Comparison of molecular linkage maps and agronomic trait loci between DH and RIL populations derived from the same rice cross

Doubled haploid (DH) and recombinant inbred line (RIL) populations are two types of permanent populations for rice (Oryza sativa L.) breeding and genetic mapping. In this study, we report the comparison of molecular maps and mapped agronomic trait loci between DH and RIL populations derived from the same rice cross, ZYQ8 (indica) x JXI7 (japonica). We investigated six agronomic traits (days to heading, plant height, number of spikelets per panicle, number of grains per panicle, 1000-grain weight, and seed set percentage) and found that five of them did not show significant differences between the two populations. Restriction fragment length polymorphism (RFLP) and microsatellite markers were selected to construct two linkage maps of the DH and RIL populations. All the DNA markers except G39 showed the same linkage groups and orders between the two populations. The genetic distance per chromosome in the RIL population was shorter than that in the DH population, and the total genetic distance of genome in the RIL population (1465 cM) was 70.5% of that in the DH population (2079 cM). In the RIL population, 27.3% markers showed distorted segregation at P < 0.01 level, of which 90% markers favored indica alleles, while in the DH population, the skewed markers favoring indica and japonica alleles were in accordance with 1:1 ratio. Eight commonly distorted regions on chromosomes 1, 3, 4, 7, 8, 10, 11, and 12 were detected in both RIL and DH populations, of which seven skewed toward indica alleles and one toward japonica allele. Five of them were located near gametophytic gene loci (ga) and/or sterility gene loci (S). We also compared the quantitative trait locus (QTL) mapping results between the DH and RIL populations and found a number of similarities in the QTL locations between these two populations. So both RIL and DH populations are equally effective in rice breeding and genetic analysis.