Understanding the genetic basis of the node of the first fruiting branch (NFFB)
      improves early-maturity cotton breeding. Here we report QTL mapping on 200 F2
      plants and derivative F2:3 and F2:4 populations by genotyping by sequencing (GBS).
      BC1F2 population was constructed by backcrossing one F2:4 line with the maternal
      parent JF914 and used for BSA-seq for further QTL mapping. A total of 1,305,642
      SNPs were developed between the parents by GBS, and 2,907,790 SNPs were
      detected by BSA-seq. A high-density genetic map was constructed containing
      11,488 SNPs and spanning 4,202.12 cM in length. A total of 13 QTL were mapped in
      the 3 tested populations. JF914 conferred favorable alleles for 11 QTL, and JF173
      conferred favorable alleles for the other 2 QTL. Two stable QTL were repeatedly
      mapped in F2:3 and F2:4, including qNFFB-D3-1 and qNFFB-D6-1. Only qNFFB-D3-
      1 contributed more than 10% of the phenotypic variation. This QTL covered about
      24.7 Mb (17,130,008–41,839,226 bp) on chromosome D3. Two regions on D3
      (41,779,195–41,836,120 bp, 41,836,768–41,872,287 bp) were found by BSA-seq
      and covered about 92.4 Kb. This 92.4 Kb region overlapped with the stable QTL
      qNFFB-D3-1 and contained 8 annotated genes. By qRT-PCR, Ghir_D03G012430
      showed a lower expression level from the 1- to 2-leaf stage and a higher
      expression level from the 3- to 6-leaf stage in the buds of JF173 than that of
      JF914. Ghir_D03G012390 reached the highest level at the 3- and 5-leaf stages in
      the buds of JF173 and JF914, respectively. As JF173 has lower NFFB and more early
      maturity than JF914, these two genes might be important in cell division and
      differentiation during NFFB formation in the seedling stage. The results of this study
      will facilitate a better understanding of the genetic basis of NFFB and benefit cotton
      molecular breeding for improving earliness traits.