Investigating genetic structure and diversity is crucial for rice improvement strategies, including mapping quantitative trait loci with the potential for improved productivity and adaptation to the upland ecology. The present study elucidated the population structure and genetic diversity of 176 rice germplasm adapted to the upland ecology using 7063 genome-wide single nucleotide polymorphism (SNP) markers from the Diversity Array Technology (DArT)-based sequencing platform (DArTseq). The SNPs were reasonably distributed across the rice genome, ranging from 432 SNPs on chromosome 9 to 989 SNPs on chromosome 1. The minimum minor allele frequency was 0.05, while the average polymorphism information content and heterozygosity were 0.25 and 0.03, respectively. The model-based (Bayesian) population structure analysis identified two major groups for the studied rice germplasm. Analysis of molecular variance revealed that all (100%) of the genetic variance was attributable to differences within the population, and none was attributable to the population structure. The estimates of genetic differentiation (PhiPT = 0.001; P = 0.197) further showed a negligible difference among the population structures. The results indicated a high genetic exchange or gene flow (number of migrants, Nm = 622.65) and a substantial level of diversity (number of private alleles, Pa = 1.52 number of different alleles, Na = 2.67; Shannon's information index, I = 0.084; and percentage of polymorphic loci, %PPL = 55.9%) within the population, representing a valuable resource for rice improvement. The findings in this study provide a critical analysis of the genetic diversity of upland rice germplasm that would be useful for rice yield improvement. We suggested further breeding and genetic analyses.

中文翻译：

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使用基于多样性阵列技术（DArT）的单核苷酸多态性（SNP）标记的旱稻种质遗传结构和多样性

研究遗传结构和多样性对于水稻改良战略至关重要，包括绘制具有提高生产力和适应高地生态潜力的数量性状基因座。本研究使用基于多样性阵列技术（DArT）的测序平台（DArTseq）的7063个全基因组单核苷酸多态性（SNP）标记阐明了176个适应旱地生态的水稻种质的种群结构和遗传多样性。SNPs在水稻基因组中分布合理，从9号染色体上的432个SNPs到1号染色体上的989个SNPs不等。最小次要等位基因频率为0.05，平均多态性信息含量和杂合度分别为0.25和0.03。基于模型的（贝叶斯）种群结构分析确定了研究水稻种质的两个主要群体。分子变异分析表明，所有（100%）的遗传变异都归因于群体内的差异，而没有一个归因于群体结构。遗传分化的估计值（PhiPT = 0.001；磷= 0.197）进一步表明人口结构之间的差异可以忽略不计。结果表明高遗传交换或基因流动（迁移数量，Nm = 622.65）和相当程度的多样性（私人等位基因数量，Pa = 1.52 不同等位基因数量，Na = 2.67；香农信息指数，一世= 0.084; 和群体中多态位点的百分比，%PPL = 55.9%），代表了水稻改良的宝贵资源。本研究的结果对旱稻种质的遗传多样性进行了批判性分析，这将有助于提高水稻产量。我们建议进一步的育种和遗传分析。