Genome-wide association study reveals the advantaged genes regulating <i>japonica</i> rice grain shape traits in northern China

Our analysis detected 15 QTLs associated with the 11 grain shape traits, of which five major QTL clusters emerged as crucial. Candidate genes, including <i>LOC_Os01g50720</i> (<i>qGL1</i>), <i>OsMKK4</i> (<i>LOC_Os02g54600</i>, influencing <i>qBA2</i>, <i>qWL2</i>, and <i>qWA2</i>), <i>GW5</i> (<i>LOC_Os05g09520</i>, controlling <i>qGW5</i>, <i>qBW5</i>, <i>qBR5</i>, <i>qWW5</i>, and <i>qWR5</i>), <i>GW6a</i> (<i>LOC_Os06g44100</i>, associated with <i>qGW6</i>, <i>qBW6</i>, <i>qBR6</i>, <i>qWW6</i>, and <i>qWR6</i>), and <i>FZP</i> (<i>LOC_Os07g47330</i>, linked to <i>qWL7</i>), were identified based on functional annotations and haplotype analysis. These findings offer valuable insights into the genetic mechanisms underlying rice grain shape and suggest promising targets for marker-assisted selection to enhance rice quality and yield.