Genetic architecture of sugarcane traits in a polyploid genomics framework

Plant materials For genome assembly and annotation, we used plant materials including, S. hybrid POJ2878, S. spontaneum 82-114 and S. officinarum XZ. These were cultivated in the greenhouse at Shenzhen. Tender leaves were collected for subsequent genome sequencing. This study also resequenced 981 sugarcane accessions, including 78 S. officinarum , 290 S. spontaneum accessions and 613 cultivated varieties. Among the cultivated varieties, 246 were non-Chinese germplasms, while 327 were core domestic cultivars or breeding lines in China. The plant materials were grown at three experimental sites representing distinct climates: (1) a tropical monsoon climate at the sugarcane research base in Lingao County, Hainan Province (19° 34′–20° 02′ N, 109° 3′–109° 53′ E, altitude: 34 m); (2) a subtropical monsoon climate in Fusui County, Guangxi Zhuang Autonomous Region (22° 38′ 06″ N, 107° 54′ 15″ E; altitude 94 m); and (3) a subtropical plateau climate in Kaiyuan City, Yunnan Province (23° 30′–23° 58′ N, 103° 04′–103° 43′ E; altitude 1,051 m). Buds were first disinfected and then planted using a single-bud method within a randomized complete block design (1.2 m row spacing; 15 cm plant spacing). To ensure uniform germination, the field was subject to standardized management, including regular irrigation and pest and weed control. DNA and RNA sequencing DNA extraction DNA extraction for single-molecule sequencing involved collecting samples and preparing long genomic DNA. …