Table 1.
Nature of SNP grouped by phenotypes.
| Phenotype categories | Genes involved (experimentally validated) | Number and nature of the molecular cause involved | No data | References | ||||||
|---|---|---|---|---|---|---|---|---|---|---|
| Total | nsSNP | InDels | 5′ or 3′UTR positions | Translocation | STR | sSNP | ||||
| Central metabolism | ||||||||||
| Nitrogen requirement, growth rate on specific nitrogen sources, ammonium and amino acid uptake, vitamin biosynthesis | GCN1, DAL1, DAL4, LST4, PUT4, GAT1, MEP2, ABZ1, ALP1, ARO1, ASI2, CPS1, LYP1, PDC1, RIM15, ASN1, AGP1, BUL2, GLT1, ADE5, ARO8, VBA3 ASI1, ARG81, BIO3, MDS3, ASP1 | 29 | 18 | 2 | 2 | 0 | 0 | 0 | 7 | (Omura et al., 2005; Marullo et al., 2007a; Ambroset et al., 2011; Kwan et al., 2011; Gutiérrez et al., 2013; Hong and Gresham, 2014; Brice et al., 2014; Ibstedt et al., 2014; Jara et al., 2014; Salinas et al., 2016; Cubillos et al., 2017) |
| Sugar catabolism, fructose, glucose, maltose, and maltotriose uptake, glucose–galactose switch, diauxic switch | HXT3, MTH1, GAL80, MAL33, MAL11, HAP4, MBR1, ADR1, BMH1, YJR030c | 10 | 10 | 0 | 0 | 0 | 0 | 0 | 0 | (Higgins et al., 1999; Segrè et al., 2006; Guillaume et al., 2007; Vidgren et al., 2009; Kvitek and Sherlock, 2011; Salinas et al., 2012) |
| Glycerol metabolism | SSK1, GPD1, HOT1, SMP1, GUT1, GAT1, YFL040W, TAO3, ADH3 | 10 | 7 | 1 | 0 | 0 | 0 | 0 | 2 | (Salinas et al., 2012; Hubmann et al., 2013a; Hubmann et al., 2013b; Swinnen et al., 2013; Wilkening et al., 2014; Tapia et al., 2018) |
| Acetic acid production | YAP1, FAS2, ASP1, ALD6 | 4 | 3 | 0 | 1 | 0 | 0 | 0 | 0 | (Inokoshi et al., 1994; Marullo et al., 2007a; Salinas et al., 2012; Cordente et al., 2013) |
| Fermentation rate and completion, fil phenotype | CYR1, GPR1, HAP4, MBR1, YJR030c, ABZ1, GDB1, MSB2, PDR1, PMA1, VMA13, PDR3, SSU1, MSN2, MSN4, RIM15, ADR1 | 18 | 15 | 1 | 1 | 1 | 0 | 0 | 0 | (Mizoguchi et al., 2002; Ambroset et al., 2011; Watanabe et al., 2011; Salinas et al., 2012; Watanabe et al., 2013; Cubillos, 2016; Martí-Raga et al., 2017; Peltier et al., 2018) |
| Resistance to toxins and stresses | ||||||||||
| Ethanol accumulation capacity, ethanol tolerance, growth on ethanol | ADE1, KIN3, SSD1, UTH1, VPS70, IAI11, APJ1, MKT1, SWS2, MEX67, PRT1, VPS70, SPT5, TAO3 | 14 | 12 | 0 | 2 | 0 | 0 | 0 | O | (Yang et al., 2011; Avrahami-Moyal et al., 2012; Salinas et al., 2012; Swinnen et al., 2012b; Hubmann et al., 2013a; Hubmann et al., 2013b; Pais et al., 2013; Duitama et al., 2014; Wilkening et al., 2014; Voordeckers et al., 2015) |
| High-temperature growth, temperature tolerance, low temperature adaptation, freezing tolerance | CDC19, IRA1, IRA2, RSP5, END3, MKT1, RHO2, NCS2, TAO3, PRP42, SMD2, GAA1, FPK1, OPT2, PET494, QCR2, OYE2, VHS1 | 18 | 14 | 0 | 2 | 0 | 0 | 1 | 1 | (Sinha et al., 2006; Sinha et al., 2008; Parts et al., 2011; Benjaphokee et al., 2012; Shahsavarani et al., 2012; Li et al., 2013; Wilkening et al., 2014; García-Ríos et al., 2017; Marullo et al., 2019) |
| Stress tolerance, oxidative, osmotic | PRO1, MPR1, AQY1, AQY2, RCK2, MOT2, MPR1, RDS2, PUT1, SPT5 | 12 | 8 | 4 | 0 | 0 | 0 | 0 | 0 | (Sekine et al., 2007; Takagi, 2008; Will et al., 2010; Diezmann and Dietrich, 2011; Dhar et al., 2011; Sasano et al., 2012; Greetham et al., 2014) |
| Toxins resistance: acidic, basic, phenolic compounds, SO2 | WAR1, ADH3, ASG1, GIS4, SKS1, COX20, CUP2, DOT5, GLO1, VMA7, HAA1, CDC23, ECM21, GPH1, IES2, MAC1, NMD4, SGT2, SPS100, LEU3, MNE1, SAP190, ADH1, MKT1, RAD5, UBP7, SSU1 | 31 | 12 | 0 | 4 | 2 | 0 | 3 | 11 | (Pérez-Ortín et al., 2002; Boaz et al., 2008; Demogines et al., 2008; Romano et al., 2010; Yang et al., 2011; Brion et al., 2013; Zimmer et al., 2014 Pinel et al., 2015; González-Ramos et al., 2016; Meijnen et al., 2016; Swinnen et al., 2017; Sardi et al., 2018) |
| Organoleptic compounds production | ||||||||||
| Acids, higher alcohols, and relative ester production | IXR1, LEU9, RGS2, RGT1, FAS2, ABZ1, TOR1, NRG1, FLX1, MDH2, AGP1, ALP1, ILV6, MAE1, AGP2, FAS1, SIR2, EAT1, SNF8 | 19 | 19 | 0 | 0 | 0 | 0 | 0 | 0 | (Akada et al., 1999; Salinas et al., 2012; Steyer et al., 2012; Trindade de Carvalho et al., 2017; Eder et al., 2018) |
| Sulfur compounds | MET10, MET5, MET2, IRC7, URE2, SKP2, MET6, CYS4, SSU1 | 9 | 5 | 1 | 0 | 1 | 0 | 0 | 2 | (Cordente et al., 2009; Linderholm et al., 2010; Huang et al., 2014; Noble et al., 2015) |
| Other aromas | PAD1, PDR8, ERG20 | 3 | 3 | 0 | 0 | 0 | 0 | 0 | 0 | (Chambon et al., 1991; Steyer et al., 2013) |
| Adhesion, flocculation, clumpiness | FLO1, SFL1, GPA1, AMN1, RGA1, CDC28, FLO8, END3, IRA2, MSS11, TRR1, FLO11 | 17 | 13 | 0 | 0 | 0 | 3 | 1 | 0 | (Yvert et al., 2003; Verstrepen et al., 2005; Fidalgo et al., 2006; Nogami et al., 2007; Yang et al., 2011; Li et al., 2013; Taylor and Ehrenreich, 2014; Wilkening et al., 2014) |