QTLs for grain shattering in the Lemont/Teqing RI population

28.QTLs for grain shattering in the Lemont/Teqing RI population D.B. ZHONG, S.B. Yu, J.L. Xu, L.J. Luo and Z.K. Li International Rice Research Instutute, P.O. Box 3127, 1271 Makati, Philippines Grain shattering is an undesirable characteristic of rice cultivars affecting field loss of grain yield before and during harvesting. A moderate degree of this character, i.e. non- shattering but easy to thresh, is a desirable feature for hand harvesting, transportation and threshing practiced by the majority of the farmers in the developing countries. There is tremendous genetic variation in rice gene pools in respect to the degree of shattering, ranging from extremely shattering to extremely hard to thresh. At least 5 genes that control shattering in rice have been reported (cf Kinoshita 1989). These include three recessive genes, shi, sh2, and sh4 located on chromosomes 11, 1, 3, and two dominant ones, Sh3 and Sh(t)* located on rice chromosomes 4 and I (Fukuta and Yagi 1998). While shattering in rice is highly heritable, modern rice varieties have shown varied degrees of shattering, suggesting its quantitative nature. We report an effort to map quantitative trait loci (QTLs) affecting shattering in rice using DNA markers. A set of 284 recombinant inbred lines (RILs) derived from a cross between Lemont (japonica) and Teqing (indica) and 182 well-distributed DNA markers were used in this study (Li et al. 1999). QTL mapping was performed using the computer software QTLMapper Version 1.0 (Wang et a!. 1999). Ten mature panicles from each of the RILs were evaluated for their shattering ability using the grasping method according to Standard Evaluation System for Rice. Lemont showed low grain shattering with less than 10% of shattered grains and Teqing had a moderate degree of shattering with approximately 40% of shattered grains. However, the RILs showed considerable transgressive segregation for grain shattering, ranging from 1% to 80%. Five main-effect QTLs were mapped to chromosomes i, 2,4, 5 and 9, which collectively accounted for about 70% of the total phenotypic variation. These QTLs had additive effects ranging from 4.5 - l1.8% grain shattering, and individually explained 4.0-27.3% of the total phenotypic variation in the RILs. The alleles at all but one QTL (QSh5) for reduced grain shattering were from Lemont. The most notable QTL was QSh2 on chromosome 2. This QTL was detected by a LOD score of 16.41 and had a large effect of 11.8% for grain shattering (R2 = 27.3%). This QTL represented a new locus for grain shattering not previously reported. The other QTLs had relatively small effects. Fukuta et a!. (1996) identified five putative QTLs for grain shattering on chromosomes 1, 2, 5, 11 and 12 using an F2 population from a cross between Nipponbare and Kasalath. In their study, the QTL on chromosome i had the strongest effect while the others showed relatively small effects. When looking closely at the QTLs for shattering identified in both studies, we found that QTLs on chromosome 2 appeared to be in the same location. There is no correspondence in genomic location for other QTLs identified in the two studies. References Fukuta, Y. and Yagi, 1998. Mapping of a shattering resistance gene in a mutant line, SR-5 induced from an indica rice variety, Nan-Jing 11. Bree. Sci. 48: 345-348 Fukuta, Y., Y.Harushima and M.Yano, 1996. Using quanitative trait locus analysis for studying genetic regulation of shattering. Rice Gentetics III: 657-662 Kinoshita, T., 1989. Report of the committee of gene symbolization , nomenclature and linkage groups. RGN 6: 2-7. LI, Z.K., L.J. Luo, H.W. Mei, A.H. Paterson, X.H. Zhao, et al., 1999. A "defeated" rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv. Oryzae. Mol.Gen.Genet. 261: 58-63. Nagato, Y. and A. Yoshimura, 1998. Report of the committee og gene symbolization , nomenclature and linkage groups.RGN 15: 13-76. Wang, D.L.,J. Thu, Z.K. Li and A. H. Paterson, 1999. Mapping QTLs with epistatic effecs and QTL x environment interactions by mixed model approaches. Theor. Appl. Genet. (in press).

28.QTLs for grain shattering in the Lemont/Teqing RI population

D.B. ZHONG, S.B. Yu, J.L. Xu, L.J. Luo and Z.K. Li

International Rice Research Instutute, P.O. Box 3127, 1271 Makati, Philippines

Grain shattering is an undesirable characteristic of rice cultivars affecting field loss of grain yield before and during harvesting. A moderate degree of this character, i.e. non- shattering but easy to thresh, is a desirable feature for hand
harvesting, transportation and threshing practiced by the majority of the farmers in the developing countries. There is tremendous genetic variation in rice gene pools in respect to the degree of shattering, ranging from extremely shattering to extremely hard to thresh. At least 5 genes that control shattering in rice have been reported (cf Kinoshita 1989). These include three recessive genes, shi, sh2, and sh4 located on chromosomes 11, 1, 3, and two dominant ones, Sh3 and Sh(t)* located on rice chromosomes 4 and I (Fukuta and Yagi 1998). While shattering in rice is highly heritable, modern rice varieties have shown varied degrees of shattering, suggesting its quantitative nature. We report an effort to map quantitative trait loci (QTLs) affecting shattering in rice using DNA markers.

A set of 284 recombinant inbred lines (RILs) derived from a cross between Lemont (japonica) and Teqing (indica) and 182 well-distributed DNA markers were used in this study (Li et al. 1999). QTL mapping was performed using the computer software QTLMapper Version 1.0 (Wang et a!. 1999). Ten mature panicles from each of the RILs were evaluated for their shattering ability using the grasping method according to Standard Evaluation System for Rice.

Lemont showed low grain shattering with less than 10% of shattered grains and Teqing had a moderate degree of shattering with approximately 40% of shattered grains. However, the RILs showed considerable transgressive segregation for grain shattering, ranging from 1% to 80%. Five main-effect QTLs were mapped to chromosomes i, 2,4, 5 and 9, which collectively accounted for about 70% of the total phenotypic variation. These QTLs had additive effects ranging from 4.5 - l1.8% grain shattering, and individually explained 4.0-27.3% of the total phenotypic variation in the RILs. The alleles at all but one QTL (QSh5) for reduced grain shattering were from Lemont. The most notable QTL was QSh2 on chromosome 2. This QTL was detected by a LOD score of 16.41 and had a large effect of 11.8% for grain shattering (R2 = 27.3%). This QTL represented a new locus for grain shattering not previously reported. The other QTLs had relatively small effects. Fukuta et a!. (1996) identified five putative QTLs for grain shattering on chromosomes 1, 2, 5, 11 and 12 using an F2 population from a cross between Nipponbare and Kasalath. In their study, the QTL on chromosome i had the strongest effect while the others showed relatively small effects. When looking closely at the QTLs for shattering identified in both studies, we found that QTLs on chromosome 2 appeared to be in the same location. There is no correspondence in genomic location for other QTLs identified in the two studies.

References
Fukuta, Y. and Yagi, 1998. Mapping of a shattering resistance gene in a mutant line, SR-5 induced from an indica rice variety, Nan-Jing 11. Bree. Sci. 48: 345-348
Fukuta, Y., Y.Harushima and M.Yano, 1996. Using quanitative trait locus analysis for studying genetic regulation of shattering. Rice Gentetics III: 657-662
Kinoshita, T., 1989. Report of the committee of gene symbolization , nomenclature and linkage groups. RGN 6: 2-7.
LI, Z.K., L.J. Luo, H.W. Mei, A.H. Paterson, X.H. Zhao, et al., 1999. A "defeated" rice resistance gene acts as a QTL against a virulent strain of Xanthomonas oryzae pv. Oryzae. Mol.Gen.Genet. 261: 58-63.
Nagato, Y. and A. Yoshimura, 1998. Report of the committee og gene symbolization , nomenclature and linkage groups.RGN 15: 13-76.
Wang, D.L.,J. Thu, Z.K. Li and A. H. Paterson, 1999. Mapping QTLs with epistatic effecs and QTL x environment interactions by mixed model approaches. Theor. Appl. Genet. (in press).