scholarly journals High-Resolution Mapping of the Novel Early Leaf Senescence Gene Els2 in Common Wheat

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 698
Author(s):  
Na Wang ◽  
Yanzhou Xie ◽  
Yingzhuang Li ◽  
Shengnan Wu ◽  
Shuxian Li ◽  
...  
Keyword(s):  
High Resolution ◽  
Leaf Senescence ◽  
Chinese Spring ◽  
Snp Array ◽  
Triticum Aestivum L ◽  
Snp Markers ◽  
F2 Population ◽  
High Resolution Map ◽  
Kasp Markers ◽  
Early Leaf Senescence

Early leaf senescence negatively impacts the grain yield in wheat (Triticum aestivum L.). Induced mutants provide an important resource for mapping and cloning of genes for early leaf senescence. In our previous study, Els2, a single incomplete dominance gene, that caused early leaf senescence phenotype in the wheat mutant LF2099, had been mapped on the long arm of chromosome 2B. The objective of this study was to develop molecular markers tightly linked to the Els2 gene and construct a high-resolution map surrounding the Els2 gene. Three tightly linked single-nucleotide polymorphism (SNP) markers were obtained from the Illumina Wheat 90K iSelect SNP genotyping array and converted to Kompetitive allele-specific polymerase chain reaction (KASP) markers. To saturate the Els2 region, the Axiom® Wheat 660K SNP array was used to screen bulked extreme phenotype DNA pools, and 9 KASP markers were developed. For fine mapping of the Els2 gene, these KASP markers and previously identified polymorphic markers were analyzed in a large F2 population of the LF2099 × Chinese Spring cross. The Els2 gene was located in a 0.24-cM genetic region flanked by the KASP markers AX-111643885 and AX-111128667, which corresponded to a physical interval of 1.61 Mb in the Chinese Spring chromosome 2BL containing 27 predicted genes with high confidence. The study laid a foundation for a map-based clone of the Els2 gene controlling the mutation phenotype and revealing the molecular regulatory mechanism of wheat leaf senescence.

scholarly journals High-Resolution Linkage Map and QTL Analyses for Machine Harvest Traits in Autotetraploid Blueberry

2020 ◽  
Author(s):  
Francesco Cappai ◽  
Rodrigo R. Amadeu ◽  
Juliana Benevenuto ◽  
Ryan Cullen ◽  
Alexandria Garcia ◽  
...  
Keyword(s):  
High Resolution ◽  
Molecular Breeding ◽  
Vaccinium Corymbosum ◽  
Average Density ◽  
Snp Markers ◽  
Total Size ◽  
Detachment Force ◽  
High Resolution Map ◽  
Trait Locus ◽  
Retention Intervals

ABSTRACTBlueberry (Vaccinium corymbosum and hybrids) is an autotetraploid crop whose commercial relevance has been growing steadily during the last twenty years. However, the ever-increasing cost of labor for hand-picking blueberry is one main constraint in competitive marketing of the fruit. Machine harvestability is, therefore, a key trait for the blueberry industry. Understanding the genetic architecture of traits through quantitative trait locus (QTL) mapping is the first step towards implementation of molecular breeding for faster genetic gains. Despite recent advances in software development for autotetraploid genetic mapping, a high-resolution map is still not available for blueberry. In this study, we crafted a map for autotetraploid low-chill highbush blueberry containing 11,292 SNP markers and a total size of 1,953.97 cM (average density of 5.78 markers/cM). This map was subsequently used to perform QTL analyses for traits relevant to machine harvesting: firmness, firmness retention, and fruit detachment force. Significant QTL peaks were identified for all the traits. The QTL intervals were further explored for putative candidate genes. Genes related to cell wall remodeling were highlighted in the firmness and firmness retention intervals. For fruit detachment force, transcription factors involved in fruit abscission were detected. Altogether, our findings provide the basis for future fine-mapping and molecular breeding efforts for machine harvesting in blueberry.

ITERATIVE TWO-PASS ALGORITHM FOR MISSING DATA IMPUTATION IN SNP ARRAYS

2009 ◽  
Vol 07 (05) ◽  
pp. 833-852 ◽  
Author(s):  
CHRISTINE SINOQUET
Keyword(s):  
Missing Data ◽  
High Resolution ◽  
Snp Array ◽  
Disease Association ◽  
Mouse Strains ◽  
Data Imputation ◽  
Inference Method ◽  
Missing Data Imputation ◽  
Sliding Windows ◽  
High Resolution Map

Though nowadays high-throughput genotyping techniques' quality improves, missing data still remains fairly common. Studies have shown that even a low percentage of missing SNPs is detrimental to the reliability of down-stream analyses such as SNP-disease association tests. This paper investigates the potentiality for improving the accuracy of an SNP inference method based on the algorithm formerly designed by Roberts and co-workers (NPUTE, 2007). This initial algorithm performs a single scan of an SNP array, inferring missing SNPs in the context of sliding windows. We have first designed a variant, KNNWinOpti, which fully exploits backward and forward dependencies between the overlapping windows and thus restores the genuine dependency of inference upon direction scanning. Our major contribution, algorithm SNPShuttle, therefore iterates bi-directional scanning to predict SNP values with more confidence. We have run simulations on realistic benchmarks built after the high resolution map of mouse strains published by the Perlegen Project. For each of the 20 mouse chromosomes and for missing data percentage varying in range 5%–30%, SNPShuttle has always been shown to increase yet high KNNWinOpti's accuracies.

scholarly journals Identification of QTLs for resistance to leaf and stem rusts in bread wheat (Triticum aestivum L.) using a mapping population of ‘Pamyati Azieva × Paragon’

2019 ◽  
Vol 23 (7) ◽  
pp. 887-895 ◽  
Author(s):  
Y. Genievskaya ◽  
Y. Fedorenko ◽  
A. Sarbayev ◽  
A. Amalova ◽  
S. Abugalieva ◽  
...  
Keyword(s):  
Triticum Aestivum ◽  
Bread Wheat ◽  
Mapping Population ◽  
Recombinant Inbred Lines ◽  
Snp Array ◽  
Initial Step ◽  
Triticum Aestivum L ◽  
Field Trials ◽  
Snp Markers ◽  
The North

Leaf rust (LR) and stem rust (SR) are harmful fungal diseases of bread wheat (Triticum aestivum L.). The purpose of this study was to identify QTLs for resistance to LR and SR that are effective in two wheat-growing regions of Kazakhstan. To accomplish this task, a population of recombinant inbred lines (RILs) of ‘Pamyati Azieva × Paragon’ was grown in the northern and southeastern parts of Kazakhstan, phenotyped for LR/SR severities, and analyzed for key yield components. The study revealed a negative correlation between disease severity and plant productivity in both areas. The mapping population was genotyped using a 20,000 Illumina SNP array. A total of 4595 polymorphic SNP markers were further selected for linkage analysis after filtering based on missing data percentage and segregation distortion. Windows QTL Cartographer was applied to identify QTLs associated with LR and SR resistances in the RIL mapping population studied. Two QTLs for LR resistance and eight for SR resistance were found in the north, and the genetic positions of eight of them have matched the positions of the known Lr and Sr genes, while two QTLs for SR were novel. In the southeast, eight QTLs for LR and one for SR were identified in total. The study is an initial step of the genetic mapping of LR and SR resistance loci of bread wheat in Kazakhstan. Field trials in two areas of the country and the genotyping of the selected mapping population have allowed identification of key QTLs that will be effective in regional breeding projects for better bread wheat productivity.

Tomato chromosome 6: a high resolution map of the long arm and construction of a composite integrated marker-order map

1996 ◽  
Vol 92 (8) ◽  
pp. 1065-1072 ◽  
Author(s):  
M. F. van Wordragen ◽  
R. L. Weide ◽  
E. Coppoolse ◽  
P. Zabel ◽  
M. Koornneef
Keyword(s):  
High Resolution ◽  
Marker Order ◽  
Chromosome 6 ◽  
Tomato Chromosome ◽  
High Resolution Map ◽  
Resolution Map

scholarly journals A high-resolution map of bacteriophage ϕX174 transcription

Virology ◽  
2020 ◽  
Vol 547 ◽  
pp. 47-56 ◽  
Author(s):  
Dominic Y. Logel ◽  
Paul R. Jaschke
Keyword(s):  
High Resolution ◽  
High Resolution Map ◽  
Resolution Map

scholarly journals A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

2016 ◽  
Vol 33 (5) ◽  
pp. 1378-1378 ◽  
Author(s):  
Elad Firnberg ◽  
Jason W. Labonte ◽  
Jeffrey J. Gray ◽  
Marc Ostermeier
Keyword(s):  
High Resolution ◽  
Fitness Landscape ◽  
High Resolution Map ◽  
Resolution Map

A high-resolution map of the chromosomal region surrounding the nude gene

Genomics ◽  
1995 ◽  
Vol 26 (2) ◽  
pp. 308-317 ◽  
Author(s):  
C.C. Blackburn ◽  
J. Griffith ◽  
G. Morahan
Keyword(s):  
High Resolution ◽  
Chromosomal Region ◽  
High Resolution Map ◽  
Resolution Map

scholarly journals SNP array analysis in hematologic malignancies: avoiding false discoveries

Blood ◽  
2010 ◽  
Vol 115 (21) ◽  
pp. 4157-4161 ◽  
Author(s):  
Stefan Heinrichs ◽  
Cheng Li ◽  
A. Thomas Look
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Resolution ◽  
Snp Array ◽  
Hematologic Malignancies ◽  
Cancer Genome ◽  
Patient Specific ◽  
Nucleotide Polymorphism ◽  
Array Analysis ◽  
Single Nucleotide ◽  
Therapeutic Decisions

Comprehensive analysis of the cancer genome has become a standard approach to identifying new disease loci, and ultimately will guide therapeutic decisions. A key technology in this effort, single nucleotide polymorphism arrays, has been applied in hematologic malignancies to detect deletions, amplifications, and loss of heterozygosity (LOH) at high resolution. An inherent challenge of such studies lies in correctly distinguishing somatically acquired, cancer-specific lesions from patient-specific inherited copy number variations or segments of homozygosity. Failure to include appropriate normal DNA reference samples for each patient in retrospective or prospective studies makes it difficult to identify small somatic deletions not evident by standard cytogenetic analysis. In addition, the lack of proper controls can also lead to vastly overestimated frequencies of LOH without accompanying loss of DNA copies, so-called copy-neutral LOH. Here we use examples from patients with myeloid malignancies to demonstrate the superiority of matched tumor and normal DNA samples (paired studies) over multiple unpaired samples with respect to reducing false discovery rates in high-resolution single nucleotide polymorphism array analysis. Comparisons between matched tumor and normal samples will continue to be critical as the field moves from high resolution array analysis to deep sequencing to detect abnormalities in the cancer genome.

Sign in / Sign up

Export Citation Format

Share Document