-wide Association Studies (GWAS) analysis identified a significant signal associated with the fiber content of stem barks in ramie, and whole_GLEAN_10016511 was near this signal ( Huang et al, 2021 ). Therefore, whole_GLEAN_10016511 might be the candidate of CF13 and was further examined.…”

“…The rapid development of next-generation sequencing technology has recently led to the identification of large-scale single-nucleotide polymorphisms (SNPs) in ramie, resulting in several high-density genetic maps ( Liu et al, 2017 ; Zeng et al, 2019 ). Consequently, the genetic architecture of many agronomic traits, such as fiber yield, quality, and flowering time, has been systematically characterized using linkage mapping and genome-wide association mapping ( Zhu et al, 2016 ; Liu et al, 2017 ; Chen et al, 2018 , 2019 ; Zeng et al, 2019 , 2022 ; Huang et al, 2021 ; Wang et al, 2021 ), and several candidates across various loci have been documented ( Liu et al, 2017 ; Wang et al, 2021 ; Zeng et al, 2022 ). Recently, ramie feeding traits have also been researched, and the genetic basis of six forage yield-related traits was characterized, resulting in 78 significant association signals from 43 genomic regions ( Bai et al, 2022 ).…”