Agronomy and Horticulture, Department of


Document Type


Date of this Version



2023) Genetics, 223 (4), DOI: 10.1093/genetics/iyad012


Used by permission.


Understanding the genetic basis responding to nitrogen (N) fertilization in crop production is a long-standing research topic in plant breeding and genetics. Albeit years of continuous efforts, the genetic architecture parameters, such as heritability, polygenicity, and mode of selection, underlying the N responses in maize remain largely unclear. In this study, about n = 230 maize inbred lines were phenotyped under high N (HN) and low N (LN) conditions for two consecutive years to obtain six yield-related traits. Heritability analyses suggested that traits highly responsive to N treatments were less heritable. Using publicly available SNP genotypes, the genome-wide association study (GWAS) was conducted to identify n = 231 and n = 139 trait-associated loci (TALs) under HN and LN conditions, respectively, and n = 162 TALs for N-responsive (NR) traits. Furthermore, genome-wide complex trait Bayesian (GCTB) analysis, a method complementary to GWAS, was performed to estimate genetic parameters, including genetic polygenicity and the mode of selection (S). GCTB results suggested that the NR value of a yield component trait was highly polygenic and that four NR traits exhibited negative correlations between SNP effects and their minor allele frequencies (or the S value < 0) — a pattern consistent with negative selection to purge deleterious alleles. This study reveals the complex genetic architecture underlying N responses for yield-related traits and provides insights into the future direction for N resilient maize development.