TABLE 2.

Candidate genes associated with pod number.

Pod number			High		Low
Published QTL marker	Ref.	SNP id	NR	Ref	NR	Ref	p-value	Candidate gene	Fold change	Gene function
Chr11:15649090	1	ss715609881	11	1#	0	12$	9.60E-06	Glyma.11G164800	3.17*	LOB domain-containing protein 4
Chr15:5252046	1	ss715622826-7	3	9	11	1	2.80E-03	Glyma.15G068500	8.6*	60S ribosomal protein L26-1-like
Chr18:55626229	2	ss715632229	5	7	12	0	4.60E-03	Glyma.18G274000	16.83*	RING finger protein 165-like
Chr11:5338661	3	ss715610851-6	8	4	1	11	9.40E-03	Glyma.11G071000	1.28*	Auxilin-like protein 1-like
Chr02:40368201	3	ss715582578	6	6	12	0	1.40E-02	Glyma.02G216500	2.44*	TRAF-type zinc finger-related
Chr02:40368201	3	ss715582578	6	6	12	0	1.40E-02	Glyma.02G216600	1.39*	AGAMOUS-like 16
Chr11:33902439	1	ss715610584	8	4	2	10	3.60E-02	Glyma.11G245300	0.72	63 kDa inner membrane protein
Chr18:55662445	2	ss715632230	7	5	12	0	3.70E-02	Glyma.18G274200	0.08	Pollen Ole e1 extensin family protein

NR, non-reference allele; Ref, reference allele. The numbers of NR and Ref indicate the number of varieties out of 24 PIs. Low and High are the pod numbers and are defined as pod numbers below or above average, respectively. The p-values were calculated using fisher’s exact test. Candidate genes were selected with 50 Kb window of enriched SNP based on published 50K SNP data. References: 1. Zhang J. et al. (2015). 2. Fang et al. (2017). 3. Hao et al. (2012). SNP id ss715622826-7 means ss715622826 and ss715622827. SNP id ss715610851-6 means ss715610851, ss715610852, ss715610853, ss715610854, ss715610855, and ss715610856. The genes marked with asterisk (*) have log₂fold change > 1 indicating the candidate genes are expressed more than two-fold higher in shoot apical meristem than in leaves. # and $ mark the numbers described in the main text.