Hui Feng | Search PubMed

PubMed2025

Hyperspectral imaging of grains uncovers the genetic architecture of nitrogen response of development in bread wheat.

UNLABELLED: Unraveling the genetic architecture of nitrogen response of development is critical for improving wheat productivity while reducing nitrogen inputs. In this study, hyperspectral imaging (HSI) was applied to wheat grains obtained from nitrogen-deficient and normal conditions, combined with genome-wide association studies (GWAS), to investigate the nitrogen response of development in a diverse wheat panel. The 1,792 i-traits were acquired via hyperspectral imaging system, which reflect detailed phenotypic assessments of wheat development, capturing subtle variations in nitrogen response. A total of 3,556 significant loci and 3,648 candidate genes were identified. Key candidate genes involved in nitrogen uptake and utilization were identified by integrating agronomic traits with i-traits, including TaARE1-7A, TaPTR9-7B, TaNAR2.1, and Rht-B1. This approach underscores the potential of combining HSI on grains with GWAS to dissect complex traits like nitrogen response, offering valuable genetic insights for breeding nitrogen-efficient wheat varieties and enhancing sustainability in crop production. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-025-01609-6.

Bread wheat↗

PubMed2025

Genomic analyses of three Acanthus L. species provide insight into polyploidization-driven speciation and evolution.

Allopolyploidy fundamentally influences plant evolution, yet the genomic dynamics of allotetraploidization remain incompletely understood. We investigated Acanthus tetraploideus (2n = 4x = 96), an ecologically significant allotetraploid true mangrove from Indo-West Pacific intertidal zones. Our prior integrative investigations indicate that A. tetraploideus originated through hybridization of the diploid species A. ilicifolius and A. ebracteatus with subsequent chromosome doubling. Here, we present complete chromosome-scale genome assemblies for all three species, representing the first genomic resources for true mangrove polyploid research. Our analysis reveals that the three species have experienced at least four rounds of polyploidization events, with the most recent, approximately 53 mya, possibly an Acanthus-specific event. The allotetraploid A. tetraploideus, which emerged between 1.5 and 2.2 mya, has A. ebracteatus as its maternal progenitor and A. ilicifolius as its paternal one. Through a comprehensive genomic comparison and analysis of homoeologous gene expression, we propose a gradual evolutionary trajectory for allotetraploidy in A. tetraploideus. Despite the allotetraploidization event dating back to around 2 mya, A. tetraploideus retains a high degree of colinearity with its ancestral genomes, with the majority (76.2%) of duplicated genes retained and no significant sub-genome bias in gene expression. Furthermore, we have identified positive selection in specific genes that may facilitate the adaptation of Acanthus mangrove species to their intertidal habitats. These findings establish A. tetraploideus as a model for studying allopolyploid evolution while providing new insights into mangrove speciation processes.

Genome, Plant↗