Table 3.
Comparison of SNP markers significantly associated with biomass yield under water stress (WS) and control (CTL) in different harvesting periods in the alfalfa association panel.
| Trait | Marker | SNP | Chr | 1st cut | 2nd cut | 3rd cut | Candidate | |||
|---|---|---|---|---|---|---|---|---|---|---|
| p-value | r2 | p-value | r2 | p-value | r2 | |||||
| Yield/WS | S1_11398797 | T/G | 1 | 1.45E-04 | 0.11 | 3.03E-11 | 0.31 | 3.03E-06 | 0.17 | |
| Yield/WS | S1_20593175 | A/T | 1 | 1.82E-04 | 0.1 | 1.98E-11 | 0.3 | 2.36E-06 | 0.15 | LRR |
| Yield/WS | S1_20593179 | C/T | 1 | 1.36E-04 | 0.1 | 1.70E-11 | 0.3 | 2.75E-06 | 0.15 | LRR |
| Yield/WS | S1_20593180 | A/G | 1 | 1.80E-04 | 0.1 | 1.95E-11 | 0.3 | 2.73E-06 | 0.15 | LRR |
| Yield/WS | S1_20593182 | G/T | 1 | 1.82E-04 | 0.1 | 1.98E-11 | 0.3 | 2.36E-06 | 0.15 | LRR |
| Yield/WS | S1_368369179 | T/C | 1* | 1.56E-04 | 0.1 | 1.92E-11 | 0.3 | 2.26E-06 | 0.15 | Exp1 |
| Yield/WS | S1_50692984 | T/C | 2 | 1.88E-04 | 0.1 | 1.43E-11 | 0.31 | 3.45E-06 | 0.15 | IF2 |
| Yield/WS | S1_41503160 | T/A | 2 | 5.02E-04 | 0.07 | 3.82E-06 | 0.12 | NS | NS | |
| Yield/WS | S1_324999216 | T/G | 2* | 4.45E-05 | 0.12 | 2.46E-11 | 0.31 | 3.32E-06 | 0.15 | NTF |
| Yield/WS | S1_92116984 | T/C | 3 | 3.84E-05 | 0.1 | 2.33E-12 | 0.32 | 5.38E-07 | 0.15 | |
| Yield/WS | S1_71309379 | G/C | 3 | NS | NS | NS | NS | 8.34E-06 | 0.14 | |
| Yield/WS | S1_71309383 | G/A | 3 | NS | NS | NS | NS | 8.95E-06 | 0.14 | |
| Yield/WS | S1_73439383 | A/C | 3 | NS | NS | NS | NS | 7.68E-05 | 0.12 | |
| Yield/WS | S1_276968267 | G/C | 3* | 3.92E-04 | 0.1 | 8.09E-08 | 0.21 | 3.88E-04 | 0.1 | B3 |
| Yield/WS | S1_276968408 | G/A | 3* | 4.77E-04 | 0.1 | 8.09E-08 | 0.21 | NS | NS | B3 |
| Yield/WS | S1_121767803 | C/A | 4 | 5.59E-05 | 0.12 | 1.52E-11 | 0.31 | 6.23E-07 | 0.17 | |
| Yield/WS | S1_104541975 | G/T | 4 | 1.00E-04 | 0.11 | 1.09E-11 | 0.32 | 3.00E-06 | 0.15 | |
| Yield/WS | S1_140803955 | C/T | 4 | 1.07E-04 | 0.1 | 1.69E-11 | 0.3 | 3.14E-06 | 0.15 | P4H |
| Yield/WS | S1_122448799 | T/A | 4 | 2.15E-04 | 0.1 | NS | NS | NS | NS | PPL |
| Yield/WS | S1_164595559 | G/A | 5 | 2.47E-04 | 0.09 | 6.27E-07 | 0.17 | 3.83E-05 | 0.12 | |
| Yield/WS | S1_326753692 | T/G | 6* | 8.66E-07 | 0.15 | 6.63E-05 | 0.09 | NS | NS | NCR |
| Yield/WS | S1_326753690 | T/G | 6* | 2.56E-06 | 0.13 | 1.19E-04 | 0.08 | NS | NS | NCR |
| Yield/WS | S1_323917811 | T/C | 6* | 1.89E-04 | 0.1 | 1.98E-11 | 0.3 | 3.45E-06 | 0.15 | |
| Yield/WS | S1_212244210 | C/A | 7 | 7.95E-05 | 0.13 | 7.89E-06 | 0.2 | NS | NS | PAPD7 |
| Yield/WS | S1_352766048 | A/G | 7* | 1.16E-04 | 0.1 | 2.10E-11 | 0.3 | 3.07E-06 | 0.15 | LTV1 |
| Yield/WS | S1_255810503 | T/C | 8 | 8.12E-05 | 0.11 | 1.87E-11 | 0.31 | 2.18E-06 | 0.16 | LN |
| Yield/WS | S1_251014656 | T/C | 8 | 2.01E-04 | 0.1 | 9.45E-06 | 0.13 | NS | NS | NBS-LRR |
| Yield/WS | S1_328564258 | A/G | 8* | 1.69E-04 | 0.1 | 1.61E-11 | 0.3 | 3.31E-06 | 0.15 | KIN4 |
| Yield/CTL | S1_6017132 | A/G | 1 | 2.63E-08 | 0.23 | 1.18E-08 | 0.25 | NS | NS | B3 |
| Yield/CTL | S1_276968267 | G/C | 3* | NS | NS | NS | NS | 5.80E-05 | 0.12 | B3 |
| Yield/CTL | S1_144642771 | C/T | 4 | 1.52E-05 | 0.13 | 5.92E-08 | 0.19 | NS | NS | XLIM |
| Yield/CTL | S1_213944479 | G/T | 7 | 2.89E-08 | 0.23 | 1.83E-09 | 0.28 | NS | NS | |
Chr, chromosome, “*”, markers that were reassigned to chromosomes based on the BLAST search. Underlined markers with the same 1st 5 digitals were located at the same locus. Markers identified in three and two harvests are highlighted in yellow and blue, respectively. The abbreviations of putative candidate genes are: LRR, leucine-rich repeat receptor-like kinase; Exp1, exportin 1-like protein; IF2, translation initiation factor IF-2; NTF, nucleotidyltransferase family protein; P4H, prolyl 4-hydroxylase subunit alpha-like protein; PPL, phospholipase-like protein; NCR, Nodule Cysteine-Rich (NCR) secreted peptide; PAPD7, poly(A) RNA polymerase PAPD7, LTV1, protein LTV1 homolog; LN, late nodulin, NBS-LRR, NBS-LRR type disease resistance protein, KIN4, serine/threonine-protein kinase KIN4; B3, B3 DNA-binding domain protein; XLI, xylose isomerase.