Table 5.
Summary of the best candidate genes at the major locus qPD5.1-Pv, according to the expression data (i.e. RNA-seq and real-time qRT–PCR), the presence of a selection signature (Bellucci et al., 2014; Schmutz et al., 2014), and gene annotation of the common bean gene and its orthologues in A. thaliana and other crops
| Gene (Phvul.005) |
Location (Pv05:) | Description | Notes | Further notes |
|---|---|---|---|---|
| G156700 | 38553404–38557416 | K15718: linoleate 9S-lipoxygenase (LOX1_5) | 2 | Tightly associated with the best associated SNP S5_38611412 for pod shattering occurrence (IL population mapping) |
| G156900 | 38579286–38583074 | K15718: linoleate 9S-lipoxygenase (LOX1_5) | 2 | Tightly associated with the best associated SNP S5_38611412 for pod shattering occurrence (IL population mapping) |
| G157000 | 38584392–38587980 | K15718: linoleate 9S-lipoxygenase (LOX1_5) | 2, 4 | Tightly associated with the best associated SNP S5_38611412 for pod shattering occurrence (IL population mapping) |
| G157600 | 38638487–38640559 | PTHR10641:SF656: MYB DOMAIN PROTEIN 26 | 1, 2, 3 | A. thaliana MYB26 orthologue, tightly associated with the best associated SNP S5_38611412 for pod shattering occurrence (IL population mapping) |
| G163800 | 39127757–39136117 | LEUCINE-RICH REPEAT PROTEIN KINASE-RELATED | 2 | Tightly associated with the highly associated SNP for pod shattering occurrence SNP S5_39120955 (IL population mapping) |
| G163901 | 39140725–39145086 | PTHR27003:SF105: LEUCINE-RICH REPEAT PROTEIN KINASE-RELATED | 2, 3 | Tightly associated with the highly associated SNP for pod shattering occurrence SNP S5_39120955 (IL population mapping) |
| G161900 | 38987320–38989140 | PTHR12565:SF174: TRANSCRIPTION FACTOR BHLH87 | 3 | Similar to A. thaliana ATIND (Indehiscent) |
| G161800 | 38972673–38978648 | 2.1.1.189: 23S rRNA [uracil(747)-C(5)]- methyltransferase | 3 | |
| G165900 | 39320080–39324951 | LYSM DOMAIN RECEPTOR-LIKE KINASE | 2, 3 | |
| G157200 | 38600977–38601816 | PF12023: Domain of unknown function (DUF3511) (DUF3511) | 2, 4 | |
| G164800 | 39245115–39246843 | PTHR22835//PTHR22835:SF170: ZINC FINGER FYVE DOMAIN CONTAINING PROTEIN // SUBFAMILY NOT NAMED | 2 |
Target candidate for seed shattering based on:
Note 1: orthologues in A. thaliana and/or in other crop species have known or putative functions in the dehiscence processes, or have potentially related activities (e.g. cell wall modification, flower and fruit development).
Note 2: gene is differentially expressed (i.e. RNA-seq data), with an interesting expression pattern.
Note 3: Gene is differentially expressed (i.e. qRT–PCR) in the comparison of the near isogenic lines (three highly dehiscent introgression lines versus totally indehiscent Midas).
Note 4: presence of selection signature.