4.6 Article

A medium-density genotyping platform for cultivated strawberry using DArTag technology

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Plant Sciences

Genetic analysis of resistance to bean leaf crumple virus identifies a candidate LRR-RLK gene

Daniel Ariza-Suarez et al.

Summary: This study identifies the resistance locus BLC7.1 against Bean leaf crumple virus (BLCrV) in common bean and provides novel diagnostic markers for marker-assisted selection. The study highlights the potential of previous breeding efforts for virus resistance in accumulating positive alleles against newly emerging viruses.

PLANT JOURNAL (2023)

Article Plant Sciences

Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry

Nicolas P. Jimenez et al.

Summary: This study investigates the development of resistance to Phytophthora crown rot in strawberry cultivars. The research shows that there have been negligible genetic gains in breeding for resistance, despite the high heritability of the resistance trait. Through genome-wide association studies, a significant genetic locus associated with resistance was identified. Adding underutilized gene bank resources to the breeding population increased the genetic variance and improved the accuracy of genomic selection. Parent selection based on genomic-estimated breeding values and genetic variances holds promise for enhancing resistance in strawberries.

PLANT GENOME (2023)

Article Plant Sciences

Development of molecular inversion probes for soybean progeny genomic selection genotyping

Haichuan Wang et al.

Summary: The increasing rate of genetic gain for agronomic traits in farming requires the development of new molecular tools for genome-wide screening. The cost of current methods limits their use in screening breeding populations. Molecular inversion probes (MIPs) are a cost-effective and high-throughput genotyping method that can be used for soybean breeding programs. A set of 1K MIP SNPs for soybean was developed and tested on diverse germplasm, showing high genotyping accuracy and low cost. This makes MIPs a powerful tool for genomic selection in soybean breeding programs.

PLANT GENOME (2023)

Article Plant Sciences

Development of a new AgriSeq 4K mid-density SNP genotyping panel and its utility in pearl millet breeding

Janani Semalaiyappan et al.

Summary: We have developed a new mid-density 4K SNP panel and demonstrated its utility in genetic studies of pearl millet. The panel successfully differentiated the accessions into two major groups, B and R lines, through genetic diversity analysis. This newly developed SNP panel will be useful in genomics and molecular breeding experiments in pearl millet.

FRONTIERS IN PLANT SCIENCE (2023)

Article Plant Sciences

High-quality haplotype-resolved genome assembly of cultivated octoploid strawberry

Jianxin Mao et al.

Summary: In this study, a high-quality genome of the cultivated octoploid strawberry was obtained using single molecule real-time sequencing and high-throughput chromosome conformation capture technology. The genome was phased into two haplotypes, and a 10 Mb inversion and translocation was identified on chromosome 2-1.

HORTICULTURE RESEARCH (2023)

Article Genetics & Heredity

Genomic prediction of strawberry resistance to postharvest fruit decay caused by the fungal pathogen Botrytis cinerea

Stefan Petrasch et al.

Summary: Gray mold, caused by Botrytis cinerea, affects strawberries economically postharvest. Genetic studies found heritability for resistance to gray mold, while correlations showed that traits affecting fruit quality also impacted susceptibility. Genomic selection showed potential for reducing lesion diameter and increasing mycelium emergence, especially in long shelf life populations.

G3-GENES GENOMES GENETICS (2022)

Article Plant Sciences

Multienvironment QTL analysis delineates a major locus associated with homoeologous exchanges for water-use efficiency and seed yield in canola

Harsh Raman et al.

Summary: This study identified quantitative trait loci (QTL) associated with water-use efficiency (WUE) in canola through analysis of a doubled haploid population. Sequencing data and RNA sequencing were used to develop markers and analyze gene expression related to carbon isotope discrimination (Delta C-13), a trait linked to WUE. The study also identified QTLs influencing Delta C-13 and yield, and discovered a multiple-trait QTL on chromosome A09. Transcriptome analysis revealed differentially expressed genes related to Delta C-13 QTL.

PLANT CELL AND ENVIRONMENT (2022)

Article Agronomy

Novel Fusarium wilt resistance genes uncovered in natural and cultivated strawberry populations are found on three non-homoeologous chromosomes

Dominique D. A. Pincot et al.

Summary: This study reveals that resistance to Fusarium wilt races 1 and 2 in strawberry is widespread and determined by multiple genes located on non-homoeologous chromosomes. The underlying genes have not been cloned and characterized yet, but potential candidates have been identified. High-throughput genotyping assays were developed for marker-assisted selection. This study lays the foundation for further research on identifying the genes and developing resistant cultivars to prevent a Fusarium wilt pandemic.

THEORETICAL AND APPLIED GENETICS (2022)

Article Genetics & Heredity

Average semivariance directly yields accurate estimates of the genomic variance in complex trait analyses

Mitchell J. Feldmann et al.

Summary: Genomic prediction integrates all genetic data in a mixed model framework, with the primary method being genomic best linear unbiased prediction. Different methods for calculating the genomic relationship matrix can affect estimates of genomic variance and genomic heritability. Proposed new matrix K-ASV directly produces accurate estimates of sigma(2)(g) and h(g)(2) in the observed population.

G3-GENES GENOMES GENETICS (2022)

Article Plant Sciences

Development and validation of an optimized marker set for genomic selection in southern US rice breeding programs

Tommaso Cerioli et al.

Summary: The study aims to develop a marker set for genomic selection (GS) and demonstrate its effectiveness in rice breeding programs in southern U.S. Through several years of breeding data and experiments, the utility of the marker set has been proven, showing high predictive ability in different market classes and yield trials, similar to phenotypic selection.

PLANT GENOME (2022)

Article Biochemical Research Methods

A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar

Erik Garrison et al.

Summary: The author presents a range of free and open source software tools used in biomedical sequencing workflows for DNA/RNA variations. The importance of the variant call format (VCF) is highlighted, and the article discusses how to handle more complex variations.

PLOS COMPUTATIONAL BIOLOGY (2022)

Article Biochemical Research Methods

PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data

Roeland E. Voorrips et al.

Summary: This study presents a new method to reconstruct haplotypes from SNP dosages derived from genotyping arrays in polyploids. The method shows higher accuracy compared to existing software, especially in the presence of full-sib families. The results demonstrate the usefulness of this method in polyploid genetic analysis.

BMC BIOINFORMATICS (2022)

Article Genetics & Heredity

Independent Validation of Genomic Prediction in Strawberry Over Multiple Cycles

Luis F. Osorio et al.

Summary: The University of Florida strawberry breeding program has successfully implemented genomic prediction as a tool for selecting outstanding parents for crosses, reducing the breeding cycle duration. Results show that relatedness between training and testing populations is crucial for predictive abilities in breeding values.

FRONTIERS IN GENETICS (2021)

Article Biochemistry & Molecular Biology

Unraveling the Complex Hybrid Ancestry and Domestication History of Cultivated strawberry

Michael A. Hardigan et al.

Summary: The cultivated strawberry, originating from early 18th-century Europe, has undergone significant genomic changes over 300 years of breeding history, leading to global expansion in production. Research shows increased heterozygosity in interspecific hybrids, selective sweeps across the genome, and substantial allelic diversity in octoploid species. Despite genetic gains in modern cultivars, nucleotide diversity and heterozygosity are lower, suggesting potential trade-offs in agricultural selection.

MOLECULAR BIOLOGY AND EVOLUTION (2021)

Article Genetics & Heredity

Discovery of three loci increasing resistance to charcoal rot caused by Macrophomina phaseolina in octoploid strawberry

Jonathan R. Nelson et al.

Summary: The study identified two major QTLs enhancing resistance to charcoal rot, as well as a novel locus in hybrid varieties. These findings are of significance for DNA-informed breeding for resistance to charcoal rot in cultivated strawberries.

G3-GENES GENOMES GENETICS (2021)

Article Biology

Twelve years of SAMtools and BCFtools

Petr Danecek et al.

Summary: SAMtools and BCFtools are widely used tools for processing high-throughput sequencing data, with a history of 12 years of continuous development and improvement. These packages have been utilized in various software projects and genomic pipelines and are freely available on GitHub.

GIGASCIENCE (2021)

Article Plant Sciences

Genetic Analysis of Methyl Anthranilate, Mesifurane, Linalool, and Other Flavor Compounds in Cultivated Strawberry (Fragaria x ananassa)

Christopher R. Barbey et al.

Summary: This study integrates multiomic analyses to identify QTL and candidate genes for multiple aroma compounds in a complex strawberry breeding population, revealing novel fruit volatile QTL and shared QTLs for various aroma compounds. The fruit transcriptomes from a subset of individuals helped in identifying candidate genes, indicating potential new opportunities for breeding improved flavor in commercial strawberries.

FRONTIERS IN PLANT SCIENCE (2021)

Article Plant Sciences

Genomic Characterization of the Fruity Aroma Gene, FaFAD1, Reveals a Gene Dosage Effect on γ-Decalactone Production in Strawberry (Fragaria x ananassa)

Youngjae Oh et al.

Summary: This study explored the genomic structure of FaFAD1 and its impact on gamma-D production in cultivated octoploid strawberry. Genome-wide association studies confirmed FaFAD1 as a major regulator of gamma-D production. A major presence-absence variation of FaFAD1 was discovered among gamma-D producers and non-producers, suggesting the role of gene dosage effect in the production of fruity aroma in strawberry fruit.

FRONTIERS IN PLANT SCIENCE (2021)

Article Plant Sciences

Chromosome Level Assembly of Homozygous Inbred Line 'Wongyo 3115' Facilitates the Construction of a High-Density Linkage Map and Identification of QTLs Associated With Fruit Firmness in Octoploid Strawberry (Fragaria x ananassa)

Hye-Eun Lee et al.

Summary: In this study, a chromosome-level assembly of homozygous octoploid strawberry 'Wongyo 3115' was generated, and a high-density genetic map was constructed to identify QTLs associated with fruit firmness. Five QTLs related to firmness were identified on chromosomes 3-3, 5-1, 6-1, and 6-4 using firmness data from 'BS F-2' populations. Candidate genes associated with firmness in strawberries were predicted by utilizing transcriptome data and QTL information.

FRONTIERS IN PLANT SCIENCE (2021)

Review Plant Sciences

A roadmap for research in octoploid strawberry

Vance M. Whitaker et al.

HORTICULTURE RESEARCH (2020)

Article Genetics & Heredity

Origin and evolution of the octoploid strawberry genome

Patrick P. Edger et al.

NATURE GENETICS (2019)

Article Horticulture

The Strawberry DNA Testing Handbook

Youngjae Oh et al.

HORTSCIENCE (2019)

Article Genetics & Heredity

polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids

Lindsay V. Clark et al.

G3-GENES GENOMES GENETICS (2019)

Article Biotechnology & Applied Microbiology

Efficiency of different strategies to mitigate ascertainment bias when using SNP panels in diversity studies

Dorcus Kholofelo Malomane et al.

BMC GENOMICS (2018)

Article Genetics & Heredity

Genome-Wide Association Mapping Uncovers Fw1, a Dominant Gene Conferring Resistance to Fusarium Wilt in Strawberry

Dominique D. A. Pincot et al.

G3-GENES GENOMES GENETICS (2018)

Article Plant Sciences

An experimental validation of genomic selection in octoploid strawberry

Salvador A. Gezan et al.

HORTICULTURE RESEARCH (2017)

Article Multidisciplinary Sciences

Calibrating genomic and allelic coverage bias in single-cell sequencing

Cheng-Zhong Zhang et al.

NATURE COMMUNICATIONS (2015)

Article Biochemical Research Methods

MIPgen: optimized modeling and design of molecular inversion probes for targeted resequencing

Evan A. Boyle et al.

BIOINFORMATICS (2014)

Review Biochemistry & Molecular Biology

Critical review of NGS analyses for de novo genotyping multigene families

Jackie Lighten et al.

MOLECULAR ECOLOGY (2014)

Article Biochemical Research Methods

The variant call format and VCFtools

Petr Danecek et al.

BIOINFORMATICS (2011)

Article Genetics & Heredity

The genome of woodland strawberry (Fragaria vesca)

Vladimir Shulaev et al.

NATURE GENETICS (2011)

Article Biochemical Research Methods

BEDTools: a flexible suite of utilities for comparing genomic features

Aaron R. Quinlan et al.

BIOINFORMATICS (2010)

Article Biochemistry & Molecular Biology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Aaron McKenna et al.

GENOME RESEARCH (2010)

Article Biochemical Research Methods

BLAST plus : architecture and applications

Christiam Camacho et al.

BMC BIOINFORMATICS (2009)

Article Genetics & Heredity

Genomic Selection Using Low-Density Marker Panels

D. Habier et al.

GENETICS (2009)