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Journal of Integrative Agriculture  2022, Vol. 21 Issue (6): 1539-1550    DOI: 10.1016/S2095-3119(21)63701-2
Special Issue: 水稻遗传育种合辑Rice Genetics · Breeding · Germplasm Resources
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China
XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long
State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, P.R.China
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Abstract  Milling and appearance quality are important contributors to rice grain quality.  Abundant genetic diversity and a suitable environment are crucial for rice improvement.  In this study, we investigated the milling and appearance quality-related traits in a panel of 200 japonica rice cultivars selected from Liaoning, Jilin and Heilongjiang provinces in Northeast China.  Pedigree assessment and genetic diversity analysis indicated that cultivars from Jilin harbored the highest genetic diversity among the three geographic regions.  An evaluation of grain quality indicated that cultivars from Liaoning showed superior milling quality, whereas cultivars from Heilongjiang tended to exhibit superior appearance quality.  Single- and multi-locus genome-wide association studies (GWAS) were conducted to identify loci associated with milling and appearance quality-related traits.  Ninety-nine significant single-nucleotide polymorphisms (SNPs) were detected.  Three common SNPs were detected using the mixed linear model (MLM), mrMLM, and FASTmrMLM methods.  Linkage disequilibrium decay was estimated and indicated three candidate regions (qBRR-1, qBRR-9 and qDEC-3) for further candidate gene analysis.  More than 300 genes were located in these candidate regions.  Gene Ontology (GO) analysis was performed to discover the potential candidate genes.  Genetic diversity analysis of the candidate regions revealed that qBRR-9 may have been subject to strong selection during breeding.  These results provide information that will be valuable for the improvement of grain quality in rice breeding.
Keywords:  rice        grain quality        GWAS        genetic diversity  
Received: 02 December 2020   Accepted: 02 April 2021
Fund: This research was funded by the National Key Research and Development Program of China (2016YFD0100902–07), the Central Public-interest Scientific Institution Basal Research Fund, China (CPSIBRF-CNRRI-202101), and the Chinese Academy of Agricultural Sciences (CAAS-ASTIP-201X-CNRRI).
About author:  Correspondence YANG Yao-long, Tel: +86-571-63370539, E-mail:; WEI Xing-hua, Tel: +86-571-63370366, E-mail:

Cite this article: 

XU Xin, YE Jun-hua, YANG Ying-ying, LI Ruo-si, LI Zhen, WANG Shan, SUN Yan-fei, ZHANG Meng-chen, XU Qun, FENG Yue, WEI Xing-hua, YANG Yao-long. 2022. Genetic diversity analysis and GWAS reveal the adaptive loci of milling and appearance quality of japonica (oryza sativa L.) in Northeast China. Journal of Integrative Agriculture, 21(6): 1539-1550.

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