Kenneth L. McNally

The paper presents 11 new chromosome-level genome assemblies of Oryza species, revealing core genome conservation and subgenome plasticity, and highlights implications for crop improvement.

The paper examines gene expression variation in rice under salinity stress, finding trans-eQTLs dominate and cis-trans reinforcement is more common than compensation.

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

The paper presents an HPC-based workflow for genome variant calling using GATK, demonstrating SNP detection in four plant species and identifying novel SNPs in rice.

The paper introduces RGI, a pan-genome database for Asian rice, integrating 16 reference genomes and transcriptome data to provide gene information and visualization tools.

The paper constructs a pan-genome inversion index for Asian rice using 16 genomes and finds a high inversion rate with functional implications.

The paper generates 12 new high-quality rice reference genomes to expand the genetic diversity coverage of cultivated rice, forming a comprehensive pan-genome resource with 16 reference sequences.

The paper analyzes genetic diversity in Japonica rice using the 3K RG dataset, identifying multiple introgression streams from different geographic regions and subgroups.

This study uses marker stability to predict agronomic traits and perform association mapping in rice landraces, showing improved performance over GEMMA for simulated traits and identifying markers in known QTL regions.