Table 1 Lead SNPs significantly associated with 10 agronomic traits according to the genome-wide association study performed for the 129 peach accessions and related candidate genes.

Trait	Scaffold	Lead SNP	Major allele	Minor allele	minor allele frequency	−Log₁₀ P value*	−Log ₁₀ P value ^†	Explained variation (%)	Candidate genes	Annotation
Flesh adhesion	4	22,695,515^b,c	A	C	0.31	10.20		30.9	ppa006857m	Polygalacturonase
Flesh texture	4	22,695,495^a,b	C	T	0.49	14.22		36.5	ppa006857m	Polygalacturonase
Flesh colour around stone	7	12,901,845^a,b	G	T	0.18	6,89		22.6	—	—
Kernel taste	5	12,622,852^b,c	T	A	0.03	40.93		78.1	ppa015634m	Transcription factor bHLH14
Fruit hairiness	5	17,576,893^a,b	A	G	0.22	27.11	121.92	80.6	ppa010316m	Pre-mRNA-splicing factor SPF27 homolog
Fruit flesh colour	1	24,968,892^b,c	C	A	0.47	13.72	25.43	30.2	ppa027093m	Flavonol synthase/flavanone 3-hydroxylase
Fruit shape	6	25,060,196^a,b,c	A	T	0.04	26.04	182.72	91.6	ppa003772m	CAD1 (constitutively activated cell death 1)
Non-acid fruit	5	541,075^b	T	C	0.21	20.77	89.42	71.3	ppa006339m	Auxin efflux carrier family protein
Flower shape-doubleF	2	21,480,531^a,b	A	G	0.09	46.55	20.64	25.6	ppb023753m	Cyclic nucleotide-gated ion channel 1
Flower shape-ShowyF	8	13,740,117^a,b,c	A	C	0.15	23.86	121.47	82.0	ppa016980m	Predicted protein

The letters ‘a’, ‘b’ and ‘c’, present in the column ‘lead SNP’, indicate that the locus was identified in an association study using GLM-no PCA, GLM-PCA and MLM models, respectively.
^*The association values resulting from resequencing 129 accessions. Among them, the P value of the association signals of flesh adhesion and flesh texture were selected from the results derived from the GLM-PCA model, since the GLM-PCA and MLM models presented the same result.
^†The P value of the associations resulting from the Sequenom MassARRAY analysis of 345 accessions.

Quick links

Search