To identify the genetic loci that control grain length, width, lengthwidth ratio, thickness, 100grain weight and the percentage of grains with chalkiness (GL, GW, LWR, GT, HGW, PGWC), we constructed an F2 population by crossing an elite indica maintainer line Gang 46B(G46B) with K1075, an introgression line of G46B derived from multibackcross with an US rice variety Lemont, with low percentage of chalkiness and narrow grain. All six investigated traits followed a continuous phenotypic distribution. Significantly positive or negative correlations were observed between all six traits, except the GL and GW. A genetic map was constructed with 30 simple sequence repeat (SSR) markers and a total of 14 QTLs for grain shape and chalkiness were detected by composite interval mapping (CIM). Among which, two were for GL (qGL2 and qGL5), two for GW (qGW5 and qGW8), five for LWR (qLWR2, qLWR5, qLWR6, qLWR8 and qLWR12), one for GT (qGT5), one for HGW (qHGW5), and three for PGWC (qPGWC5, qPGWC6 and qPGWC8). The G46B alleles contributed to increasing GW, GT, HGW and PGWC, while decreasing GL and LWR at all detected loci. The major QTLs controlling GW, GT, GW, PGWC and LWR were located in the same region RM17990RM18004RM18068 on chromosome 5, which was correspondent to the results identified in extreme phenotype plants using linkage and linkage disequilibrium.
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