Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice

Pingping Qu; Jinhui Shi; Tianxiao Chen; Kai Chen; Congcong Shen; Jiankang Wang; Xiangqian Zhao; Guoyou Ye; Jianlong Xu; Luyan Zhang

doi:10.1186/s12284-020-0373-z

Construction and integration of genetic linkage maps from three multi-parent advanced generation inter-cross populations in rice

Rice (N Y). 2020 Feb 14;13(1):13. doi: 10.1186/s12284-020-0373-z.

Authors

Pingping Qu, Jinhui Shi, Tianxiao Chen¹, Kai Chen¹, Congcong Shen¹, Jiankang Wang², Xiangqian Zhao³, Guoyou Ye⁴, Jianlong Xu⁵, Luyan Zhang⁶

Affiliations

¹ Agricultural Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen, 518210, China.
² The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
³ Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Science, Hangzhou, 310021, China.
⁴ Genetics and Biotechnology Division, International Rice Research Institute, Baños, Laguna, Philippines.
⁵ The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. xujianlong@caas.cn.
⁶ The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. zhangluyan@caas.cn.

Abstract

Background: The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Pure lines derived from multiple parents provide more abundant genetic variation than those from bi-parent populations. Two four-parent pure-line populations (4PL1 and 4PL2) and one eight-parent pure-line population (8PL) were developed from eight homozygous indica varieties of rice by the International Rice Research Institute (IRRI). To the best of our knowledge, there have been no reports on linkage map construction and their integration in multi-parent populations of rice.

Results: We constructed linkage maps for the three multi-parent populations and conducted quantitative trait locus (QTL) mapping for heading date (HD) and plant height (PH) based on the three maps by inclusive composite interval mapping (ICIM). An integrated map was built from the three individual maps and used for QTL projection and meta-analysis. QTL mapping of the three populations was also conducted based on the integrated map, and the mapping results were compared with those from meta-analysis. The three linkage maps developed for 8PL, 4PL1 and 4PL2 had 5905, 4354 and 5464 bins and were 1290.16, 1720.01 and 1560.30 cM in length, respectively. The integrated map was 3022.08 cM in length and contained 10,033 bins. Based on the three linkage maps, 3, 7 and 9 QTLs were detected for HD while 6, 9 and 10 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. In contrast, 19 and 25 QTLs were identified for HD and PH by meta-analysis using the integrated map, respectively. Based on the integrated map, 5, 9, and 10 QTLs were detected for HD while 3, 10, and 12 QTLs were detected for PH in 8PL, 4PL1 and 4PL2, respectively. Eleven of these 49 QTLs coincided with those from the meta-analysis.

Conclusions: In this study, we reported the first rice linkage map constructed from one eight-parent recombinant inbred line (RIL) population and the first integrated map from three multi-parent populations, which provide essential information for QTL linkage mapping, meta-analysis, and map-based cloning in rice genetics and breeding.

Keywords: Integrated map; Linkage map; Multi-parent population; QTL mapping; Quantitative trait locus (QTL).

Abstract

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