ArticlePlant physiology2010
An integrative approach to genomic introgression mapping.
Article in Plant physiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- GmGLU1 and GmRR4 contribute to iron deficiency tolerance in soybean.Frontiers in plant science · 2024Article
- Predicting the genomic resolution of bulk segregant analysis.G3 (Bethesda, Md.) · 2022Article
- Comparing Early Transcriptomic Responses of 18 Soybean (International journal of molecular sciences · 2021Article
- Identification and mapping of new genes for resistance to downy mildew in lettuce.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
- Examining Short-Term Responses to a Long-Term Problem: RNA-Seq Analyses of Iron Deficiency Chlorosis Tolerant Soybean.International journal of molecular sciences · 2020Article
- Dynamic gene expression changes in response to micronutrient, macronutrient, and multiple stress exposures in soybean.Functional & integrative genomics · 2020Article
- Characterization of genetic heterogeneity within accessions in the USDA soybean germplasm collection.The plant genome · 2020Article
- Deconstructing the genetic architecture of iron deficiency chlorosis in soybean using genome-wide approaches.BMC plant biology · 2020Article
- Legume genomics and transcriptomics: From classic breeding to modern technologies.Saudi journal of biological sciences · 2020Review
- Comprehensive mapping of abiotic stress inputs into the soybean circadian clock.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Gene Expression Profiling of Iron Deficiency Chlorosis Sensitive and Tolerant Soybean Indicates Key Roles for Phenylpropanoids under Alkalinity Stress.Frontiers in plant science · 2018Article
- Searching for an Accurate Marker-Based Prediction of an Individual Quantitative Trait in Molecular Plant Breeding.Frontiers in plant science · 2017Review
- Fast neutron-induced structural rearrangements at a soybean NAP1 locus result in gnarled trichomes.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Article
- An RNA-Seq-based reference transcriptome for Citrus.Plant biotechnology journal · 2016Article
- Long Non-coding RNAs in Urologic Malignancies: Functional Roles and Clinical Translation.Journal of Cancer · 2016Review
- Identification of candidate genes involved in early iron deficiency chlorosis signaling in soybean (Glycine max) roots and leaves.BMC genomics · 2014Article
- Legume genomics: understanding biology through DNA and RNA sequencing.Annals of botany · 2014Review
- Molecular and cellular characterization of a zebrafish optic pathway tumor line implicates glia-derived progenitors in tumorigenesis.PloS one · 2014Article
- Genome-wide association studies identifies seven major regions responsible for iron deficiency chlorosis in soybean (Glycine max).PloS one · 2014Article
- Genomic heterogeneity and structural variation in soybean near isogenic lines.Frontiers in plant science · 2013Article
Corrections and comments
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Authors and funding
13 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Near-isogenic lines (NILs) are valuable genetic resources for many crop species, including soybean (Glycine max). The development of new molecular platforms promises to accelerate the mapping of genetic introgressions in these materials. Here, we compare some existing and emerging methodologies for genetic introgression mapping: single-feature polymorphism analysis, Illumina GoldenGate single nucleotide polymorphism (SNP) genotyping, and de novo SNP discovery via RNA-Seq analysis of next-generation sequence data. We used these methods to map the introgressed regions in an iron-inefficient soybean NIL and found that the three mapping approaches are complementary when utilized in combination. The comparative RNA-Seq approach offers several additional advantages, including the greatest mapping resolution, marker depth, and de novo marker utility for downstream fine-mapping analysis. We applied the comparative RNA-Seq method to map genetic introgressions in an additional pair of NILs exhibiting differential seed protein content. Furthermore, we attempted to optimize the comparative RNA-Seq approach by assessing the impact of sequence depth, SNP identification methodology, and post hoc analyses on SNP discovery rates. We conclude that the comparative RNA-Seq approach can be optimized with sufficient sampling and by utilizing a post hoc correction accounting for gene density variation that controls for false discoveries.
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