QTL Mapping And Genetic Analysis For Rice Quality Traits

The demand for superior grain quality is increasingly becoming a priority for international export markets in all of the cultivated rice-producing areas worldwide. The primary components of rice grain quality include appearance, eating, cooking, and milling quality, and nutritional qualities, all values that are determined by their physical-chemical properties and other socio-cultural factors. Among these quality properties, consumers pay more attention to the fine appearance, high eating and nutritional quality. Therefore, these are major goals in rice quality improvement. In order to characterized the genetic components, including additive effects, epistasis, and QTL-by-environment interaction, that are involved in the control of grain quality, data were collected from replicated tests of a recombinant inbred line population derived from the cross between Koshihikari, a top elite japonica variety with superior grain quality, and Guichao2, a high-yield indica variety with poor grain quality, in two successive years. The results are as follows:1. A molecular linkage map consisting of 172 SSR markers was constructed using 184 individual plants of the RIL population. Linkage map consisting of 172 SSR markers spanning a total of 2,139.8 cM was constructed, with an average marker interval of 12.4 cM. Marker order on the chromosomes agreed well with that of the published map.2. The RIL population showed bimodal segregations for amylase content, indicating the involvement of a major gene for it; whereas, normal distributions of the others, indicating qualititative-inherited.3. A total of 27 QTL were identified with significant additive effects on nine chromosomes except chromosomes 8, 11 and 12. Each QTL explained 1.63-55.63% of the phenotypic variance, although only qAC-6 for amylase content had the largest effects. Epistasis analysis detected 13 significant additive-by-additive interactions on the traits. For grain length of milled rice (MGL), two additive QTL (qMGL-9 and qMGL-10b)were detected that interacted with environment..Only one additive QTL, qRPC-4, interacted with the environments for rice protein content (RPC). For length-width ratio, only one pair of QTL with significant epistasis-by-environment interaction was detected, which contributed 12.01% to the trait variation. For the other traits, neither additive-by-environment interaction nor epistasis-by-environment interaction was detected. Compared with QTL previously reported for these traits, eleven additive QTL, namely qMGL-6b, qMGL-9, qMGW-10, qLWR-4, qLWR-10, qRPC-3, qRFC-2, qRFC-3, qRFC-6b, qRFC-7 and qAC-1, are novel loci. Interestingly, the QTL qRFC-6a for RFC with the highest LOD score was located in the interval RM190-RM588 on chromosome 6, which corresponded to the waxy gene region.4. Based on the dissection of genetic basis in controlling grain quality, it revealed that grain length of milled rice, grain width of milled rice and fat content were mainly determined by additive QTL; additive effect and epistatic effect were the main genetic components for length-width ratio and thousand-seed weight rice; rice protein content was controlled by additive and epistic QTL as well as QTL-by-environment (QE) effect; and amylose content was controlled by Wx and multiple minor loci.