Phenotypic analysis of wheat processing quality
The five parents of the NAM population had different dough rheological characteristics (Fig. 1A). Among of them, HU (Hussar) had the best dough characteristics, while the dough characteristics of YZ (Yanzhan 1) and YN (Yunnanxiaomai) were poor. We found that the common parent YZ had a longer MlPT (midline peak time), wider PkWd (peak width) and wider WdEm (width at eight minutes) compared with other parents, CY (Chayazheda 29) and YN, and had the smallest MlPH (midline peak height) compared with the other four donor parents. HU had the highest values in all dough rheological characteristics compared with the other four parents, which indicated that HU had optimal dough characters. CY had a longer MlPT, wider PkWd and wider WdEm than YN. YN had a wider MlPH than YZ, CY and YT, but the shortest MlPT and the narrowest WdEm compared with the other four parents. Compared with YZ, CY and YN, YT (Yutiandaomai) had the longest MlPT, widest WdEm and narrowest PkWd. Observing the phenotypic data distribution of the NAM population, there is strong transgressive segregation for all dough rheological characteristic in each RIL population except for the MlPT of HU-RILs (Fig. 1B, Table S1).
To evaluate the pairwise correlations between dough rheological characteristics, the Pearson’s correlation was estimated using BLUP (best linear unbiased prediction) values combined over four environments (Fig. 1C). WdEm was significantly positively correlated with MlPT and PkWd, but significantly negatively correlated with MlPH. PkWd was significantly positively correlated with MlPT and MlPH. The correlation between MlPT and MlPH was not significant.
The heritabilities of dough rheological characteristics in the NAM population were 42.7–84.7%, and it was differed largely in four RIL populations (Table S2). PKWD is a relatively important dough rheological parameter to measure wheat processing quality, and its phenotype is greatly affected by the environment (42.7 –59.7%). Among them, the heritabilities of HU-RILs and YT-RILs populations were higher, whereas that in the YN-RILs population was lower.
QTL analysis of wheat processing quality
A total of 49 QTL were detected on chromosomes 1A (2), 1B (17), 1D, 2A, 2B (3), 3B (11), 4A, 4B, 4D (2), 5A, 5B (3), 5D, 6A (2), 7A, and 7B (2) for wheat processing quality in four individual environments and combined QTL analysis (Fig. 2, Table S3). Ten, eighteen, eleven, and ten QTL were identified for MlPT, MlPH, PkWd and WdEm, respectively. These QTL explained 0.36–10.82% of the phenotypic variation. Thirty-four of these QTL were identified in the individual environment and the combined environment analysis. The favorable alleles of two, seven, six, ten and twenty-four QTL were provided by parents CY, YN, YT, HU and YZ, respectively (Table S4).
For MlPT, ten QTL were found on chromosomes 1A, 1B (4), 3B (2), 4B, 5A, and 7B in four environments and the combined environment analysis, explaining a range of 1.47% to 8.29% of the phenotypic variation (Fig. 2, Table S3). Six of those QTL were detected in the individual environment and combined environment analyses. One stable QTL, QMlPT-1B.2, had a favorable allele from YT and was found in two individual environments and the combined environment analysis, explaining 2.20–3.66% of the phenotypic variation. The donor parent YN contributed the best favorable allele for QMlPT-3B.1, which was stably detected in three individual environments, explaining 2.86–4.14% of the phenotypic variation. Five QTL, including QMlPT-1A, QMlPT-1B.3, QMlPT-1B.4, QMlPT-4B and QMlPT-7B, were identified in one environment and the combined environment analysis, with 4.15–8.29%, 2.80–3.28%, 3.31–4.19%, 2.74–3.11% and 1.47–4.02% of the phenotypic variation, respectively. QMlPT-1B.1, QMlPT-3B.2 and QMlPT-5A with respectively 3.71–6.38, 3.08–8.03 and 2.66–4.88 of the LOD value, were found in two environments, accounting for 2.24–5.42%, 2.07–3.70% and 1.78–1.82% of the phenotypic variation, respectively. The favorable alleles of two and three QTL of the ten QTL were provided by semi-wild parents YN and YT, respectively, while the one and four QTL of the remaining QTL were provided by domesticated parents HU and YZ, respectively (Table S4).
For MlPH, 18 QTL were identified, which were distributed on chromosomes 1B (6), 2B, 3B (5), 4D, 5B (2), 5D, 6A, and 7B in four environments and the combined environment analysis, explaining 0.36–10.82% of the phenotypic variation (Fig. 2, Table S3). Twelve of the eighteen QTL were detected in both individual environments and the combined environment analysis. The favorable alleles of two stable QTL (QMlPH-3B.3 and QMlPH-3B.4) were contributed by HU, which were identified in all four environments and the combined environment analysis, explaining 1.50–8.60% and 1.71–10.82% of the phenotypic variation, respectively. QMlPH-1B.4, a favorable allele from common parent YZ, was stably found in four environments, with 4.01–9.75 of the LOD value and 1.42–4.50% of the phenotypic variation. QMlPH-1B.3 and QMlPH-5D with 5.18–10.25 and 3.21–5.99 of the LOD value, respectively, were stably detected in two environments and the combined environment analysis, accounting for 1.15–4.90% and 1.10–2.21% of the phenotypic variation, respectively. Eight QTL, including QMlPH-1B.5, QMlPH-1B.6, QMlPH-3B.1, QMlPH-4D, QMlPH-5B.1, QMlPH-5B.2, QMlPH-6A and QMlPH-7B, were detected in one environment and the combined environment analysis. In addition, five QTL, including QMlPH-1B.1, QMlPH-1B.2, QMlPH-2B, QMlPH-3B.2 and QMlPH-3B.5, were identified in two environments. Three OTL with favorable alleles were detected in the three semi-wild parents CY, YN, and YT (Table S4). Compared with the other four parents, the alleles of domesticated parent HU increased the MlPH for five QTL, while the common parent YZ decreased MlPH for ten QTL.
For PkWd, eleven QTL were stably detected on chromosomes 1A, 1B (4), 2B, 3B (2), 4A, 6A, and 7A, explaining 0.55–6.09% of the phenotypic variation (Fig. 2, Table S3). All of these QTL except for QPkWd-1B.1 were identified in both individual environments and the combined environment analysis. QPkWd-3B.1 and QPkWd-3B.2 are favorable alleles from common parent YZ, and were detected in three and more environments. In five QTL (QPkWd-1B.2, QPkWd-1B.3, QPkWd-1B.4, QPkWd-4A and QPkWd-6A), the alleles increasing PkWd were provided by YZ, accounting for 1.74–5.31%, 1.85–4.70%, 1.93–4.85%, 0.76–3.02% and 1.49–3.37% of the phenotypic variation, respectively. In QPkWd-1A and QPkWd-7A, the alleles increasing PkWd were donated by HU, with 5.85–7.29 and 3.04–3.36 of the LOD value, respectively, and accounting for 2.15–2.81% and 1.12–2.88% of the phenotypic variation respectively. In addition, in QPkWd-1B.1 and QPkWd-2B, the alleles decreasing PkWd were provided by CY and YT, respectively, accounting for 0.96–4.80% and 0.55–4.16% of the phenotypic variation, respectively.
For WdEm, ten QTL were detected on chromosomes 1B (3), 1D, 2A, 2B, 3B (2), 4D, and 5B in individual environmental and combined environment analysis, accounting for 0.51–9.70% of the phenotypic variation (Fig. 2, Table S3). Six QTL were identified in both individual environments and the combined environment analysis. Two QTL, QWdEm-1B.2 and QWdEm-3B.1, were stably identified in three environments and the combined environment analysis, with 4.70–5.78 and 4.44–16.13 of the LOD value, respectively, and explaining 0.51–2.42% and 2.14–8.82% of the phenotypic variation, respectively. QWdEm-1B.1 and QWdEm-1B.3 had 4.14–4.89 and 4.87–6.87 of the LOD value, respectively, and were detected in two environments and the combined environment analysis. In these two QTL, the alleles decreasing WdEm were donated by YN, accounting for 1.19–2.73% and 1.75–3.25% of the phenotypic variation, respectively. The alleles in HU had increased WdEm for two QTL, QWdEm-2A and QWdEm-4D, which explained 2.34–4.05% and 0.85–2.12% of the phenotypic variation, respectively. For QWdEm-1D and QWdEm-2B, favorable alleles were donated by YT and YN, respectively. Favorable alleles of three QTL, QWdEm-3B.1, QWdEm-3B.2, and QWdEm-5B, were provided by common parent YZ. Among the ten QTL for WdEm, the favorable alleles of four and one QTL were provided by semi-wild parents YN and YT, respectively. In addition, two and three QTL were provided by domesticated parents HU and YZ, respectively (Table S4).
Eight important genetic regions for wheat processing quality
In this study, eight important genetic regions were found on chromosomes 1B (4), 3B (3), and 4D (Table 1). QG-3B.1 was associated with all dough rheological characteristics, QMlPT-3B.1, QMlPH-3B.3, QPkWd-3B.1, and QWdEm-3B.1, within 4.71 Mb of physical distance. Three genetic regions, QG-1B.3, QG-3B.2, and QG-4D, influence MlPH and WdEm. QG-1B.2, located on flank markers BS00047700_51–IAAV4866, was associated with MlPT, MlPH, and PkWd. QG-1B.4, located on flank marker tplb0048b10_1365–Ku_c28580_432, influences dough rheological characteristics MlPT, MlPH, and WdEm. In addition, QG-1B.1 and QG-3B.3 were located on flank markers wsnp_Ku_rep_c70742_70379526–tplb0059c20_2221 and wsnp_Ex_c64005_62987067–wsnp_BE497740B_Ta_2_1 respectively, which influence PkWd and WdEm, and PkWd and MlPT, respectively.