Association Mapping
Across all models and isolates, a total of 151 MTA were identified, resulting in the identification of 62 unique QTL, of which 36 are suspected of being novel and 26 previously reported and consolidated by Zhang et al. (2020) and more recent publications (Büttner et al. 2020; Cope et al. 2021; Hautsalo et al. 2021). However, when selecting only the best model for each isolate, a total of 31 MTA (28 unique SNP makers) were identified, resulting in 21 unique QTL, of which 13 are novel and nine have been previously reported and consolidated by Zhang et al. (2020). The BLINK algorithm model was selected as the best model for four isolates (GPS71-U, 13GPS149, 13GPS203 and 13GPS207), whereas the FarmCPU algorithm model was selected as the best for the remaining two isolates (E4 and 13GPS109). Using only the best model, a total of one, four, four, three, six, and three QTL were identified on barley chromosomes 1H, 2H, 3H, 4H, 5H and 7H, respectively (Fig. 4; Table 2). There was one QTL identified on the “unassigned” chromosome and no QTL identified on barley chromosome 6H, which was surprising given that chromosome 5H is typically depleted for QTL in barley - R. commune interactions. Barley row type was used as a control phenotype with most significant SNP marker (SSM) SCRI_RS_13565 on chromosome 2H at position 655,112,232 corresponding to the known row type vrs1 locus (Supplemental Figs. 3 & 4).
Isolate E4
The best model for isolate E4 was the mixed model using the FarmCPU algorithm and one principal component. Seven unique QTL were identified at the 0.01 significance threshold and an additional four at the 0.05 significance threshold, of which five are hypothesized to be novel (Table 2). Three QTL were identified on chromosome 2H, two QTL on chromosome 3H, three QTL on chromosome 5H and two QTL on chromosome 7H (Fig. 2). The loci QRrs-2H.1, QRrs-2H.2, QRrs-5H.2 and QRrs-7H.3 were all novel. QRrs-2H.1 and QRrs-2H.2 were identified on chromosome 2H at positions 579,016,838 − 579,380,380 with SSMs 12_30724 and 11_21166 and position 622,777,603 (SSM 11_20947), respectively. QRrs-5H.2 was identified on chromosome 5H at position 610,172,204 (SSM 12_10633). The last novel locus QRrs-7H.3, was identified on chromosome 7H at position 573,627,082 (SSM SCRI_RS_200020) approximately 14 Mb proximal to the locus qS271_7 (Coulter et al. 2019), but there are three insignificant markers in between QRrs-7H.3 and qS271_7 (Table 2). The first previously reported locus is QRrs-2H.3 identified on chromosome 2H at position 655,112,232 (SSM SCRI_RS_13565), approximately 3.4 Mb distal of QSc.TxFr-2H (Li and Zhou 2011), 1.5 Mb proximal of QA2 (Looseley et al. 2018). The second previously reported locus is QRrs-3H.2 identified on chromosome 3H at position 493,556,092 (SSM 12_30829), approximately 6.1 Mb distal of qC174_3 (Coulter et al. 2019), 9.9 Mb proximal of QTLSR‐3H‐2015 (Zhang et al. 2019), and within the Qsc_3H_2 locus (Hautsalo et al. 2021). The third previously identified locus is QRrs-3H.3 located on chromosome 3H at position 574,441,946 (SSM SCRI_RS_162539) located approximately 0.9 Mb distal of Rrs1, QTLSHN1999, QTLSHS2000 and QTLSHG2001 (Genger et al. 2003; Read et al. 2003), and may colocalize with the undesignated 3H locus reported in the HEB-25 association mapping (Büttner et al. 2020). The locus QRrs-5H.4 located on chromosome 5H at position 557,014,868 (SSM 11_20549) is at the same position as QTLCW5H.1 (Looseley et al. 2012) and an unnamed locus reported in the Bere landrace association mapping study using the isolate L77 (Cope et al. 2021). The locus QRrs-5H.6 was identified on chromosome 5H at location 640,002,824 (SSM SCRI_RS_155322) and is within the Qsc_5H_1 locus (Hautsalo et al. 2021). The locus QRrs-7H.2 was identified on chromosome 7H at position 66,021,760 (SSM 12_30181) located approximately 3.9 Mb proximal to QTLSR‐7H‐2017 (Zhang et al. 2019).
Isolate GPS71-U
The best model for isolate GPS71-U was the random model using the BLINK algorithm and nine principal components. A total of five QTL were identified at the 0.01 significance threshold, with one additional QTL at the 0.05 significance threshold, with a total of three out of the six being novel QTL. One QTL was identified on chromosome 3H, one QTL on chromosome 4H, three QTL on 5H and one locus that has not been assigned to a chromosome (Fig. 2). The loci QRrs-3H.1, QRrs-5H.1, and QRrs-Un.1 were all novel and identified on chromosomes 1H, 5H, and the unassigned chromosome at positions 169,952,332 (SSM 11_20866), 459,971,602 (SSM 11_21344), and 75,893,225 (SSM SCRI_RS_139563), respectively (Table 2). The first previously identified locus is QRrs-4H.1 located at position 7,870,312 (SSM 12_30540), 6.1 Mb distal of Rrs16 Hb1, Rrs16 Hb2 (Pickering et al. 2006), QSc.VlWa.4H.2 (Wang et al. 2014b), QTLVB4H.1, and QTLVB4H.3 (Wallwork et al. 2014), 6.4 Mb distal from Qsc_4H_1 (Hautsalo et al. 2021), and 2.2 Mb proximal to QA6 (Looseley et al. 2018). The second previously reported locus QRrs-5H.4, was also identified with isolate E4 as described above. The last previously identified locus was QRrs5H.6 identified on chromosome 5H at position 642,241,089 (SSM 12_30566) embedded within the Qsc_5H_1 locus (Hautsalo et al. 2021).
Isolate 13GPS109
The best model for isolate 13GPS109 was the mixed model using the FarmCPU algorithm and Q population structure. Similar to isolate GPS71-U, a total of six QTL were identified using isolate 13GPS109 at the 0.01 significance threshold and one additional QTL at the 0.05 significance threshold, with three being novel. One QTL was identified on chromosomes 1H, 2H, 3H, 4H, 5H and 7H (Fig. 2). The novel loci QRrs-1H.1, QRrs-3H.4, and QRrs-4H.3 were identified on chromosomes 1H, 3H, and 4H at positions 508,780,596 (SSM 11_10433), 667,790,880 (SSM 12_31161), and 617,971,329 (SSM 12_10824), respectively (Table 2). The first previously identified locus QRrs-2H.3 was identified on chromosome 2H at position 655,324,614 (SSM SCRI_RS_3376), approximately 3.6 Mb distal of QSc.TxFr-2H (Li and Zhou 2011) and 1.3 Mb proximal of QA2 (Looseley et al. 2018). The second previously identified locus QRrs5H.6 was identified on chromosome 7H at position 638,951,179 (SSM 12_30162) embedded within the Qsc_5H_1 locus (Hautsalo et al. 2021). The third previously identified locus QRrs-7H.1 was identified on chromosome 7H at position 15,857,316 (SSM SCRI_RS_139563) approximately 7.1 Mb distal from the boundary of Qsc_7H_1 (Hautsalo et al. 2021), 5 Mb distal of Rh2 (Schweizer et al. 1995) and 0.2 Mb proximal to Rrs12 (Abbott et al. 1991; Genger et al. 2003).
Isolate 13GPS149
The best model for isolate 13GPS149 was the mixed model using the BLINK algorithm and four principal components. A total of two QTL were identified at the 0.01 significance threshold, with one additional QTL at the 0.05 significance threshold, with two of the three being novel QTL. These QTL were identified on chromosomes 2H, 3H and 4H (Fig. 2). The novel loci QRrs-2H.1 and QRrs-4H.2 were identified on chromosomes 2H and 4H at positions 567,016,838 (SSM 12_30724) and 27,327,299 (SSM 12_10860), respectively (Table 2). The previously identified locus QRrs-3H.2 was also identified using the isolate E4 on chromosome 3H at position 493,556,092 (SSM 12_30829), approximately 6.1 Mb distal of qC174_3 (Coulter et al. 2019) and 9.9 Mb proximal of QTLSR-3H‐2015 (Zhang et al. 2019), and embedded within the Qsc_3H_2 locus (Hautsalo et al. 2021).
Isolate 13GPS203
The best model for isolate 13GPS203 was the mixed model using the BLINK algorithm and nine principal components. A total of three QTL were identified at the 0.01 significance threshold, of which two were novel and identified on chromosome 5H (Fig. 2). No additional QTL were detected at the 0.05 significance threshold. The novel loci QRrs-5H.3 and QRrs-5H.5, and QRrs-5H.6 were identified on chromosome 5H at positions 528,355,024 (SSM 12_31427), and 599,128,110 (SSM 12_30930), respectively (Table 2). The locus QRrs-5H.6 at position 638,951,179 (SSM 12_30162) was previously identified and embedded within the locus Qsc_5H_1 (Hautsalo et al. 2021).
Isolate 13GPS207
The best model for isolate 13GPS207 was the mixed model using the BLINK algorithm and four principal components. One QTL was identified at the 0.01 significance threshold and one additional QTL at the 0.05 significance threshold, with no novel loci. The first previously identified locus QRrs-5H.6 was identified on chromosome 5H at position 649,232,960 (SSM 11_10600) and embedded within the Qsc_5H_1 locus (Hautsalo et al. 2021). The previously identified locus QRrs-7H.1 was identified on chromosome 7H at position 22,774,581 (SSM 11_20495) approximately 6.7 Mb distal of Rrs12 (Abbott et al. 1991; Genger et al. 2003).