SNP markers developed by RAD-seq can generate a large number of markers, increasing the density of the map. A genetic map based on the Sorghum bicolor BTx623 x IS3620c RIL population was constructed with 399 individuals and 616 SNP markers and the map spanned 1,404.8 cM on 10 linkage groups with a 3.8 cM average between-marker distance [24]. Cui et al., (2014) [25] used three related RIL populations derived from the cross between the common parent Weimai 8 and Jimai 20, Yannong 19 and Luohan 2 to construct a genetic map containing 1,127 markers with a total length of 2,976.75 cM. Zhang et al., (2018) [26] used two related RIL populations developed from crosses of linseed and fiber flex parents to construct a consensus linkage map containing 4,497 SNP markers on 15 linkage groups with an average between-marker distance of 2.71 cM. We developed a large number of SNP markers using Rad-Seq sequencing technology and constructed a genetic map of 1,610 markers covering 10 chromosomes. The map length was 2,329 cM with the average between-marker distance of 1.45 cM. In our previous study, we constructed a genetic map of 1,065 markers with a total length of 1191.7 cM from an RIL population between sorghum Tx623A and sudangrass Sa also using RAD-seq [17]. The two maps share 18 markers and were aligned as shown in Supplementary Fig. S1. Both mapping populations use Tx623A as male parent with S722 and Sa sudangrass variety as the female parent, respectively. S722 is 17–23% taller than Tx623A (Table 2) while Sa is 30–99% taller than Tx623A [17]. Interestingly, broad-sense heritability of the same five traits ranges from 0.84 ~ 0.95 in the Tx623A × S722 population (Table 2), higher than those in the Tx623A × Sa population (0.51 ~ 0.73; Jin et al., 2021) measured in the same environments.
Among the 19 QTLs mapped in this study, 16 overlapped with previously identified QTLs (Table 4). The other three QTLs (qFW7, qDW2.1, qDW2.2) are newly discovered in this study and are of great significance for crop breeding. PH is controlled by the phytohormones through internodal elongation. Four major PH loci (Dw1, Dw2, Dw3, and Dw4) have been widely used in sorghum breeding programs. Dw1 (Sobic. 009g230800) on Chr 9 is a novel brassinosteroid (BR) signaling component and controls plant height by regulating sorghum internode length [27]. Dw2 (Sobic.006G067700) encodes a protein kinase and modifies the length of internode [27]. Dw3 on Chr 7, the first cloned Dw gene, is homologous to the maize Br2 gene and encodes a P-glycoprotein that controls auxin transport in stems [28]. Dw4 has not been identified [29].
Table 4
Colocalization of QTLs mapped in this study with previously mapped ones
This study | Previous studies |
Trait | QTL | Location | QTL | Location | Reference* |
PH | qPH1.1 | 1:12,130 − 38,171,644 | QHGHT1.35 | 0–13,145,267 | Liu et al 2019 |
QHGHT1.3 | 12,440,782 − 12,574,938 | Higgins et al 2014 |
qPH1.2 | 1:1,650,767-1,661,157 | qPH.1A.H6.1 | 0–2,100,000 | Kong et al. 2021 |
SD | qSD3 | 3:37,925,962 − 67,503,983 | QSTDM3.3 | 16,435,677 − 51,381,887 | Shiringani et al 2010 |
QSTDM3.4 | 63,660,172 − 68,225,538 | Shiringani et al 2010 |
qBD3.1 | 61,400,000–63,400,000 | Kong et al. 2020 |
SD_S3_66578380 | 66,578,380 | Wang et al. 2022 |
qSD4 | 4:2,011,330-6,901,648 | QSTDM4.1 | 2,651,777 − 11,222,066 | Shehzad and Okuno 2015 |
QSTDM4.2 | 4,415,864-7,407,064 | Shehzad and Okuno 2015 |
qSD7 | 7: 57,700,988 − 64,546,537 | qBD7.1 | 58,400,000–60,100,000 | Kong et al. 2020 |
qMD7.1 | 57,700,000–59,500,000 | Kong et al. 2020 |
qSD7.2 | 58,885,433 − 62,720,932 | Jin et al. 2021 |
TN | qTN5 | 5:51,198,317 − 51,606,021 | QTNUM5.6 | 9,124,158 − 62,582,946 | Paterson et al 1995 |
QTNUM5.5 | 10,946,850 − 54,875,177 | Shiringani et al 2010 |
qTN6 | 6:51,419,263 − 52,148,041 | QTNUM6.9 | 51,117,351 − 52,426,686 | Alam et al 2014 |
qTN6.2 | 45,156,899 − 55,463,230 | Jin et al. 2021 |
qTN7 | 7:5,092,139 − 62,923,231 | QTNUM7.4 | 7,540,868 − 58,184,111 | Kong et al 2014 |
QTNUM7.5 | 9,128,540 − 58,270,104 | Paterson et al 1995 |
TN_S7_58337639 | 58,337,639 | Wang et al. 2022 |
qTN7.1 | 55,938,458 − 57,230,541 | Jin et al. 2021 |
qTN10 | 10:18,302,795 − 56,855,620 | QTNUM10.1 | 8,804,764 − 49,486,871 | Shiringani et al 2010 |
QTNUM10.2 | 8,896,696 − 49,732,414 | Alam et al 2014 |
TN_S10_51545993 | 51,545,993 | Wang et al. 2022 |
FW | qFW1.2 | 1:12,130 − 38,171,644 | QFBMS1.1 | 12,493,718 − 15,732,609 | Guan et al 2011 |
qFW1 | 18,112,348 − 19,225,646 | Jin et al. 2021 |
qFW1.1 | 1:1,779,302 − 57,679,428 | QFBMS1.2 | 54,115,571 − 58,598,506 | Guan et al 2011 |
qFW1 | 18,112,348 − 19,225,646 | Jin et al. 2021 |
qFW2 | 2:6,206,915-6,517,439 | QFBMS2.2 | 6,052,918-6,127,702 | Shiringani & Friedt 2011 |
DW | qDW1.1 | 1:22,119,393 − 55,061,036 | QTDBM1.8 | 24,700,039–49,720,395 | Moghimi et al 2019 |
qDW1.2 | 1:8,745,436 − 74,367,828 | QTDBM1.2 | 60,851,531 − 60,987,349 | Ritter et al 2008 |
qDW1.1 | 73,913,116 − 74,754,306 | Jin et al. 2021 |
qDW7 | 7:146,957 − 13,320,446 | QTDBM7.15 | 1,336,986-1,438,127 | Moghimi et al 2019 |
| QTDBM7.2 | 7,090,658 − 55,635,259 | Felderhoff et al 2012 |
| QTDBM7.4 | 7,869,055 − 45,159,879 | Murray et al 2008 |
qDW9 | 9:4,830,760 − 57,773,165 | QTDBM9.1 | 52,235,353 − 57,911,830 | Felderhoff et al 2012 |
qDW9 | 53,517,584 − 59,086,146 | Jin et al. 2021 |
*References before 2019 was compiled by Mace et al. (2019). |
However, the PH locus qPH1.2 on chromosome 1 from 1650767–1661157 bp overlaps with qPH.1A.H6.1 located between 0-2.1 Mb mapped by Kong et al., (2021) [30] (Table 4). The qPH1.2 in 1650767–1661157 bp covers the 3’ end of Sobic.001G019800 (ubiquinone biosynthesis monooxygenase Coq6) and the whole promoter and coding region of Sobic.001G019900 (a C3HC4 zinc finger RING protein) located between 1658659 and 1661648 bp (Supplementary Figure S1). A tobacco C3HC4 zinc finger RING protein, NbZFP1, has been shown to be localized in the chloroplast, especially those in the cells surrounding leaf stoma and has been hypothesized to interact with ABA to regulate stomata opening and closing [31]. ABA is known to regulate internode elongation [32]. Overexpressing NbZFP1 in tobacco shortens internode length which produces sturdy stems [31].
Several QTLs identified in this study completely overlap with those mapped in previous studies (Table 4). qSD3 completely covers qBD3.1 mapped by Kong et al., (2020) [33] and almost completely covers QSTDM3.4 mapped by Shiringani et al., (2010) [34]. On the other hand, qSD7 completely covers both qBD7.1 and qMD7.1 mapped by Kong et al., (2020) [33] and qSD7.2 by Jin et al., (2021) [17]. Similarly, qTN10 maps a large segment of chromosome 10 as in QTNUM10.1 [34] and QTNUM10.2 [35], and qTN7 a large segment of chromosome 7 as in QTNUM7.4 [36] and QTNUM7.5 [37].
QTLs identified in this study but not previously mapped (Table 4) contains orthologs of maize SD candidate genes. For example, qSD3 is mapped to 37,925,962 − 67,503,983 bp on sorghum chromosome 3. A sorghum ortholog (Sobic.003G206600 encoding CASC3/Barentsz eIF4AIII binding protein) of the maize SD candidate gene Zm00001d011272 is located on chromosome 3 between 53720275–53728645 bp [35]. For the qSD7 locus on chromosome 7 from 57700988–64546537 bp, there are two maize SD gene orthologs. The Zm00001d031531 ortholog Sobic.007G201900 is located on chromosome 7 between 63283856–63288793 bp and code for an unknown protein and the Zm00001d031485 [38] ortholog Sobic.007G207700 is located between 63707363–63709522 bp also on chromosome 7 and code for cyclin-dependent kinase. Mutation in cyclin-dependent kinase gene in pea plants significantly reduces stem diameter [39].
In conclusion, this study mapped QTLs for PH, SD, TN, FW and DW using an RIL population derived from a sorghum × sudangrass cross. Comparison between the map generated in this study and other maps in sorghum and maize identified candidate SD genes. These genes may be examined in their role in SD in sorghum for their application in molecular breeding of forage sorghum-sudangrass hybrids.