Mapping of quantitative trait loci (QTLs) for rice protein and fat content using doubled haploid lines

Hu, Zhong-Li; Li, Ping; Zhou, Ming-Quan; Zhang, Zhi-Hong; Wang, Ling-Xia; Zhu, Li-Huang; Zhu, Ying-Guo
January 2004
Euphytica;Jan2004, Vol. 135 Issue 1, p47
Academic Journal
Rice protein content (RPC) and rice fat content (RFC) are two important components of rice nutritional quality. In order to examine the genetic basis of these traits, a doubled haploid (DH) population and an RFLP linkage map consisting of 232 marker loci were used to search QTLs for the traits with the computer program QTLMapper1.0. This program is based on mixed linear models and allows simultaneous mapping of both main-effect and digenic epistastic QTLs in a DH population. RPC and RFC were evaluated based on a dry weight basis of head rice by the Kjeldahl and Soxhlet methods respectively. A total of five main-effect QTLs for RPC were resolved. The five QTLs collectively explained 74% of the phenotypic variation with LOD=15.2. Among these QTLs, the major QTL qRPC-5 with the largest effect was mapped in the interval of RG435-RG172a on chromosome 5. It accounted for 35% of the phenotypic variation with a LOD of 16.7. At this locus the allele from the parent `Gui 630' increased RPC by 1.32%. The second QTL qRPC-7 was mapped in the interval ZG34B-G20 on chromosome 7. It explained 23% of the phenotypic variance with a LOD of 6.1. Its positive alleles, also from the parent `Gui 630', increased RPC by 1.05%. As for the remaining three QTLs, their additive effects were relatively small and their positive alleles were all inherited from the parent `02428'. Three QTLs for RFC were mapped on chromosome 1, 2 and 5 respectively. They collectively explained 44% of the phenotypic variation. Among these loci, QTLs qRFC-2 and qRFC-5 with larger effects individually accounted for 24% and 26% of the phenotypic variance respectively. At QTL qRFC-2 the positive allele came from the parent `Gui 630', while at QTL qRFC-5 the positive allele from the parent `02428'. The fact that both parents possess the positive alleles at the QTLs for the two traits provides an appropriate explanation for the large transgressive segregation observed in the DH lines. Furthermore, only one pair of epistatic loci explaining only 5.1% of the phenotypic variance was detected for RPC, whereas seven pairs of epistatic loci were resolved for RFC. The total absolute effects of these RFC interactions amounted to 0.97% which is much larger than that (0.42%) of the three main-effect QTLs for the trait. Along with the observation that RPC showed a high heritability (78%), these results demonstrate that RPC in the DH population could be mainly controlled by relatively few QTLs with large main-effects. As for RFC, epistatic interactions might be an even more important component of the genetic basis and the segregation of the DH lines could be largely explained by a few main-effect QTLs and many epistatic loci. In addition, a highly negative correlation (r = –0.45) between RPC and RFC in the DH population was observed. This correlation could be largely explained by the linkage of qRPC-5 and qRFC-5 with the directions of effects opposite and the co-locations of the two epistatic loci for RFC respectively with two different main-effect QTLs for RPC. The information reported in the present paper may be useful for improving rice nutritional quality by means of marker-assisted selection.


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