Experimental materials

The association mapping panel consisted of 169 Upland cotton backbone cultivars (lines). Among them, 159 cultivars were selected from major cotton regions in China (Yellow River, Yangtze River, Northwestern China, and Northern China), and 10 were introduced from abroad (Li et al. 2018a). All the accessions were legally planted in the ecological cotton-growing areas of the Yellow River (Xinxiang City, Henan Province) (113°52′ E, 35°18′ N, 95 m above sea level) and Northwestern China (Shihezi City, Xinjiang Province) (85°56′, 44°16′ N, 442 m above sea level) in 2012 and 2013 with two replications. The climate characteristics of the four environments are listed in Table 1. Because of the large climatic differences between Yellow River, with a longer frost-free season, and Northwestern China, with a shorter frost-free season, we performed corresponding cultivation measures for the two locations. In Xinxiang, 14–16 plants were arranged in each row, with a row length of 5 m and a row interval of 1.0 m, while in Shihezi, 38–40 plants were arranged in each row, with a row length of 5 m and a row interval of 0.45 m. All the activities were performed as per normal local management practices. The four environments, 2012Xinxiang, 2013Xinxiang, 2012Shihezi, and 2013Shihezi, were designated E1, E2, E3, and E4, respectively.

Climate characteristic of four environments

E1, E2, E3, and E4 indicate four environments: 2012Xinxiang, 2013Xinxiang, 2012Shihezi, and 2013Shihezi, respectively.