Fine linkage mapping enables dissection of closely linked quantitative trait loci for seed dormancy and heading in rice

Abstract

Two quantitative trait loci (QTLs) for seed dormancy (tentatively designated Sdr1) and heading date ( Hd8) have been mapped to approximately the same region on chromosome 3 by interval mapping of backcross inbred lines derived from crosses between the rice cultivars Nipponbare (japonica) and Kasalath (indica). To clarify whether Sdr1 and Hd8 could be dissected genetically, we carried out fine-scale mapping with an advanced backcross progeny. We selected a BC(4)F(1) plant, in which a small chromosomal region including Sdr1 and Hd8, on the short arm of chromosome 3, remained heterozygous, whereas all the other chromosomal regions were homozygous for Nipponbare. Days-to-heading and seed germination rate in the BC(4)F(2) plants showed continuous variation. Ten BC(4)F(2) plants with recombination in the vicinity of Sdr1 and Hd8 were selected on the basis of the genotypes of the restriction fragment length polymorphism (RFLP) markers flanking both QTLs. Genotypes of those plants for Sdr1 and Hd8 were determined by advanced progeny testing of BC(4)F(4) families. Sdr1 was mapped between the RFLP markers R10942 and C2045, and co-segregated with C1488. Hd8 was also mapped between C12534S and R10942. Six recombination events were detected between Sdr1 and Hd8. These results clearly demonstrate that Sdr1 and Hd8 were tightly linked. Nearly isogenic lines for Sdr1 and Hd8 were selected by marker-assisted selection.

Isolation of three dormancy QTLs as Mendelian factors in rice

“…Several dormancy QTL regions have been isolated in introgression or near isogenic lines for Arabidopsis, barley, and rice (Han et al, 1999;Alonso-Blanco et al, 2003;Gao et al, 2003;Takeuchi et al, 2003). Fine mapping these regions suggests: (1) a dormancy QTL may consist of a gene cluster (Han et al, 1999); (2) some dormancy QTLs may lose their effect in a nondormant genetic background (Alonso-Blanco et al, 2003); (3) some QTLs are especially sensitive to the environment during seed development (Gao et al, 2003); and (4) an influence of flowering time on dormancy may be due to tight linkage between loci for both traits (Takeuchi et al, 2003).…”

“…Fine mapping these regions suggests: (1) a dormancy QTL may consist of a gene cluster (Han et al, 1999); (2) some dormancy QTLs may lose their effect in a nondormant genetic background (Alonso-Blanco et al, 2003); (3) some QTLs are especially sensitive to the environment during seed development (Gao et al, 2003); and (4) an influence of flowering time on dormancy may be due to tight linkage between loci for both traits (Takeuchi et al, 2003). Some of the introgression lines were used to estimate geneadditive effects for the QTL.…”

Validation of QTLs for Eating Quality of Japonica Rice ‘Koshihikari’ Using Backcross Inbred Lines

“…Takeuchi et al (2003) carried out fine mapping of QTLs for DTH and seed dormancy in this region. Hori et al (2010) detected a QTL for preharvest sprouting that is allelic with qLTG3-1 identified by Fujino et al (2008).…”

Evaluation of Cultivar Differences in Preharvest Sprouting of Common Buckwheat (Fagopyrum esculentumMoench)

“…There is accumulating evidence that QTL of domestication-related traits are clustered close together on the same linkage group (Koinange et al, 1996;Takeuchi et al, 2003;Gu et al, 2005;Hancock, 2005). In buckwheat, summer ecotype cultivars are considered to have differentiated from the late-summer ecotype cultivars as a result of adaptation to the long-day condition of summer cropping in high latitude regions (Minami and Namai, 1986).…”