GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein

Abstract

The GS3 locus located in the pericentromeric region of rice chromosome 3 has been frequently identified as a major QTL for both grain weight (a yield trait) and grain length (a quality trait) in the literature. Near isogenic lines of GS3 were developed by successive crossing and backcrossing Minghui 63 (large grain) with Chuan 7 (small grain), using Minghui 63 as the recurrent parent. Analysis of a random subpopulation of 201 individuals from the BC3F2 progeny confirmed that the GS3 locus explained 80-90% of the variation for grain weight and length in this population. In addition, this locus was resolved as a minor QTL for grain width and thickness. Using 1,384 individuals with recessive phenotype (large grain) from a total of 5,740 BC3F2 plants and 11 molecular markers based on sequence information, GS3 was mapped to a DNA fragment approximately 7.9 kb in length. A full-length cDNA corresponding to the target region was identified, which provided complete sequence information for the GS3 candidate. This gene consists of five exons and encodes 232 amino acids with a putative PEBP-like domain, a transmembrane region, a putative TNFR/NGFR family cysteine-rich domain and a VWFC module. Comparative sequencing analysis identified a nonsense mutation, shared among all the large-grain varieties tested in comparison with the small grain varieties, in the second exon of the putative GS3 gene. This mutation causes a 178-aa truncation in the C-terminus of the predicted protein, suggesting that GS3 may function as a negative regulator for grain size. Cloning of such a gene provided the opportunity for fully characterizing the regulatory mechanism and related processes during grain development.

An improved anther culture procedure for obtaining new commercial Mediterranean temperate <i>japonica</i> rice (<i>Oryza sativa</i>) genotypes

“…The 1,000-grain weight (determined by grain length, width and thickness) of the lines was in average 31.6 g, comparable among them since the humidity range was 13.6-14.2%. Of the assayed lines, all of them with the exception of F 2 -30.C1, as seen in Table 2, showed a 1,000-grain weight higher than NRVC980385 and other indica and japonica varieties (Fan et al 2006;Koutroubas and Ntanos 2003). The whole grains percentage was variable among the 9 lines assayed but ranged between 60-70%, similar to NRVC980385 and several other Spanish varieties values (Català et al 2009), thus these lines are suitable for large scale production.…”

A Quantitative Trait Locus for Chlorophyll Content and its Association with Leaf Photosynthesis in Rice

“…The genetics of sink size (e.g., grain size and grain number) has been well analyzed in rice plants, and several QTLs controlling grain number per panicle and grain size have been identified (Ashikari et al 2005;Fan et al 2006;Song et al 2007;Shomura et al 2008;Huang et al 2009). On the other hand, genetic analyses of factors affecting source capacity, such as photosynthetic rate, have been limited, probably because of the need for time- C1006 G2009 C479 C383 G1068 C145 R646 R1440 R2394 R2677 R1245 C847 R1789 G379 C596 C924 C213 8 R1943 G278 C277 C1121 C1107 G104 C347 R1394A G1073 S10622 G187 R2382 R202 S14074 G1149 R2662 R1963 9 C711 G36 R1164 R1751 G385 R2272 S1057 C609 C1263 C570 C506 G1445 10 C701 S2083 R2174 C148 R1629 C1166 R2447 R3285 C1286 R1877 R844 G2155 R716 C16 C809 C405 11 G24A R77 R3202 C794A S1057 C410 C477 G320B G320A C535 G44 C3 R728 G257 C1172 S723 C50 G1465 C82 C950 G181 12 G24B R1957 C1336 R2672A R367 R3375 R...…”

A map of rice genome variation reveals the origin of cultivated rice

“…2c). For example, at the causal SNP site for GS3 (a major QTL for grain shape 33,34 ), the null allele mainly existed in the wild rice populations in the Guangxi and Guangdong provinces of southern China. This allele rapidly extended to become the major …”