MAP-Based Analysis Of Polymorphism Of Chinese Rice Genetic Resources Detected By SSRs (Microsatelites)

In the present study, using 60 microsatellies of cultivated rice, map-based analysis of SSLPs of a total of 117 genotypes of Oryza rufipogon, O. officinalis and O. granulata, as well as 57 varieties of cultivated rice O. sativa, representing their geographical distribution in China were conducted to detect their genetic diversity and relatedness. Meanwhile, a comparative study on genetic diversity and population genetic structure of five natural populations of O. rufipogon of China were completed using 21 microsatellites and 22 allozyme loci. The results were as follows:1 Using 60 SSR primer pairs of rice, a total of 60 genotypes of three Chinese wild rice were amplified by PCR. The results suggest that O. granulata, O. officinalis, and O. rufipogon had the transferability rate of 73.3％, 90.0％and 100％, respectively, indicating that the closer a wild relative is to cultivated rice, the higher transferability rate of rice microsatellites it has.2 A total of 1492 alleles were detected in 117 genotypes of 4 species of the genus Oryza. of them, 815, 454, 150 and 73 alleles were found in Oryza rufipogon, O. sativa, O. officinalis and O. granulata, respectively. Among 60 loci examined, the most alleles were found in RM247(47), the fewest alleles were scored in RM83(5), and other loci varied between 20 to 40.. Based on the numbers of alleles of the loci and chromosomes examined, the four species can be listed as: O. rufipogon＞O. sativa＞0. officinalis＞0. granulata. O. rufipogon had more alleles than O. sativa in 12 chromosomes. O. rufipogon had more alleles than O. sativa in 56 loci except OSR19 and RM222, which showed fewer alleles than O. sativa and RM224 and RM 235, which had the same alleles to O. sativa.3 A total of 638 specific alleles were detected within 117 genotypes of 4 species of the genus Oryza. Of them, 437, 454, 65 and 11 specific alleles were found in O. rufipogon, O. sativa, O. officinalis and O. granulata, respectively. Among 60 loci examined, the most specific alleles were found in RM209 and OSR27(22), the fewest alleles were scored in RM83(1), and other loci varied between 10 to 20.. Based on the numbers of specific alleles of the loci and chromosomes examined, the four species can be listed as: O. rufipogon＞O. sativa＞O. officinalis＞O. granulata. O. rufipogon generally had more specific alleles than O. sativa in 12 chromosomes. O. rufipogon had far more alleles than O. sativa at 58 loci of 12 chromosomes.4 In the genomes of O. rufipogon, O. sativa and O. officinalis, there were different numbers of total alleles and specific alleles both in 12 chromosomes and loci of each chromosome. However, no significant differences of both total and specific alleles detected were found in chromosomes and loci, which probably results from small sampling size.5 UPGMA dendrograms of 35 genotypes of O. rufipogon using 5 loci of each chromosome and a total of 60 loci of 12 chromosomes were produced. The results indicate that: (1) the dendrograms were different from each other using 5 loci of each chromosome, which means the numbers of groups and clustering patterns were different from each other. It suggests that there are differences of genetic diversity among different chromosomes and different relationships among these genotypes observed based on different chromosomes; (2) every 5 loci of 11 chromosomes except No. 9 chromosome, all genotypes may be easily discriminated. All genotypes examined showed significant differences at chromosomes and loci levels; and(3) genetic relationships among these genotypes of O. rufipogon were not significantly related to geographical distances.6 UPGMA dendrograms of 21 genotypes of O. officinalis using 5 loci of each chromosome and a total of 60 loci of 12 chromosomes were produced. The results indicate: (1) the dendrograms were different from each other using 5 loci of each chromosome, suggesting that there are differences of levels and distribution of genetic diversity among different chromosomes; (2)all genotypes might easily be distinguished using 60 loci of 12 chromosomes. However, they could not be discriminated by any one chromosome; and(3) clustering patters showed that genetic relationships among these genotypes of O. officinalis were closely related to geographical distances.7 UPGMA dendrograms of 57 varieties of O. sativa using 5 loci of each chromosome and a total of 60 loci of 12 chromosomes were produced. The results indicate that:(1) the dendrograms were different from each other using 5 loci of each chromosome, suggesting that there are differences of genetic diversity among different chromosomes. Additionally, detected by every 5 loci of 12 chromosomes most of the genotypes might easily be discriminated;(2) there were different japonica-indica differentiation among different chromosomes; and(3) compared with the landraces, most of the cultivars, popular grown varieties as well as major parents for rice breeding had high genetic similarity, indicating they have narrow genetic bases.8 Although similar patters of levels of genetic diversity were observed among five populations using allozyme and microsatellite loci, levels of genetic diversity were far higher at microsatellite loci(A=3.1, P=73.3％, Ho=0.358 and He=0.345) than those at allozyme loci(A=1.2, P=12.7％, Ho=0.020 and He=0.030) for these same five populations, and each value detected at microsatellite loci was higher than that at allozyme loci, suggesting there were higher polymorphisms at microsatellite loci than allozyme loci;(2) there were slightly different population genetic structure detected at microsatellite and allozyme loci: allozyme analysis suggests that most of populations deviated from Hardy-Weinberg equilibrium within populations and a deficiency of hyterozygotes (F_IS=0.337), but microsatellite analysis indicates that most of populations deviated from Hardy-Weinberg equilibrium within populations and an excess of hyterozygotes(F_IS=-0.69). More hyterozygotes detected by microsatellite probably lead to the result observed. There were higher genetic differentiation detected by microsatellite analysis(F_ST=0.468) than allozyme analysis (F_ST=0.338), which was also supported by lower mean genetic identity for microsatellite analysis(1=0.463) than allozyme analysis(1=0.973). Higher polymorphisms at microsatellite loci may probably result in the results observed.9 Above results show that:(1) microsatellites are powerful tool for distinguish rice genetic resources;(2) map-based analysis of genetic diversity shows great significance in exploring and utilizing gene resources in the future rice breeding programs; (3) this study suggests that O. rufipogon harbored abundant genetic variability as well as a great deal of specific alleles for rice breeding; and(4) as a molecular marker, microsatellite loci are prior to allozyme loci for studying population genetic structure of O. rufipogon.