Mapping phenotypic performance and novel SNPs for cold tolerance in tomato (Solanum lycopersicum) genotypes through GWAS and population genetics

Table 5 Top significant marker trait associations under different environments

S. No	ENV	Trait name	SNPs	Chromosome	Position	p-value	maf	Effect	PVE (%)
1	E3	Proline content	CH08_9484802	chr8	9,484,802	8.75*10⁻⁶	0.48	-0.73699	48.34
2	E3	Proline content	CH08_9484810	chr8	9,484,810	8.75*10⁻⁶	0.48	0.73699	48.34
3	E3	Proline content	CH08_9528421	chr8	9,528,421	7.65*10⁻⁵	0.44	-0.60225	36.37
4	E2	No of fruits per plant	CH12_49436823	chr12	49,436,823	4.18*10⁻⁵	0.5	204.3378	45.26
5	E4	No of fruits per plant	CH12_49436823	chr12	49,436,823	1.11*10⁻⁴	0.5	307.8472	38.19
6	E5	No of fruits per plant	CH12_49436823	chr12	49,436,823	8.19*10⁻⁴	0.5	151.2753	27.97
7	E5	No of days to first fruit set	CH09_32796951	chr9	32,796,951	2.4721*10⁻⁴	0.43	-9.63575	27.39
8	E5	No of days to first fruit set	CH11_13438935	chr11	13,438,935	7.27*10⁻⁴	0.38	-8.06909	20.52
9	E4	Fruit shape index	CH08_9435068	chr8	9,435,068	8.31*10⁻⁷	0.5	16.60184	26.22
10	E4	Fruit shape index	CH08_9452288	chr8	9,452,288	1.75*10⁻⁵	0.47	9.82668	18.52
11	E4	Fruit shape index	CH08_9452289	chr8	9,452,289	1.75*10⁻⁵	0.47	9.82668	18.52
12	E4	Fruit shape index	CH08_9454260	chr8	9,454,260	2.31*10⁻⁵	0.46	7.677636	17.88
13	E4	Fruit shape index	CH08_9454275	chr8	9,454,275	2.31*10⁻⁵	0.46	7.677636	17.88

E2: Polyhouse sown (2019); E3: Field, early sown (2020); E4: Field, normal sown (2020); E5: Field, late sown (2020)

ISSN: 2730-6844