Association mapping of starch chain length distribution and amylose content in pea (Pisum sativum L.) using carbohydrate metabolism candidate genes

Table 2 Summary of the associations between candidate carbohydrate metabolism gene sequences and starch chain length distribution (CLD) peak areas

Environment Glasshouse 2010. All PSP lines, n = 92.
Gene	Sequence alignment ^a	Site(s) on alignment ^b	CLD peak with lowest p-value	p-value	R² (%)	Q-value
Starch branching enzyme I (r locus)	n/a ^c	n/a	DP17	7.50 E-39	83.4	1.92 E-36
Cell wall invertase	694,183,574	24 (T/G)	DP39	1.23 E-04	17.3	0.010
ADP glucose pyrophosphorylase S2 subunit	694,187,965	237 (indel)	DP10	1.83 E-04	14.3	9.13E-03
UDP glucose pyrophosphorylase	694,186,492	18 (T/G), 25 (C/G), 56 (T/G), 274 (T/G)	DP16	8.50 E-04	12.3	0.039
Second sucrose synthase	694,184,180	148 (C/T), 299 (indel)	DP34	1.52 E-03	11.8	0.015
Environment Glasshouse 2010. Round seeded PSP lines, n = 83.
Second sucrose synthase	694,184,180	128 (T/A), 134 (T/indel/C)	DP29	2.68E-04	16.9	0.027
Invertase inhibitor	694,182,042	357 (T/C)	DP18	3.07 E-04	15.6	0.086
ADP glucose pyrophosphorylase S2 subunit	694,187,965	517 (G/T)	DP10	1.16 E-03	12.4	0.062
Environment Field 2011. All PSP lines, n = 92.
Starch branching enzyme I (r locus)	n/a	n/a	DP18	8.81 E-53	88.6	1.72 E-50
UDP glucose pyrophosphorylase	694,186,492	25 (C/G), 56 (T/G), 274 (T/G)	DP17	2.62 E-06	22.2	1.02 E-04
ADP glucose pyrophosphorylase S2 subunit	694,187,965	72 (T/C)	DP23	6.58 E-04	12.1	0.027
ADP glucose pyrophosphorylase L1 subunit (rb locus)	694,185,424	9 (A/C)	DP23	8.94 E-04	12.1	0.027
Starch synthase II (rug5 locus)	1,206,484,033	307 (G/A)	DP17	1.26 E-03	15.9	0.027

^aGenBank PopSet identification number
^bWhere more than one site is shown in this column, they all had the same p-value; (major/minor) alleles are shown
^cNot applicable. The r locus genotype was determined by recording the round or wrinkled seed shape, so the alignment and site information are not applicable
Associations were identified using the mixed linear model approach with adjustment for population structure using Q + K matrices, implemented in the Tassel package. For all the pea lines (n = 92), associations that meet the α < 0.05 criterion for minimising the false discovery rate (FDR) are shown, while for the round only pea lines (n = 83) associations that meet the α < 0.10 criterion are shown

ISSN: 1471-2229