Fig. 2

GWAS and QTL co-located of major loci on chromosome A09. a, b Circular Manhattan plots of the 60 K population and WGR population. From the inner ring to the outer ring are results of the FarmCPU, Blink, CMLM, GLM, and MLM models. c Scatterplot of association results from an MLM model analysis of SL on chromosome A09. Negative log10-transformed P values from the GWAS analysis are plotted against the genomic physical position. The green line indicates the threshold level log(1/N) = 5.58. d Major QTL loci on the chromosome A09 were repeatedly detected in multiple environments by QTL mapping in an RIL population. 16SL-cq, 17SL-cq, and 18SL-cq represent silique length from Chongqing in 2016, 2017, and 2018, respectively; 18SL-xa and 19SL-xa represent silique length from Xi’an in 2018 and 2019, respectively; BLUP and BLUE represent best linear unbiased predictions and best linear unbiased estimates, respectively. e Location of the reference genome region on A09 corresponding to the major effective loci and LD block analysis of this region. The red gene ID represents that the gene is an important candidate gene. f, i FPKM value and qRT–PCR validation of candidate genes in A09. The upper half represents qRT–PCR results, and the normalized levels ST1 were arbitrarily set to 1. The lower part is the FPKM value obtained by RNA-seq. Statistically significant differences were revealed using a Student’s t test: ns ≥ 0.05, *p < 0.05, **p < 0.01, ***p < 0.001