Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice
Tóm tắt
The gene GS3 has major effect on grain size and plays an important role in rice breeding. The C to A mutation in the second exon of GS3 was reported to be functionally associated with enhanced grain length in rice. In the present study, besides the C-A mutation at locus SF28, three novel polymorphic loci, SR17, RGS1, and RGS2, were discovered in the second intron, the last intron and the final exon of GS3, respectively. A number of alleles at these four polymorphic loci were observed in a total of 287 accessions including Chinese rice varieties (Oryza sativa), African cultivated rice (O. glaberrima) and AA-genome wild relatives. The haplotype analysis revealed that the simple sequence repeats (AT)n at RGS1 and (TCC)n at RGS2 had differentiated in the wild rice whilst the C-A mutation occurred in the cultivated rice recently during domestication. It also indicated that A allele at SF28 was highly associated with long rice grain whilst various motifs of (AT)n at RGS1 and (TCC)n at RGS2 were mainly associated with medium to short grain in Chinese rice. The C-A mutation at SF28 explained 33.4% of the grain length variation in the whole rice population tested in this study, whereas (AT)n at RGS1 and (TCC)n at RGS2 explained 26.4 and 26.2% of the variation, respectively. These results would be helpful for better understanding domestication of GS3 and its manipulation for grain size in rice. The genic marker RGS1 based on the motifs (AT)n was further validated as a functional marker using two sets of backcross recombinant inbred lines. These results suggested that the functional markers developed from four different loci within GS3 could be used for fine marker-assisted selection of grain length in rice breeding.
Tài liệu tham khảo
Agrama HA, Eizenga GC, Yan WG (2007) Association mapping of yield and its components in rice cultivars. Mol Breed 19:341–356
Andersen JR, Lübberstedt T (2003) Functional markers in plants. Trends Plant Sci 8:554–559
Bao JS, Corke H, Sun M (2006) Microsatellite, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). Theor Appl Genet 113:1185–1196
Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635
Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Am J Hum Genet 19:233–257
Doebley JF, Gaut BS, Smith BD (2006) The molecular genetics of crop domestication. Cell 127:1309–1321
Fan CC, Xing YZ, Mao HL, Lu TT, Han B, Xu CG, Li XH, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171
Fan CC, Yu SB, Wang CR, Xing YZ (2009) A causal C-A mutation in the second exon of GS3 highly associated with rice grain length and validated as a functional marker. Theor Appl Genet 118:465–472
Gepts P (2004) Crop domestication as a long-term selection experiment. Plant Breed Rev 24:1–44
Ji YT, Qu CQ, Cao BY (2007) An optimal method of DNA silver staining in polyacrylamide gels. Electrophoresis 28:1173–1175
Juliano BO, Villareal CP (1993) Grain quality evaluation of world rice. International Rice Research Institute, Manila
Juliano AB, Naredo MEB, Lu BR, Jackson MT (2005) Genetic differentiation in Oryza meridionalis Ng based on molecular and crossability analyses. Genet Resour Crop Evol 52:435–445
Kovach MJ, Sweeney MT, McCouch SR (2007) New insights into the history of rice domestication. Trends Genet 23:578–587
Li Q, Wan JM (2005) SSRHunter: development of a local searching software for SSR sites. Yi Chuan 27:808–810 (in Chinese with an English abstract)
Liu K, Muse SV (2005) PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21:2128–2129
McKenzie KS, Rutger JN (1983) Genetic analysis of amylose content, alkali spreading score, and grain dimensions in rice. Crop Sci 23:306–313
Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucl Acids Res 8:4321–4325
Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Mol Biol 12:357–358
Paterson AH, Lin YR, Li ZK, Schertz KF, Doebley JF, Pinson SR, Liu SC, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic-loci. Science 269:1714–1718
Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959
Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457:843–848
Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028
Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630
Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, Padhukasahasram B, Bustamante C, Yoshimura A, Doi K, McCouch S (2009) Evolutionary history of GS3, a gene conferring grain length in rice. Genetics 182:1323–1334
Takeda S, Matsuoka M (2008) Genetic approaches to crop improvement: responding to environmental and population changes. Nat Rev 9:444–457
Tan YF, Zhang QF (2001) Correlation of simple sequence repeat (SSR) variants in the leader sequence of the waxy gene with amylose content of the grain in rice. Acta Bot Sin 43:146–150
Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, Zhang L, He W, Lu B, Lin H, Ma H, Zhang G, He Z (2008) Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet 40(11):1273–1275
Wen W, Mei H, Feng F, Yu S, Huang ZC, Wu JH, Chen L, Xu XY, Luo LJ (2009) Population structure and association mapping on chromosome 7 using a diverse panel of Chinese germplasm of rice (Oryza sativa L.). Theor Appl Genet 119:459–470
Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209
Xu Y, McCouch SR, Zhang Q (2005) How can we use genomics to improve cereals with rice as a reference genome? Plant Mol Biol 59:7–26
Young ND (1999) A cautiously optimistic vision for marker-assisted breeding. Mol Breed 5:505–510