Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in Arabidopsis thaliana

Genetics
David J WolynJoanne Chory

Abstract

Genetic analysis of natural variation in ecotypes of Arabidopsis thaliana can facilitate the discovery of new genes or of allelic variants of previously identified genes controlling physiological processes in plants. We mapped quantitative trait loci (QTL) for light response in recombinant inbred lines (RILs) derived from the Columbia and Kashmir accessions via two methods: composite interval mapping and eXtreme array mapping (XAM). After measuring seedling hypocotyl lengths in blue, red, far-red, and white light, and in darkness, eight QTL were identified by composite interval mapping and five localized near photoreceptor loci. Two QTL in blue light were associated with CRY1 and CRY2, two in red light were near PHYB and PHYC, and one in far-red light localized near PHYA. The RED2 and RED5 QTL were verified in segregating lines. XAM was tested for the identification of QTL in red light with pools of RILs selected for extreme phenotypes. Thousands of single feature polymorphisms detected by differential DNA hybridized to high-density oligo-nucleotide arrays were used to estimate allele frequency differences between the pools. The RED2 QTL was identified clearly; differences exceeded a threshold of significance determined by simu...Continue Reading

References

Nov 1, 1994·Genetics·G A Churchill, R W Doerge
Apr 1, 1994·Genetics·Z B Zeng
Jan 1, 1993·Annual Review of Genetics·S D Tanksley
Feb 1, 1994·The Plant Journal : for Cell and Molecular Biology·L WesterR A Sharrock
Sep 1, 1993·The Plant Cell·K DeheshP H Quail
Jan 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·G A ChurchillS D Tanksley
Mar 1, 1997·The Plant Journal : for Cell and Molecular Biology·M Ahmad, A R Cashmore
Dec 1, 2001·Nature Genetics·S El-Din El-AssalM Koornneef
Dec 1, 2001·Nature Genetics·J N MaloofJ Chory
Feb 12, 2002·Nature Reviews. Molecular Cell Biology·Peter H Quail
Dec 1, 1991·The Plant Cell·D. E. SomersP. H. Quail
Jan 7, 2003·Plant & Cell Physiology·Yuriko Kobayashi, Hiroyuki Koyama
Jan 17, 2003·Plant Physiology·Olivier LoudetFrançoise Daniel-Vedele
Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
Mar 6, 2003·Genome Research·Justin O BorevitzJoanne Chory
Mar 26, 2003·Physiologia Plantarum·Eva Kevei, Ferenc Nagy
Apr 25, 2003·Trends in Plant Science·Haiyang Wang, Xing Wang Deng

❮ Previous
Next ❯

Citations

Mar 8, 2005·Trends in Plant Science·Ruairidh J H SawersThomas P Brutnell
Oct 20, 2010·Proceedings of the National Academy of Sciences of the United States of America·Sima FakheranLindsay A Turnbull
Sep 6, 2012·Proceedings of the National Academy of Sciences of the United States of America·Wen HuangTrudy F C Mackay
May 24, 2005·Plant Physiology·Samuel P HazenSteve A Kay
Jun 16, 2005·Plant Physiology·Kentaro K Shimizu, Michael D Purugganan
May 23, 2006·Plant Physiology·Grégory MouilleMarkus Pauly
May 16, 2007·Genome Génome / Conseil National De Recherches Canada·José M Jiménez-GómezJosé M Martínez-Zapater
Jun 5, 2007·Genome Génome / Conseil National De Recherches Canada·Yuling LiDangqun Cui
Oct 29, 2008·Genome Génome / Conseil National De Recherches Canada·Eiji HayashiDavid W Still
Aug 28, 2009·BMC Genetics·Wayne Wenzhong XuGary J Muehlbauer
Jun 29, 2007·BMC Genomics·Peter WenzlAndrzej Kilian
May 14, 2010·PLoS Genetics·Benjamin BrachiFabrice Roux
Sep 15, 2010·PLoS Genetics·José M Jiménez-GómezJulin N Maloof
Mar 21, 2007·PloS One·Rajesh KumarHenry T Nguyen
Feb 3, 2009·PloS One·Sureshkumar BalasubramanianDetlef Weigel
Jan 15, 2010·PloS One·Hunter B Fraser, Eric E Schadt
Feb 8, 2011·PloS One·Anthony BeckerIvan Baxter
May 16, 2012·PloS One·Sanzhen LiuPatrick S Schnable
May 17, 2006·Genetics·Rong JiangSimon Tavaré
Jan 30, 2010·International Journal of Molecular Sciences·Valérie LefebvreMylène Durand-Tardif
Jul 22, 2006·PLoS Biology·Ayellet V SegrèJun-Yi Leu
Oct 16, 2004·Proceedings of the National Academy of Sciences of the United States of America·Ji-Ming GongJulian I Schroeder
Jul 14, 2007·Proceedings of the National Academy of Sciences of the United States of America·Justin O BorevitzJoseph R Ecker
Aug 21, 2014·Nature Reviews. Genetics·Korbinian Schneeberger
Oct 16, 2004·Annual Review of Genomics and Human Genetics·Justin O Borevitz, Joseph R Ecker
Mar 29, 2011·Trends in Plant Science·Korbinian Schneeberger, Detlef Weigel
Apr 10, 2007·Trends in Plant Science·Tong Zhu, John Salmeron
Mar 12, 2005·The New Phytologist·Q C B Cronk
Jun 3, 2006·The Plant Journal : for Cell and Molecular Biology·Eunkyoo OhGiltsu Choi
Apr 10, 2008·The Plant Journal : for Cell and Molecular Biology·Jens StaalChristina Dixelius
Feb 20, 2007·Molecular Ecology·Amy Bouck, Todd Vision
Oct 19, 2007·PLoS Genetics·Adam M WentzellDaniel J Kliebenstein
Apr 18, 2008·PLoS Biology·Erin N Smith, Leonid Kruglyak

❮ Previous
Next ❯

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