SSR markers associated with fiber yield traits in ramie (Boehmeria nivea L. Gaudich)

Luan, Mingbao; Liu, Chenchen; Wang, Xiaofei; Xu, Ying; Sun, Zenghui; Chen, Jianhua

doi:10.1016/j.indcrop.2017.05.065

Cited by 21 publications

(23 citation statements)

References 26 publications

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“…Thus, it should present with lower LD levels than those of self-pollinated crops. Despite several earlier association studies on ramie [2,21,22], none of them reported any LD decay values. Here, the genome-wide LD decayed to r 2 = 0.1 was 11.75 kb in physical distance.…”

Section: Population Structure and Linkage Disequilibriummentioning

confidence: 84%

“…Numerous statistical models are available to calculate the significance of the associations between SNPs and traits [38]. Luan et al [2] detected 16 stable molecular markers from an association analysis of fiber yield traits in ramie based on the MLM-Q+K model. However, this model considers the effects of Q for the population structure, analyzes K for the genetic relationships, and Bonferroni correction is required for multiple tests.…”

Section: Genome-wide Association Study (Gwas)mentioning

confidence: 99%

“…Thirteen plant traits were measured and the data were applied to the association mapping (Table 1). Measurements were made according to the methods of Luan et al [2].…”

Section: Plant Materials and Phenotypingmentioning

confidence: 99%

“…Fiber yield and quality limit ramie cultivation in China [3]. While, fiber yield is a complex quantitative trait comprising ramet number, stem diameter, plant height, skin thickness, and fiber percentage [2]. Qualitative fiber characteristics include length, strength, and fineness.…”

mentioning

confidence: 99%

“…Chen et al [3] identified 4,230 SSR loci and developed 2,431 SSR markers from the ramie transcriptome at different developmental stages. Using SSR markers, Liu et al [8] and Luan et al [2] identified several agronomic trait-related quantitative trait loci (QTLs) in ramie. Nevertheless, it is difficult to use them for cloning or breeding programs due to these QTLs with large intervals.…”

mentioning

confidence: 99%

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

Huang

Shi

Pan

et al. 2019

Preprint

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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 single-nucleotide 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 geographic origins. The genome-wide linkage disequilibrium (LD) decayed to r2 = 0.1 was ~11.75 kb in physical distance. One, seven, one, seven, and twenty-seven significant SNP marker associations were detected for fiber fineness (third season), stem diameter (third season), stem skin thickness (third season), fiber percentage (second season), and fiber percentage (third season), respectively. Two promising candidate genes, whole_GLEAN_10029622 and whole_GLEAN_10029638 resided in the significant trait-SNP association for fiber fineness (third season), which annotated as a cotton fiber-expressed protein and an Arabidopsis thaliana homeobox protein ATH1, respectively and validated by qPCR. Conclusions: These results provide information for understanding the population structure, LD decay and genetic variation in ramie natural population. The identified loci or genes for fiber fineness and yield may provide the basis for future research on fiber fineness and yield and marker-assisted selection breeding for ramie.

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Section: Population Structure and Linkage Disequilibriummentioning

confidence: 84%

Section: Genome-wide Association Study (Gwas)mentioning

confidence: 99%

“…Thirteen plant traits were measured and the data were applied to the association mapping (Table 1). Measurements were made according to the methods of Luan et al [2].…”

Section: Plant Materials and Phenotypingmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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

Huang

Shi

Pan

et al. 2019

Preprint

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Ramie (Boehmeria nivea L. Gaud) Genetic Improvement

Satya

Mitra

Ray

2019

Advances in Plant Breeding Strategies: Industrial and Food Crops

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Genomic variation and candidate genes dissect quality and yield traits in Boehmeria nivea (L.) Gaudich

Shi,

Huang,

Chen

et al. 2024

Cellulose

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Ramie is a perennial and traditional Chinese cellulose ber crop and accessible for harvesting three times within one year in some region of China. Besides, ramie can also be used in medicine, feed and material industries. The genetic basis over quality-and yield-related traits in ramie is poorly understood and insu cient owing to the lack of assessment in different environments. A core collection comprising 319 accessions with 25.31-fold coverage resequencing depth for evaluating population structure and genomic variation. Combined with linkage mapping method detecting favorable variation and candidate genes associated with yield and quality related traits.We obtained approximately 3.49 million high quality single nucleotide polymorphisms (SNPs), 2,089,798 insertions and deletions (Indels) and 88,087 structure variation (SV) in whole genome. None distinct population structure was found in ramie population based on geographical distribution. Some loci and genes were detected to relate to three yield traits and ber neness. A pleiotropic genes encoding NAC domain containing protein (BnNAC29), was identi ed signi cantly correlated with stem diameter and bark thickness. The variation of large-fragment deletion and indels in two candidate genes may responsible for the two traits. Moreover, we also detected pleiotropic loci and candidate genes for plant height and stem diameter. Our study provides new insights into the genetic architecture of ramie yield and ber quality. The identi ed loci and candidate genes are expected to facilitate genomics-based breeding for higher ber yield and quality improvement in ramie.

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SSR markers associated with fiber yield traits in ramie (Boehmeria nivea L. Gaudich)

Cited by 21 publications

References 26 publications

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

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

Ramie (Boehmeria nivea L. Gaud) Genetic Improvement

Genomic variation and candidate genes dissect quality and yield traits in Boehmeria nivea (L.) Gaudich

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