The LKF locus, which regulates grain size in the rice cultivar ‘Fusayoshi’ showing large grain, has been mapped to the proximal part of the long arm of chromosome 3. An incomplete dominant allele, Lkf, caused large grain size of Fusayoshi. The structure and function of this locus, however, have not yet been determined. In a similar position to LKF on chromosome 3, two loci, Os03g0407400 (GS3) and LOC_Os03g44500, have been already reported as loci also regulating rice grain size. The objective of the present study was to determine the nucleotide sequences of both Os03g0407400 and LOC_Os03g44500 for different alleles at the LKF locus. Results showed that only one known single nucleotide polymorphism (SNP) in exon 10 of LOC_Os03g44500 was detected between a large-grain allele (Lkf) and a small-grain allele at the LKF locus, whereas no polymorphisms in Os03g0407400. This SNP, visualized using a dCAPS marker, clearly demonstrated nearly complete co-segregation with grain length in an F2 population segregating the Lkf at LKF. Other large-grain mutant lines with large-grain alleles at the LKF locus, which originated from another cultivar ‘Gimbozu’, also showed the same SNP in exon 10 of LOC_Os03g44500. It was concluded from these results that LKF is identical to LOC_Os03g44500, and the detected SNP in exon 10, at least, which is included in Kelch-like repeat motif, could be essential for expression of the large-grain phenotype.
dCAPS marker Grain size GS3Serine/threonine protein phosphatase Kelch-like repeat motif Rice Single nucleotide polymorphism
This is a preview of subscription content, log in to check access.
We sincerely thank to Y. Fujiwara, Y. Iguchi, K. Matsumoto and N. Ueda, for their technical assistance to this study.
Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15Google Scholar
Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, 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 112:1164–1171CrossRefPubMedGoogle Scholar
Hu Z, He H, Zhang S, Sun F, Xin X, Wang W, Qian X, Yang J, Luo X (2012) A Kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice. J Integr Plant Biol 54:979–990CrossRefPubMedGoogle Scholar
Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi A, Miyagawa H, Katoh E (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet 45:707–711CrossRefPubMedGoogle Scholar
Kato T (1990) Genetic analysis on the mutant alleles for long grains induced in a rice cultivar, Gimbozu. SABRAO J 22:123–129Google Scholar
Li Y, Fan Y, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269CrossRefPubMedGoogle Scholar
Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107:19579–19584CrossRefPubMedPubMedCentralGoogle Scholar
Neff MM, Yurk E, Kalishman M (2002) Web-based primer design for single nucleotide polymorphism analysis. Trends Genet 18:613–615CrossRefPubMedGoogle Scholar
Qi P, Lin YS, Song XJ, Shen JB, Huang W, Shan JX, Zhu MZ, Jiang L, Gao JP, Lin HX (2012) The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Res 22:1666–1680CrossRefPubMedPubMedCentralGoogle Scholar
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 169:1023–1028CrossRefGoogle Scholar
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 39:623–630CrossRefPubMedGoogle Scholar
Takamure I, Kinoshita T (1985) Genic identification of big-grain types between “Shiokari” mutant and “Fusayoshi” in rice. Jpn J Breed 35(Suppl 2):80–81 (In Japanese)Google Scholar
Takano-Kai N, Jiang H, Kubo T, Sweeney M, Masumoto 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 182:1323–1334CrossRefPubMedPubMedCentralGoogle Scholar
Takeda K, Saito K (1980) Major genes controlling grain shape in rice. Jpn J Breed 30:280–282 (In Japanese)CrossRefGoogle Scholar
Wang C, Chen S, Yu S (2011) Functional markers developed from multiple loci in GS3 for fine marker-assisted selection of grain length in rice. Theor Appl Genet 122:905–913CrossRefPubMedGoogle Scholar
Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954CrossRefPubMedGoogle Scholar
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 119:459–470CrossRefPubMedGoogle Scholar
Zhang X, Wang J, Huang J, Lan H, Wang C, Yin C, Wu Y, Tang H, Qian Q, Li J, Zhang H (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci USA 109:21534–21539CrossRefPubMedPubMedCentralGoogle Scholar