Genetic Analysis of a Collection of Rice Germplasm (Oryza sativa L.) through High-Density SNP Array Provides Useful Information for Further Breeding Practices

Ping Huang; Qiongyao Gu; Yong Hu; Huahui Li; Zhigang Wu; Weihua Liu; Zhenhua Zhu; Pingrong Yuan; Liu Duan; Ying Zhou; Hanyu Luo; Shuyan Kou; Li Liu

doi:10.3390/genes13050830

Genetic Analysis of a Collection of Rice Germplasm (Oryza sativa L.) through High-Density SNP Array Provides Useful Information for Further Breeding Practices

Genes (Basel). 2022 May 6;13(5):830. doi: 10.3390/genes13050830.

Authors

Ping Huang¹, Qiongyao Gu¹, Yong Hu², Huahui Li¹, Zhigang Wu¹, Weihua Liu¹, Zhenhua Zhu¹, Pingrong Yuan¹, Liu Duan², Ying Zhou³, Hanyu Luo⁴, Shuyan Kou¹, Li Liu²

Affiliations

¹ Institute of Food Crops, Yunnan Academy of Agriculture Sciences, Kunming 650205, China.
² State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan 430062, China.
³ College of Life Science and Health, Wuhan University of Science and Technology, Wuhan 430065, China.
⁴ Yunnan Inntra Intelligence System Co., Ltd., 22/F, Junhao building, Kegao Road High-Tech Zone, Kunming 650101, China.

Abstract

Traditional breeding strategies mainly focus on the evaluation of trait performance, but pay less attention to the changing genetic background. A comprehensive understanding of the genetic diversity of germplasms is crucial for the deliberate improvement of specific traits. A collection of 154 highland rice varieties were collected as the initial genetic resource in our breeding program to improve the pathogen resistance and eating and cooking qualities. These varieties were analyzed using a whole-genome SNP array and were clustered into three groups. Further analysis revealed that the favorable alleles of pathogen resistance genes are mostly absent in our collected varieties. However, it showed that most varieties possess favorable alleles of Waxy (Wx) and ALKALI DEGENERATION (ALK), which are able to enhance the eating and cooking qualities. Moreover, only about one fifth of all varieties harbors favorable the allele of fragrance gene Betainealdehyde dehydrogenase (BADH2). Together, these results give an overall view of the genetic constitution of the target traits, which provide useful information for future genetic improvement in breeding practices.

Keywords: SNP; genetic diversity; local variety; rice.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Alleles
Genetic Testing
Oryza* / genetics
Phenotype
Plant Breeding

Grants and funding

This work was supported by the Personnel Training Program of Yunnan Technical Innovation (2018HB113), the Outstanding Young Scholar Program of Yunnan Province, the Yunnan Science Foundation (202001AT070361, 202101BD070001-091), Yunling Scholar Program of Yunnan Province and Major Projects of Yunnan Science and Technology (202102AE090004) and the National Natural Science Foundation of China (31971410).