Characterization of plant genomic SSR loci and exploration of an experiential method of developing SSR markers

The next - generation sequencing platform has revealed the genomic sequences of numer-ous plant species that are ideal resources for simple sequence repeat （SSR） locus screening. In this stud-y, we performed a comparative genomic SSR analysis on 9 sequenced plants. This showed that the total numbers of mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeat SSRs and compound SSRs ranged from 45,552 to 326,319, and the frequencies varied from 177.9 to 573.7 with an average of 401. 3 per Mb. The SSR numbers decreased as the size of the repeat unit increased. The mono-and di-nucleotide SSRs and compound SSRs accounted for more than 78% of the total SSRs in these plants. A/T-rich re-peat motifs were generally dominant in most plants. The sizes of different SSRs varied from 10 to 7288 bp, but at least 85% of them were less than 45 bp. The polymorphism rates of different SSR types ranged from 1.5% to 14.4% in Sesamum indicum, and the mono- and di-nucleotide SSRs displayed the highest polymorphism, followed by the compound SSRs （11.2% ） . These results provide comprehensive insight into the SSR loci of plants and serve as an experimental reference for improvement of SSR marker devel-opment based on plant genomic sequences.

Syntenic quantitative trait loci and genomic divergence for Sclerotinia resistance and ?owering time in Brassica napus

Oilseed rape(Brassica napus) is an allotetraploid with two subgenomes descended from a common ancestor. Accordingly, its genome contains syntenic regions with many duplicate genes, some of which may have retained their original functions, whereas others may have diverged. Here, we mapped quantitative trait loci(QTL) for stem rot resistance(SRR), a disease caused by the fungus Sclerotinia sclerotiorum, and flowering time(FT) in a recombinant inbred line population. The population was genotyped using B.napus 60 K single nucleotide polymorphism arrays and phenotyped in six(FT) and nine(SSR) experimental conditions or environments. In total, we detected 30 SRR QTL and 22 FT QTL and show that some of the major QTL associated with these two traits were co-localized,suggesting a genetic linkage between them. Two SRR QTL on chromosome A2 and two on chromosome C2 were shown to be syntenic, suggesting the functional conservation of these regions. We used the syntenic properties of the genomic regions to exclude genes for selection candidates responsible for QTL-associated traits. For example, 152 of the 185 genes could be excluded from a syntenic A2–C2 region. These findings will help to elucidate polyploid genomics in future studies, in addition to providing useful information for B. napus breeding programs.