Combining genome-wide association study and linkage mapping in the genetic dissection of amylose content in maize (Zea mays L.).

KEY MESSAGE: Integrated linkage and association analysis revealed genetic basis across multiple environments. The genes Zm00001d003102 and Zm00001d015905 were further verified to influence amylose content using gene-based association study. Maize kernel amylose is an important source of human food and industrial raw material. However, the genetic basis underlying maize amylose content is still obscure. Herein, we used an intermated B73 × Mo17 (IBM) Syn10 doubled haploid population composed of 222 lines and a germplasm set including 305 inbred lines to uncover the genetic control for amylose content under four environments. Linkage mapping detected 16 unique QTL, among which four were individually repeatedly identified across multiple environments. Genome-wide association study revealed 17 significant (P = 2.24E-06) single-nucleotide polymorphisms, of which two (SYN19568 and PZE-105090500) were located in the intervals of the mapped QTL (qAC2 and qAC5-3), respectively. According to the two population co-localized loci, 20 genes were confirmed as the candidate genes for amylose content. Gene-based association analysis indicated that the variants in Zm00001d003102 (Beta-16-galactosyltransferase GALT29A) and Zm00001d015905 (Sugar transporter 4a) affected amylose content across multi-environment. Tissue expression analysis showed that the two genes were specifically highly expressed in the ear and stem, respectively, suggesting that they might participate in sugar transport from source to sink organs. Our study provides valuable genetic information for breeding maize varieties with high amylose.

A combination of QTL mapping and genome-wide association study revealed the key gene for husk number in maize.

KEY MESSAGE: Two key genes Zm00001d021232 and Zm00001d048138 were identified by QTL mapping and GWAS. Additionally, they were verified to be significantly associated with maize husk number (HN) using gene-based association study. As a by-product of maize production, maize husk is an important industrial raw material. Husk layer number (HN) is an important trait that affects the yield of maize husk. However, the genetic mechanism underlying HN remains unclear. Herein, a total of 13 quantitative trait loci (QTL) controlling HN were identified in an IBM Syn 10 DH population across different locations. Among these, three QTL were individually repeatedly detected in at least two environments. Meanwhile, 26 unique single nucleotide polymorphisms (SNPs) were detected to be significantly (p < 2.15 × 10-6) associated with HN in an association pool. Of these SNPs, three were simultaneously detected across multiple environments or environments and best linear unbiased prediction (BLUP). We focused on these environment-stable and population-common genetic loci for excavating the candidate genes responsible for maize HN. Finally, 173 initial candidate genes were identified, of which 22 were involved in both multicellular organism development and single-multicellular organism process and thus confirmed as the candidate genes for HN. Gene-based association analyses revealed that the variants in four genes were significantly (p < 0.01/N) correlated with HN, of which Zm00001d021232 and Zm00001d048138 were highly expressed in husks and early developing ears among different maize tissues. Our study contributes to the understanding of genetic and molecular mechanisms of maize husk yield and industrial development in the future.

PIP family-based association studies uncover ZmPIP1;6 involved in Pb accumulation and water absorption in maize roots.

Excessive lead (Pb) in the soil affects crop growth and development, thus threatening human beings via food chains. Plasma membrane intrinsic proteins (PIPs) facilitate the transport of substrates across cell membranes. Herein, we characterized maize PIPs and identified eight Pb accumulation-associated PIP genes using association studies. Among these, ZmPIP1;6 was simultaneously correlated with root Pb concentrations under various Pb treatment stages. Significant correlations were observed between the ZmPIP1;6 expression abundance and Pb accumulation in maize roots. Ectopic expression in yeast showed that ZmPIP1;6 conferred Pb accumulation in the cells and affected Pb tolerance in yeast. Overexpression in maize demonstrated that ZmPIP1;6 altered the Pb concentration performance and root moisture content under Pb stress. Meanwhile, protein interaction analyses suggested that ZmPIP1; 6 and three PIP2 members formed isoforms and facilitate water uptake in maize roots. However, ZmPIP1; 6 improved Pb absorption in maize roots probably by interacting with CASP-like protein 2C3 and/or another metal transporter. Moreover, the significant variants in the ZmPIP1;6 promoter caused the variations in ZmPIP1;6 expression level and Pb accumulation among various maize germplasms. Our study will contribute to understanding of PIP family-mediated Pb accumulation in crops and bioremediation of Pb-polluted soils.