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Identification and DUS Testing of Rice Varieties through Microsatellite Markers.

ABSTRACT: Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of microsatellite markers to separate varieties utilizing the best combination of markers. For this research, 12 microsatellite markers were used. In total, 83 polymorphic alleles (6.91 alleles per locus) were found. In addition, the variation of PIC was calculated from 0.52 to 0.9. The results of cluster analysis showed the complete discrimination of varieties from each other except for IR58025A and IR58025B. Moreover, cluster analysis could detect the most of the improved varieties from local varieties. Based on the best combination of markers analysis, five pair primers together have shown the same results of all markers for detection among all varieties. Considering the results of this research, we can propose that microsatellite markers can be used as a complementary tool for morphological characteristics in DUS tests.

SUBMITTER: Pourabed E

PROVIDER: S-EPMC4337753 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Identification and DUS Testing of Rice Varieties through Microsatellite Markers.

Pourabed Ehsan E Jazayeri Noushabadi Mohammad Reza MR Jamali Seyed Hossein SH Moheb Alipour Naser N Zareyan Abbas A Sadeghi Leila L

International journal of plant genomics 20150208

Identification and registration of new rice varieties are very important to be free from environmental effects and using molecular markers that are more reliable. The objectives of this study were, first, the identification and distinction of 40 rice varieties consisting of local varieties of Iran, improved varieties, and IRRI varieties using PIC, and discriminating power, second, cluster analysis based on Dice similarity coefficient and UPGMA algorithm, and, third, determining the ability of mi ...[more]

PMID: 25755666

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Project description:Wheat has been widely cultivated all over the world. In China, the number of approved wheat varieties has steadily grown since 2010, with the most notable trend in the Huang-Huai-Hai region. Distinctiveness, uniformity, and stability (DUS) are the prerequisites for a new wheat variety to obtain a release permit. Yet, few reports are available on DUS testing characteristics of released wheat varieties. Here, 32 DUS testing characteristics of 195 wheat varieties released in the Huang-Huai-Hai region were investigated to study their artificial selection trend. The results showed that the means, ranges, and coefficients of variation for eight measured characteristics varied greatly, among which the number of sterile spikelets had the largest variation coefficient of all three wheat-growing areas in the Huang-Huai-Hai region. The difference in plant height between the three wheat-growing areas was the most significant. The mean plant height in the northern winter wheat area was the largest, while that in south Huanghuai was the smallest. The released varieties of the three wheat-growing areas in the region had similar artificial selection trends in some characteristics. For instance, flag leaf length and flag leaf width, grain number per ear, and grain volume weight showed an overall upward trend, while the plant height gradually decreased. The clustering results based on DUS testing characteristics showed that artificial selection of characteristics was consistent with ecological adaptation and breeding process as well as pedigree sources. Our findings indicated that with the current breeding objectives, the selection of some non-economic characteristics of wheat varieties, such as awn color, stem color, and glume color, seemed to be able to enrich the genetic diversity of varieties in the Huang-Huai-Hai region. These results could provide guidance for subsequent wheat breeding and production in this region, screening similar varieties, and determining the distinctness of applied varieties in DUS testing.

Project description:Background:Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak. Methods:A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy-Weinberg equilibrium without linkage disequilibrium. Results:Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak. Discussion:Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were suitable for parentage analysis in polled yak populations.

Project description:BACKGROUND:Microsatellites, or simple sequence repeats (SSRs), represent important DNA variations that are widely distributed across the entire plant genome and can be used to develop SSR markers, which can then be used to conduct genetic analyses and molecular breeding. Cultivated peanut (A. hypogaea L.), an important oil crop worldwide, is an allotetraploid (AABB, 2n = 4× = 40) plant species. Because of its complex genome, genomic marker development has been very challenging. However, sequencing of cultivated peanut genome allowed us to develop genomic markers and construct a high-density physical map. RESULTS:A total of 8,329,496 SSRs were identified, including 3,772,653, 4,414,961, and 141,882 SSRs that were distributed in subgenome A, B, and nine scaffolds, respectively. Based on the flanking sequences of the identified SSRs, a total of 973,984 newly developed SSR markers were developed in subgenome A (462,267), B (489,394), and nine scaffolds (22,323), with an average density of 392.45 markers per Mb. In silico PCR evaluation showed that an average of 88.32% of the SSR markers generated only one in silico-specific product in two tetraploid A. hypogaea varieties, Tifrunner and Shitouqi. A total of 39,599 common SSR markers were identified among the two A. hypogaea varieties and two progenitors, A. duranensis and A. ipaensis. Additionally, an amplification effectiveness of 44.15% was observed by real PCR validation. Moreover, a total of 1276 public SSR loci were integrated with the newly developed SSR markers. Finally, a previously known leaf spot quantitative trait locus (QTL), qLLS_T13_A05_7, was determined to be in a 1.448-Mb region on chromosome A05. In this region, a total of 819 newly developed SSR markers were located and 108 candidate genes were detected. CONCLUSIONS:The availability of these newly developed and public SSR markers both provide a large number of molecular markers that could potentially be used to enhance the process of trait genetic analyses and improve molecular breeding strategies for cultivated peanut.

Dataset Information

Identification and DUS Testing of Rice Varieties through Microsatellite Markers.

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Identification and DUS Testing of Rice Varieties through Microsatellite Markers.

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