Dissection of closely linked QTLs controlling stigma exsertion rate in rice by substitution mapping

Key message Through substitution mapping strategy, two pairs of closely linked QTLs controlling stigma exsertion rate were dissected from chromosomes 2 and 3 and the four QTLs were fine mapped. Abstract Stigma exsertion rate (SER) is an important trait affecting the outcrossing ability of male sterility lines in hybrid rice. This complex trait was controlled by multiple QTLs and affected by environment condition. Here, we dissected, respectively, two pairs of tightly linked QTLs for SER on chromosomes 2 and 3 by substitution mapping. On chromosome 2, two linkage QTLs, qSER-2a and qSER-2b, were located in the region of 1288.0 kb, and were, respectively, delimited to the intervals of 234.9 kb and 214.3 kb. On chromosome 3, two QTLs, qSER-3a and qSER-3b, were detected in the region of 3575.5 kb and were narrowed down to 319.1 kb and 637.3 kb, respectively. The additive effects of four QTLs ranged from 7.9 to 9.0%. The epistatic effect produced by the interaction of qSER-2a and qSER-2b was much greater than that of qSER-3a and qSER-3b. The open reading frames were identified within the maximum intervals of qSER-2a, qSER-2b and qSER-3a, respectively. These results revealed that there are potential QTL clusters for SER in the two regions of chromosome 2 and chromosome 3. Fine mapping of the QTLs laid a foundation for cloning of the genes of SER.

Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

Background: Stigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula , a wild Oryza species. Results: Seven QTLs for SER were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an estimated interval of 898.8kb by secondary substitution mapping. qSER-5 , qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to an estimated region of 551.9kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, which were higher than those of most loci for SER reported previously. Conclusions: qSER-1a and qSER-1b are novel loci for SER on chromosome 1. All of the 7 QTLs have major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

Substitution mapping of the major quantitative trait loci controlling stigma exsertion rate from Oryza glumaepatula

Background: Stigma exsertion rate (SER) is a key determinant for outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. Outcrossing ability in cultivated rice varieties has diminished during the process of domestication, while wild Oryza species keep strong outcrossing ability. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula, a wild Oryza species.Results: Seven QTLs for SER, qSER-1a, qSER-1b, qSER-3a, qSER-3b, qSER-5, qSER-9 and qSER-10, were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an interval of 931.0kb by secondary substitution mapping. qSER-5, qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to a region of 608.2kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, and the additive contribution variances explained by each of the QTLs were from 36.3% to 50.6%, which were higher than those of most loci for SER reported previously.Conclusions: qSER-1a and qSER-1b were novel loci for SER on chromosome 1. All of the 7 QTLs had major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.