Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Hackett, Christine A.; Milne, Linda; Smith, Kay; Hedley, Pete; Morris, Jenny; Simpson, Craig G.; Preedy, Katharine; Graham, Julie

doi:10.1186/s12863-018-0666-z

Table 4 QTLs detected using a HMM

From: Enhancement of Glen Moy x Latham raspberry linkage map using GbS to further understand control of developmental processes leading to fruit ripening

Env	LG	Trait	Pos. (cM)	Mean_AC	Mean_AD	Mean_BC	Mean_BD	%var	LOD	se_AC	se_AD	se_BC	se_BD	Nearest SNP	Detected previously	Key parent
Field	2	Red	57	46.02	46.31	46.59	47.09	9.10	4.57	0.163	0.156	0.177	0.180	s986_p33227_R52	No	Both
Field	2	PCO1	63	−0.10	0.03	−0.04	0.10	10.27	5.42	0.029	0.029	0.032	0.032	s1650_p8516_R1	Yes	Both
Field	2	Open	85	13.36	15.03	13.69	15.16	9.99	5.03	0.309	0.336	0.335	0.338	s976_p36734_R52	No	Moy
Field	2	%late	86	0.06	0.09	0.27	0.28	11.58	5.91	0.036	0.039	0.038	0.039	s3294_p23887_F36	Yes	Latham
Field	2	PCO4	88	−0.01	−0.05	0.03	0.03	15.22	7.46	0.010	0.012	0.011	0.011	s22199_p1017_F46	Yes	Latham
Field	3	Red	8	46.17	45.97	46.81	46.89	9.64	4.70	0.161	0.174	0.167	0.169	s2456_p19264_F31	No	Latham
Poly	3	Red	9	50.68	51.00	51.73	51.77	14.70	5.25	0.171	0.210	0.197	0.196	s2456_p19264_F31	No	Latham
Field	3	PCO1	16	−0.11	−0.08	0.05	0.12	17.07	8.91	0.027	0.032	0.029	0.029	s88_p165011_R50	Yes	Latham
Field	3	Open	17	13.22	13.64	14.76	15.46	12.95	6.64	0.306	0.347	0.319	0.325	s88_p165011_R50	Yes	Latham
Field	3	Green	49	25.76	25.89	26.46	26.27	10.20	5.17	0.108	0.131	0.118	0.127	s59561_p275_R31	Yes	Latham
Poly	3	PCO1	56	−0.06	−0.09	0.06	0.08	12.06	4.95	0.025	0.033	0.026	0.036	s4830_p9111_R31	Yes	Latham
Poly	3	Open	62	21.10	20.03	22.55	22.42	8.68	3.91	0.368	0.554	0.427	0.524	s3246_p13440_F35	Yes	Latham
Poly	3	%flower	66	49.80	62.33	41.67	41.96	11.96	5.02	2.371	3.681	2.790	3.619	s2005_p3000_F19	Yes	Both
Field	3	PCO4	76	0.02	0.01	−0.04	−0.01	6.99	3.75	0.010	0.013	0.011	0.013	s4615_p65_R31	No	Latham
Poly	3	Set	76	24.96	25.17	26.88	25.96	8.51	3.73	0.314	0.451	0.376	0.462	s4615_p65_R31	Yes	Latham
Field	3	PCO2	94	0.06	0.00	−0.05	−0.05	9.98	5.10	0.017	0.019	0.018	0.022	s37694_p610_F60	Yes	Latham
Field	3	Set	102	21.33	22.15	22.72	22.92	11.17	5.96	0.215	0.252	0.251	0.293	s4_p124533_F28	Yes	Both
Field	3	Green	105	25.75	25.95	26.40	26.49	11.21	5.66	0.102	0.119	0.124	0.143	s65_p181620_R20	Yes	Both
Field	4	PCO2	35	0.01	0.02	−0.08	0.02	8.80	4.50	0.019	0.017	0.020	0.020	s2217_p870_F28	No	Both
Field	4	Green/Red	39	41.31	41.56	43.88	40.40	10.28	5.41	0.526	0.475	0.508	0.550	s702_p32282_F17	No	Both
Field	4	Red	42	46.52	46.45	46.94	45.90	7.49	3.81	0.172	0.155	0.172	0.181	s39775_p439_F60	No	Both
Field	5	Set	1	21.40	21.62	22.43	23.20	14.96	7.34	0.232	0.249	0.258	0.238	s376_p49208_R48	Yes	Both
Field	5	Green	1	25.70	25.95	26.27	26.45	10.15	5.08	0.114	0.123	0.128	0.118	s376_p49208_R48	Yes	Both
Field	5	PCO4	17	0.03	0.02	−0.03	−0.01	7.69	3.95	0.011	0.012	0.012	0.011	s54868_p407_F20	Yes	Latham
Field	5	PCO1	40	−0.07	−0.06	0.00	0.09	6.99	3.74	0.031	0.031	0.033	0.029	s608_p18443_F46	Yes	Both
Field	5	Open	40	13.46	13.57	14.23	15.64	13.08	6.62	0.318	0.328	0.346	0.307	s608_p18443_F46	Yes	Both
Field	5	PCO2	72	−0.05	−0.03	−0.01	0.08	10.87	5.42	0.020	0.017	0.018	0.020	s1838_p21919_F22	No	Both
Field	6	PCO2	3	0.06	0.07	−0.08	−0.04	19.26	9.48	0.019	0.019	0.018	0.016	s4321_p5696_R54	Yes	Latham
Field	6	Green/Red	3	40.48	39.57	43.35	43.14	17.75	8.76	0.521	0.531	0.492	0.436	s4321_p5696_R54	Yes	Latham
Field	6	PCO4	5	0.01	0.05	−0.04	−0.01	11.72	5.89	0.012	0.012	0.011	0.010	s5202_p10092_F12	Yes	Latham
Field	6	Set	9	22.02	21.11	22.85	22.44	10.47	5.44	0.263	0.268	0.251	0.225	s666_p20259_R9	No	Latham
Field	6	Green	9	26.06	25.53	26.38	26.24	11.61	6.04	0.126	0.128	0.120	0.107	s666_p20259_R9	No	Latham
Poly	6	Green/Red	46	47.03	47.46	49.35	49.05	11.69	4.43	0.452	0.430	0.416	0.455	s75795_p432_F40	No	Latham
Field	7	Set	20	21.65	21.45	22.66	22.62	7.70	4.00	0.271	0.267	0.240	0.240	s21_p135135_R49	No	Latham

Env environment, LG linkage group, Pos is the position of the maximum LOD in cM, Mean_AC etc. are the means of the four offspring genotype classes AC, AD, BC, BD (assuming a QTL model of Latham having genotype AB and Moy having genotype CD), se_AC etc. are the corresponding standard errors, %var. is the % trait variance explained by this QTL, ‘Detected previously’ indicates whether it was reported by Graham et al. (2009b) and ‘Key parent’ indicates whether one or both parents’ alleles are significant, based on pairwise t-tests of the estimated genotype means

Back to article page

ISSN: 2730-6844

Contact us

General enquiries: journalsubmissions@springernature.com

BMC Genomic Data

Contact us