Genomewide prediction to target russet formation in apple

Ashley A. Powell; Sarah A. Kostick; Rex Bernardo; James J. Luby; Ashley A. Powell; Sarah A. Kostick; Rex Bernardo; James J. Luby

doi:10.48130/frures-0024-0016

Figures (0) Tables (2)

Trait^a	Training set^b	Fixed effects^c	Mean predictive ability (r)^d	SD^e	Minimum^f	Maximum^g
Shoulder	All families	No	0.33	0.15	0.12	0.60
	Honeycrisp-derived families		0.30	0.15	0.11	0.57
	Minneiska-derived families		0.28	0.15	0.09	0.46
	All families	Yes	0.33	0.15	0.10	0.62
	Honeycrisp-derived families		0.31	0.15	0.09	0.58
	Minneiska-derived families		0.35	0.18	0.08	0.48
Lenticel	All families	No	0.34	0.10	0.23	0.53
	Honeycrisp-derived families		0.30	0.11	0.11	0.47
	Minneiska-derived families		0.35	0.10	0.26	0.46
^aShoulder russet ratings and the dual lenticel russet ratings; ^bThree training sets were used: (1) all breeding germplasm minus untested family, (2) all 'Honeycrisp'-derived families minus untested family, and (3) all 'Minneiska'-derived families minus untested family; ^cFixed effect model included two SNPs at the previously reported LG2 and LG6 shoulder russet QTLs^[8] as fixed effects; ^dCorrelation between observed and predicted values using Pearson correlation averaged across testing set families; ^eStandard deviation of r all runs for each trait-training-model set; ^fMinimum r within each trait-training-model set; ^gMaximum r within each trait-training-model set.

Table 1.

Summary of genomewide prediction for shoulder and dual lenticel russet ratings.

Model – Trait^a	Testing set^b	Culling criteria	Cull (n)	Keep (n)	Type A error (%)^c	Type B error (%)^d
GS – Shoulder	Full-sib families	Over 2.0	461	548	26.0	10.2
		Over 2.5	248	761	15.0	10.8
		Over 3.0	105	906	7.1	11.5
MAS – Shoulder		< 2 LOW alleles	461	548	28.2	9.7
GS – Lenticel		Over 2.5	885	124	22.6	7.1
		Over 5.0	331	678	17.0	21.1
		Over 7.5	13	996	0.9	14.4
GS – Shoulder	Selections	Over 2.0	87	76	–	–
		Over 2.5	47	116	–	–
		Over 3.0	17	146	–	–
MAS – Shoulder*		< 2 LOW alleles	57	73	–	–
GS – Lenticel		Over 2.5	149	14	–	–
		Over 5.0	63	100	–	–
		Over 7.5	13	150	–	–
^a Model comparison between genomewide selection (GS) with all markers as random effects using the all training set and marker-assisted selection (MAS); targeted traits were shoulder russet formation and lenticel russet formation; ^b Germplasm used in the testing set; Breeding = all 13 'Honeycrisp'- and 'Minneiska'-derived families were used as a testing family (n = 1,009); Selections = all advanced selections (n = 163), * Only 130 individuals were assessed for MAS due to unresolved QTL alleles; ^c Type 1 error defined as individuals that were culled based upon predicted values but would have been kept based upon observed values; ^d Type 2 error defined as individuals that were kept based upon predicted values but would have been culled based upon observed values.

Table 2.

Comparison of culling using genomewide selection (GS) at different thresholds and marker-assisted (MAS) for shoulder russet and genomewide selection at different thresholds for lenticel russet formation.