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.
Highlights
The Oryza genus comprises more than 22 species with 10 recognized genomic types, six of which are diploid genome sets (2n = 24, AA, BB, CC, EE, FF, and GG) and four of which are tetraploid (2n = 4x = 48, BBCC, CCDD, HHJJ, and HHKK) [1]
According to their genome constitution, species in this genus can be classified into four main complexes [2]: Oryza ridleyi complex; Oryza granulate complex; Oryza officinalis complex; and Oryza sativa complex
The goal of this study was to develop the first set of microsatellite markers for the BBCC Oryza genome using generation sequencing (NGS) technology. 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 for marker-assisted breeding programs that include accessions with the AA genome, especially Oryza sativa
Summary
The Oryza genus comprises more than 22 species with 10 recognized genomic types, six of which are diploid genome sets (2n = 24, AA, BB, CC, EE, FF, and GG) and four of which are tetraploid (2n = 4x = 48, BBCC, CCDD, HHJJ, and HHKK) [1]. Some populations of wild species of Oryza have been identified as extremely valuable resources that can be used to broaden the genetic background of cultivated rice to increase its resistance to adverse factors
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