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 (h2 = 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.

Genome-wide association study presents insights into the genetic architecture of drought tolerance in maize seedlings under field water-deficit conditions

“…The plotting script is available online on the webpage https://aozhangchina.github.io/R/LDdecay/LDdecayPlotTool.html . Then, we used the uniform Bonferroni-corrected threshold of α = 1 for the mixed linear model’s significance cutoff as reported in previous studies ( Mao et al., 2015 ; Liu et al., 2022 ). Therefore, the suggested P-value was computed with 1/n (n = 97,862, total markers used), and we obtained a P-value threshold of 1.02×10 -5 for GWAS.…”

Plant microphenotype: from innovative imaging to computational analysis

“…With the precise identification of microphenotypic traits, an increasing number of genes that regulate microphenotypes of vasculature, such as the metaxylem vessel number ( KNAT7 , ZmTIP1 ), stele area ( OsNACs , Mei2‐like gene), cortical cell ( bHLH121 ), and stem xylem and phloem traits ( NAC91, ZmTIP1, CLE41/44 , etc. ), are being uncovered, which provides insights for the genetic improvement of crop yield and stress resistance (Barrieu et al ., 1998 ; Li et al ., 2021b ; Liu et al ., 2022 ; Schneider et al ., 2023 ).…”

Utilizing Two Populations Derived from Tropical Maize for Genome-Wide Association Analysis of Banded Leaf and Sheath Blight Resistance

“…Through GWAS, Li Ning [18] successfully identified a gene, ZmFBL4, associated with banded leaf and sheath blight. Numerous studies have successfully identified QTLs related to crucial agronomic traits, thereby showcasing the practicality and efficiency of GWAS [19][20][21][22]. In crops like maize, GWAS has proven invaluable in exploring key genes and identifying potential disease-resistant genes.…”