Fig. 2: ZmACO2 is the candidate gene of qEL7 and negatively affects yield-related traits.
From: An ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield
a By fine mapping, qEL7 was delineated into a 50.8 kb interval with only one predicted gene ZmACO2; detailed information is presented in Supplementary Fig. 1d. b Sequence variations identified in ZmACO2 genomic regions between NILs; the positions (relative to transcript start site, TSS) were listed beside genotypes information; the genotypes were presented as qEL7SL17/qEL7Ye478; the nucleotide bases and numbers represent the genotypes of SNPs and base pairs of InDels, respectively; white box, UTR region; black box, exon; arrowhead, gene direction. c ZmACO2 expression was lower in the 2 mm (p = 4.33 × 10−7) and 5 mm (p = 0.0034) ears of qEL7Ye478 (blue bar) than that in qEL7SL17 (orange bar), data are presented as means ± SD and **p-value ≤ 0.01, ***p-value ≤ 0.001, from a two-tailed, two-sample t-test. d Five variants in ZmACO2 promoter show association with ear length in diversity inbred lines; the red dash line indicates the threshold of significant association at p ≤ 1.79 × 10‒4; the white to black heatmap shows the pairwise linkage disequilibrium pattern by R2; the genotypes and positions (relative to TSS) of five significant association loci are shown on the top and indicated by green and blue dash lines. HapYe478 haplotype has a longer ear (e, p = 6.94 × 10−5), more kernel number per row (f, p = 0.0041) and lower ZmACO2 expression (g, p = 0.0014, H = 10.26) than HapSL17 haplotype among diverse inbred lines; orange box, HapSL17 haplotype (n = 56 in e and f, n = 16 in g); blue box, HapYe478 haplotype (n = 158 in e and f, n = 24 in g); each box represents the median and interquartile range, and whiskers extend to maximum and minimum values; **p-value ≤ 0.01, ***p-value ≤ 0.001 from a two-tailed, two-sample t-test (e, f) and Kruskal–Wallis test (g). For expression level is measured by qRT-PCR; three biological replicates and three technical replicates in (c); one biological replicate and three technical replicates for each line in (g); approximately 20 ears were used in each biological replicate. n is the number of inbred lines examined in (e−g).
