Phenotypic analysis
The IT was used to assess the SR of adult plants. The average IT of the female parent Chuanmai 42 was 3.00, reflecting its resistance to stripe rust, whereas the average IT of the male parent 86–741 was 5.80, indicative of its susceptibility to stripe rust (Fig. 1). The IT values varied considerably more for the RIL population (i.e., wider range) than for the parents (Fig. 1), indicating both parents carried SR genes. Among the yield-related traits, the PH, GNP, TGW, GWP, and YLD values were much higher for Chuanmai 42 than for 86–741, but there were no significant differences in SN between the two parents (Fig. 1). The SCC values were also higher for Chuanmai 42 (red wheat) than for 86–741 (white wheat). With the exception of GNP, the values for all examined traits varied substantially more for the RILs (i.e., wider range) than for the parents (Fig. 1). In addition, h2 ranged from 15.22% (SN) to 76.75%, with the h2 of PH, SCC, SR, and TGW exceeding 40% (Fig. 1).
In this study, SR and yield-related traits were investigated separately in different field trials, which revealed SR was not significantly correlated with the yield-related traits (Table 1). Additionally, SCC was significantly positively correlated only with TGW. Among the yield-related traits, YLD was significantly positively correlated with PH, TGW, GNP, SN, and GWP, with correlation coefficients of at least 0.50 (Table 1). Significant positive correlations were also detected between GWP and PH, TGW, and GNP (Table 1). Moreover, GNP was significantly positively correlated with SN (correlation coefficient > 0.30), but it was significantly negatively correlated with TGW, with a correlation coefficient of − 0.16 (Table 1). There was no significant correlation between SN and TGW (Table 1)
Table 1
Correlation coefficients for the investigated traits in all environments
| PH | SCC | TGW | GNP | SN | GWP | YLD |
SR | 0.00 | -0.00 | 0.07 | 0.06 | 0.07 | 0.10 | 0.06 |
PH | | -0.11 | 0.50** | 0.22** | 0.01 | 0.56** | 0.50** |
SCC | | | 0.17* | -0.11 | 0.12 | 0.06 | 0.12 |
TGW | | | | -0.16* | 0.04 | 0.68** | 0.58** |
GNP | | | | | 0.31** | 0.61** | 0.52** |
SN | | | | | | 0.26** | 0.61** |
GWP | | | | | | | 0.86** |
Significance at *P = 0.05 and **P = 0.01 |
GISH and FISH analysis
The results of the analysis of the root-tip metaphase chromosomes of both parents using rye genomic DNA, Oligo-pSc119.2, and Oligo-pTa535 as probes indicated the genome of the male parent 86–741 was modified by the 1RS.1BL translocation and the 3R (3D) substitution with rye chromosomes 1RS and 3R, whereas the Chuanmai 42 genome lacks rye chromosomal fragments (Fig. 2A, B). When the F1 hybrids with 1RS.1BL/1B and 3R/3D chromosome combinations were used to produce the subsequent generations, chromosomal aberrations were detected in the advanced RILs. For example, centromere breakage and fusion occurred in some of the F8 RILs. More specifically, in RIL No. 017 (i.e., RIL017), the centromere of chromosome 2A was broken, leading to the separation of 2AS and 2AL (Fig. 2C). In RIL177, the centromere breakage and fusion of chromosomes 5B and 7B created two new translocations (5BS.7BS and 5BL.7BL) (Fig. 2D). Moreover, chromosomal breaks also occurred in other regions, such as the long arm of 1B in RIL016, which resulted in the loss of the small chromosome fragment (i.e., deletion) (Fig. 2E). The rye chromosomes 1RS.1BL and 3R from 86–741 were stably retained through normal meiotic activities in several RILs, including RIL018, RIL081 (Fig. 2F), and RIL131.
Genetic map of chromosomes 1BS/1RS and 3D/3R
In this study, the 90K iSelect Wheat SNP chip was used to genotype the RILs and their parents. Along with SSR and CAPS markers, 1,764 markers were used to construct genetic maps (Data S1). A genetic linkage map with 32 linkage groups was constructed for 185 RILs and their genotypes. The map covered 2,913 cM, with an average interval between adjacent markers of 1.65 cM (Fig. 3).
Because of the 1RS.1BL translocation and 3R (3D) substitution in the male parent 86–741 (Fig. 2B), we analyzed the collinearity between the genetic and physical maps for chromosomes 1BS/1RS and 3D/3R (Data S2). On chromosome 1RS/1BS, the physical interval from RAC875_c13855_882 to IAAV5246 (17.3 to 173.1 Mb) was estimated to correspond to a genetic length of 2.3 cM (Fig. 4), with an average chromosomal recombination rate of 0.01 cM/Mb. However, for another homologous group 1 chromosome, the physical interval from BobWhite_c359_1026 to wsnp_Ex_c16720_25268525 (0.4 to 199.1 Mb) on chromosome arm 1DS corresponded to 37.1 cM in this RIL population, with an average chromosomal recombination rate of 0.2 cM/Mb (Fig. 4). The rate of the recombination between 1RS of 86–741 and 1BS of Chuanmai 42 was approximately 20-fold lower than the rate of the recombination of chromosome 1DS between the two parents.
For chromosome 3R/3D, the region from 50.0 Mb (RFL_Contig854_2253) to 760.1 Mb (GENE-1785_118) was estimated to correspond to a genetic length of 11.2 cM (Fig. 4), with a chromosomal recombination rate (0.02 cM/Mb) that was much lower than that (0.18 cM/Mb) for the region from 2.5 Mb (RAC875_s113853_61) to 778.3 Mb (BS00070211_51) on chromosome 3B. The rate of the recombination between 3R of 86–741 and 3D of Chuanmai 42 was more than 9-fold lower than the rate of the recombination of chromosome 3B between the two parents.
QTL mapping
On the basis of the genetic map and the recorded phenotypic data, the ICIM method was used for detecting QTLs. Four QTLs related to the IT of adult plants infected with stripe rust were identified on chromosomes 1B, 2AL, 4BL, and 7BL, with all QTLs detected in both field trials (Table 2). Among these four QTLs for SR, the QTL with a peak from Kukri_c28541_635 to wsnp_Ex_c66106_64268316 on chromosome 1B had the highest LOD value and explained approximately 40.0% of the phenotypic variation. The average LOD value and PVE of the QTL with a peak from BS00021717_51 to BS00108630_51 on chromosome 7BL were about 10.55 and 10.16%, respectively (Table 2). The alleles for both of these SR-related QTLs were from the female parent Chuanmai 42 (Table 2). Among the three stably expressed QTLs for PH, the QTL on 4DS had the highest LOD value and PVE. The male parent 86–741 had the QTL allele for decreased PH. Moreover, 86–741 also carried the minor QTL for decreased PH on chromosome 5AL (Table 2).
Table 2
QTLs for the investigated traits in the RIL population derived from a wheat-rye 1RS.1BL translocation and 3R/3D substitution line
Chromosome | Position | Trial | Left Marker of QTL peak | Right Marker of QTL peak | LOD | PVE (%) | Adda | |
Stripe rust resistance (SR) |
1B/1RS.1BL | 107 | 2015PD | Kukri_c28541_635: 336.27 Mb | IAAV5246: 336.21 Mb | 34.44 | 41.37 | -1.15 | |
1B/1RS.1BL | 108 | 2016PD | BobWhite_c4328_1345 | wsnp_Ex_c66106_64268316 | 26.91 | 38.37 | -1.13 | |
2A | 67 | 2015PD | BS00023214_51: 693.29 Mb | RAC875_c8093_605: 694.47 Mb | 5.26 | 4.36 | -0.36 | |
2A | 60 | 2016PD | wsnp_Ex_c21709_30869795: 703.88 Mb | Ra_c26702_797: 701.48 Mb | 3.26 | 3.49 | -0.33 | |
4B | 44 | 2015PD | Kukri_c1784_225: 581.31 Mb | Kukri_c322_1394: 520.24 Mb | 4.48 | 3.54 | 0.32 | |
4B | 43 | 2016PD | Tdurum_contig10137_89: 612.33 Mb | Kukri_c1784_225: 581.31 Mb | 5.96 | 6.52 | 0.45 | |
7B | 11 | 2015PD | BS00021717_51: 734.39 Mb | Excalibur_c1688_436: 733.61 Mb | 16.68 | 15.41 | -0.68 | |
7B | 18 | 2016PD | BS00010953_51: 719.72 Mb | BS00108630_51: 714.05 Mb | 4.41 | 4.91 | -0.39 | |
Plant height (PH) |
4D.1 | 45 | 2014GH | Kukri_rep_c68594_530: 12.77 Mb | wsnp_Ex_rep_c107564_91144523: 26.48 Mb | 12.43 | 23.59 | 6.86 | |
4D.1 | 44 | 2017DT | Kukri_rep_c68594_530: 12.77 Mb | wsnp_Ex_rep_c107564_91144523: 26.48 Mb | 16.73 | 28.44 | 8.44 | |
4D.2 | 6 | 2014GH | Xwmc48: 515.85 Mb | Xbarc48: 504.20 Mb | 3.02 | 7.61 | -4.23 | |
4D.2 | 0 | 2017DT | Xwmc48: 515.85 Mb | Xbarc48: 504.20 Mb | 4.58 | 6.25 | -4.56 | |
5A | 102 | 2014GH | BS00098207_51: 540.06 Mb | BS00072155_51: 540.61 Mb | 3.50 | 5.60 | 3.32 | |
5A | 102 | 2017DT | BS00098207_51: 540.06 Mb | BS00072155_51: 540.61 Mb | 4.65 | 6.44 | 3.99 | |
Grain number per spike (GNP) |
1A | 80 | 2014GH | Kukri_rep_c102900_1715: 29.19 Mb | GENE-0507_285: 31.78 Mb | 2.10 | 5.43 | 1.67 | |
1A | 63 | 2016DT | wsnp_Ex_c29914_38896441: 76.03 Mb | BobWhite_c34661_208: 96.47 Mb | 2.20 | 5.34 | 1.64 | |
1A | 79 | 2017DT | Tdurum_contig61515_259: 36.57 Mb | Tdurum_contig41233_94 | 3.11 | 6.06 | 1.88 | |
2B | 52 | 2016DT | RFL_Contig1987_3440: 555.84 Mb | BS00066545_51: 452.81 Mb | 3.97 | 9.28 | -2.08 | |
2B | 52 | 2017DT | RFL_Contig1987_3440: 555.84 Mb | BS00066545_51: 452.81 Mb | 3.91 | 8.29 | -2.33 | |
5D | 8 | 2014GH | RAC875_c4792_754: 445.32 Mb | IACX3123: 479.88 Mb | 3.60 | 10.64 | 3.61 | |
6B | 92 | 2014GH | RAC875_c6190_1173: 30.28 Mb | Excalibur_c100270_78: 31.01 Mb | 2.68 | 5.79 | 2.67 | |
Seed coat color (SCC) |
2A | 39 | 2014GH | BS00082084_51: 732.57 Mb | BS00057059_51: 729.29 Mb | 7.66 | 4.73 | -0.27 | |
3D/3R | 5 | 2014GH | D_contig05095_504: 515.26 | GENE-1785_626: 379.04 Mb | 47.54 | 50.85 | 0.89 | |
5B | 113 | 2014GH | BS00067701_51: 19.46 Mb | Excalibur_c30273_138: 17.55 Mb | 12.07 | 10.80 | 0.42 | |
6A | 11 | 2014GH | IACX5481: 609.45 Mb | TA005330-0793: 608.12Mb | 3.79 | 2.36 | 0.19 | |
Thousand grain weight (TGW) |
1B/1RS.1BL | 75 | 2014GH | Tdurum_contig42755_886: 553.14 Mb | Kukri_rep_c111991_498: 553.02 Mb | 3.09 | 5.74 | -1.69 | |
3B | 110 | 2014GH | Excalibur_c20863_179: 152.97 Mb | Tdurum_contig93037_960: 23.96Mb | 3.74 | 7.51 | -1.91 | |
3D/3R | 25 | 2016DT | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 3.55 | 7.06 | 2.11 | |
3D/3R | 3 | 2017DT | D_contig75662_409: 548.82 Mb | Xgwm314: 556.89 Mb | 6.80 | 10.46 | 2.51 | |
4D | 46 | 2016DT | Kukri_rep_c68594_530: 12.77 Mb | wsnp_Ex_rep_c107564_91144523: 26.48 Mb | 4.53 | 8.46 | 2.13 | |
4D | 45 | 2017DT | Kukri_rep_c68594_530: 12.77 Mb | wsnp_Ex_rep_c107564_91144523: 26.48 Mb | 5.64 | 8.67 | 2.31 | |
5B | 103 | 2017DT | BS00040350_51: 404.19 Mb | Kukri_rep_c105540_177: 357.11 Mb | 3.61 | 5.16 | -1.88 | |
7B | 93 | 2014GH | Kukri_c48870_115: 488.41 Mb | wsnp_Ex_c43096_49510164: 569.96 Mb | 4.56 | 9.99 | 2.26 | |
Spike number per plant (SN) |
1B/1RS.1BL | 47 | 2016DT | RAC875_c4908_1539: 622.47 Mb | BS00108257_51: 621.27 Mb | 4.46 | 7.52 | 0.35 | |
3D/3R | 26 | 2016DT | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 2.40 | 10.45 | 0.32 | |
3D/3R | 23 | 2017DT | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 6.24 | 15.14 | 0.41 | |
4D | 56 | 2016DT | Xbarc48: 504.20 Mb | D_GB5Y7FA01AGCKH_224: 506.00 Mb | 5.71 | 9.72 | 0.41 | |
5A | 111 | 2017DT | BS00013829_51: 526.40 Mb | RAC875_c10310_1486: 510.56 Mb | 3.69 | 6.40 | -0.25 | |
6A.2 | 73 | 2016DT | BS00022840_51: 545.11 Mb | TA004297-0876: 497.79 Mb | 3.06 | 5.04 | -0.28 | |
Grain weight per spike (GWP) |
2B | 43 | 2016DT | BS00090235_51: 680.41 Mb | BobWhite_c41676_137: 672.53 Mb | 7.05 | 9.94 | -0.15 | |
2B | 43 | 2017DT | BS00090235_51: 680.41 Mb | BobWhite_c41676_137: 672.53 Mb | 2.77 | 4.27 | -0.12 | |
3D/3R | 21 | 2014GH | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 4.91 | 10.97 | 0.22 | |
3D/3R | 25 | 2016DT | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 5.30 | 7.84 | 0.13 | |
3D/3R | 21 | 2017DT | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 5.43 | 12.12 | 0.19 | |
4D.1 | 48 | 2016DT | wsnp_Ex_c15977_24392258: 388.93 Mb | wsnp_Ex_rep_c79748_75305162: 408.79 Mb | 3.12 | 4.40 | 0.09 | |
4D.2 | 56 | 2014GH | wsnp_Ex_c15977_24392258: 388.93 Mb | wsnp_Ex_rep_c79748_75305162: 408.79 Mb | 2.73 | 4.09 | 0.13 | |
4D.2 | 55 | 2017DT | wsnp_Ex_c15977_24392258: 388.93 Mb | wsnp_Ex_rep_c79748_75305162: 408.79 Mb | 3.36 | 5.46 | 0.12 | |
5D | 5 | 2014GH | RAC875_c4792_754: 445.32 Mb | IACX3123: 479.88 Mb | 5.39 | 10.33 | 0.20 | |
Yield per plant (YLD) |
3D/3R | 25 | 2016DT | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 5.32 | 12.76 | 1.69 | |
3D/3R | 18 | 2017DT | GENE-1785_626: 379.04 Mb | Kukri_c88294_60: 1.75 Mb | 3.80 | 10.12 | 1.26 | |
5A | 52 | 2016DT | BS00021968_51: 677.63 Mb | BS00020605_51: 689.61 Mb | 2.94 | 7.47 | 1.20 | |
aPositive and negative, Chuanmai 42 and 86–741 allele produced larger value, respectively |
For GNP (i.e., yield component), two QTLs on chromosomes 1AS and 2BL were detected in multiple environments and were derived from Chuanmai 42 and 86–741 with increased GNP, respectively (Table 2). Two major QTLs for SCC were identified on chromosomes 3D/3R and 5BS. The QTL allele from 86–741 was associated with a white wheat seed coat. The QTL for SCC on 3D/3R explained more than 50% of the phenotypic variation. On chromosomes 3D/3R and 4DS, two QTLs for TGW were detected during both trials in the Middle–Lower Yangtze River Valley. The QTL alleles associated with increased TGW were from Chuanmai 42. Of the QTLs for SN, the QTL on 3D/3R was detected in both trials and had a PVE exceeding 10%. Furthermore, in comparison to the rye chromosome 3R of 86–741, chromosome 3D in Chuanmai 42 had QTL/allele for increased SN (Table 2).
Three stably expressed QTLs for GWP were detected on chromosomes 2BL, 3D/3R, and 4DS. The comparison with chromosomes 3R and 4D in 86–741 resulted in the detection of other QTLs for increased GWP on chromosomes 3D and 4D in Chuanmai 42. Additionally, the QTL for increased GWP on chromosome 2BL was derived from 86–741 (Table 2). One stably expressed QTL related to YLD with a PVE > 10% was detected on chromosome 3D/3R. The comparison with 3R of 86–741 indicated chromosome 3D in Chuanmai 42 contained QTL/allele for increased YLD (Table 2).
Genetic effects of rye chromosomes 1RS and 3R
Using the RIL population derived from a wheat-breeding founder parent (Chuanmai 42) from southwestern China, we examined the genetic effects of rye chromosomes 1RS and 3R by comparing the traits of RILs carrying 1RS or 3R with the traits of RILs containing 1BS or 3D. In this study, rye chromosome 1RS or 3R of 86–741 and 1BS or 3D of Chuanmai 42 were identified in the RIL population using SNP markers.
The mean IT for the RILs carrying 1RS was 5.27, suggesting they were susceptible to stripe rust, whereas the mean IT for the RILs carrying 1BS from Chuanmai 42 was 3.08, indicative of their resistance to the disease (Fig. 5). This resistance was attributed to the QTL for SR on chromosome 1BL (Table 2). Chromosome 1RS significantly affected TGW. Compared with the effects of 1BS from Chuanmai42, the presence of 1RS from 86–741 increased TGW by at least 3 g, but it also resulted in significant decreases in GNP and SN (Fig. 5). There were no differences in PH, GWP and YLD between 1RS and 1BS (Fig. 5).
For SCC, rye chromosome 3R was associated with white wheat and a decrease in the SCC value of approximately 2 (Fig. 5), likely because of the major SCC-related QTL on 3R/3D (Fig. 5). Compared with the effects of 3D from Chuanmai 42, rye chromosome 3R significantly decreased the values for several traits (TGW, SN, GWP, and YLD) (Fig. 5), but it did not significantly affect SR, PH, and GNP (Fig. 5).