Abstract
BackgroundThe 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.ResultsWe 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.ConclusionsIn 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.
Highlights
The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies
In Eight-parent recombinant inbred line (RIL) population (8PL), The first four-parent RIL population (4PL1) and The second four-parent RIL population (4PL2), there were 279, 252 and 270 markers whose missing rates were greater than 10%; percent of 13.17, 12.03, and 4.48 of the markers had a heterozygosity level over 3%, respectively (Additional file 8: Figure 1B)
In summary, individual linkage maps were constructed from three multi-parent rice populations, and an integrated map was built based on the three individual maps
Summary
The construction of genetic maps based on molecular markers is a crucial step in rice genetic and genomic studies. Construction of linkage map by using molecular markers is a crucial step in genetic and genomic analysis that facilitates the discovery of quantitative trait locus/ loci (QTLs) and provides chromosomal information for gene cloning and marker-assisted breeding (Meng et al 2015; Palumbo et al 2019). Harushima et al (1998) reported a genetic linkage map containing 2275 cDNA markers covering 1521.6 cM in an F2 population of Nipponbare × Kasalath. Yin et al (2015) constructed a linkage map containing 143 SSR markers in one japonica × indica genetic population consisting of 215 recombinant inbred lines (RILs). De Leon et al (2016) constructed a high-density GBSderived SNP linkage map with 2817 bins from a rice RIL population. Kim (2018) developed a SNP map with 1954 bins for an F2 population
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