Figure 2.

Key candidate genes and lignin biosynthesis genes that display expression changes upon C. campestris infestation. A–C, The normalized expressions levels (CPM, counts per million) of genes in susceptible cultivar H9775 and in resistant hybrid cultivar H9553 and H9492 under C. campestris infestation. – and + indicates without or with C. campestris infection treatments, respectively. Biologically independent replicates: RNA-seq libraries: H9775−Cc, n = 5; H9775+Cc, n = 7; H9492−Cc, n = 4; H9492+Cc, n = 4; H9553−Cc, n = 5; H9553+Cc, n = 5. Data are assessed using two-tailed t test. *P < 0.04, **P < 0.01, ***P < 0.005. The boxplot consists of a box extending from the 25th quantile to the 75th quantile. The centerline in the box indicates the median. The length of the box is the IQR, which is the difference between the 25th quantile and the 75th quantile. The whiskers extend from the ends of the box to the outermost data point that falls within 1.5 times of IQR. Points outside of the whiskers are outliers. D, The lignin biosynthesis pathway with key enzyme expression levels. Genes that are differentially expressed were selected and the normalized expression values across three cultivars were color coded according to z-score. + Cc indicates with C. campestris infection treatments. TAL, tyrosine ammonia-lyase; 4CL, 4-coumarate CoA ligase; HCT, hydroxycinnamoyl-CoA shikimate/Quinate hydroxycinnamoyltransferase; C3H, p-coumarate 3-hydroxylase; CCoAOMT, caffeoyl-CoA O-methyltransferase; CCR, cinnamoyl-CoA reductase; CAD, cinnamyl alcohol dehydrogenase; LAC, laccase. 3D structure images of phenylalanine, tyrosine, cinnamic acid, p-coumaric acid, p-coumaroyl shikimic acid, caffeoyl shikimic acid, p-coumaraldehyde, p-coumaryl alcohol, caffeyl aldehyde, caffeyl alcohol, coniferaldehyde, coniferyl alcohol, sinapaldehyde, and sinapyl alcohol are from PubChem (National Center for Biotechnology Information, 2021a, 2021b, 2021c, 2021d, 2021e, 2021f, 2021g, 2021h, 2021i, 2021j, 2021k, 2021l, 2021m, 2021n).