Abstract:

Littledalea racemosa is a herb with significant ecological and economic value belonging to the Poaceae family and endemic to Qinghai-Xizang Plateau. Identification of a suitable set of simple sequence repeat （SSR） molecular markers offers an important technical means for studying genetic diversity， phylogenetics， and species distribution patterns. In this study， 14089 SSR sequences were obtained using MISA software from 30624 Unigene sequences derived from the L. racemosa full-length transcriptome with the Pacbio sequencing platform. The value of incidence of SSR was 33.85%. Analysis of SSR characteristics， indicated six types of SSR locus nucleotide repeats， with mono-nucleotide， di-nucleotide， and tri-nucleotide being the dominant repeat motifs and accounting for 97.35% of all nucleotide types. Among these three dominant motif types， tri-nucleotide SSRs were the most frequently encountered， with a total of 10 detected. The CCG/CGG motif type was most common and occurred at a total of 1736 SSR sites， accounting for 31.32% of the total SSR tri-nucleotide sites. Twelve samples of L. racemosa were selected randomly from different populations and used by PCR amplification and agarose gel electrophoresis examination for 160 pairs of primers， and 15 pairs of SSR primers with stable amplification and specificity were finally obtained. For these 15 pairs of SSR primers， polymorphism of 81 individuals from 27 populations was analyzed， and a total of 132 alleles could be amplified， with an average of 8.8 alleles amplified per primer pair. The effective allele number （Ne）， Shannon information index （I）， polymorphic information content （PIC）， observed heterozygosity （Ho）， and expected heterozygosity （He）， were 4.7799， 1.6959， 0.7270， 0.8575， and 0.7648， respectively. Cluster analysis was conducted using the UPGMA method based on Nei’s genetics distance， and the results showed that there were explicit genetic relationships among the populations and individuals within a population of L. racemosa. The genetic distance between different populations may be related to geographical distance. The 15 pairs of SSR primers developed in this study have rich genetic diversity， which can provide effective marker selection for genetic variation research in germplasm resourcesof L. racemosa.

Key words: Littledalea racemosa, transcriptome, SSR, molecular marker