Table 6 Summary for GWAS results reported so far in sesame
From: Genome-wide association study and its applications in the non-model crop Sesamum indicum
Sample size | Targeted traits | Group of traits | SNP size | SNP density | Significant associations identified | Number of candidate genes | Potential genes | References |
|---|---|---|---|---|---|---|---|---|
705 | 56 | Oil content, nutrient composition, yield components, morphological characteristics, growth cycle, coloration and disease resistance | 1,805,413 | 1SNP/50bp | 446 | 46 | - SiGL3 ~flower in lip colour - SiMYB113 & SiMYB23 ~ petiole colour - SiPPO ~oil content, seed coat color, protein content - SIN_1016759 encodes a predicted PPO ~seed coat color - CXE17 & GDSL-like lipases ~ encoding lipase - SIN_1019167 & SIN_1009923 ~encoding lipid transfer protein - SiACNA, SiDGAT2, SiFATA, SiFATB and SiSAD~ fatty acid composition - SiFAD2 ~ oleic acid desaturase - SiACS~ seed yield | [15] |
705 | 39 | Yield index, seed traits, capsule number, capsule size, and capsule pericarp | 1,805,413 | 1SNP /50bp | 646 | 48 | - SiACS8 ~capsule number - SiLPT3 ~ capsule length | [34] |
490 | 4 | Drought and salt tolerances | 1,005,413 | 2,7SNP / kb | 252 | 40 | - SiOPR3 ~ increase of abscisic acid during desiccation - SiWRKY69 ~ functioning in response to dehydration stress - SiCCD8 ~ functions as a carotenoid cleavage dioxygenase - SiMLP31~ salicylic acid synthesis - SiANTH ~ phosphatidic acid-binding protein - SiHKT1 ~ sodium transporter - SIN_1021330, SIN_1021327, SIN_1021326, SIN_1021325, SIN_1021324, SIN_1021323 and SIN_1021322~ encoding sesame peroxidase | [33] |
400 | 5 | Drought (stem length, survival rate, wilting level, capsule number and seed yield) | 1,000,939 | 5SNP /kb | 569 | 102 | - SiABI4 ~ involved in abscisic acid signal transduction - SiTTM3, SiGOLS1, SiPOD3 & SiNIMIN1 ~ involved in drought tolerance - SiSAM ~ modulates polyamine levels | [35] |
96 | 1 | Vitamin E | 5,962 | 2.3SNP /100 kb | 8 | 12 | - LG08_6621957 loci ~ γ-tocopherol - SLG03_13104062 loci ~β-tocotrienol | [36] |
87 | 1 | Phytophthora disease-resistant | 8,883 | NA | 44 | 68 | - SIN_1019026 & SIN_1019021~ regulation of pathogen-induced signaling - SIN_1019014 & SIN_1018999~ encoded F-box - SIN_1019019 & SIN_1018986~ cytochrome P450 family protein - SIN_1019026 & SIN_1019021~ encoding ubiquitin ligases and ubiquitin-related modifiers | [135] |
366 | 1 | Seed coat color | 42,781 | 1SNP/2.6kb | 224 | 92 | - SIN_1016759 ~ PPO - SIN_1023237 ~ laccase3 - SIN_1006022 ~ cytochrome P450 - SIN_1023226 & SIN_1024895 ~ WRKY and bHLH130 | [136] |
327 | 7 | Root traits | 1,000,000 | 5SNP /kb | 409 | 32 | - SiBRB | [148] |