Evaluation of the genetic diversity of japonica from different ecological zones：Using whole genome sequencing and agronomic trait analysis
Authors: Yan Zhiqiang , Deng Ruyue , Li Jiali , Xia Zhongmin , Zhu Susong 
Published: June 2022

Background
Japonica rice (Oryza sativa L.) is a subspecies of the Asian cultivated rice and is popular because of its better quality. The genetic diversity of japonica rice germplasm resources is the basis for japonica variety breeding and improvement. Genetic diversity is evaluated by means of phenotypic identification and molecular markers. Molecular markers are more stable and less susceptible to interference by environmental factors, whereas phenotypes are susceptible to environmental factors. In this study, 150 japonica rice varieties from different ecological zones were used to analyze their kinship and population structure by next-generation sequencing technology. The phenotypic diversity was then evaluated using ten agronomic traits under two different environmental conditions, Guiyang and Hainan, respectively, and the effect of different environmental conditions on the phenotypic diversity evaluation was analyzed. The present study will provide a comprehensive assessment of the genetic diversity of japonica rice varieties from different ecological zones and provide a theoretical foundation for parental selection in conventional japonica rice breeding.
Result
The results of sequencing and population structure analysis showed that the 150 japonica varieties were abundant in genetic variation, without homogeneity and subgroup differentiation. The identification of phenotypic diversity also showed that the phenotypes of these japonica rice varieties from different ecological zones are rich in diversity under different environmental conditions. In addition, different environments had a significant impact on the results of phenotypic diversity evaluation such as diversity index, enrichment intervals, agronomic trait correlations, and composite scores based on regression analysis for japonica rice varieties from different ecological zones. In Guiyang, the top 10 overall agronomic traits were Yungingnuo (JR_LN38), Chugeng37 (JR_LN32), Chugeng28 (JR_LN34), Fuhedao255 (JR_LN50), Guangminggeng2Hao (JR_LN96), Chugeng7 (JR_LN39), Chugeng40 (JR_LN33), Liaogeng401 (JR_LN102), Bigeng44 (JR_LN107), Sugeng45 (JR_LN76), however, in Hainan, the top 10 in terms of overall performance were, respectively, Chugeng7 (JR_LN39), Lemont (JR_LN149), Chugeng32 (JR_LN43), Chugeng28 (JR_LN34), Bidao126 (JR_LN105), Tenggeng2 (JR_LN45), Chugeng26 (JR_LN41), Tengxi138 (JR_LN153), Hexi27-2 (JR_LN145), Chugeng39 (JR_LN44).
Conclusion
150 Japonica rice varieties from different ecological zones are abundantly genetically diverse, with no homogeneity and no subpopulation differentiation that can be utilized as parental resources for Japonica rice variety breeding. In conventional breeding, breeders often rely on phenotypes as an important basis for parental selection. Given that different environments have a strong influence on the evaluation of phenotypic diversity of japonica rice germplasm resources, it is necessary to conduct a comprehensive evaluation of germplasm resources based on a large amount of agronomic trait data obtained in the local environment to screen for desirable parents after the breeding target has been determined.