Abstract: 【Objective】 The paper is order to identify quantitative trait loci (QTLs) for grain length (GL), width (GW) and thickness(GT), and further to narrow down the genomic region containing the major QTL for GT and analyze the possible candidate genes, which would help us to understand the genetic basis underlying the formation of slender grains and facilitate the efforts to the marker-assisted improvement of yield in a cytoplasmic male-sterile (CMS) maintainer line Chuan106B (C-106B). 【Method】 In this study, C-106B, which has a long slender grain type and good grain quality, was crossed with Chuan345B (C-345B), another CMS maintainer line with thicker and wider grain, to produce F₂ population for a preliminary QTL analysis. The chromosome interval of QTLs for grain shape was identified by composite interval mapping (CIM) using QTL Catographer v2.5. Then, a BC₃F₂ population derived from the same cross was developed and those plants with thinner grain were further picked out for the fine mapping of the major QTL (qGT8) for GT. Sequencing analysis and quantitative real-time PCR for the candidate gene were also conducted. In addition, a pair of nearisogenic lines (NIL) carrying the C-106B (NIL-gt8^C-106B) and C-345B (NIL-GT8^C-345B) alleles at qGT8 locus were bred and applied to survey for yield and quality traits, respectively.【Result】Significant differences were observed for GL, GW and GT between C-106B and C-345B. Using the phenotype and genotype data of the F₂ population, two QTLs for GL, three for GW and three for GT were identified. Among these, the major QTL for GL, accounting for 68.23% of phenotypic variance was mapped to the region between RM21892 and RM3589 on chromosome 7. The allele from C-106B was responsible for increasing GL by 0.47 mm at this locus. Two major QTLs (qGW8 and qGT8) controlled GW and GT, each explaining up to 26.48% and 34.89% of the variation, respectively, were found in the same interval of RM6070-RM447 on chromosome 8. The C-345B alleles contributed to the increase in GW and GT at the two loci. Furthermore, using 1732 plants with recessive phenotype (thinner grain) from the BC₃F₂ population and 11 markers including in the region RM6070-RM447, qGT8 was delimitated to a region bounded by insertion/deletion (Indel) markers SG930 and SG950, with a physical interval of 11.2 kb, which contains only one predicted gene (LOC_os08g41940, OsSPL16). Comparison of the nucleotide sequencesof the C-106B and C-345B alleles of qGT8 uncovered seven nucleotide changes within the promoter region upstream of the ATG start codon and five polymorphisms in the coding region. One of these, a 2-bp insertion（c.1006_1007 ins CT）in exon 3 at miR156 target site in qGT8 of C-106B, result in a frameshift mutation, which is probably associated with the formation of a more slender grain. Expression analysis indicated that qGT8 was preferentially accumulated in developing panicles. The expression patterns of qGT8 at eight panicle developmental stages were similar between C-106B and C-345B, which gradually increased at early stages (panicles length ranging 1-8 cm), peaked at the 8 cm young panicle and then declined in panicles of 12 cm to 23 cm in length. However, the levels of transcript for qGT8 were different at every developing stage between two parents. Comparison of the two NILs showed that NIL-GT8^C-345B increased significantly in GW, GT, 1000-grain weight, grain yield per plant and the percentage of grain with chalkiness, while no significant differences were observed in other measured traits such as GL, transparency, plant height, number of panicles per plant, panicle length, number of filled grains per panicle, seed setting ratio and heading date. 【Conclusion】 A major QTL affecting grain length in C-106B was mapped to a region flanked by markers RM21892 and RM3589 on chromosome 7, while two major QTLs (qGW8 and qGT8) governing grain width and thickness, respectively, were found in the same interval of RM6070-RM447 on chromosome 8. Furthermore, qGT8 was fine mapped to a DNA region only covering GW8 gene and this result suggested that qGT8 may play a key regulator role in grain shape and yield traits. However, a coupling link of the increasing for grain weight and high chalkiness in NILs implied its counteracting effects on grain yield and quality at same locus.

Key words: rice, grain shape, grain thickness, QTL, yield, quality