An integrative approach to genomic introgression mapping.

Plant Physiology
Andrew J SeverinRobert M Stupar

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 th...Continue Reading

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Citations

Nov 23, 2010·Plant Physiology·Arnis DrukaRobbie Waugh
Dec 13, 2012·Genome Génome / Conseil National De Recherches Canada·Filipe de Carvalho VictoriaAntônio Costa de Oliveira
Feb 14, 2013·PloS One·Saakshi JalaliVinod Scaria
Apr 29, 2014·Annals of Botany·Jamie A O'RourkeCarroll P Vance
Aug 12, 2015·Plant Biotechnology Journal·Javier TerolManuel Talon
Jun 11, 2016·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Benjamin W CampbellRobert M Stupar
Apr 18, 2014·Biology of Reproduction·Frédéric ChalmelBernard Jégou
Nov 5, 2019·Proceedings of the National Academy of Sciences of the United States of America·Meina LiWei Wang
Oct 28, 2019·Functional & Integrative Genomics·Jamie A O'RourkeMichelle A Graham
May 23, 2020·International Journal of Molecular Sciences·Adrienne N Moran LauterMichelle A Graham
Jun 8, 2013·Plant, Cell & Environment·Sarah E AtwoodMichelle A Graham
Nov 1, 2020·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Lorena ParraRichard Michelmore

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