Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection
Identifieur interne : 000630 ( Ncbi/Merge ); précédent : 000629; suivant : 000631Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection
Auteurs : Jorge Duitama [Colombie] ; Alexander Silva [Colombie] ; Yamid Sanabria [États-Unis] ; Daniel Felipe Cruz [Colombie] ; Constanza Quintero [Colombie] ; Carolina Ballen [Colombie] ; Mathias Lorieux [Colombie, France] ; Brian Scheffler [États-Unis] ; Andrew Farmer [États-Unis] ; Edgar Torres [Colombie] ; James Oard [États-Unis] ; Joe Tohme [Colombie]Source :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of
Url:
DOI: 10.1371/journal.pone.0124617
PubMed: 25923345
PubMed Central: 4414565
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<front><div type="abstract" xml:lang="en"><p>Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of <italic>Oryza sativa</italic>
. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within <italic>O. sativa</italic>
allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene <italic>GBSSI</italic>
, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.</p>
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</author>
<author><name sortKey="Kosugi, S" uniqKey="Kosugi S">S Kosugi</name>
</author>
<author><name sortKey="Yoshida, K" uniqKey="Yoshida K">K Yoshida</name>
</author>
<author><name sortKey="Natsume, S" uniqKey="Natsume S">S Natsume</name>
</author>
<author><name sortKey="Takagi, H" uniqKey="Takagi H">H Takagi</name>
</author>
<author><name sortKey="Kanzaki, H" uniqKey="Kanzaki H">H Kanzaki</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="He, Z" uniqKey="He Z">Z He</name>
</author>
<author><name sortKey="Zhai, W" uniqKey="Zhai W">W Zhai</name>
</author>
<author><name sortKey="Wen, H" uniqKey="Wen H">H Wen</name>
</author>
<author><name sortKey="Tang, T" uniqKey="Tang T">T Tang</name>
</author>
<author><name sortKey="Wang, Y" uniqKey="Wang Y">Y Wang</name>
</author>
<author><name sortKey="Lu, X" uniqKey="Lu X">X Lu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huang, X" uniqKey="Huang X">X Huang</name>
</author>
<author><name sortKey="Wei, X" uniqKey="Wei X">X Wei</name>
</author>
<author><name sortKey="Sang, T" uniqKey="Sang T">T Sang</name>
</author>
<author><name sortKey="Zhao, Q" uniqKey="Zhao Q">Q Zhao</name>
</author>
<author><name sortKey="Feng, Q" uniqKey="Feng Q">Q Feng</name>
</author>
<author><name sortKey="Zhao, Y" uniqKey="Zhao Y">Y Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huang, X" uniqKey="Huang X">X Huang</name>
</author>
<author><name sortKey="Kurata, N" uniqKey="Kurata N">N Kurata</name>
</author>
<author><name sortKey="Wei, X" uniqKey="Wei X">X Wei</name>
</author>
<author><name sortKey="Wang, Zx" uniqKey="Wang Z">ZX Wang</name>
</author>
<author><name sortKey="Wang, A" uniqKey="Wang A">A Wang</name>
</author>
<author><name sortKey="Zhao, Q" uniqKey="Zhao Q">Q Zhao</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Arai Kichise, Y" uniqKey="Arai Kichise Y">Y Arai-Kichise</name>
</author>
<author><name sortKey="Shiwa, Y" uniqKey="Shiwa Y">Y Shiwa</name>
</author>
<author><name sortKey="Ebana, K" uniqKey="Ebana K">K Ebana</name>
</author>
<author><name sortKey="Shibata Hatta, M" uniqKey="Shibata Hatta M">M Shibata-Hatta</name>
</author>
<author><name sortKey="Yoshikawa, H" uniqKey="Yoshikawa H">H Yoshikawa</name>
</author>
<author><name sortKey="Yano, M" uniqKey="Yano M">M Yano</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lyu, J" uniqKey="Lyu J">J Lyu</name>
</author>
<author><name sortKey="Zhang, S" uniqKey="Zhang S">S Zhang</name>
</author>
<author><name sortKey="Dong, Y" uniqKey="Dong Y">Y Dong</name>
</author>
<author><name sortKey="He, W" uniqKey="He W">W He</name>
</author>
<author><name sortKey="Zhang, J" uniqKey="Zhang J">J Zhang</name>
</author>
<author><name sortKey="Deng, X" uniqKey="Deng X">X Deng</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xu, X" uniqKey="Xu X">X Xu</name>
</author>
<author><name sortKey="Liu, X" uniqKey="Liu X">X Liu</name>
</author>
<author><name sortKey="Ge, S" uniqKey="Ge S">S Ge</name>
</author>
<author><name sortKey="Jensen, Jd" uniqKey="Jensen J">JD Jensen</name>
</author>
<author><name sortKey="Hu, F" uniqKey="Hu F">F Hu</name>
</author>
<author><name sortKey="Li, X" uniqKey="Li X">X Li</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yang, Cc" uniqKey="Yang C">Cc Yang</name>
</author>
<author><name sortKey="Kawahara, Y" uniqKey="Kawahara Y">Y Kawahara</name>
</author>
<author><name sortKey="Mizuno, H" uniqKey="Mizuno H">H Mizuno</name>
</author>
<author><name sortKey="Wu, J" uniqKey="Wu J">J Wu</name>
</author>
<author><name sortKey="Matsumoto, T" uniqKey="Matsumoto T">T Matsumoto</name>
</author>
<author><name sortKey="Itoh, T" uniqKey="Itoh T">T Itoh</name>
</author>
</analytic>
</biblStruct>
<biblStruct></biblStruct>
<biblStruct><analytic><author><name sortKey="Famoso, An" uniqKey="Famoso A">AN Famoso</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
<author><name sortKey="Clark, Rt" uniqKey="Clark R">RT Clark</name>
</author>
<author><name sortKey="Tung, Cw" uniqKey="Tung C">CW Tung</name>
</author>
<author><name sortKey="Wright, Mh" uniqKey="Wright M">MH Wright</name>
</author>
<author><name sortKey="Bustamante, C" uniqKey="Bustamante C">C Bustamante</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Mcnally, Kl" uniqKey="Mcnally K">KL McNally</name>
</author>
<author><name sortKey="Childs, Kl" uniqKey="Childs K">KL Childs</name>
</author>
<author><name sortKey="Bohnert, R" uniqKey="Bohnert R">R Bohnert</name>
</author>
<author><name sortKey="Davidson, Rm" uniqKey="Davidson R">RM Davidson</name>
</author>
<author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
<author><name sortKey="Ulat, Vj" uniqKey="Ulat V">VJ Ulat</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Norton, Gj" uniqKey="Norton G">GJ Norton</name>
</author>
<author><name sortKey="Douglas, A" uniqKey="Douglas A">A Douglas</name>
</author>
<author><name sortKey="Lahner, B" uniqKey="Lahner B">B Lahner</name>
</author>
<author><name sortKey="Yakubova, E" uniqKey="Yakubova E">E Yakubova</name>
</author>
<author><name sortKey="Guerinot, Ml" uniqKey="Guerinot M">ML Guerinot</name>
</author>
<author><name sortKey="Pinson, Srm" uniqKey="Pinson S">SRM Pinson</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
<author><name sortKey="Wright, M" uniqKey="Wright M">M Wright</name>
</author>
<author><name sortKey="Kimball, J" uniqKey="Kimball J">J Kimball</name>
</author>
<author><name sortKey="Eizenga, G" uniqKey="Eizenga G">G Eizenga</name>
</author>
<author><name sortKey="Mcclung, A" uniqKey="Mcclung A">A McClung</name>
</author>
<author><name sortKey="Kovach, M" uniqKey="Kovach M">M Kovach</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Zhao, K" uniqKey="Zhao K">K Zhao</name>
</author>
<author><name sortKey="Tung, Cw" uniqKey="Tung C">CW Tung</name>
</author>
<author><name sortKey="Eizenga, Gc" uniqKey="Eizenga G">GC Eizenga</name>
</author>
<author><name sortKey="Wright, Mh" uniqKey="Wright M">MH Wright</name>
</author>
<author><name sortKey="Ali, Ml" uniqKey="Ali M">ML Ali</name>
</author>
<author><name sortKey="Price, Ah" uniqKey="Price A">AH Price</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huang, P" uniqKey="Huang P">P Huang</name>
</author>
<author><name sortKey="Molina, J" uniqKey="Molina J">J Molina</name>
</author>
<author><name sortKey="Flowers, Jm" uniqKey="Flowers J">JM Flowers</name>
</author>
<author><name sortKey="Rubinstein, S" uniqKey="Rubinstein S">S Rubinstein</name>
</author>
<author><name sortKey="Jackson, Sa" uniqKey="Jackson S">SA Jackson</name>
</author>
<author><name sortKey="Purugganan, Md" uniqKey="Purugganan M">MD Purugganan</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Xie, X" uniqKey="Xie X">X Xie</name>
</author>
<author><name sortKey="Molina, J" uniqKey="Molina J">J Molina</name>
</author>
<author><name sortKey="Hernandez, R" uniqKey="Hernandez R">R Hernandez</name>
</author>
<author><name sortKey="Reynolds, A" uniqKey="Reynolds A">A Reynolds</name>
</author>
<author><name sortKey="Boyko, Ar" uniqKey="Boyko A">AR Boyko</name>
</author>
<author><name sortKey="Bustamante, Cd" uniqKey="Bustamante C">CD Bustamante</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Caicedo, Al" uniqKey="Caicedo A">AL Caicedo</name>
</author>
<author><name sortKey="Williamson, Sh" uniqKey="Williamson S">SH Williamson</name>
</author>
<author><name sortKey="Hernandez, Rd" uniqKey="Hernandez R">RD Hernandez</name>
</author>
<author><name sortKey="Boyko, A" uniqKey="Boyko A">A Boyko</name>
</author>
<author><name sortKey="Fledel Alon, A" uniqKey="Fledel Alon A">A Fledel-Alon</name>
</author>
<author><name sortKey="York, Tl" uniqKey="York T">TL York</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Molina, J" uniqKey="Molina J">J Molina</name>
</author>
<author><name sortKey="Sikora, M" uniqKey="Sikora M">M Sikora</name>
</author>
<author><name sortKey="Garud, N" uniqKey="Garud N">N Garud</name>
</author>
<author><name sortKey="Flowers, Jm" uniqKey="Flowers J">JM Flowers</name>
</author>
<author><name sortKey="Rubinstein, S" uniqKey="Rubinstein S">S Rubinstein</name>
</author>
<author><name sortKey="Reynolds, A" uniqKey="Reynolds A">A Reynolds</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yamamoto, E" uniqKey="Yamamoto E">E Yamamoto</name>
</author>
<author><name sortKey="Yonemaru, Ji" uniqKey="Yonemaru J">Ji Yonemaru</name>
</author>
<author><name sortKey="Yamamoto, T" uniqKey="Yamamoto T">T Yamamoto</name>
</author>
<author><name sortKey="Yano, M" uniqKey="Yano M">M Yano</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Varshney, Rk" uniqKey="Varshney R">RK Varshney</name>
</author>
<author><name sortKey="Terauchi, R" uniqKey="Terauchi R">R Terauchi</name>
</author>
<author><name sortKey="Mccouch, Sr" uniqKey="Mccouch S">SR McCouch</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Shure, M" uniqKey="Shure M">M Shure</name>
</author>
<author><name sortKey="Wessler, S" uniqKey="Wessler S">S Wessler</name>
</author>
<author><name sortKey="Fedoroff, N" uniqKey="Fedoroff N">N Fedoroff</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Silva, J" uniqKey="Silva J">J Silva</name>
</author>
<author><name sortKey="Scheffler, B" uniqKey="Scheffler B">B Scheffler</name>
</author>
<author><name sortKey="Sanabria, Y" uniqKey="Sanabria Y">Y Sanabria</name>
</author>
<author><name sortKey="De Guzman, C" uniqKey="De Guzman C">C De Guzman</name>
</author>
<author><name sortKey="Galam, D" uniqKey="Galam D">D Galam</name>
</author>
<author><name sortKey="Farmer, A" uniqKey="Farmer A">A Farmer</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Goff, Sa" uniqKey="Goff S">SA Goff</name>
</author>
<author><name sortKey="Vaughn, M" uniqKey="Vaughn M">M Vaughn</name>
</author>
<author><name sortKey="Mckay, S" uniqKey="Mckay S">S McKay</name>
</author>
<author><name sortKey="Lyons, E" uniqKey="Lyons E">E Lyons</name>
</author>
<author><name sortKey="Stapleton, Ae" uniqKey="Stapleton A">AE Stapleton</name>
</author>
<author><name sortKey="Gessler, D" uniqKey="Gessler D">D Gessler</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Lappalainen, I" uniqKey="Lappalainen I">I Lappalainen</name>
</author>
<author><name sortKey="Lopez, J" uniqKey="Lopez J">J Lopez</name>
</author>
<author><name sortKey="Skipper, L" uniqKey="Skipper L">L Skipper</name>
</author>
<author><name sortKey="Hefferon, T" uniqKey="Hefferon T">T Hefferon</name>
</author>
<author><name sortKey="Spalding, Jd" uniqKey="Spalding J">JD Spalding</name>
</author>
<author><name sortKey="Garner, J" uniqKey="Garner J">J Garner</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Monaco, Mk" uniqKey="Monaco M">MK Monaco</name>
</author>
<author><name sortKey="Stein, J" uniqKey="Stein J">J Stein</name>
</author>
<author><name sortKey="Naithani, S" uniqKey="Naithani S">S Naithani</name>
</author>
<author><name sortKey="Wei, S" uniqKey="Wei S">S Wei</name>
</author>
<author><name sortKey="Dharmawardhana, P" uniqKey="Dharmawardhana P">P Dharmawardhana</name>
</author>
<author><name sortKey="Kumari, S" uniqKey="Kumari S">S Kumari</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sakai, H" uniqKey="Sakai H">H Sakai</name>
</author>
<author><name sortKey="Lee, Ss" uniqKey="Lee S">SS Lee</name>
</author>
<author><name sortKey="Tanaka, T" uniqKey="Tanaka T">T Tanaka</name>
</author>
<author><name sortKey="Numa, H" uniqKey="Numa H">H Numa</name>
</author>
<author><name sortKey="Kim, J" uniqKey="Kim J">J Kim</name>
</author>
<author><name sortKey="Kawahara, Y" uniqKey="Kawahara Y">Y Kawahara</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Kawahara, Y" uniqKey="Kawahara Y">Y Kawahara</name>
</author>
<author><name sortKey="De La Bastide, M" uniqKey="De La Bastide M">M de la Bastide</name>
</author>
<author><name sortKey="Hamilton, Jp" uniqKey="Hamilton J">JP Hamilton</name>
</author>
<author><name sortKey="Kanamori, H" uniqKey="Kanamori H">H Kanamori</name>
</author>
<author><name sortKey="Mccombie, Wr" uniqKey="Mccombie W">WR McCombie</name>
</author>
<author><name sortKey="Ouyang, S" uniqKey="Ouyang S">S Ouyang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Duitama, J" uniqKey="Duitama J">J Duitama</name>
</author>
<author><name sortKey="Quintero, Jc" uniqKey="Quintero J">JC Quintero</name>
</author>
<author><name sortKey="Cruz, Df" uniqKey="Cruz D">DF Cruz</name>
</author>
<author><name sortKey="Quintero, C" uniqKey="Quintero C">C Quintero</name>
</author>
<author><name sortKey="Hubmann, G" uniqKey="Hubmann G">G Hubmann</name>
</author>
<author><name sortKey="Foulquie Moreno, Mr" uniqKey="Foulquie Moreno M">MR Foulquie-Moreno</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Langmead, B" uniqKey="Langmead B">B Langmead</name>
</author>
<author><name sortKey="Salzberg, Sl" uniqKey="Salzberg S">SL Salzberg</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Milne, I" uniqKey="Milne I">I Milne</name>
</author>
<author><name sortKey="Shaw, P" uniqKey="Shaw P">P Shaw</name>
</author>
<author><name sortKey="Stephen, G" uniqKey="Stephen G">G Stephen</name>
</author>
<author><name sortKey="Bayer, M" uniqKey="Bayer M">M Bayer</name>
</author>
<author><name sortKey="Cardie, L" uniqKey="Cardie L">L Cardie</name>
</author>
<author><name sortKey="Thomas, Wtb" uniqKey="Thomas W">WTB Thomas</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Alkan, C" uniqKey="Alkan C">C Alkan</name>
</author>
<author><name sortKey="Kidd, Jm" uniqKey="Kidd J">JM Kidd</name>
</author>
<author><name sortKey="Marques Bonet, T" uniqKey="Marques Bonet T">T Marques-Bonet</name>
</author>
<author><name sortKey="Aksay, G" uniqKey="Aksay G">G Aksay</name>
</author>
<author><name sortKey="Antonacci, F" uniqKey="Antonacci F">F Antonacci</name>
</author>
<author><name sortKey="Hormozdiari, F" uniqKey="Hormozdiari F">F Hormozdiari</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Huson, Dh" uniqKey="Huson D">DH Huson</name>
</author>
<author><name sortKey="Bryant, D" uniqKey="Bryant D">D Bryant</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Falush, D" uniqKey="Falush D">D Falush</name>
</author>
<author><name sortKey="Stephens, M" uniqKey="Stephens M">M Stephens</name>
</author>
<author><name sortKey="Pritchard, Jk" uniqKey="Pritchard J">JK Pritchard</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Krzywinski, M" uniqKey="Krzywinski M">M Krzywinski</name>
</author>
<author><name sortKey="Schein, J" uniqKey="Schein J">J Schein</name>
</author>
<author><name sortKey="Birol, I" uniqKey="Birol I">I Birol</name>
</author>
<author><name sortKey="Connors, J" uniqKey="Connors J">J Connors</name>
</author>
<author><name sortKey="Gascoyne, R" uniqKey="Gascoyne R">R Gascoyne</name>
</author>
<author><name sortKey="Horsman, D" uniqKey="Horsman D">D Horsman</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Purcell, S" uniqKey="Purcell S">S Purcell</name>
</author>
<author><name sortKey="Neale, B" uniqKey="Neale B">B Neale</name>
</author>
<author><name sortKey="Todd Brown, K" uniqKey="Todd Brown K">K Todd-Brown</name>
</author>
<author><name sortKey="Thomas, L" uniqKey="Thomas L">L Thomas</name>
</author>
<author><name sortKey="Ferreira, Mar" uniqKey="Ferreira M">MAR Ferreira</name>
</author>
<author><name sortKey="Bender, D" uniqKey="Bender D">D Bender</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Christiaens, Jf" uniqKey="Christiaens J">JF Christiaens</name>
</author>
<author><name sortKey="Van Mulders, Se" uniqKey="Van Mulders S">SE Van Mulders</name>
</author>
<author><name sortKey="Duitama, J" uniqKey="Duitama J">J Duitama</name>
</author>
<author><name sortKey="Brown, Ca" uniqKey="Brown C">CA Brown</name>
</author>
<author><name sortKey="Ghequire, Mg" uniqKey="Ghequire M">MG Ghequire</name>
</author>
<author><name sortKey="De Meester, L" uniqKey="De Meester L">L De Meester</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Delwiche, Sr" uniqKey="Delwiche S">SR Delwiche</name>
</author>
<author><name sortKey="Bean, Mm" uniqKey="Bean M">MM Bean</name>
</author>
<author><name sortKey="Miller, Re" uniqKey="Miller R">RE Miller</name>
</author>
<author><name sortKey="Webb, Bd" uniqKey="Webb B">BD Webb</name>
</author>
<author><name sortKey="Williams, Pc" uniqKey="Williams P">PC Williams</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Bonferroni, Ce" uniqKey="Bonferroni C">CE Bonferroni</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Jacquemin, J" uniqKey="Jacquemin J">J Jacquemin</name>
</author>
<author><name sortKey="Chaparro, C" uniqKey="Chaparro C">C Chaparro</name>
</author>
<author><name sortKey="Laudie, M" uniqKey="Laudie M">M Laudié</name>
</author>
<author><name sortKey="Berger, A" uniqKey="Berger A">A Berger</name>
</author>
<author><name sortKey="Gavory, F" uniqKey="Gavory F">F Gavory</name>
</author>
<author><name sortKey="Goicoechea, Jl" uniqKey="Goicoechea J">JL Goicoechea</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yu, P" uniqKey="Yu P">P Yu</name>
</author>
<author><name sortKey="Wang, Ch" uniqKey="Wang C">CH Wang</name>
</author>
<author><name sortKey="Xu, Q" uniqKey="Xu Q">Q Xu</name>
</author>
<author><name sortKey="Feng, Y" uniqKey="Feng Y">Y Feng</name>
</author>
<author><name sortKey="Yuan, Xp" uniqKey="Yuan X">XP Yuan</name>
</author>
<author><name sortKey="Yu, Hy" uniqKey="Yu H">HY Yu</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Yamamoto, E" uniqKey="Yamamoto E">E Yamamoto</name>
</author>
<author><name sortKey="Takashi, T" uniqKey="Takashi T">T Takashi</name>
</author>
<author><name sortKey="Morinaka, Y" uniqKey="Morinaka Y">Y Morinaka</name>
</author>
<author><name sortKey="Lin, S" uniqKey="Lin S">S Lin</name>
</author>
<author><name sortKey="Wu, J" uniqKey="Wu J">J Wu</name>
</author>
<author><name sortKey="Matsumoto, T" uniqKey="Matsumoto T">T Matsumoto</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Sazuka, T" uniqKey="Sazuka T">T Sazuka</name>
</author>
<author><name sortKey="Kamiya, N" uniqKey="Kamiya N">N Kamiya</name>
</author>
<author><name sortKey="Nishimura, T" uniqKey="Nishimura T">T Nishimura</name>
</author>
<author><name sortKey="Ohmae, K" uniqKey="Ohmae K">K Ohmae</name>
</author>
<author><name sortKey="Sato, Y" uniqKey="Sato Y">Y Sato</name>
</author>
<author><name sortKey="Imamura, K" uniqKey="Imamura K">K Imamura</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Dobo, M" uniqKey="Dobo M">M Dobo</name>
</author>
<author><name sortKey="Ayres, N" uniqKey="Ayres N">N Ayres</name>
</author>
<author><name sortKey="Walker, G" uniqKey="Walker G">G Walker</name>
</author>
<author><name sortKey="Park, Wd" uniqKey="Park W">WD Park</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Ayres, Nm" uniqKey="Ayres N">NM Ayres</name>
</author>
<author><name sortKey="Mcclung, Am" uniqKey="Mcclung A">AM McClung</name>
</author>
<author><name sortKey="Larkin, Pd" uniqKey="Larkin P">PD Larkin</name>
</author>
<author><name sortKey="Bligh, Hfj" uniqKey="Bligh H">HFJ Bligh</name>
</author>
<author><name sortKey="Jones, Ca" uniqKey="Jones C">CA Jones</name>
</author>
<author><name sortKey="Park, Wd" uniqKey="Park W">WD Park</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Larkin, Pd" uniqKey="Larkin P">PD Larkin</name>
</author>
<author><name sortKey="Park, Wd" uniqKey="Park W">WD Park</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Duan, J" uniqKey="Duan J">J Duan</name>
</author>
<author><name sortKey="Zhang, Jg" uniqKey="Zhang J">JG Zhang</name>
</author>
<author><name sortKey="Deng, Hw" uniqKey="Deng H">HW Deng</name>
</author>
<author><name sortKey="Wang, Yp" uniqKey="Wang Y">YP Wang</name>
</author>
</analytic>
</biblStruct>
<biblStruct><analytic><author><name sortKey="Fukuoka, S" uniqKey="Fukuoka S">S Fukuoka</name>
</author>
<author><name sortKey="Saka, N" uniqKey="Saka N">N Saka</name>
</author>
<author><name sortKey="Koga, H" uniqKey="Koga H">H Koga</name>
</author>
<author><name sortKey="Ono, K" uniqKey="Ono K">K Ono</name>
</author>
<author><name sortKey="Shimizu, T" uniqKey="Shimizu T">T Shimizu</name>
</author>
<author><name sortKey="Ebana, K" uniqKey="Ebana K">K Ebana</name>
</author>
</analytic>
</biblStruct>
</listBibl>
</div1>
</back>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id>
<journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id>
<journal-id journal-id-type="publisher-id">plos</journal-id>
<journal-id journal-id-type="pmc">plosone</journal-id>
<journal-title-group><journal-title>PLoS ONE</journal-title>
</journal-title-group>
<issn pub-type="epub">1932-6203</issn>
<publisher><publisher-name>Public Library of Science</publisher-name>
<publisher-loc>San Francisco, CA USA</publisher-loc>
</publisher>
</journal-meta>
<article-meta><article-id pub-id-type="pmid">25923345</article-id>
<article-id pub-id-type="pmc">4414565</article-id>
<article-id pub-id-type="publisher-id">PONE-D-14-47425</article-id>
<article-id pub-id-type="doi">10.1371/journal.pone.0124617</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
</subj-group>
</article-categories>
<title-group><article-title>Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection</article-title>
<alt-title alt-title-type="running-head">WGS of Rice Cultivars as a Resource for Marker Assisted Selection</alt-title>
</title-group>
<contrib-group><contrib contrib-type="author"><name><surname>Duitama</surname>
<given-names>Jorge</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="corresp" rid="cor001">*</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Silva</surname>
<given-names>Alexander</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Sanabria</surname>
<given-names>Yamid</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Cruz</surname>
<given-names>Daniel Felipe</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Quintero</surname>
<given-names>Constanza</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Ballen</surname>
<given-names>Carolina</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="currentaff001"><sup>¤</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Lorieux</surname>
<given-names>Mathias</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="aff" rid="aff005"><sup>5</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Scheffler</surname>
<given-names>Brian</given-names>
</name>
<xref ref-type="aff" rid="aff003"><sup>3</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Farmer</surname>
<given-names>Andrew</given-names>
</name>
<xref ref-type="aff" rid="aff004"><sup>4</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Torres</surname>
<given-names>Edgar</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Oard</surname>
<given-names>James</given-names>
</name>
<xref ref-type="aff" rid="aff002"><sup>2</sup>
</xref>
<xref ref-type="author-notes" rid="econtrib001"><sup>‡</sup>
</xref>
</contrib>
<contrib contrib-type="author"><name><surname>Tohme</surname>
<given-names>Joe</given-names>
</name>
<xref ref-type="aff" rid="aff001"><sup>1</sup>
</xref>
<xref ref-type="author-notes" rid="econtrib001"><sup>‡</sup>
</xref>
</contrib>
</contrib-group>
<aff id="aff001"><label>1</label>
<addr-line>Agrobiodiversity research area, International Center for Tropical Agriculture, Cali, Colombia</addr-line>
</aff>
<aff id="aff002"><label>2</label>
<addr-line>Rice Research Station, Louisiana State University Agricultural Center, Rayne, Louisiana, United States of America</addr-line>
</aff>
<aff id="aff003"><label>3</label>
<addr-line>Genomics and Bioinformatics Research Unit, Agricultural Research Service, United States Department of Agriculture, Jamie Whitten Delta States Research Center, Stoneville, Mississippi, United States of America</addr-line>
</aff>
<aff id="aff004"><label>4</label>
<addr-line>National Center for Genome Resources, Santa Fe, New Mexico, United States of America</addr-line>
</aff>
<aff id="aff005"><label>5</label>
<addr-line>Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement, Montpellier, France</addr-line>
</aff>
<contrib-group><contrib contrib-type="editor"><name><surname>Jaiswal</surname>
<given-names>Pankaj</given-names>
</name>
<role>Academic Editor</role>
<xref ref-type="aff" rid="edit1"></xref>
</contrib>
</contrib-group>
<aff id="edit1"><addr-line>Oregon State University, UNITED STATES</addr-line>
</aff>
<author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>
The authors have declared that no competing interests exist.</p>
</fn>
<fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: JO BS JT ET ML. Performed the experiments: CQ JO BS AF YS AS. Analyzed the data: JD AS YS DFC CB AF. Contributed reagents/materials/analysis tools: JD AF. Wrote the paper: JD AS JO.</p>
</fn>
<fn fn-type="current-aff" id="currentaff001"><label>¤</label>
<p>Current address: Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America</p>
</fn>
<fn fn-type="other" id="econtrib001"><p>‡ These authors contributed equally to this work and should be considered joint last authors.</p>
</fn>
<corresp id="cor001">* E-mail: <email>j.duitama@cgiar.org</email>
</corresp>
</author-notes>
<pub-date pub-type="collection"><year>2015</year>
</pub-date>
<pub-date pub-type="epub"><day>29</day>
<month>4</month>
<year>2015</year>
</pub-date>
<volume>10</volume>
<issue>4</issue>
<elocation-id>e0124617</elocation-id>
<history><date date-type="received"><day>21</day>
<month>10</month>
<year>2014</year>
</date>
<date date-type="accepted"><day>2</day>
<month>3</month>
<year>2015</year>
</date>
</history>
<permissions><license xlink:href="https://creativecommons.org/publicdomain/zero/1.0/"><license-p>This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the <ext-link ext-link-type="uri" xlink:href="https://creativecommons.org/publicdomain/zero/1.0/">Creative Commons CC0</ext-link>
public domain dedication</license-p>
</license>
</permissions>
<self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0124617.pdf"></self-uri>
<abstract><p>Current advances in sequencing technologies and bioinformatics revealed the genomic background of rice, a staple food for the poor people, and provided the basis to develop large genomic variation databases for thousands of cultivars. Proper analysis of this massive resource is expected to give novel insights into the structure, function, and evolution of the rice genome, and to aid the development of rice varieties through marker assisted selection or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of <italic>Oryza sativa</italic>
. We identified repetitive elements and recurrent copy number variation covering about 200 Mbp of the rice genome. Genotyping of over 18 million polymorphic locations within <italic>O. sativa</italic>
allowed us to reconstruct the individual haplotype patterns shaping the genomic background of elite varieties used by farmers throughout the Americas. Based on a reconstruction of the alleles for the gene <italic>GBSSI</italic>
, we could identify novel genetic markers for selection of varieties with high amylose content. We expect that both the analysis methods and the genomic information described here would be of great use for the rice research community and for other groups carrying on similar sequencing efforts in other crops.</p>
</abstract>
<funding-group><funding-statement>This work was supported by the Agricultural Research Service of the United States Department of Agriculture (USDA/ARS); the RiceCAP project (USDA/CSREES <ext-link ext-link-type="uri" xlink:href="http://www.uark.edu/ua/ricecap/">http://www.uark.edu/ua/ricecap/</ext-link>
) (2004-35317-14867 to J.O. and B.S.); The Mississippi Rice Promotion Board (<ext-link ext-link-type="uri" xlink:href="http://rice.msstate.edu/members.html">http://rice.msstate.edu/members.html</ext-link>
); The Rice Foundation (<ext-link ext-link-type="uri" xlink:href="http://www.usarice.com/index.php">http://www.usarice.com/index.php</ext-link>
); the Louisiana Rice Research Board (<ext-link ext-link-type="uri" xlink:href="http://www.lsuagcenter.com/en/crops_livestock/crops/rice/Rice+Research+Board+Reports/From-the-Louisiana-Rice-Research-Board.htm">http://www.lsuagcenter.com/en/crops_livestock/crops/rice/Rice+Research+Board+Reports/From-the-Louisiana-Rice-Research-Board.htm</ext-link>
); the International Center for Tropical Agriculture (<ext-link ext-link-type="uri" xlink:href="http://ciat.cgiar.org/">http://ciat.cgiar.org/</ext-link>
); the Global Rice Science Partnership (GRiSP) project (<ext-link ext-link-type="uri" xlink:href="http://www.grisp.net/main/summary">http://www.grisp.net/main/summary</ext-link>
); and the National Science Foundation (NSF) (0965420 to J.T.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
<counts><fig-count count="4"></fig-count>
<table-count count="1"></table-count>
<page-count count="20"></page-count>
</counts>
<custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name>
<meta-value>All sequencing data generated for this work are available from the NCBI short read archive database (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/sra">http://www.ncbi.nlm.nih.gov/sra</ext-link>
) with accession number (SRP023273). SNPs, small indels, and structural variants predicted in this study are available at dryad (<ext-link ext-link-type="uri" xlink:href="http://datadryad.org/">http://datadryad.org/</ext-link>
) with digital object identifier (doi:<ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5061/dryad.8hg32">10.5061/dryad.8hg32</ext-link>
).</meta-value>
</custom-meta>
</custom-meta-group>
</article-meta>
<notes><title>Data Availability</title>
<p>All sequencing data generated for this work are available from the NCBI short read archive database (<ext-link ext-link-type="uri" xlink:href="http://www.ncbi.nlm.nih.gov/sra">http://www.ncbi.nlm.nih.gov/sra</ext-link>
) with accession number (SRP023273). SNPs, small indels, and structural variants predicted in this study are available at dryad (<ext-link ext-link-type="uri" xlink:href="http://datadryad.org/">http://datadryad.org/</ext-link>
) with digital object identifier (doi:<ext-link ext-link-type="uri" xlink:href="http://dx.doi.org/10.5061/dryad.8hg32">10.5061/dryad.8hg32</ext-link>
).</p>
</notes>
</front>
</pmc>
<affiliations><list><country><li>Colombie</li>
<li>France</li>
<li>États-Unis</li>
</country>
<region><li>Louisiane</li>
<li>Nouveau-Mexique</li>
<li>État du Mississippi</li>
</region>
<settlement><li>Montpellier</li>
</settlement>
</list>
<tree><country name="Colombie"><noRegion><name sortKey="Duitama, Jorge" sort="Duitama, Jorge" uniqKey="Duitama J" first="Jorge" last="Duitama">Jorge Duitama</name>
</noRegion>
<name sortKey="Ballen, Carolina" sort="Ballen, Carolina" uniqKey="Ballen C" first="Carolina" last="Ballen">Carolina Ballen</name>
<name sortKey="Cruz, Daniel Felipe" sort="Cruz, Daniel Felipe" uniqKey="Cruz D" first="Daniel Felipe" last="Cruz">Daniel Felipe Cruz</name>
<name sortKey="Lorieux, Mathias" sort="Lorieux, Mathias" uniqKey="Lorieux M" first="Mathias" last="Lorieux">Mathias Lorieux</name>
<name sortKey="Quintero, Constanza" sort="Quintero, Constanza" uniqKey="Quintero C" first="Constanza" last="Quintero">Constanza Quintero</name>
<name sortKey="Silva, Alexander" sort="Silva, Alexander" uniqKey="Silva A" first="Alexander" last="Silva">Alexander Silva</name>
<name sortKey="Tohme, Joe" sort="Tohme, Joe" uniqKey="Tohme J" first="Joe" last="Tohme">Joe Tohme</name>
<name sortKey="Torres, Edgar" sort="Torres, Edgar" uniqKey="Torres E" first="Edgar" last="Torres">Edgar Torres</name>
</country>
<country name="États-Unis"><region name="Louisiane"><name sortKey="Sanabria, Yamid" sort="Sanabria, Yamid" uniqKey="Sanabria Y" first="Yamid" last="Sanabria">Yamid Sanabria</name>
</region>
<name sortKey="Farmer, Andrew" sort="Farmer, Andrew" uniqKey="Farmer A" first="Andrew" last="Farmer">Andrew Farmer</name>
<name sortKey="Oard, James" sort="Oard, James" uniqKey="Oard J" first="James" last="Oard">James Oard</name>
<name sortKey="Scheffler, Brian" sort="Scheffler, Brian" uniqKey="Scheffler B" first="Brian" last="Scheffler">Brian Scheffler</name>
</country>
<country name="France"><noRegion><name sortKey="Lorieux, Mathias" sort="Lorieux, Mathias" uniqKey="Lorieux M" first="Mathias" last="Lorieux">Mathias Lorieux</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>
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