Analysis of Genetic Structure in the USDA Rice Mini-Core Collection Using the SQUAMOSA Promoter-binding-like Gene Family

The SQUAMOSA (SQUA) promoter-binding-like ( SPL ) gene family is a plant specific transcription factor family and has many important biological functions. In this study, 19 pairs of primers were designed based on 19 Oryza sativa L. SQUAMOSA promoter-binding-like ( OsSPL ) gene sequences and used for a polymorphism analysis with 171 accessions as a set of the United States Department of Agriculture (USDA) rice mini-core collection established in the US. This mini-core represents the core of 1 794 accessions and the entire collection of 18 412 accessions. In total, 140 bands were amplified, and 128 of them were polymorphic, occupying a great majority (up to 91.4%) of the mini-core collection. The average number of alleles per locus was 7.4. The cluster and principal coordinate analysis agreeably classified the 171 accessions into six subgroups (subgroups â… -â…¥), and those in the same subgroup were distributed throughout similar geographical and ecological regions worldwide. Days to heading for subgroup â…¥ was significantly greater than the overall mean. Similarly, the plant height for subgroup â…i and spikelets per panicle for subgroups â…  and â…¢ were significantly different from the overall mean, respectively. Thus, the OsSPL genes were associated with the days to heading, plant height and spikelets per panicle.