Fig. 2

NAL1 haplotype analysis. a The gene structure of NAL1. The five exons are indicated as black boxes, 3′ UTR and 5′ UTR are indicated as white boxes, and single nucleotide polymorphism (SNP) positions are connected to the haplotype table by lines (SNP frequency > 5%). Sixteen haplotypes, classified by SNP and insertion/deletion (InDel) variations, are detected in the collection (indicated as either blue or white). Numbers show the length of the InDel in bp. The number and subpopulation identity of varieties carrying each haplotype are indicated in columns to the right. The eight wild rice varieties of O.rufipogon are indicated by WR1–4. b The phylogenetic network of NAL1. The phylogenetic network of haplotypes in Oryza sativa and O. rufipogon are constructed for NAL1. c–d Grain number per panicle (c), flag leaf width (d) are compared among the NAL1–2, NAL1–4, NAL1–5 and NAL1–6 haplotypes in geng rice (Oryza sativa). e–f Grain number per panicle (e), flag leaf width (f) are compared among the NAL1–1, NAL1–2 and NAL1–3 haplotypes in xian rice (Oryza sativa). Letters on histograms (a, and b) are ranked by Duncan’s test at P < 0.05.Light pink, light yellow and light blue colors indicate in 2014, 2015 and 2016, respectively