21. Comparative mapping of quantitative trait loci controlling the cooking and eating quality of rice (Oryza Sativa L.) in two years
  Z.F. LI1, J.M. WAN1, J.F. XIA2, W.Y. WANG2 and M. YANO3

1) State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Provincial Center of Plant Gene Engineering, Nanjing Agricultural University, Nanjing 210095, China
2) Rice Research Institute, Anhui Academy of Agricultural Sciences, Hefei 230031, China
3) Department of Molecular Genetics, National Institute of Agrobiological Resources, Tsukuba, Japan

Cooking and eating qualities of rice present a major problem in many rice producing areas. The traits which greatly affect eating and cooking qualities of rice are amylose content (AC), gelatinization temperature (GT) and gel consistency (GC). Some studies to map quantitative trait loci (QTL) for AC, GT and GC by molecular markers have been carried out (He et al. 1999, Tan et al. 1999, Yan et al. 2001). Eating and cooking qualities of rice are also affected by environmental factors, however, there are few reports on QTL mapping for these traits in different environments. In this study, we compared QTL mapping of AC, GT and GC for two consecutive years to elucidate genotype and environment interaction, to get a better understanding of genetic control of the three traits.

Backcross inbred lines (BILs) were used as a mapping population derived from an intersubspecies backcross, Nipponbare (japonica) / Kasalath (indica) // Nipponbare by single seed descent method. Nipponbare is a Japanese cultivar with low AC, relatively low GT and high GC. Kasalath is a landrace from Assam of India with high AC, medium GT and high GC. AC, GT and GC were evaluated according to China National Standards NY 147-88, and GT was expressed by alkali spreading score (ASS).

Composite interval mapping was implemented using QTL Cartographer software (Basten et al. 1999), with a model specifying five co-factors to control for genetic background and a window size of 10 cM that blocked out a region of 5 cM on either side of the markers flanking the test site. Specific co-factors used were obtained by forward-backward stepwise regression, with Fin = 0.01 and Fout = 0.01. A LOD threshold of 2.0 was used to declare the presence of putative QTL in a given genomic region. A total of 12 QTLs located on six chromosomes for the three traits were detected by composite interval mapping, based on the phenotypic performance of BIL population in 2000 and 2001 (Table 1, Fig. 1). Four QTLs for AC were detected. qAC-5 and qAC-6 were significant in both years. qAC-6 explained over 80% of phenotypic variance and was located in the wx region on the short arm of chromosome 6. The other two QTLs for AC with small additive effects were detected significantly only in2001. Three QTLs for GT were identified. qGT-6a and qGT-6b were significant in both years. qGT-6a was a major gene located in the alk region on chromosome 6. qGT-3 on chromosome 3 was significant only in 2001. Five QTLs for GC were detected and all were significant only in one year. These results showed that AC and GT were genetically controlled by a major gene with modification of some minor genes, and GC was a multi-gene inherited

trait. The QTL-environment interactions were observed by comparing QTL mapping of the same population grown in two consecutive years, but were trait dependent. QTLs for AC and GT were rather stable for two years, while QTLs for GC were very sensitive to the environment. This suggests that QTLs for AC and GT would are more useful for marker-assisted selection to improve the quality of rice.


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Tan, Y. F., J. X. Li, S.B. Yu, Y. Z. Xing, C. G. Xu and Q. Zhang, 1999. The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor. Appl. Genet. 99:: 642-648.

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