Fine Mapping Of The QTL Controlling Heading Date, Plant Height And Spikelets Number Per Panicle And Map-based Cloning The Gene Controlling Gel Consistency And Gelatinization Temperature In Shanyou 63

Heading date, plant height and number of spikelets per panicle are 3 important agricultural traits in rice. In our previous studies, one putative QTL affecting heading date, plant height and number of spikelets per panicle were identified in the pericentromeric region of rice chromosome 7 using a recombinant inbred population. In order to determine that whether the 3 traits were controlled by a single locus with pleiotropic effects or by 3 tightly linked genes, we construct a near isogenic lines Hd1, with the background of Zhenshan 97 and 4 region from Minghui 63. Among them, only the region of chromosome 7 was relation with the 3 traits. In order to fine mapping the QTL, an F₂ population between Zhenshan 97 and the NIL containing 8400 individuals was developed. The phenotype of F₂ population was divided into two types: the type with shorter heading date, shorter plant height and much number of spikelets per panicle and the type with longer heading date, longer plant height and less number of spikelets per panicle, the ratio is 1:3(χ²=0.11,P=0.740).1082 plants with extremely short heading date of the F₂ population were selected to fine mapping the QTL. All the extremely short heading date plants were with short plant height and less number of spikelets per panicle. No recombination were detected among the 3 traits in the extremely population. By analyzing the recombination of marker and the trait, the QTL were narrowed down to an interval between marker RM3859 and C39, and cosegregated with RM5436 and RM5499. The marker RM3859 and C39 spanning a physical distance of more than 2500kb, and the distance of RM5436 and RM5499 is 912.4kb. As the recombination suppression occurred in the region, it is difficult to narrow down the region by enlarge the population.Amylose content, gel consistency and gelatinization temperature are the three most important traits determining the cooking and eating quality of rice. Using populations derived from Shanyou 63, an elite rice hybrid, we previously mapped the major genes for these three traits to a region tightly linked to the Wx locus on the short arm of rice chromosome 6. In order to determine that whether the 3 traits were controlled by a single locus with pleiotropic effects or by 3 tightly linked genes, an F₂ population between Zhenshan 97 and the NIL containing 5280 individuals was developed. A total of 1080 plants with the trait combination of Minghui 63 were identified from this population. Molecular marker analysis located the gene(s) for the 3 traits to a single BAC clone, 35M22, isolated from a Minghui 63 BAC library, and got a corresponding Zhenshan 97 BAC, 2N1. The two BAC clones were then sequenced using the shotgun strategy. Further recombinant analysis using polymorphism between the parents identified by the subclones localized the genes(s) for the three traits to an interval between two polymorphic markers, C6 and P80. Comparing the sequences of C6 and P80 with 35M22 indicated that the distance between these two subclones is approximately 14kb. In the 14kb region,there are two ORFs. One is the Wx gene, encoding granule bound starch synthase. The other one is an uncomplete retrotransposon. The result show that the three traits were controlled by the Wx gene in the population.We identified the 3 traits to Wx gene, but some research thought the Alk gene has effect on GT and GC. So here we selected 97 cultivars to check the correction of the 2 genes and the 3 traits. Univariate analyzed of the traits of AC, GT and GC by two genes Wx and Alk by software of SPSS 15.0, respectively. The result showed that AC only is controlled by Wx gene and Alk gene no effect on AC and 91.8% of the total variation of GT is explained by Alk gene and 7.1% of variation is explained by Wx gene and 36.9% of variation of GC if explained by Alk gene and 55.9% of it is explained by Wx gene. And no epistatic effect was detected between the two genes.We sequenced a 6.2 kb DNA fragment including Wx gene of 33 cultivars. 43 single nucleotide polymorphisms (SNPs) and 8 insertion/deletions (InDels) were identified. Of them 2 SNPs and 2 InDels can explained all the variation of AC. A new SNP mutation of G substituted A at site of-1126 were detected, result in the AC increase from intermediate AC to high AC.We analyzed the expression of genes in the progress of starch synthesis, including 5 families 23 genes, by Affymetrix chip. The result showed the 23 genes were divided into 3 groups: the type expressing in endosperm tissue, the type expressing in photosynthesis tissue and the type expressing in both these tissues. The starch, synthesized in photosynthesis tissue, is the temporary starch, as source for plant development. And the starch, synthesized in endosporm cell, is storing starch, as the nutrition for seed pullulation.We checked the difference of Zhenshan 97 and Zhenshan 97 (Wx^b) in microstructure by transmission electron microscope, the result showed that the endosporm cell of Zhenshan 97 (Wx^b) was more easily broken but the starch graunle was tighter than Zhenshan 97. It maybe result to that Zhenshan 97 (Wx^b) more difficult to gelatinize and extend. Thus, it maybe is the reason of Zhenshan 97 (Wx^b) with higher GT and shorter GC.