scholarly journals A set of SNP markers for timber tracking of Larix spp. in Europe and Russia

2018 ◽  
Vol 91 (5) ◽  
pp. 614-628 ◽  
Author(s):  
Céline Blanc-Jolivet ◽  
Yulai Yanbaev ◽  
Birgit Kersten ◽  
Bernd Degen
Keyword(s):  
Snp Markers ◽  
Timber Tracking

scholarly journals Development of nuclear SNP markers for Mahogany (Swietenia spp.)

2020 ◽  
Vol 12 (4) ◽  
pp. 585-587
Author(s):  
Birte Pakull ◽  
Lasse Schindler ◽  
Malte Mader ◽  
Birgit Kersten ◽  
Celine Blanc-Jolivet ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Population Genetic ◽  
Snp Markers ◽  
Genetic Studies ◽  
Timber Tracking

Abstract Swietenia species are the most valuable American tropical timbers and have been heavily overexploited for decades. The three species are listed as either vulnerable or endangered by IUCN and are included on Appendix II of CITES, yet illegal exploitation continues. Here, we used restriction associated DNA sequencing to develop a new set of 120 SNP markers for Swietenia sp., suitable for MassARRAY®iPLEX™ genotyping. These markers can be used for population genetic studies and timber tracking purposes.

scholarly journals Development of nuclear SNP markers for the timber tracking of the African tree species Sapelli, Entandrophragma cylindricum

2017 ◽  
Vol 10 (3) ◽  
pp. 539-541 ◽  
Author(s):  
Céline Blanc-Jolivet ◽  
Birgit Kersten ◽  
Nils Bourland ◽  
Erwan Guichoux ◽  
Adline Delcamp ◽  
...  
Keyword(s):  
Tree Species ◽  
Snp Markers ◽  
Timber Tracking

scholarly journals Short note: Development of a new set of SNP markers to measure genetic diversity and genetic differentiation of Mongolian oak (Quercus mon­golica Fisch. ex Ledeb.) in the Far East of Russia

2019 ◽  
Vol 68 (1) ◽  
pp. 85-91
Author(s):  
Hilke Schröder ◽  
Yulai Yanbaev ◽  
Birgit Kersten ◽  
Bernd Degen
Keyword(s):  
Genetic Differentiation ◽  
Russian Far East ◽  
Short Note ◽  
Far East ◽  
Snp Markers ◽  
Practical Application ◽  
Timber Tracking ◽  
Mongolian Oak ◽  
The City ◽  
The Russian Far East

Abstract We developed a new set of 25 nuclear (nc), 12 chloroplast (cp) and 7 mitochondrial (mt) SNPs and used it to genotype 371 Mongolian oak (Quercus mongolica Fisch. ex Ledeb.) trees from seven locations in a 200 km by 400 km area in the Russian Far East. One of the locations in an area of 15 km by 25 km east of the city Ussuriusk was analyzed more intensively with 188 collected trees. The genetic differentiation at the nuclear SNPs was small to moderate and for the plastid SNPs it was high when considering all trees from the seven locations. The gene pool distances between locations were for 19 out of 21 pairs statistically highly significant. There was no correlation of genetic and spatial distances. Only three different multilocus-haplotypes could be identified and 42 two-loci-combinations of plastid SNPs could be used to identify them. Conclusions for the practical application such as timber tracking and gene conservation are discussed.

Revealing the genetic diversity of wheat varieties (lines) in China based on SNP markers

2019 ◽  
Vol 46 (2) ◽  
pp. 307-314
Author(s):  
Yu-Qing ZHANG ◽  
Juan ZOU ◽  
Yi-Ke LIU ◽  
Wei-Jie HE ◽  
Zhan-Wang ZHU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Snp Markers ◽  
Wheat Varieties

An enrichment method for mapping ambiguous reads to the reference genome for NGS analysis

2019 ◽  
Vol 17 (06) ◽  
pp. 1940012
Author(s):  
Yuan Liu ◽  
Yongchao Ma ◽  
Evan Salsman ◽  
Frank A. Manthey ◽  
Elias M. Elias ◽  
...  
Keyword(s):  
Reference Genome ◽  
Association Studies ◽  
Large Fraction ◽  
Snp Markers ◽  
Alternative Methods ◽  
Probability Method ◽  
Genome Wide Association Studies ◽  
Enrichment Method ◽  
Allele Distribution ◽  
Random Method

Mapping short reads to a reference genome is an essential step in many next-generation sequencing (NGS) analyses. In plants with large genomes, a large fraction of the reads can align to multiple locations of the genome with equally good alignment scores. How to map these ambiguous reads to the genome is a challenging problem with big impacts on the downstream analysis. Traditionally, the default method is to assign an ambiguous read randomly to one of the many potential locations. In this study, we explore two alternative methods that are based on the hypothesis that the possibility of an ambiguous read being generated by a location is proportional to the total number of reads produced by that location: (1) the enrichment method that assigns an ambiguous read to the location that has produced the most reads among all the potential locations, (2) the probability method that assigns an ambiguous read to a location based on a probability proportional to the number of reads the location produces. We systematically compared the performance of the proposed methods with that of the default random method. Our results showed that the enrichment method produced better results than the default random method and the probability method in the discovery of single nucleotide polymorphisms (SNPs). Not only did it produce more SNP markers, but it also produced SNP markers with better quality, which was demonstrated using multiple mainstay genomic analyses, including genome-wide association studies (GWAS), minor allele distribution, population structure, and genomic prediction.

scholarly journals Prototype for developing SNP markers from GWAS and biparental QTL for rice panicle and grain traits

ael ◽  
2021 ◽  
Vol 6 (2) ◽  
Author(s):  
Georgia C. Eizenga ◽  
Aaron K. Jackson ◽  
Jeremy D. Edwards
Keyword(s):  
Snp Markers

Development and application of rose (Rosa chinensis Jacq.) SNP markers based on SLAF-seq technology

2021 ◽  
Author(s):  
Ao-Nan Xia ◽  
Ao-Ao Yang ◽  
Xian-Shui Meng ◽  
Gui-Zhi Dong ◽  
Xiao-Juan Tang ◽  
...  
Keyword(s):  
Snp Markers ◽  
Rosa Chinensis

scholarly journals High resolution mapping and candidate gene identification of downy mildew race 16 resistance in spinach

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gehendra Bhattarai ◽  
Wei Yang ◽  
Ainong Shi ◽  
Chunda Feng ◽  
Braham Dhillon ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Downy Mildew ◽  
Association Analysis ◽  
Spinacia Oleracea ◽  
Genotyping By Sequencing ◽  
Significant Snps ◽  
Snp Markers ◽  
Resistance Locus ◽  
Downy Mildew Resistance ◽  
Mildew Resistance

Abstract Background Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant host and comprises 19 reported races and many novel isolates. Sixteen new P. effusa races were identified during the past three decades, and the new pathogen races are continually overcoming the genetic resistances used in commercial cultivars. A spinach breeding population derived from the cross between cultivars Whale and Lazio was inoculated with P. effusa race 16 in an environment-controlled facility; disease response was recorded and genotyped using genotyping by sequencing (GBS). The main objective of this study was to identify resistance-associated single nucleotide polymorphism (SNP) markers from the cultivar Whale against the P. effusa race 16. Results Association analysis conducted using GBS markers identified six significant SNPs (S3_658,306, S3_692697, S3_1050601, S3_1227787, S3_1227802, S3_1231197). The downy mildew resistance locus from cultivar Whale was mapped to a 0.57 Mb region on chromosome 3, including four disease resistance candidate genes (Spo12736, Spo12784, Spo12908, and Spo12821) within 2.69–11.28 Kb of the peak SNP. Conclusions Genomewide association analysis approach was used to map the P. effusa race 16 resistance loci and identify associated SNP markers and the candidate genes. The results from this study could be valuable in understanding the genetic basis of downy mildew resistance, and the SNP marker will be useful in spinach breeding to select resistant lines.

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