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

2020 ◽  
Author(s):  
Kunyong Huang ◽  
Yaliang Shi ◽  
Yicheng Zhong ◽  
Aiguo Zhu ◽  
Zhimin Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Natural Fiber ◽  
Stem Diameter ◽  
Genome Wide Association ◽  
Skin Thickness ◽  
Ramie Fiber ◽  
Fiber Yield ◽  
Genome Wide ◽  
Fiber Fineness

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 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 r 2 = 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.

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

2019 ◽  
Author(s):  
Kunyong Huang ◽  
Yaliang Shi ◽  
Yicheng Zhong ◽  
Aiguo Zhu ◽  
Zhimin Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Natural Fiber ◽  
Stem Diameter ◽  
Genome Wide Association ◽  
Skin Thickness ◽  
Ramie Fiber ◽  
Fiber Yield ◽  
Genome Wide ◽  
Fiber Fineness

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 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.

Genome-wide association for β-glucan content, population structure, and linkage disequilibrium in elite oat germplasm adapted to subtropical environments

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Cristiano M. Zimmer ◽  
Ian G. McNish ◽  
Kathy Esvelt Klos ◽  
Tatiana Oro ◽  
Klever M. A. Arruda ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals Epstein Barr virus genomes reveal population structure and type 1 association with endemic Burkitt lymphoma

2019 ◽  
Author(s):  
Yasin Kaymaz ◽  
Cliff I. Oduor ◽  
Ozkan Aydemir ◽  
Micah A. Luftig ◽  
Juliana A. Otieno ◽  
...  
Keyword(s):  
Population Structure ◽  
Burkitt Lymphoma ◽  
Epstein Barr Virus ◽  
Genome Wide Association ◽  
Viral Dna ◽  
Barr Virus ◽  
Genome Wide ◽  
Epstein Barr

AbstractEndemic Burkitt lymphoma (eBL), the most prevalent pediatric cancer in sub-Saharan Africa, is associated with malaria and Epstein Barr virus (EBV). In order to better understand the role of EBV in eBL, we improved viral DNA enrichment methods and generated a total of 98 new EBV genomes from both eBL cases (N=58) and healthy controls (N=40) residing in the same geographic region in Kenya. Comparing cases and controls, we found that EBV type 1 was significantly associated with eBL with 74.5% of patients (41/55) versus 47.5% of healthy children (19/40) carrying type 1 (OR=3.24, 95% CI=1.36 - 7.71,P=0.007). Controlling for EBV type, we also performed a genome-wide association study identifying 6 nonsynonymous variants in the genes EBNA1, EBNA2, BcLF1, and BARF1 that were enriched in eBL patients. Additionally, we observed that viruses isolated from plasma of eBL patients were identical to their tumor counterpart consistent with circulating viral DNA originating from the tumor. We also detected three intertypic recombinants carrying type 1 EBNA2 and type 2 EBNA3 regions as well as one novel genome with a 20 kb deletion resulting in the loss of multiple lytic and virion genes. Comparing EBV types, genes show differential variation rates as type 1 appears to be more divergent. Besides, type 2 demonstrates novel substructures. Overall, our findings address the complexities of EBV population structure and provide new insight into viral variation, which has the potential to influence eBL oncogenesis.Key PointsEBV type 1 is more prevalent in eBL patients compared to the geographically matched healthy control group.Genome-wide association analysis between cases and controls identifies 6 eBL-associated nonsynonymous variants in EBNA1, EBNA2, BcLF1, and BARF1 genes.Analysis of population structure reveals that EBV type 2 exists as two genomic sub groups.

scholarly journals Korean soybean core collection: Genotypic and phenotypic diversity population structure and genome-wide association study

PLoS ONE ◽  
2019 ◽  
Vol 14 (10) ◽  
pp. e0224074 ◽  
Author(s):  
Namhee Jeong ◽  
Ki-Seung Kim ◽  
Seongmun Jeong ◽  
Jae-Yoon Kim ◽  
Soo-Kwon Park ◽  
...  
Keyword(s):  
Population Structure ◽  
Association Study ◽  
Core Collection ◽  
Genome Wide Association Study ◽  
Phenotypic Diversity ◽  
Genome Wide Association ◽  
Genome Wide

scholarly journals A New Diversity Panel for Winter Rapeseed (Brassica napus L.) Genome-Wide Association Studies

Agronomy ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2006
Author(s):  
David P. Horvath ◽  
Michael Stamm ◽  
Zahirul I. Talukder ◽  
Jason Fiedler ◽  
Aidan P. Horvath ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Brassica Napus ◽  
Association Studies ◽  
Decay Rates ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
High Quality ◽  
Brassica Napus L ◽  
Genome Wide ◽  
Quality Markers

A diverse population (429 member) of canola (Brassica napus L.) consisting primarily of winter biotypes was assembled and used in genome-wide association studies. Genotype by sequencing analysis of the population identified and mapped 290,972 high-quality markers ranging from 18.5 to 82.4% missing markers per line and an average of 36.8%. After interpolation, 251,575 high-quality markers remained. After filtering for markers with low minor allele counts (count > 5), we were left with 190,375 markers. The average distance between these markers is 4463 bases with a median of 69 and a range from 1 to 281,248 bases. The heterozygosity among the imputed population ranges from 0.9 to 11.0% with an average of 5.4%. The filtered and imputed dataset was used to determine population structure and kinship, which indicated that the population had minimal structure with the best K value of 2–3. These results also indicated that the majority of the population has substantial sequence from a single population with sub-clusters of, and admixtures with, a very small number of other populations. Analysis of chromosomal linkage disequilibrium decay ranged from ~7 Kb for chromosome A01 to ~68 Kb for chromosome C01. Local linkage decay rates determined for all 500 kb windows with a 10kb sliding step indicated a wide range of linkage disequilibrium decay rates, indicating numerous crossover hotspots within this population, and provide a resource for determining the likely limits of linkage disequilibrium from any given marker in which to identify candidate genes. This population and the resources provided here should serve as helpful tools for investigating genetics in winter canola.

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