| Asian cultivated rice (Oryza sativa L.) is an important food crop in the world. As permanent populations, doubled haploid (DH) populations are unique genetic resources that have various applications in plant genetics and genomics studies. So far, except a small number of DH lines obtained from the hybrid Pei’ai 64S/02428, all rice DH populations do not carry wide compatibility gene S5n. To generate new germplasm resources for rice genetic studies and breeding, this study developed a DH population by anther culture from the hybrid of a japonica elite line 668B and a wide compatible indica line T23 with 178 non-redundant lines. The DH lines were characterized using three S5 locus specific markers as well as 34 InDel markers that can specifically differentiate indica and japonica. Futhermore, the agronomic traits of the DH population were investingated and a selection of DH lines were further crossed to three different indica and japonica male sterile lines and their F1 hybrids were assessed. The main results are as follows:1. Development of a DH population. By anther culture of the F1 hybrid of 668B X T23, a DH population that consist of 178 non-redundant DH lines was developed.2. Chractarization of the DH population for indica-japonica attribute and analysis of S5 haplotype. Each DH line of the population was genotyped for the indica/japonica specific InDel markers; the results showed that most (74.15%) of the DH lines belong to the intermediate type, only a few lines belong to typical indica-type (1.8%) and japonica-type (0.6%). However, among the intermediate-type DH lines, the frequency of japonica allele (Fi <0.5) in the DH population is less than the frequency of indica allele. Genotyping of the S5 locus with three allele-specific markers for ORF3, ORF4 and ORF5 revealed that there were 65 lines having the haplotype similar to 668B (ORF3-/ORF4+/ORF5j) and 109 lines having haplotype similar to T23 (ORF3+/ORF4-/ORF5n). In addition, there were four DH lines having a new haplotype, i.e.ORF3+/ORF4+/ORF5j. This result showed that the ORF3-ORF4 region is likely to be a recombination hotspot.3. Subspecies specificity and genetic similarity of DH population:Haplotyping analysis revealed higher frequency of indica allele in the DH population. In addition, less than half (13/34) InDel markers fit the 1:1 segregation ratio, the rest of the markers were either over-represented by indica alleles (12/34) or by japonica alleles (9/34). In addition, a few markers are present at frequencies as low as 1.8% or as high as 98.3%. According to cluster analysis of the DH population, DH lines had similarity coefficients between 0.51-0.97 with an average of 0.74. When the similarity coefficient is less than 0.6, the DH population could be divided into 8 main types, this revealed high genetic similarity of DH population.4. Analysis of seed set of F1 hybrids. A selection of 54 DH lines were crossed to three male sterile lines Hua201S, GS113 and 668A. Consequently,139 hybrids were produced. Based on whether carrying the wide compatibility gene S5", the DH lines were divided into two categories, i.e. Sub-S5n and Sub-S5J. The result showed that the F1 hybrids of Hua201S and GS113 with Sub-S5n and Sub-S5J has little difference on seed setting rate, while seed setting rate of 668A X Sub-S5n and Sub-S5J of combinations are generally higher, indicating that 668A has higher affinity. Further analysis showed that genetic distance of two parents had little effect on seed settingTaken together, the present study advanced understanding of the genetics of wide crosses between the two rice subspecies, and the new DH population generated will become a useful resource for rice genetic study and breeding in the future. |
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