Genetic Analysis of the Awn Length Gene in the Rice Chromosome Segment Substitution Line CSSL29

Awn length is a significant agronomic trait in rice. To analyze the genetic mechanism of awn length in the chromosome segment substitution line 29 (CSSL29) derived from 9311 (recipient) into Nipponbare (NIP, donor), an F₂ segregated population was constructed from 9311 (indica) and CSSL29. The population and candidate genes were analyzed using quantitative trait loci sequencing (QTL-seq), yeast two-hybrid assays, and 3 k and 10 k rice population databases. The results indicated that the awn length in the F₂ segregating population followed a normal distribution, and the long-awn phenotype in CSSL29 was controlled by multiple genes. Through BSA sequencing data, a major QTL qAWN4 associated with rice awn length was identified on chromosome 4, containing the cloned gene An-2. Further investigation of the CSSL29 long-awn substitution segment revealed the presence of the awn length gene An-1, with both genes exhibiting an additive effect on the regulation of the long-awn phenotype. Yeast two-hybrid experiments confirmed no interaction between An-2 and An-1, suggesting that additive effect awn length regulation is not mediated through simple protein-to-protein binding. Population genetic analysis indicated that the An-2 allele was artificially selected during domestication but did not significantly differ between indica and japonica subspecies. These findings enhance our understanding of the genetic regulation of rice awn length and the domestication of long-awn rice, laying the groundwork for future research in this area.