Development of mitochondrial SNP markers in different Populus species

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.

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Comparative genome-wide mapping versus extreme pool-genotyping and development of diagnostic SNP markers linked to QTL for adult plant resistance to stripe rust in common wheat

Theoretical and Applied Genetics ◽

10.1007/s00122-018-3113-7 ◽

2018 ◽

Vol 131 (8) ◽

pp. 1777-1792 ◽

Cited By ~ 12

Author(s):

Jianhui Wu ◽

Shuo Huang ◽

Qingdong Zeng ◽

Shengjie Liu ◽

Qilin Wang ◽

...

Keyword(s):

Common Wheat ◽

Stripe Rust ◽

Plant Resistance ◽

Adult Plant Resistance ◽

Snp Markers ◽

Adult Plant ◽

Comparative Genome ◽

Genome Wide ◽

Pool Genotyping ◽

Mapping Versus

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

ael ◽

10.1002/ael2.20047 ◽

2021 ◽

Vol 6 (2) ◽

Author(s):

Georgia C. Eizenga ◽

Aaron K. Jackson ◽

Jeremy D. Edwards

Keyword(s):

Snp Markers

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

Genetic Resources and Crop Evolution ◽

10.1007/s10722-021-01215-3 ◽

2021 ◽

Author(s):

Ao-Nan Xia ◽

Ao-Ao Yang ◽

Xian-Shui Meng ◽

Gui-Zhi Dong ◽

Xiao-Juan Tang ◽

...

Keyword(s):

Snp Markers ◽

Rosa Chinensis

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Dense Genetic Linkage Maps of Three Populus Species (Populus deltoides, P. nigra and P. trichocarpa) Based on AFLP and Microsatellite Markers

Genetics ◽

10.1093/genetics/158.2.787 ◽

2001 ◽

Vol 158 (2) ◽

pp. 787-809 ◽

Cited By ~ 1

Author(s):

Maria-Teresa Cervera ◽

Véronique Storme ◽

Bart Ivens ◽

Jaqueline Gusmão ◽

Ben H Liu ◽

...

Keyword(s):

Populus Deltoides ◽

Female Parent ◽

Aflp Markers ◽

Linkage Maps ◽

Important Species ◽

Mapping Strategy ◽

Sequence Tagged Sites ◽

Fundamental Research ◽

Populus Species ◽

The Individual

Abstract Populus deltoides, P. nigra, and P. trichocarpa are the most important species for poplar breeding programs worldwide. In addition, Populus has become a model for fundamental research on trees. Linkage maps were constructed for these three species by analyzing progeny of two controlled crosses sharing the same female parent, Populus deltoides cv. S9-2 × P. nigra cv. Ghoy and P. deltoides cv. S9-2 × P. trichocarpa cv. V24. The two-way pseudotestcross mapping strategy was used to construct the maps. Amplified fragment length polymorphism (AFLP) markers that segregated 1:1 were used to form the four parental maps. Microsatellites and sequence-tagged sites were used to align homoeologous groups between the maps and to merge linkage groups within the individual maps. Linkage analysis and alignment of the homoeologous groups resulted in 566 markers distributed over 19 groups for P. deltoides covering 86% of the genome, 339 markers distributed over 19 groups for P. trichocarpa covering 73%, and 369 markers distributed over 28 groups for P. nigra covering 61%. Several tests for randomness showed that the AFLP markers were randomly distributed over the genome.

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

BMC Genomics ◽

10.1186/s12864-021-07788-8 ◽

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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