A Genome-Wide Association Study Dissects the Genetic Architecture of the Metaxylem Vessel Number in Maize Brace Roots

Abstract

Metaxylem vessels in maize brace roots are key tissue, and their number (MVN) affects plant water and inorganic salt transportation and lodging resistance. Dissecting the genetic basis of MVN in maize brace roots can help guide the genetic improvement of maize drought resistance and lodging resistance during late developmental stages. In this study, we used 508 inbred lines with tropical, subtropical, and temperate backgrounds to analyze the genetic architecture of MVN in maize brace roots. The phenotypic variation in MVN in brace roots was evaluated in three environments, which revealed broad natural variation and relative low levels of heritability (h ² = 0.42). Stiff-stalk lines with a temperate background tended to have higher MVNs than plants in other genetic backgrounds. MVN was significantly positively correlated with plant height, tassel maximum axis length, ear length, and kernel number per row, which indicates that MVN may affect plant morphological development and yield. In addition, MVN was extremely significantly negatively correlated with brace root radius, but significantly positively correlated with brace root angle (BRA), diameter, and number, thus suggesting that the morphological function of some brace root traits may be essentially determined by MVN. Association analysis of MVN in brace roots combined 1,253,814 single nucleotide polymorphisms (SNPs) using FarmCPU revealed a total of nine SNPs significantly associated with MVN at P < 7.96 × 10^-7. Five candidate genes for MVN that may participate in secondary wall formation (GRMZM2G168365, GRMZM2G470499, and GRMZM2G028982) and regulate flowering time (GRMZM2G381691 and GRMZM2G449165). These results provide useful information for understanding the genetic basis of MVN in brace root development. Further functional studies of identified candidate genes should help elucidate the molecular pathways that regulate MVN in maize brace roots.

Keywords: GWAS; brace root; candidate gene; maize (Zea mays L.); metaxylem vessel number.

FIGURE 1

Boxplot of metaxylem vessel number (MVN) in maize brace roots distribution in different environments and subgroups. Analysis of variance (ANOVA) was applied to examine the difference of phenotypes among different environments and subgroups. Different letters indicate statistically significant differences at P ≤ 0.05. (A) Different environments, (B) different subgroups.

FIGURE 2

Correlation coefficients of metaxylem vessel number (MVN) in maize brace roots with 17 other agronomic traits based on BLUP values. *, significant at P ≤ 0.05; **, significant at P ≤ 0.01. PH, plant height; EH, ear height; ELW, ear leaf width; ELL, ear leaf length; TMAL, tassel maximum axis length; TBN, tassel branch number; LNAE, leaf number above ear; EL, ear length; ED, ear diameter; CD, cob diameter; KNPR, kernel number per row; CGW, cob grain weight; CW, cob weight; KW, kernel width; DTA, days to anthesis; DTS, days to silking; DTH, days to heading.

FIGURE 3

Correlation coefficients of metaxylem vessel number (MVN) in maize brace roots with five other brace root traits based on BLUP values. BRT, brace root tier number; RBR, brace root radius; BRN, brace root number; BRA, brace root angle; BRD, brace root diameter, *, significant at P ≤ 0.05; **, significant at P ≤ 0.01.

FIGURE 4

GWAS-derived Manhattan plots showing significant SNPs associated with metaxylem vessel number (MVN) in maize brace roots using FarmCPU. Each dot represents a SNP. The red solid line represents the Bonferroni-corrected significance threshold of 7.96 × 10^–7. From the inside to the outside: LN, JL, HN, and across all environments.

FIGURE 5

The boxplot of phenotypic difference between the major alleles and minor alleles for significant SNPs associated with metaxylem vessel number (MVN) in maize brace roots. The P-values (Student’s t-test) of the allelic effects of MVN are exhibited above each small plot. (A–J) Ten significant SNPs associated with MVN in maize brace roots with three individual environments and across all environments.

FIGURE 6

Co-localization between the significant SNPs associated with metaxylem vessel number in brace roots and QTL for aerial nodal root number and day to pollen. Colored lines represent QTL region for different traits, The asterisk represents the significant SNPs associated with metaxylem vessel number.

FIGURE 7

Heat map of expression patterns of candidate genes identified by GWAS in different tissues. The values used in the figure were the log10 (n + 1) transformed of normalized TPM valve. Columns and rows were ordered according to similarity (hierarchical cluster analysis at the top and left). The red and blue represented higher and lower expression level in different tissues, respectively.