Table 3 Candidate genes for amino acid traits as identified by a priori candidate genes from amino acid biosynthesis and degradation pathways
Trait | SNP | Chr | Position (bp)a | candidate gene | Distance (kb)b | Annotation | Pathwayc |
|---|---|---|---|---|---|---|---|
Asp family | 1:10068032 | 1 | 10,068,032 | Sobic.001G127700 | −25.64 | similar to Lysine Decarboxylase, putative | lysine degradation I |
Leu/BCAA | 1:1014946 | 1 | 1,014,946 | Sobic.001G011700 | −4.06 | similar to Aspartokinase | superpathway of lysine, threonine and methionine biosynthesis II |
Val/BCAA | 1:24852243 | 1 | 24,852,243 | Sobic.001G241200 | −21.77 | similar to EDR1 | threonine degradation III (to methylglyoxal) |
Ile/BCAA | 1:69010559 | 1 | 69,010,559 | Sobic.001G405500 | 4.08 | similar to Pyruvate decarboxylase isozyme 2 | superpathway of leucine, valine, and isoleucine biosynthesis |
Phe/Shikimate family | 1:69010559 | 1 | 69,010,559 | Sobic.001G405500 | 4.08 | similar to Pyruvate decarboxylase isozyme 2 | superpathway of leucine, valine, and isoleucine biosynthesis |
Tyr/Shikimate | 1:69010559 | 1 | 69,010,559 | Sobic.001G405500 | 4.08 | similar to Pyruvate decarboxylase isozyme 2 | superpathway of leucine, valine, and isoleucine biosynthesis |
Leu/BCAA | 1:72963758 | 1 | 72,963,758 | Sobic.001G453100 | −10.87 | similar to Homocysteine S-methyltransferase 1 | superpathway of lysine, threonine and methionine biosynthesis II |
Lys | 2:13818293 | 2 | 13,818,293 | Sobic.002G113600 | 15.98 | similar to Rac GTPase activating protein 3-like protein | superpathway of lysine, threonine and methionine biosynthesis II |
Ile/Asp family | 2:4671226 | 2 | 4,671,226 | Sobic.002G049200 | −15.65 | weakly similar to PHD finger transcription factor-like | superpathway of leucine, valine, and isoleucine biosynthesis |
Thr/Asp family | 2:58060555 | 2 | 58,060,555 | Sobic.002G193800 | 15.95 | GLUCOSE TRANSPORTER TYPE 1 | superpathway of lysine, threonine and methionine biosynthesis II |
Leu/Pyruvate | 3:11583493 | 3 | 11,583,493 | Sobic.003G126500 | 17.82 | similar to Os01g0269000 protein | leucine degradation I |
Ala/Pyruvate | 3:3063590 | 3 | 3,063,590 | Sobic.003G033900 | 26.43 | similar to 1-aminocyclopropane-1-carboxylic acid synthase | phenylalanine degradation III |
Ala/total | 3:5411028 | 3 | 5,411,028 | Sobic.003G061300 | −17.63 | Thiamine pyrophosphate dependent pyruvate decarboxylase family protein | superpathway of leucine, valine, and isoleucine biosynthesis |
Leu/Pyruvate | 3:57321213 | 3 | 57,321,213 | Sobic.003G234701 | 12.80 | similar to Pectin-glucuronyltransferase-like | arginine degradation I (arginase pathway) |
Gly | 3:70271670 | 3 | 70,271,670 | Sobic.003G391600 | 9.40 | similar to Putative 4-coumarate:coenzyme A ligase | superpathway of lysine, threonine and methionine biosynthesis II |
Lys | 4:11594929 | 4 | 11,594,929 | Sobic.004G114500 | −18.26 | Core-2/I-branching beta-1,6-N-acetylglucosaminyltransferase family protein | glycine cleavage complex |
Ser | 4:1351183 | 4 | 1,351,183 | Sobic.004G016800 | −22.65 | similar to Putative serine/threonine protein kinase | threonine degradation III (to methylglyoxal) |
Thr/total | 4:49321838 | 4 | 49,321,838 | Sobic.004G156000 | 10.33 | similar to Putative steroleosin | lysine degradation II |
Leu/Pyruvate family | 4:65472831 | 4 | 65,472,831 | Sobic.004G319400 | −16.93 | similar to DNA helicase RECQE-like | superpathway of leucine, valine, and isoleucine biosynthesis |
Val/BCAA | 4:65472831 | 4 | 65,472,831 | Sobic.004G319400 | −16.93 | similar to DNA helicase RECQE-like | superpathway of leucine, valine, and isoleucine biosynthesis |
Glu/Glutamate family | 5:3605534 | 5 | 3,605,534 | Sobic.005G039700 | 10.91 | similar to Rac GTPase activating protein 1 | superpathway of lysine, threonine and methionine biosynthesis II |
Pro | 5:3605534 | 5 | 3,605,534 | Sobic.005G039700 | 10.91 | similar to Rac GTPase activating protein 1 | superpathway of lysine, threonine and methionine biosynthesis II |
Pro/Glutamate family | 5:3605534 | 5 | 3,605,534 | Sobic.005G039700 | 10.91 | similar to Rac GTPase activating protein 1 | superpathway of lysine, threonine and methionine biosynthesis II |
Lys | 5:5579891 | 5 | 5,579,891 | Sobic.005G055300 | – | similar to Tropinone reductase | lysine degradation II |
Lys | 5:5579891 | 5 | 5,579,891 | Sobic.005G055300 | – | similar to Tropinone reductase | phenylalanine degradation III |
Lys | 5:5579891 | 5 | 5,579,891 | Sobic.005G055400 | 1.07 | similar to Amidase family protein | arginine degradation X (arginine monooxygenase pathway) |
Val/BCAA | 5:63968450 | 5 | 63,968,450 | Sobic.005G164200 | 2.49 | similar to Putative uncharacterized protein | superpathway of leucine, valine, and isoleucine biosynthesis |
Val/BCAA | 5:63968450 | 5 | 63,968,450 | Sobic.005G164300 | 6.84 | similar to Putative uncharacterized protein | superpathway of leucine, valine, and isoleucine biosynthesis |
Ile/BCAA | 5:67881473 | 5 | 67,881,473 | Sobic.005G194900 | −22.93 | similar to Phosphoserine phosphatase | superpathway of serine and glycine biosynthesis I |
Val/Pyruvate | 5:67881473 | 5 | 67,881,473 | Sobic.005G194900 | −22.93 | similar to Phosphoserine phosphatase | superpathway of serine and glycine biosynthesis I |
Val/BCAA | 5:67881473 | 5 | 67,881,473 | Sobic.005G194900 | −22.93 | similar to Phosphoserine phosphatase | superpathway of serine and glycine biosynthesis I |
Val/total | 5:67881473 | 5 | 67,881,473 | Sobic.005G194900 | −22.93 | similar to Phosphoserine phosphatase | superpathway of serine and glycine biosynthesis I |
Met/Asp family | 5:69690963 | 5 | 69,690,963 | Sobic.005G210500 | 20.74 | similar to ATP-dependent DNA helicase, RecQ family protein, expressed | superpathway of leucine, valine, and isoleucine biosynthesis |
Leu/BCAA | 6:54237869 | 6 | 54,237,869 | Sobic.006G187900 | −0.29 | similar to Acc synthase | phenylalanine degradation III |
Leu/BCAA | 6:54237869 | 6 | 54,237,869 | Sobic.006G187900 | −0.29 | similar to Acc synthase | tyrosine degradation I |
Tyr/total | 7:60330803 | 7 | 60,330,803 | Sobic.007G168200 | −14.06 | similar to Peptidyl-prolyl cis-trans isomerase | phenylalanine degradation III |
Tyr/total | 7:60330803 | 7 | 60,330,803 | Sobic.007G168200 | −14.06 | similar to Peptidyl-prolyl cis-trans isomerase | tyrosine degradation I |
Leu/Pyruvate | 8:1074094 | 8 | 1,074,094 | Sobic.008G012400 | −27.01 | similar to Os11g0142500 protein | superpathway of leucine, valine, and isoleucine biosynthesis |
Ala/total | 8:51569085 | 8 | 51,569,085 | Sobic.008G111100 | 1.99 | Predicted transporter (major facilitator superfamily) | superpathway of lysine, threonine and methionine biosynthesis II |
Leu/Pyruvate | 8:52368227 | 8 | 52,368,227 | Sobic.008G114900 | 18.62 | similar to Rac GTPase activating protein 3, putative, expressed | superpathway of lysine, threonine and methionine biosynthesis II |
Leu/Pyruvate | 8:59438201 | 8 | 59,438,201 | Sobic.008G160700 | −28.52 | similar to Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor | leucine degradation I |
Glu/Glutamate family | 8:5993722 | 8 | 5,993,722 | Sobic.008G057500 | 1.10 | similar to Aldehyde dehydrogenase family protein | arginine degradation I (arginase pathway) |
Pro/Glu family | 8:5993722 | 8 | 5,993,722 | Sobic.008G057500 | 1.10 | similar to Aldehyde dehydrogenase family protein | arginine degradation I (arginase pathway) |
Hist/total | 10:6862967 | 10 | 6,862,967 | Sobic.010G080300 | −16.74 | similar to Putative aminoacylase | superpathway of lysine, threonine and methionine biosynthesis II |
Cys | 10:8489698 | 10 | 8,489,698 | Sobic.010G094900 | 9.71 | similar to Putative uncharacterized protein | Tryptophan degradation III (eukaryotic) |
Cys/total | 10:8489698 | 10 | 8,489,698 | Sobic.010G094900 | 9.71 | similar to Putative uncharacterized protein | Tryptophan degradation III (eukaryotic) |
Val/BCAA | 10:55465480 | 10 | 55,465,480 | Sobic.010G212000 | 25.56 | similar to Putative uncharacterized protein | arginine degradation I (arginase pathway) |
Val/BCAA | 10:55465480 | 10 | 55,465,480 | Sobic.010G212000 | 25.56 | similar to Putative uncharacterized protein | proline degradation I |
Val/BCAA | 10:55465480 | 10 | 55,465,480 | Sobic.010G212000 | 25.56 | similar to Putative uncharacterized protein | proline degradation II |
Val/BCAA | 10:55465480 | 10 | 55,465,480 | Sobic.010G212000 | 25.56 | similar to Putative uncharacterized protein | valine degradation I |