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Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica.

Schatz MC, Maron LG, Stein JC, Hernandez Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie WR.

Genome Biol. 2014;15(11):506.


Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.).

Xu J, Zhao Q, Du P, Xu C, Wang B, Feng Q, Liu Q, Tang S, Gu M, Han B, Liang G.

BMC Genomics. 2010 Nov 24;11:656. doi: 10.1186/1471-2164-11-656.


Resequencing rice genomes: an emerging new era of rice genomics.

Huang X, Lu T, Han B.

Trends Genet. 2013 Apr;29(4):225-32. doi: 10.1016/j.tig.2012.12.001. Epub 2013 Jan 4. Review.


Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application.

Chin JH, Gamuyao R, Dalid C, Bustamam M, Prasetiyono J, Moeljopawiro S, Wissuwa M, Heuer S.

Plant Physiol. 2011 Jul;156(3):1202-16. doi: 10.1104/pp.111.175471. Epub 2011 May 20.


Genetic variation and association mapping for 12 agronomic traits in indica rice.

Lu Q, Zhang M, Niu X, Wang S, Xu Q, Feng Y, Wang C, Deng H, Yuan X, Yu H, Wang Y, Wei X.

BMC Genomics. 2015 Dec 16;16:1067. doi: 10.1186/s12864-015-2245-2.


Development and application of gene-based markers for the major rice QTL Phosphorus uptake 1.

Chin JH, Lu X, Haefele SM, Gamuyao R, Ismail A, Wissuwa M, Heuer S.

Theor Appl Genet. 2010 Apr;120(6):1073-86. doi: 10.1007/s00122-009-1235-7. Epub 2009 Dec 25. Erratum in: Theor Appl Genet. 2010 Apr;120(6):1087-8.


Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication.

Zhang F, Xu T, Mao L, Yan S, Chen X, Wu Z, Chen R, Luo X, Xie J, Gao S.

BMC Plant Biol. 2016 Apr 26;16:103. doi: 10.1186/s12870-016-0788-2.


Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.

Zhou P, Silverstein KA, Ramaraj T, Guhlin J, Denny R, Liu J, Farmer AD, Steele KP, Stupar RM, Miller JR, Tiffin P, Mudge J, Young ND.

BMC Genomics. 2017 Mar 27;18(1):261. doi: 10.1186/s12864-017-3654-1.


QTL analysis of novel genomic regions associated with yield and yield related traits in new plant type based recombinant inbred lines of rice (Oryza sativa L.).

Marathi B, Guleria S, Mohapatra T, Parsad R, Mariappan N, Kurungara VK, Atwal SS, Prabhu KV, Singh NK, Singh AK.

BMC Plant Biol. 2012 Aug 9;12:137. doi: 10.1186/1471-2229-12-137.


The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency.

Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S.

Nature. 2012 Aug 23;488(7412):535-9. doi: 10.1038/nature11346.


Identification of a Rice stripe necrosis virus resistance locus and yield component QTLs using Oryza sativa x O. glaberrima introgression lines.

Gutiérrez AG, Carabalí SJ, Giraldo OX, Martínez CP, Correa F, Prado G, Tohme J, Lorieux M.

BMC Plant Biol. 2010 Jan 8;10:6. doi: 10.1186/1471-2229-10-6.


Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63.

Zhang J, Chen LL, Xing F, Kudrna DA, Yao W, Copetti D, Mu T, Li W, Song JM, Xie W, Lee S, Talag J, Shao L, An Y, Zhang CL, Ouyang Y, Sun S, Jiao WB, Lv F, Du B, Luo M, Maldonado CE, Goicoechea JL, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou ZW, Hurtado BE, Danowitz A, Wing RA, Zhang Q.

Proc Natl Acad Sci U S A. 2016 Aug 30;113(35):E5163-71. doi: 10.1073/pnas.1611012113. Epub 2016 Aug 17.


A Rice Genetic Improvement Boom by Next Generation Sequencing.

Zhou X, Bai X, Xing Y.

Curr Issues Mol Biol. 2018;27:109-126. doi: 10.21775/cimb.027.109. Epub 2017 Sep 8. Review.


Indica rice genome assembly, annotation and mining of blast disease resistance genes.

Mahesh HB, Shirke MD, Singh S, Rajamani A, Hittalmani S, Wang GL, Gowda M.

BMC Genomics. 2016 Mar 16;17:242. doi: 10.1186/s12864-016-2523-7.


Updates and perspectives on the utilization of molecular makers of complex traits in rice.

Li G, Kwon SW, Park YJ.

Genet Mol Res. 2012 Dec 3;11(4):4157-68. doi: 10.4238/2012.September.10.4. Review.


Identification of genome-wide variations among three elite restorer lines for hybrid-rice.

Li S, Wang S, Deng Q, Zheng A, Zhu J, Liu H, Wang L, Gao F, Zou T, Huang B, Cao X, Xu L, Yu C, Ai P, Li P.

PLoS One. 2012;7(2):e30952. doi: 10.1371/journal.pone.0030952. Epub 2012 Feb 23.


Deep re-sequencing of a widely used maintainer line of hybrid rice for discovery of DNA polymorphisms and evaluation of genetic diversity.

Hu Y, Mao B, Peng Y, Sun Y, Pan Y, Xia Y, Sheng X, Li Y, Tang L, Yuan L, Zhao B.

Mol Genet Genomics. 2014 Jun;289(3):303-15. doi: 10.1007/s00438-013-0807-z. Epub 2014 Jan 12.


Genomewide SNP variation reveals relationships among landraces and modern varieties of rice.

McNally KL, Childs KL, Bohnert R, Davidson RM, Zhao K, Ulat VJ, Zeller G, Clark RM, Hoen DR, Bureau TE, Stokowski R, Ballinger DG, Frazer KA, Cox DR, Padhukasahasram B, Bustamante CD, Weigel D, Mackill DJ, Bruskiewich RM, Rätsch G, Buell CR, Leung H, Leach JE.

Proc Natl Acad Sci U S A. 2009 Jul 28;106(30):12273-8. doi: 10.1073/pnas.0900992106. Epub 2009 Jul 13.


Levels and patterns of nucleotide variation in domestication QTL regions on rice chromosome 3 suggest lineage-specific selection.

Xie X, Molina J, Hernandez R, Reynolds A, Boyko AR, Bustamante CD, Purugganan MD.

PLoS One. 2011;6(6):e20670. doi: 10.1371/journal.pone.0020670. Epub 2011 Jun 6.


Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum.

Hass-Jacobus BL, Futrell-Griggs M, Abernathy B, Westerman R, Goicoechea JL, Stein J, Klein P, Hurwitz B, Zhou B, Rakhshan F, Sanyal A, Gill N, Lin JY, Walling JG, Luo MZ, Ammiraju JS, Kudrna D, Kim HR, Ware D, Wing RA, San Miguel P, Jackson SA.

BMC Genomics. 2006 Aug 8;7:199.

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