Table 5.
Genomic regions harboring stable QTL for plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand grain weight (TGW), and grain weight per spike (GWS) in the ND3338/JD6 doubled haploid (DH) population.
| Chromosome | Genetic interval (cM)a | Physical distance (Mb)b | Traitsc | Included QTLd | Detected environmente | References |
|---|---|---|---|---|---|---|
| Chr.1B.1 | 31.2–42.0 | 598.43–641.84 | PH (J) | QPh.cau-1B.1 | E1/E2/E3/E4/E5/E6/E7/E8/C | Griffiths et al., 2012 |
| TGW(J) | QTgw.cau-1B.1 | E2/E4/C | Cui et al., 2014 | |||
| SPP (N) | QSpp.cau-1B.2 | E7 | ||||
| GWS (J) | QGws.cau-1B.1 | E1 | ||||
| Chr.2A | 112.9–133.8 | 639.07–733.92 | TGW (J) | QTgw.cau-2A.3 | E2/E5/E6/E10/C | Cui et al., 2014 |
| SPP (N) | QSpp.cau-2A.1 | E2/E6/C | ||||
| GWS (J) | QGws.cau-2A.3 | E1/E5/E7 | ||||
| GWS (J) | QGws.cau-2A.2 | E1/E2/E5/C | ||||
| Chr.2B | 111.6–131.9 | 177.65–657.73 | GNS (N) | QGns.cau-2B.4 | E1/E2/E4/E7/C | Liu G. et al., 2014 |
| GWS (N) | QGws.cau-2B.1 | E2/E5/E8/C | Liu G. et al., 2014 | |||
| GWS (N) | QGws.cau-2B.2 | E2/E3/E8/C | ||||
| SPP (J) | QSpp.cau-2B.5 | E4 | ||||
| Chr.2D.1 | 26.9–69.8 | PH (N) | QPh.cau-2D.2 | E1/E2/E3/E4/E5/E6/E7/E8/C | ||
| PH (N) | QPh.cau-2D.3 | E1/E2/E3/E4/E5/E6/E7/E8/C | Wu et al., 2010;Zhai et al., 2016 | |||
| TGW (N) | QTgw.cau-2D.1 | E5/E6/E7/C | Cui et al., 2014 | |||
| GNS (N) | QGns.cau-2D.1 | E4 | ||||
| GWS (N) | QGws.cau-2D.1 | E4 | ||||
| Chr.3A | 65.8–105.8 | 705.31–749.11 | PH (J) | QPh.cau-3A.1 | E1/E2/E3/E4/E5/E6/E7/E8/C | Zanke et al., 2014 |
| PH (J) | QPh.cau-3A.2 | E1/E2/E3/E4/E5/E7/E8/C | ||||
| PH (J) | QPh.cau-3A.3 | E1/E2/E3/E4/E5/E6/E7/E8/C | ||||
| GNS (N) | QGns.cau-3A.2 | E6 | ||||
| Chr.4A | 84.6–108.5 | 622.19–685.00 | GNS (N) | QGns.cau-4A.3 | E1/E2/E3/E6/E7 | |
| GNS (N) | QGns.cau-4A.4 | E2/E3/E4/E5/E6/E7/E8/C | Gao et al., 2015;Cui et al., 2017 | |||
| TGW (J) | QTgw.cau-4A.2 | E1/E4/E6/E8 | Cui et al., 2014 | |||
| TGW (J) | QTgw.cau-4A.3 | E1/E2/E3/E4/E6/E7/E8/E9/E11/E12/C | Gao et al., 2015;Cui et al., 2016 | |||
| GWS (N) | QGws.cau-4A.3 | E5 | ||||
| GWS (N) | QGws.cau-4A.4 | E5 | ||||
| SPP (J) | QSpp.cau-4A.3 | E6 | ||||
| Chr.4B | 22.3–95.8 | 13.98–567.18 | TGW (J) | QTgw.cau-4B.1 | E2/E3/E5/E6/E8/E9/E10/C | |
| TGW (J) | QTgw.cau-4B.2 | E2/E3/E5/E6/E8/E9/E10/C | Chen et al., 2014 | |||
| TGW (J) | QTgw.cau-4B.3 | E1/E3/E4/E5/E6/E7/E8/E12/C | Liu G. et al., 2014;Kumar et al., 2016 | |||
| TGW (J) | QTgw.cau-4B.4 | E3/E4/E5/E7/E8/E11/E12/C | Liu G. et al., 2014;Kumar et al., 2016 | |||
| TGW (J) | QTgw.cau-4B.5 | E4/E8/E11 | Kumar et al., 2016 | |||
| SPP (N) | QEp.cau-4B.3 | E4/E6/E7/E8/C | Liu G. et al., 2014 | |||
| SPP (N) | QEp.cau-4B.4 | E1/E4/E6/E7/E8/C | Cui et al., 2014;Liu G. et al., 2014 | |||
| PH (J) | QPh.cau-4B.2 | E1/E2/E3/E4/E5/E6/E7/E8/C | Wu et al., 2010;Gao et al., 2015 | |||
| GWS (J) | QGws.cau-4B.3 | E1/E5/E6/E7/C | Liu G. et al., 2014 | |||
| GWS (J) | QGws.cau-4B.4 | E3/E4/C | Liu G. et al., 2014 | |||
| GWS (J) | QGws.cau-4B.5 | E3/E4/C | ||||
| GWS (J) | QGws.cau-4B.6 | E4 | ||||
| Chr.4D | 22.3–62.0 | 12.77–62.47 | PH (J) | QPh.cau-4D.1 | E1/E2/E3/E4/E5/E6/E7/E8/C | Liu G. et al., 2014;Gao et al., 2015 |
| PH (J) | QPh.cau-4D.2 | E2/E3/E5/E8/C | ||||
| SPP (J) | QEp.cau-4D.1 | E1/E3/E4/C | ||||
| TGW (J) | QTgw.cau-4D.2 | E1/E3/E4/E5/E7/E8 | Liu G. et al., 2014 | |||
| TGW (J) | QTgw.cau-4D.3 | E4 | ||||
| Chr.5A | 23.2–63.9 | 11.05–460.52 | GNS (J) | QGns.cau-5A.1 | E3/E6/E7/C | |
| GNS (J) | QGns.cau-5A.2 | E1/E2/E3/E4/E6/C | Cui et al., 2014 | |||
| TGW (N) | QTgw.cau-5A.2 | E3/E4/E5/E11/C | Gao et al., 2015;Wu et al., 2015 | |||
| TGW (N) | QTgw.cau-5A.3 | E5/E11 | Wu et al., 2015 | |||
| GWS (J) | QGws.cau-5A.1 | E7 | ||||
| Chr.6A | 71.5–79.0 | 38.43–596.59 | TGW (J) | QTgw.cau-6A.5 | E3/E4/E5/E7 | Gao et al., 2015;Tian et al., 2017 |
| TGW (N) | QTgw.cau-6A.4 | E3/E6/E7/E12/C | ||||
| PH (J) | QPh.cau-6A.2 | E1/E2/E3/E4/E5/E6/E7/E8/C | Tian et al., 2017;Würschum et al., 2017 | |||
| GWS (N) | QGws.cau-6A.4 | E8 | ||||
| GNS (N) | QGns.cau-6A.2 | E1/E8 | ||||
| Chr.7A | 39.5–61.9 | 7.13–612.38 | GNS (J) | QGns.cau-7A.3 | E1/E2/E3/E5/E8/C | Quarrie et al., 2006 |
| GNS (J) | QGns.cau-7A.2 | E1/E2/E3/E8/C | Quarrie et al., 2006; Zhai et al., 2017 | |||
| GNS (J) | QGns.cau-7A.4 | E1/E3/E8/C | Quarrie et al., 2006 | |||
| GWS (J) | QGws.cau-7A.2 | E2/E7/E8/C | ||||
| PH (J) | QPh.cau-7A.6 | E4/E5/E6/E8/C | Wu et al., 2010 | |||
| PH (J) | QPh.cau-7A.5 | E1 | ||||
| SPP (N) | QSpp.cau-7A.1 | E4 | ||||
| Chr.7A | 90.9–121.7 | 672.03–719.57 | TGW (N) | QTgw.cau-7A.2 | E2/E6/E9/C | Quarrie et al., 2006 |
| TGW (N) | QTgw.cau-7A.3 | E2/E6/E9/E10/E11/C | Quarrie et al., 2006 | |||
| TGW (N) | QTgw.cau-7A.4 | E2/E6/E9/E11/C | Quarrie et al., 2006 | |||
| SPP (N) | QSpp.cau-7A.2 | E2/E3 | Quarrie et al., 2006 | |||
| GNS (J) | QGns.cau-7A.5 | E5/E6/E7/C | Quarrie et al., 2006 | |||
| GNS (J) | QGns.cau-7A.6 | E2/E5 | Quarrie et al., 2006 |
Additional details regarding the SNP markers within each QTL region can be found in Tables S6, S7.
The corresponding physical distances (Mb) of the QTL regions on chromosomes 1B.1, 2A, 2B, 2D.1, 3A, 4A, 4B, 4D, 5A, 6A, and 7A were obtained by blasting the flanking sequences of SNP markers to the Chinese Spring RefSeq v1.0 sequence (Table S4).
The traits include plant height (PH), spikes per plant (SPP), grain number per spike (GNS), thousand grain weight (TGW), and grain weight per spike (GWS). The letters within the brackets indicate the origin of the increasing alleles with “N” and “J” representing ND3338 and JD6, respectively.
QTL shown in bold are stable QTL that were detected in ≥3 individual environments and the BLUP analysis.
C indicates the combined QTL analysis based on BLUP values.