Genome-wide association study for mapping QTLs and candidate gene analysis of rice chalkiness

<bold>Objective</bold> Rice chalkiness is one of the key indicators affecting the commercial value of rice grains.Although progress has been made in the identification of quantitative trait loci（QTLs）and genes associated with rice grain chalkiness，it still cannot fully meet the needs of rice breeding. Therefore，mining more chalkiness-related QTLs and genes from rice germplasm resources is of great significance for promoting the breeding of new high-quality rice varieties. <bold>Method</bold> A total of 144 representative rice varieties were used as experimental materials.These materials were planted at the experimental bases in Nanchang and Gao’an in 2023.After harvest at the maturity stage，the chalky grain rate and chalkiness degree of rice were determined，and genome-wide association analysis was performed using GEMMA software combined with genotypes. <bold>Result</bold> Under the Nanchang environment，16 chalkiness-related QTLs were identified，including 12 associated with the percentage of chalky grains and 4 associated with chalkiness degree.Under the Gao’an environment，3 chalkiness-related QTLs were detected，with 1 related to the percentage of chalky grains and 2 related to chalkiness degree.The results showed that <italic>qPGWCNC10-2</italic>，<italic>qPGWCGA10-2</italic>，<italic>qDECNC-10</italic>，and <italic>qDECGA-10</italic> on chromosome 10 were localized in the same interval.Further analysis of QTLs on chromosome 10 led to the screening of 3 candidate genes associated with grain chalkiness，namely <italic>LOC_Os10g14870</italic>，<italic>LOC_Os10g17690</italic>，and <italic>LOC_Os10g17930</italic>. <bold>Conclusion</bold> This study identified new chalkiness-related loci in rice and analyzed the candidate genes，providing a reference for the cloning of new chalkiness-related QTLs（genes）and the genetic improvement of chalkiness.