Ethnic minorities living in Guizhou Province, China, have produced numerous rice landraces that are rich in genetic variations. Studying the genetic diversity and population structure of rice landraces in Guizhou has therefore become a topic of great research interest. However, the influence of ethnic minorities and their traditional food cultures on rice landraces remains unclear. We analyzed the genetic diversity of 598 rice landraces using simple sequence repeat (SSR) markers. Furthermore, we analyzed the nucleotide variations between two similar populations collected during two different time periods using a single-nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The three major results were as follows: (1) The genetic diversity index of rice landraces in six ecologically distinct rice farming zones of Guizhou Province was high (He = 0.7721), and Southwest Guizhou, which has a large population of ethnic minorities, is the center of genetic diversity of rice landraces in the province; this region had the highest He at 0.7823 and the highest polymorphic information content (PIC) at 0.7562. (2) A neighbor-joining (NJ) phylogenetic tree and a model of the population structure showed that the rice landraces from the southwest, south, and southeast of Guizhou had unique genetic structures and genetic backgrounds, which are closely related to the traditional diet cultures of the local ethnic minorities. (3) A nucleotide variation analysis of similar rice landraces collected in 1980 and 2015 revealed that, after 35 years of domestication by ethnic minorities, the original dominant haplotypes were well-preserved; the frequency of the most favorable haplotypes gradually increased to adapt to the traditional food culture. This study is expected to promote the protection and sustainable utilization of rice landraces from this unique region and to provide valuable germplasm materials and information for future rice breeding and basic research efforts.

Ethnic minorities living in Guizhou Province have a long history of rice farming and traditional culture, and they produce numerous of rice landraces, which are rich in genetic variation. Therefore, studying the genetic structure and diversity of rice landraces in Guizhou has become a hot topic. However, the influence of ethnic minorities and their traditional farming system and culture on rice landraces remains unclear. In this study, we analyzed the genetic diversity and population structure in 598 rice landraces in six eco-rice farming zones using simple sequence repeat (SSR) markers and the nucleotide variation between two similar populations collected during different periods using single nucleotide polymorphism (SNP) haplotype analysis of six unlinked nuclear loci. The results were as follows: 1) The genetic diversity level of rice landraces in six different eco-rice farming zones of Guizhou Province was high (He = 0.7659), and the genetic background was rich. Qianxinan Miao and Buyi Autonomous Prefecture is the genetic diversity center of rice landraces in Guizhou, with the highest He (0.7549) and PIC (0.7278). 2) The neighbor-joining (N-J) tree and the STRUCTURE model showed the same genetic structure, and the population structure of japonica was correlated with geographical origin. Under the influence of the domestication of the Buyi, Miao and Dong people, rice landraces in the III and IV eco-rice farming zones were isolated into a subgroup, forming a special ecological type of landrace. 3) Nucleotide variation analysis was performed on similar rice landraces collected in 1980 and 2015. The results showed that after 35 years of domestication, the original dominant haplotypes could be preserved well, and the frequency of the most favorable haplotypes gradually increased, while the frequency of a few unfavorable haplotypes gradually decreased to adapt to the corresponding environment and traditional culture. This study can promote the protection and sustainable utilization of rice landraces and provide more valuable germplasm materials and information for rice breeding and basic research.