Table 3.
Description of the 33 selected genomic regions being associated with at least four traits
| Region | MTA-QTLs | Chr | Region (Mb) | Associated traits | Genes | Closest gene | Annotation | Co-localize |
|---|---|---|---|---|---|---|---|---|
| R1A.1 | 1A.3, 1A.4 | 1A | 34.02–42.08 | Ar, Majell, Minell, TKW** | 90 | TraesCS1A03G0122300 | RING/U-box superfamily protein | – |
| R1A.2 | 1A.16 | 1A | 463.47–464.49 | Perim, Majell, GrnSpk**, SpkLng | 15 | TraesCS1A03G0679900 | Chaperone protein dnaJ | – |
| R1B.2 | 1B.32, 1B.33, 1B.34 | 1B | 505.29–525.4 | Ar, Perim, Majell, Minell, TKW***, SpkLng | 110 | TraesCS1B03G0804700 | UPF0503 protein, chloroplastic | Ma et al. (2022) |
| R1B.4 | 1B.39 | 1B | 573.83—578.27 | Ar, Perim, Majell, TKW** | 37 | TraesCS1B03G0935200 | Formin-like protein | Liu et al. (2020), Ma et al. (2022) |
| R1D.1 | 1D.60 | 1D | 422.94–435.17 | Ar, Perim, Majell, TKW* | 145 | TraesCS1D03G0780700 | Formin-like protein | Ma et al. (2022) |
| R2B.1 | 2B.91 | 2B | 230.57–235.85 | Ar, Perim, Majell, SpkLng | 29 | TraesCS2B03G0551900 | Protein phosphatase-2c, putative | Cao et al. (2020), Yang et al. (2021) |
| R2B.2 | 2B.92, 2B.93 | 2B | 237.56–245.95 | Perim, Majell, SpkLng, DM | 60 | TraesCS2B03G0568500 | Mitochondrial pyruvate carrier | Cao et al. (2020 |
| R2B.4 | 2B.100 | 2B | 690.25–697.81 | Ar, Perim, Majell, TKW** | 64 | TraesCS2B03G1224900 | Multidrug resistance protein ABC transporter family protein | Liu et al. (2020) |
| R2B.6 | 2B.110, 2B.111 | 2B | 752.7–757.03 | Ar, Perim, Majell, Minell, TKW*** | 39 | TraesCS2B03G1379000 | Methylcytosine binding domain protein | Liu et al. (2020) |
| R2B.7 | 2B.112 | 2B | 758.29–758.42 | Ar, Perim, Majell, TKW** | 4 | TraesCS2B03G1392800 | Anthocyanin 5-aromatic acyltransferase | Liu et al. (2020) |
| R3A.1 | 3A.131, 3A.132 | 3A | 550.76–568.22 | Ar, Perim, Minell, TKW** | 132 | TraesCS3A03G0766300 | Purple acid phosphatase | – |
| R3B.1 | 3B.139, 3B.140, 3B.141 | 3B | 12.61–16.82 | Ar, Perim, Majell, TKW***, SpkLng | 83 | TraesCS3B03G0058000 | Cytochrome P450, putative, expressed | Yang et al. (2021) |
| R3B.2 | 3B.145 | 3B | 249.38–258.96 | Ar, Perim, Majell, TKW*** | 62 | TraesCS3B03G0503100 | 30S ribosomal protein S5 | Liu et al. (2020) |
| R3B.3 | 3B.148, 3B.149 | 3B | 517.99–535.10 | Minell, GrnSpk, SpkLng, PH** | 70 | TraesCS3B03G0811300 | GDSL esterase/lipase | Yang et al. (2021) |
| R3B.4 | 3B.155, 3B.156, 3B.157 | 3B | 619.28–638.59 | Ar, Perim, Minell, TKW**** | 112 | TraesCS3B03G0984700 | No note registered for this gen | – |
| R4A.2 | 4A.182 | 4A | 612.61–614.01 | Perim, Majell, SplN, DM | 30 | TraesCS4A03G0817700 | DEAD-box ATP-dependent RNA helicase 52A | Cao et al. (2020), Ma et al. (2022), Yang et al. 2021) |
| R4D.1 | 4D.198 | 4D | 12.32–25.31 | Ar, Perim, Majell, TKW* | 210 | TraesCS4D03G0082900 | Zinc-finger domain of monoamine-oxidase A repressor R1, putative | Cao et al. (2020), Liu et al. (2020), Yang et al. (2021) |
| R5A.1 | 5A.200 | 5A | 49.59–136.02 | Ar, Perim, Majell, DM | 421 | TraesCS5A03G0141900 | Nitrate transporter 1.2 | Cao et al. (2020) |
| R5A.2 | 5A.202, 5A.203, 5A.204, 5A.205 | 5A | 459.1- 467.06 | Ar, Perim, Majell, SpkLng, GrnSpk* | 55 | TraesCS5A03G0617500 | Cyclin | Cao et al. (2020), Liu et al. (2020) |
| R5A.3 | 5A.212, 5A.213 | 5A | 584.83–588.52 | Ar, Perim, Majell, TKW* | 61 | TraesCS5A03G0931300 | Beta-glucosidase | Cao et al. (2020), Yang et al. (2021) |
| R5A.4 | 5A.216, 5A.217, 5A.218, 5A.219, 5A.220 | 5A | 590.25–596.91 | Ar, Perim, Majell, Minell, TKW*** | 102 | TraesCS5A03G0954900 | Zinc-finger protein | Liu et al. (2020) |
| R5A.5 | 5A.221 | 5A | 615.67–616.16 | Ar, Perim, Majell, TKW* | 9 | TraesCS5A03G1017500 | Blue copper protein | Liu et al. (2020) |
| R5A.6 | 5A.225 | 5A | 673.15–675.35 | Ar, Perim, Majell, TKW*, SpkLng | 31 | TraesCS5A03G1195900 | Sugar transporter protein | Yang et al. (2021) |
| R5A.7 | 5A.229, 5A.230, 5A.231 | 5A | 705.07–708.08 | Minell, GrnSpk**, SpkLng, PH** | 37 | TraesCS5A03G1283300 | Dirigent protein | Cao et al. (2020) |
| R5B.1 | 5B.246 | 5B | 607.47–609.33 | Ar, Perim, Majell, TKW* | 28 | TraesCS5B03G1055600 | MD-2-related lipid recognition domain-containing protein/ML domain-containing protein | Ma et al. (2022) |
| R5B.3 | 5B.249, 5B.250, 5B.251, 5B.252 | 5B | 645.07–662.73 | Ar, Perim, Majell, DM | 227 | TraesCS5B03G1158800 | Protein ELC | Ma et al. (2022) |
| R6A.1 | 6A.265, 6A.266 | 6A | 66.41–84.24 | Ar, Perim, Majell, TKW*, PH* | 166 | TraesCS6A03G0222800 | Tryptophan synthase beta chain | Cao et al. (2020), Liu et al. (2020) |
| R6A.2 | 6A.271, 6A.272 | 6A | 524.5–539.75 | Ar, Perim, Majell, Minell | 132 | TraesCS6A03G0791700 | TPR repeat-containing thioredoxin TTL4 | Cao et al. (2020) |
| R6A.3 | 6A.278, 6A.279, 6A.280 | 6A | 577.41–586.13 | Majell, TKW*, GrnSpk*, SpkLng, | 95 | TraesCS6A03G0893300 | Sugar transporter family protein, expressed | Cao et al. (2020), Yang et al. (2021) |
| R7A.1 | 7A.322, 7A.323, 7A.324 | 7A | 617.38–621.40 | Ar, Perim, Majell, Minell, TKW** | 37 | TraesCS7A03G1031200 | Serine/threonine-protein kinase | Liu et al. (2020), Ma et al. (2022) |
| R7B.1 | 7B.340 | 7B | 234.61–248.39 | Ar, Perim, Minell, TKW*** | 61 | TraesCS7B03G0447700 | Glutamate dehydrogenase | Ma et al. (2022) |
| R7B.2 | 7B.343 | 7B | 688.21–690.48 | Ar, Perim, Majell, TKW*** | 17 | TraesCS7B03G1115100 | tumour necrosis factor receptor family protein | Liu et al. (2020 |
| R7D.1 | 7D.352, 7D.353, 7D.354 | 7D | 221.8–372.34 | Ar, Perim, Majell, Minell, TKW** | 461 | TraesCS7D03G0643100 | Defective in cullin neddylation protein | Cao et al. (2020), Liu et al. (2020), Ma et al. (2022) |
Ar Area; Perim Perimeter; Majell Major Ellipse; Minell Minor ellipse; TKW Thousand Kernel Weight; SpkLng Spike Length. For TKW, number of * indicate the number of years for which associations were found