草业学报2025，Vol.34Issue(7)：107-119,13.DOI:10.11686/cyxb2024304
扇穗茅全长转录组SSR特征分析及分子标记开发
Analysis of SSR characterization in full-length transcriptome and development of SSR molecular markers for Littledalea racemosa
摘要
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 resources of L.racemosa.关键词
扇穗茅/转录组/SSR/分子标记Key words
Littledalea racemosa/transcriptome/SSR/molecular marker引用本文复制引用
富贵,刘玉萍,苏旭,曲荣举,才让扎西..扇穗茅全长转录组SSR特征分析及分子标记开发[J].草业学报,2025,34(7):107-119,13.基金项目
2023年中央林业草原生态保护恢复资金野生动植物保护项目,青海野生单子叶植物种质资源调查及其多样性评价项目(QHSY-2023-016)和青海民族大学2024年大学生创新创业训练计划项目(2024-DCXM-55)资助. （QHSY-2023-016）
