Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

Molecular Plant - Tập 8 Số 6 - Trang 946-957 - 2015
Quan-Xiu Wang1, Weibo Xie1, Hongkun Xing1, Yan Ju1, Xiang‐Zhou Meng1, Xinglei Li1, Xiangkui Fu1, Jiuyue Xu1, Xingming Lian1, Sibin Yu1, Yongzhong Xing1, Gongwei Wang1
1National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China

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Agrama, 2009, Genetic assessment of a mini-core subset developed from the USDA rice genebank, Crop Sci., 49, 1336, 10.2135/cropsci2008.06.0551

Alexander, 2009, Fast model-based estimation of ancestry in unrelated individuals, Genome Res., 19, 1655, 10.1101/gr.094052.109

Arnon, 1949, Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris, Plant Physiol., 24, 1, 10.1104/pp.24.1.1

Basten, 1997

Chen, 2012, Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1, Plant Cell Rep., 31, 863, 10.1007/s00299-011-1207-7

Fujita, 2013, NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars, Proc. Natl. Acad. Sci. USA, 110, 20431, 10.1073/pnas.1310790110

Huang, 2010, Genome-wide association studies of 14 agronomic traits in rice landraces, Nat. Genet., 42, 961, 10.1038/ng.695

Jiang, 2004, The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross, Theor. Appl. Genet., 108, 688, 10.1007/s00122-003-1465-z

Jiang, 2007, Molecular cloning and function analysis of the stay green gene in rice, Plant J., 52, 197, 10.1111/j.1365-313X.2007.03221.x

Jiang, 2010, Comparison between QTLs for chlorophyll content and genes controlling chlorophyll biosynthesis and degradation in japonica rice, Acta Agron. Sin., 36, 376, 10.3724/SP.J.1006.2010.00376

Jiang, 2012, Identification and fine mapping of qCTH4, a quantitative trait loci controlling the chlorophyll content from tillering to heading in rice (Oryza sativa L.), J. Hered., 103, 720, 10.1093/jhered/ess041

Jiang, 2014, Analysis of quantitative trait loci affecting chlorophyll content of rice leaves in a double haploid population and two backcross populations, Gene, 536, 287, 10.1016/j.gene.2013.12.010

Jung, 2003, Characterization of a rice chlorophyll-deficient mutant using the T-DNA gene-trap system, Plant Cell Physiol., 44, 463, 10.1093/pcp/pcg064

Jung, 2008, Identification and functional analysis of light-responsive unique genes and gene family members in rice, PLoS Genet., 4, e1000164, 10.1371/journal.pgen.1000164

Kusaba, 2007, Rice NON-YELLOW COLORING1 is involved in light-harvesting complex II and grana degradation during leaf senescence, Plant Cell, 19, 1362, 10.1105/tpc.106.042911

Li, 2009, Fast and accurate short read alignment with Burrows-Wheeler transform, Bioinformatics, 25, 1754, 10.1093/bioinformatics/btp324

Li, 2009, The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352

Li, 2012, Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets, Hum. Genet., 131, 747, 10.1007/s00439-011-1118-2

Lippert, 2011, FaST linear mixed models for genome-wide association studies, Nat. Methods, 8, 833, 10.1038/nmeth.1681

Livak, 2001, Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C (T)) method, Methods, 25, 402, 10.1006/meth.2001.1262

Lu, 2012, Evolution and association analysis of Ghd7 in rice, PLoS One, 7, e34021, 10.1371/journal.pone.0034021

Masuda, 2008, Regulation and evolution of chlorophyll metabolism, Photochem. Photobiol. Sci., 7, 1131, 10.1039/b807210h

McNally, 2009, Genome wide SNP variation reveals relationships among landraces and modern varieties of rice, Proc. Natl. Acad. Sci. USA, 106, 12273, 10.1073/pnas.0900992106

Ort, 2011, Optimizing antennae size to maximize photosynthetic efficiency, Plant Physiol., 155, 79, 10.1104/pp.110.165886

Peng, 2008, Progress in ideotype breeding to increase rice yield potential, Field Crop Res., 108, 32, 10.1016/j.fcr.2008.04.001

Sato, 2009, Two short-chain dehydrogenase/reductases, NON-YELLOW COLORING 1 and NYC1-LIKE, are required for chlorophyll b and light-harvesting complex II degradation during senescence in rice, Plant J., 57, 120, 10.1111/j.1365-313X.2008.03670.x

Segura, 2012, An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations, Nat. Genet., 44, 825, 10.1038/ng.2314

Takai, 2010, A quantitative trait locus for chlorophyll content and its association with leaf photosynthesis in rice, Rice, 3, 172, 10.1007/s12284-010-9047-6

Takai, 2013, A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate, Sci. Rep., 3, 2149, 10.1038/srep02149

Tan, 2012, Ghd7, a pleiotropic gene controlling flag leaf area in rice, Yi Chuan, 34, 901, 10.3724/SP.J.1005.2012.00901

Weng, 2014, Grain number, plant height, and heading date7 is a central regulator of growth, development, and stress response, Plant Physiol., 164, 735, 10.1104/pp.113.231308

Wu, 2007, A chlorophyll-deficient rice mutant with impaired chlorophyllide esterification in chlorophyll biosynthesis, Plant Physiol., 145, 29, 10.1104/pp.107.100321

Xue, 2008, Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice, Nat. Genet., 40, 761, 10.1038/ng.143

Yamatani, 2013, NYC4, the rice ortholog of Arabidopsis THF1, is involved in the degradation of chlorophyll-protein complexes during leaf senescence, Plant J., 74, 652, 10.1111/tpj.12154

Yu, 2003, Molecular diversity and multilocus organization of the parental lines used in the International Rice Molecular Breeding Program, Theor. Appl. Genet., 108, 131, 10.1007/s00122-003-1400-3

Yue, 2006, QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice, Yi Chuan Xue Bao, 33, 824

Zhang, 2006, Rice Chlorina-1 and Chlorina-9 encode ChlD and ChlI subunits of Mg-chelatase, a key enzyme for chlorophyll synthesis and chloroplast development, Plant Mol. Biol., 62, 325, 10.1007/s11103-006-9024-z

Zhang, 2011, A core collection and mini core collection of Oryza sativa L. in China, Theor. Appl. Genet., 122, 49, 10.1007/s00122-010-1421-7

Zhang, 2014, LSCHL4 from japonica cultivar, which is allelic to NAL1, increases yield of indica super rice 93-11, Mol. Plant, 7, 1350, 10.1093/mp/ssu055

Zhao, 2007, An Arabidopsis example of association mapping in structured samples, PLoS Genet., 3, e4, 10.1371/journal.pgen.0030004

Zhao, 2011, Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa, Nat. Commun., 2, 467, 10.1038/ncomms1467

Zhu, 2010, Improving photosynthetic efficiency for greater yield, Annu. Rev. Plant Biol., 61, 235, 10.1146/annurev-arplant-042809-112206