Development of Novel Microsatellite Markers for the BBCC Oryza Genome (Poaceae) Using High-Throughput Sequencing Technology

Abstract

Wild species of Oryza are extremely valuable sources of genetic material that can be used to broaden the genetic background of cultivated rice, and to increase its resistance to abiotic and biotic stresses. Until recently, there was no sequence information for the BBCC Oryza genome; therefore, no special markers had been developed for this genome type. The lack of suitable markers made it difficult to search for valuable genes in the BBCC genome. The aim of this study was to develop microsatellite markers for the BBCC genome. We obtained 13,991 SSR-containing sequences and designed 14,508 primer pairs. The most abundant was hexanuclelotide (31.39%), followed by trinucleotide (27.67%) and dinucleotide (19.04%). 600 markers were selected for validation in 23 accessions of Oryza species with the BBCC genome. A set of 495 markers produced clear amplified fragments of the expected sizes. The average number of alleles per locus (Na) was 2.5, ranging from 1 to 9. The genetic diversity per locus (He) ranged from 0 to 0.844 with a mean of 0.333. The mean polymorphism information content (PIC) was 0.290, and ranged from 0 to 0.825. Of the 495 markers, 12 were only found in the BB genome, 173 were unique to the CC genome, and 198 were also present in the AA genome. These microsatellite markers could be used to evaluate the phylogenetic relationships among different Oryza genomes, and to construct a genetic linkage map for locating and identifying valuable genes in the BBCC genome, and would also for marker-assisted breeding programs that included accessions with the AA genome, especially Oryza sativa.

The potentiality of rice microsatellite markers in assessment of cross-species transferability and genetic diversity of rice and its wild relatives

“…The remaining markers were not tried for PCR optimization as 70 SSR markers were considered enough for crossspecies amplification analysis compared with other earlier reports. The range of such successful SSR amplification rate in the present studies is similar to the result reported by other researchers (Wang et al 2014;Zheng et al 2013).…”

“…Since the SSR markers were designed using Nipponbare genome database and randomly selected from the 12 chromosomes covering the whole genome of rice, occurrence of ascertainment bias in the present study was avoided (Gao et al 2005). The cross-species amplification of SSR markers across the 18 rice genotypes which was estimated as the total number of SSR markers amplified in a particular genome type was ranged from 38.90% (RM280 and RM447) to 100% (RM490, RM318, RM279, RM18877 and RM20033, RM19303) with an average of 76.58% which is corroborated to the other reports (Wang et al 2014;Alexander et al 2018;Hernández et al 2001;Gupta et al 2003); this range was found to be higher as compared to the Melilotus with 61.40% (Yan et al 2017), Paspalum with 61% (Wang et al 2006), Siberian wildrye with 49.11% (Zhou et al 2016) and Cucumis with 12.70% (Fernandez-Silva 2008). Such differences in the rate of cross-species transferability could be explained by genetic relatedness and PCR primers used (Wang et al 2006).…”

“…The present study was not aimed at investigating the genetic diversity; a total of 341 alleles from 70 loci were detected ( Table 2). The number of alleles per locus (K) ranged from 2 to 12 with an average of 4.871 ± 2.063 which was found to be similar to previous reports on Oresitrophe and Mukdenia (Liu et al 2018) but lower than O. glaberrima (Yelome et al 2018), Melilotus (Yan et al 2017) and higher from the results reported in rice (Wang et al 2014). The RM510 marker mapped at 2.83 Mb on chromosome 6 showed the highest number of alleles (12) with mean observed and expected heterozygosity were found to be 0.361 ± 0.259 (H O ) and 0.623 ± 0.152 (H E ), respectively.…”

“…The genotyping data were used to estimate the distance matrix using the Jaccard's similarity coefficient and a corresponding dendrogram was developed. The robust dendrogram divided the 18 genotypes into three major clusters I, II and III, which are consistent with the established evolutionary relationships among the Oryza genus (Wang et al 2014;Zhang et al 2014;Zhu et al 2014); this shows the usefulness of the presently used markers in genetic analyses (Fig. 2).…”

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae)

“…Whole‐genome SSR detection has been reported in plants such as Oryza minuta and Or. punctata (Wang et al ., ), Sesamum indicum (Wei et al ., ), and Ziziphus jujuba (Xiao et al ., ) and in 30 marine animals (Jiang et al ., ), six species of birds (Huang et al ., ), six species of bovids (Qi et al ., ), Apis cerana (Liu et al ., ) and Tribolium castaneum (Demuth et al ., ). The SSRs in coding sequences (CDs) of 25 insect species have been identified and comparatively analyzed (Behura & Severson, ).…”