TABLE 1

List of QTL detected for each domestication trait

TraitQTLEggplant linkage groupTomato chromosomeLocationSignificant marker(s)P value% PVEd/a
Fruit weight (fw) fw2.1 22FRTG469-ofx0.00223–0.8
fw9.1 99NYTG589-TG350.00544–0.1
fw11.1 114S–11SFR TG523 0.00919–7.3
Fruit length (fl) fl2.1 22NYTG469-orfx-CT90.00223–0.3
22FRTG469-orfx-CT240.000429–0.4
fl9.1 99NYTG589-CD30.000827–0.1
99FRTG589-CD30.00224–0.2
fl11.1 114S–11SFRTG523-T4080.00422–3.5
Fruit diameter (fd) fd1.1 11FRTG273-TG6070.002230.8
fd11.1 114S–11SFR TG523 0.0119–6.0
Fruit shape (fs) fs2.1 22NYTG140-CT9-CT2740.00222–1.0
22FRTG140-CT90.00619–1.0
fs7.1 77NYTG639-TG216-CT1950.0008291.0
77FRCT84-TG216-CT1950.0009291.0
Ovary length (ovl)ovl1.1 (–)11NYTG224-TG83-CT1630.000835–0.3
Ovary diameter (ovd)ovd4.1 (–)44L–10SNYCD55-TG620.00329–7.0
ovd9.1 (–)99NY TG390 0.00331–0.8
ovd9.2 (–)99NYTG35-CT740.000835–2.3
Ovary shape (ovs) ovs4.1 44L–10SNYTG596-TG386-TG620.000936–3.0
Ovary locule number(oln) oln5.1 55L-12LNYCT118-CT1720.00329–1.2
Fruit anthocyanin presence (fap) fap10.1 1010L–5S–12SNYCT100-CT240-CT20<0.0001861.0
1010L–5S–12SFRCT100-CT240-TG285<0.0001931.0
Fruit anthocyanin intensity (fai)fai1.1 (–)11NYTG607-TG830.0134–0.3
fai10.1 1010L–5S–12SNYCT242-TG2410.00342–0.1
fai12.1 1211L–12SNY CT79 0.00148–5.4
Fruit color (fc)fc8.1 (–)88NYTG510-CT1480.00628–0.1
fc10.1 1010L–5S–12SNYCT99-CT240-TG285<0.0001760.5
1010L–5S–12SFRCT99-CT240-TG285<0.0001810.7
Leaf lamina anthocyanin (lla) lla2.1 22NY ovate-orfx 0.00520–4.3
lla6.1 (–)66NYTG178-CT204-CT1090.000327–0.2
66FRTG240-GP890.00522–0.2
lla9.1 99NYTG421-TG4240.0022276.0
lla10.1 1010L–5S–12SNYCT217-CT240-CT200.0002290.5
1010L–5S–12SFRCT99-CT240-TG285<0.0001600.4
Leaf rib anthocyanin (lra) lra10.1 1010L–5S–12SFRCT99-CT240-TG285<0.0001760.8
Stem anthocyanin (sa)sa6.1 (–)66NYTG178-TG240-CT2040.000133–0.2
66FRTG178-TG240-GP890.0120–0.5
sa6.2 66NYCT193-CT1090.007190.2
sa10.1 1010L–5S–12SNYCT217-CT240-TG2850.0002290.8
1010L–5S–12SFRCT217-CT240-TG241<0.0001390.9
sa12.1 (–)1211L–12SNYCT79-CT211-cLET8K40.01243.0
Prickle anthocyanin (pa) pa10.1 1010L–5S–12SNYCT100-CT240-TG285<0.0001930.8
1010L–5S–12SFRCT99-CT240-CD72A<0.0001900.9
Corolla anthocyanin (ca) ca3.1 33FR CT115 0.0007262.0
ca5.1 (–)55L–12LFRTG351-TG565-T8010.000331–5.5
ca6.1 (–)66FRTG240-GP89-CT1090.000230–0.7
ca10.1 1010L–5S–12SFRCT240-CD72A-TG2850.0009260.3
Fruit stripe (fst) fst4.1 44L–10SNYTG230-TG303-TG62<0.000167–0.9
44L–10SFRTG230-TG303-T877<0.000149–1.0
fst10.1 (–)1010L–5S–12SFRCD19-CT99-CT2420.002251.3
Leaf prickle (lp) lp6.1 66NYTG365-CT109-TG482<0.000162–0.6
66FRTG240-CT109-TG482<0.000179–0.7
lp10.1 (–)1010L–5S–12SFRCT20-TG2850.006231.8
Stem prickle (sp) sp6.1 66NYTG365-TG162-TG642<0.000137–0.5
66FRTG365-CT109-TG482<0.000164–0.5
Flower calyx prickle (flcp) flcp6.1 66FRTG240-CT193-TG642<0.000164–0.8
Fruit calyx prickle (ftcp) ftcp6.1 66NYTG292-CT109-TG482<0.000151–0.3
66FRTG240-TG162-TG642<0.000165–0.7
ftcp9.1 99NY TG328 0.006291.0
ftcp11.1 (–)114S–11SFRT408-TG1940.008199.0
ftcp11.2 (–)114S–11SNYCT175-TG3390.00334–10.0
Petiole prickle (pp) pp6.1 66FRTG240-CT109-TG482<0.000171–0.4

Traits that were measured in both locations are underlined. QTL are named according to trait abbreviations. The first number following each abbreviation indicates the linkage group and the second number distinguishes QTL that mapped to the same linkage group and affected the same trait. QTL that were identified in the same genomic region in both locations are underlined. A (–) after a QTL indicates that the parental alleles had effects opposite to those predicted by the parental phenotypes. The homeologous tomato chromosomes for each eggplant linkage group are included for reference purposes. Location is coded: NY, New York; FR, France. Significant marker(s) column includes the most significant marker (P ≤ 0.01) linked to the trait (underlined) as well as flanking markers that were significant at P ≤ 0.05 as determined by single-point linear regression. Statistics in the remaining columns pertain to the most significant marker and were obtained from simple linear regression analysis. % PVE is percentage of phenotypic variation explained. d/a is the gene action for each QTL.