Marker-trait associations and superior haplotypes for rice straw cell wall components and their relationship with digestibility and agronomic traits

Being a staple crop and growing over larger area, rice (Oryza sativa L.) generates a vast quantity of straw as a by-product. However, high fibre and silica content present in rice straw makes it difficult to utilize as a quality livestock feed or for industrial utilization, thus necessitating to identify genetic resources with lower silica content and enhanced straw digestibility. In this study, 207 diverse rice germplasm accessions belonging to 2 K rice diversity panel and 25 cultivated varieties were evaluated for straw cell wall components (silica, lignin and cellulose), agronomic traits (plant height, number of tillers, stem thickness) and in-vitro digestibility (acid detergent fibre). Wide variation was observed for silica (4.3-15.7%), lignin (4.9-29.5%), cellulose (20.3-45.2%), plant height (65.6-197.0 cm), number of tillers (4.0-19.0), stem thickness (0.9-9.2 mm) acid detergent fibre (ADF; 45.1-73.0%). Correlation analysis revealed a strong negative relationship between silica and organic as well as dry matter digestibility while lignin displayed variable effects depending on its interaction with other components. Multi-locus-Genome-wide Association Studies (ML-GWAS) with a subset of 154 rice accessions using 208,846 SNPs identified 33 significant marker-trait associations (MTAs) across genome for straw silica, lignin, cellulose, and ADF content. Major MTAs co-localized with known genes involved in silicon uptake (OsOPT2, OsOPT3, OsUCP2), lignin biosynthesis (4CL3, WRKY71, OsACS7), and cellulose synthesis (WAK12, BGLU4, OsMPS). Haplotype analyses of key candidate genes revealed superior alleles associated with up to 15.9% lower silica and 26.9% lower lignin content, with corresponding higher expression in relevant tissues. Selected rice accessions with favourable alleles and balanced ADF, lignin, and silica showed improved in-vitro digestibility, providing promising genetic resources for enhancing rice straw palatability. These findings offer valuable insights into the genetic basis of straw quality traits and identify potential donors for breeding programs aimed at developing rice varieties with improved straw value for sustainable agriculture and bioenergy use.