Identifying Novel QTLs and Candidate Genes for Tillering Ability in Sugarcane (Saccharum spp.)

Sugarcane is a tropical and subtropica cultivated crop that exhibits complex genetic traits. Key agronomic characteristics, such as tillering rate (T-rate) and the number of canes per hectare (NCPH), are crucial for yield optimization. This study employed a two-way pseudo-testcross strategy mapping approach with a 172 F1 population derived from ‘Yuenong73-204’ (low-tillering) × ‘CP72-1210’ (high-tillering). A genetic map spanning 1578.04 cM was constructed using 572 SNP identified via chip array genotyping. Through quantitative trait loci (QTL) mapping with LOD > 3, five QTLs linked to T-rate and four to NCPH were identified. Meanwhile, one QTL consistently present in at least two environments and one QTL present in both tillering traits. These QTLs accounted for the explanatory rate of phenotypic variation (PVE), ranging from 7.7 to 11.1% for T-rate and 5.6% to 10.7% for NCPH. Additionally, we screened one representative loci (AX-171307910) with one excellent genotype (GG), based on the QTL of qSE1/E2NCPH57 for NCPH, which excellent genotype will lead sugarcane toward better tillering traits. Finally, seven having this excellent genotype were screened. Further analysis revealed 3 relatively reliable candidate genes within the QTL of qSE1/E2NCPH57, including Soffic.01G0055400-1P, Soffic.01G0055410-1A, and Soffic.01G0055150-1A, respectively. However, RT-qPCR analysis discovered that the expression level of Soffic.01G0055400-1P and Soffic.01G0055150-A showed significant difference between Yuenong73-204 and CP72-1210, suggesting these two candidate genes were highly likely to be important genes affecting tillering. These insights offer valuable reference points for genetic enhancement strategies targeting tillers and for effective stalk development in sugarcane.