SER in the SSSLs derived from O. glumaepatula
At the first, a set of 168 SSSLs derived from O. glumaepatula were investigated for SER and 9 of the SSSLs with higher SER were selected. The 9 SSSLs were then tested their SER for 5 cropping seasons. Compared with the HJX74 recipient, the 9 SSSLs were showed higher SER at the P ≤ 0.001 level in every cropping season. Average SER of the 9 SSSLs in the 5 cropping seasons were from 48.1–60.8% with 18.5–31.2% higher than that of the control HJX74 (Fig. 1 and Additional file: Table S1).
The chromosomal substituted segments from O. glumaepatula in the 9 SSSLs were detected by molecular markers. The substituted segments in the 9 SSSLs were detected on chromosomes 1, 3, 5, 9 and 10, respectively. The estimated lengths of substituted segments were from 1467.0 kb to 16410.5 kb (Additional file: Table S2 and Table S3).
Eight of agronomic traits in the 9 SSSLs were investigated in two cropping seasons. Compared with HJX74, most of the traits in the SSSLs had no significant difference, except the plant height in SG25, the heading date in SG153, and so on (Additional file: Table S4).
Two QTLs for SER were mapped on chromosome 1
Four SSSLs with high SER, SG18, SG22, SG23 and SG25, carried substituted segments on chromosome 1. SG18 had a substituted segment at the interval from markers RM140 to RM5853 with the estimated length of 10741.8 kb (Fig. 1 and Additional file: Table S3). Therefore, the substituted segment of SG18 carried an QTL for SER, named qSER-1a.
Other three SSSLs, SG22, SG23, and SG25 carried substituted segments in the region of 29385.9-41082.0 kb and the substituted segments were overlapped. SG22 had the shortest substituted segment with the estimated length of 2611.3 kb from markers RM403 to RM6648. The estimated lengths of substituted segments were 5874.5 kb in SG23, and 11059.7 kb in SG25. These results indicated that the three SSSLs carried another QTL for SER, named qSER-1b, which located in the substituted segment of SG22 with the interval of 2611.3 kb (Fig. 2 and Additional file: Table S3).
Because the qSER-1b was linked to Sd1, SG25 carried the Sd1 in the substituted segment from O. glumaepatula and showed tall in plant height with 160.3 cm in FCS and 135.7 cm in SCS. SG22 and SG23 carried shorter substituted segments and had no Sd1 from O. glumaepatula. Although SG22 and SG23 were semi-dwarf in plant height, the SER had no significant difference with SG25 (Fig. 2 and Additional file: Table S4). These results indicated that the qSER-1b of SER was not influenced by plant height.
Two QTLs for SER were mapped on chromosome 3
Two SSSLs with high SER, SG59 and SG65, carried substituted segments on chromosome 3. SG59 had a substituted segment at the interval from markers RM282 to InDel3 with the estimated length of 4632.1 kb (Fig. 1 and Additional file: Table S3). Therefore, the substituted segment of SG59 carried an QTL for SER, named qSER-3a.
The SSSL SG65 carried a substituted segment at the interval of 26747.5-35843.1 kb on chromosome 3. The substituted segment was in a different region from that in SG59. Therefore, SG65 had another QTL for SER, qSER-3b, in its substituted segment (Fig. 3b, Additional file: Table S3).
To narrow the interval of qSER-3b, 5 secondary SSSLs were developed from an F2:3 population derived from the cross of HJX74/SG65. The secondary SSSL, SG65-14, carried a substituted segment in the region from markers RM15678 to ID03MC07 on the left. Two of the secondary SSSLs, SG65-48 and SG65-61, had substituted segments in the regions from PSM132 and RM186 to RM442 on the right, respectively. The three secondary SSSLs showed lower SER as HJX74. Other two secondary SSSLs, SG65-9 and SG65-55, carrying substituted segments covered the region from markers ID03MC07 to RM186 showed higher SER as SG65. These results indicated that the qSER-3b was narrowed to an interval of 931.0 kb between markers ID03MC07 and RM186 (Fig. 3).
Secondary substitution mapping of qSER-9
One SSSL, SG135, carried a substituted segment on chromosome 9. Therefore, the substituted segment had an QTL for SER, qSER-9. To further map qSER-9, 5 secondary SSSLs were developed from an F2:3 population from the cross of HJX74/SG135. Two of the secondary SSSLs, SG135-26 and SG135-30, carried respectively substituted segments in the regions from ID09M06 to ID09M16 and RM105 on the left. The secondary SSSL, SG135-6, had a substituted segment in the region from ID09M23 to RM3600 on the right. The three secondary SSSLs showed lower SER as HJX74. Other two secondary SSSLs, SG135-44 and SG135-68, carried substituted segments from ID09M16 to ID09M23, and had higher SER as SG135. These results indicated that the qSER-9 was delimited to an interval of 608.2 kb between ID09M16 and ID09M23 (Fig. 4).
Other QTLs for SER identified in the SSSLs
One SSSL, SG85, carried a substituted segment from markers RM7444 to RM291 on chromosome 5 with the estimated length of 16410.5 kb. Therefore, the SSSL had an QTL for SER, qSER-5, in the substituted segment (Fig. 1 and Additional file: Table S3).
Another SSSL, SG153, carried a substituted segment from markers RM484 to RM25886 on chromosome 10 with the estimated length of 1467.0 kb and had an QTL for SER, qSER-10, in the substituted segment (Fig. 1 and Additional file: Table S3).
Summarily, a total of 7 QTLs for SER was mapped on 5 chromosomes. Among of them, chromosomes 1 and 3 each carried two of the QTLs, and chromosomes 5, 9 and 10 each carried one of the QTLs (Fig. 5).
The additive effects of QTLs for SER identified in the SSSLs
The additive effects of the 7 QTLs for SER, qSER-1a, qSER-1b, qSER-3a, qSER-3b, qSER-5, qSER-9 and qSER-10, ranged from 10.6–14.8% and the additive contribution variances explained by each of the QTLs for SER were from 36.3–50.6%. Among of them, qSER-10 had the highest additive effect of 14.8% and the highest additive contribution variance of 50.6% (Table 1).
Table 1
Additive effects of QTLs for stigma exsertion rate detected in the SSSLs
QTL | Chr. | Interval (kb) | Estimated length (kb) | P value | A (%) | ACV (%) |
qSER-1a | 1 | 12291.6-23033.4 | 10741.8 | 2.5E-08 | 11.9 ± 0.8 | 40.7 ± 3.7 |
qSER-1b | 1 | 29608.2-32219.6 | 2611.3 | 3.6E-06 | 12.4 ± 1.8 | 42.5 ± 6.3 |
qSER-3a | 3 | 11656.8-16288.9 | 4632.1 | 1.2E-07 | 11.1 ± 1.1 | 38.0 ± 4.4 |
qSER-3b | 3 | 27677.1-28608.1 | 931.0 | 2.4E-07 | 10.7 ± 1.2 | 37.1 ± 5.5 |
qSER-5 | 5 | 3216.5-19626.9 | 16410.5 | 1.3E-09 | 13.5 ± 1.6 | 46.5 ± 6.6 |
qSER-9 | 9 | 14342.2-14950.4 | 608.2 | 3.1E-07 | 10.6 ± 1.0 | 36.3 ± 4.2 |
qSER-10 | 10 | 21132.3-22599.3 | 1467.0 | 1.2E-10 | 14.8 ± 2.0 | 50.6 ± 7.2 |
A additive effect, ACV additive contribution variance, A and ACV was represented as mean ± S.E. in five cropping seasons. |