Table 3. Most significant SNP markers associated with drought resistance index (DRI) in alfalfa.
| Trait | Marker | Ref allele | Variant | Chr | p-Value | Effect | Candidate |
|---|---|---|---|---|---|---|---|
| DRI | 1_19681672 | TCT | CCG,TTG,TCA,TCG | 1 | 3.94E-06 | 0.48 | SDD |
| DRI | 2_12216981 | T | C,G | 2 | 2.03E-06 | -0.57 | - |
| DRI | 2_15380249 | TAAT | CATT,CATC,TCAT,CAAT | 2 | 7.73E-06 | -2.61 | ALDH7A1 |
| DRI | 2_5751832 | TAAG | TGAG,TAAT | 2 | 2.05E-06 | 0.08 | - |
| DRI | contig_113898_4807 | TCAAA | CCAAG,TCAAG | 2* | 1.60E-06 | -2.63 | - |
| DRI | 3_28938985 | CACTA | GACTG,CACTAA,CTCTA,CACCA,CACTG | 3 | 6.71E-06 | -2.64 | EIG-J7 |
| DRI | 3_42400246 | CGGAT | TGGAC,CGGAC | 3 | 1.76E-06 | -2.62 | AGPL |
| DRI | 4_44343064 | AGGG | GGGA,GGGG | 4 | 2.44E-06 | -2.61 | - |
| DRI | contig_102202_1102 | GG | AA,GA | 4* | 4.74E-07 | -2.63 | SRF |
| DRI | 5_21015344 | G | A,T | 5 | 3.81E-06 | 0.24 | - |
| DRI | 5_7439536 | TG | CA,CT,CG | 5 | 2.91E-06 | -2.62 | - |
| DRI | 6_18926195 | GAG | AAC,AAG,GAC | 6 | 2.18E-06 | -0.14 | - |
| DRI | 6_19756214 | TTTGTTGT | TTTGTTGTTGT,TTCATTGT,CTTGTTGT | 6 | 4.84E-07 | -2.64 | - |
| DRI | 6_21240052 | ATTT | GTCT,GTTC,GTTT | 6 | 4.99E-06 | -2.64 | NYC1 |
| DRI | 7_11861405 | CAA | CA,CAG | 7 | 3.06E-06 | -2.63 | - |
| DRI | contig_66405_1600 | TCCT | CCCA,TCTG,TCCA,TCCG | 8* | 2.81E-06 | 0.14 | - |
| DRI | contig_69188_111 | C | A | 8* | 4.47E-08 | -2.65 | - |
| DRI | contig_72424_3165 | CATTTTG | CGTTTA,CGTTTTA,CATTCTA,CATTGTG,CATTTTA | U | 9.46E-07 | -0.29 | - |
| DRI | contig_122638_1094 | TTT | ATA,ATC,CCT,CTT | U | 4.39E-06 | -2.63 | - |
Note: Ref allele, allele from the Medicago truncatula reference genome sequence assembly (ftp://ftp.ensemblgenomes.org/pub/plants/release-26/fasta/medicago_truncatula/dna/). “Chr”, chromosome assigned based on the marker
position in Medicago truncatula. “U”, unknown chromosomal location.
“*”, Unknowns were reassigned to corresponding chromosomes based on the BLAST of the flanking sequence tags against the updated version of M. truncatula genome (Mt4.0 v1). The full names of putative candidates are listed in Fig 5.