Towards the understanding of complex traits in rice: substantially or superficially?

Abstract

Completion of the genome analysis followed by extensive comprehensive studies on a variety of genes and gene families of rice (Oryza sativa) resulted in rapid accumulation of information concerning the presence of many complex traits that are governed by a number of genes of distinct functions in this most important crop cultivated worldwide. The genetic and molecular biological dissection of many important rice phenotypes has contributed to our understanding of the complex nature of the genetic control with respect to these phenotypes. However, in spite of the considerable advances made in the field, details of genetic control remain largely unsolved, thereby hampering our exploitation of this useful information in the breeding of new rice cultivars. To further strengthen the field application of the genome science data of rice obtained so far, we need to develop more powerful genomics-assisted methods for rice breeding based on information derived from various quantitative trait loci (QTL) and related analyses. In this review, we describe recent progresses and outcomes in rice QTL analyses, problems associated with the application of the technology to rice breeding and their implications for the genetic study of other crops along with future perspectives of the relevant fields.

Figure 1

The location of Gramene QTL on rice chromosomes. In 6293 Gramene QTL with physical position of chromosome segment deduced from the sequences of corresponding DNA markers, 4090 QTL within the interval of 1 Mb or less were only plotted by using the central value of the interval in each TC. X-axis is QTL position (Mb) on each chromosome (1–12, from top to bottom). Y-axis is the number of QTL. Red circles indicate the position of the centromere on each chromosome. The 95 QTL of ‘Vigor’ at 40.9 Mb on chromosome 1 was off scale and the value is written in parentheses.

Figure 2

Scheme for the use of primary and backcrossed populations to investigate genetically complex traits in rice. (A) Two kinds of experimental populations—primary populations such as RILs and backcrossed population such as CSSLs—can be developed by crossing between a donor parent (P1) with trait of interest and a recurrent parent (P2) such as a representative cultivar. (B) Putative QTL, genotype by environmental interaction (G × E) or genotype by genotype (epistatic) interaction (G × G) are statistically estimated by QTL analysis of primary population. (C) A series of CSSL contribute to validation of the estimated QTL, G × E interaction (C1), G × G interaction (C2) and to fine mapping of the QTL followed by marker-assisted breeding and gene isolation (C3).