Assessment of genetic diversity among okra genotypes using SSR markers

Okra (Abelmoschus esculentus) is an important nutritious vegetable. Despite its high economic and industrial value, very little attention has been paid to assess genetic diversity of okra at molecular level. For effective conservation and proper deployment of germplasm, a study on diversity analysis of okra germplasm was conducted with DNA markers. Microsatellite/Simple sequence repeat (SSR) markers were utilized to evaluate the genetic diversity among 96 accessions of Abelmoschus, of which 92 accessions were of A. esculentus and one accession each of A. tuberculatus, A. moschatus, A. moschatus subspecies tuberosus and A. manihot. A set of 40 SSR primers were tested, of which 30 primers gave reproducible amplification which were used further for diversity analysis. With a mean of 7.1 bands per SSR, DNA amplification with 30 SSRs generated a total 213 bands, of which 60.66 % were recorded polymorphic. Polymorphic information content ranged between 0.11 and 0.80 with an average of 0.52, indicating that the majority of primers were informative. The Jaccard’s coefficient ranged from 0.107 to 0.969. The UPGMA analysis grouped Abelmoschus genotypes into three main clusters at a cut-off of 0.20. Results of present study revealed that sufficient variation exists among the studied accessions and GAO-5 which was found highly diverse can be exploited for okra improvement. The outcome of present research would assist to make use of Ablemoschus germplasm for okra breeding.     

Evaluation of SSR Markers for the Assessment of Genetic Diversity and Fingerprinting of Gossypium hirsutum Accessions

A total 177 simple sequence repeat (SSR) markers were screened using a set of 47 Upland cotton genotypes comprising 14 commercial varieties, 14 germplasm accessions and 19 advanced breeding lines to identify informative markers for genetic diversity assessment and fingerprinting in G. hirsutum. Only 21% (381177) of SSR markers tested showed polymorphism with a mean of 2.18 alleles per locus and with average polymorphism information content (PIC) of 0.32. The SSR markers revealed a Jaccard’ similarity coefficient ranging between 0.43 and 0.89, with an average of 0.67 among accessions. Cluster analysis using unweighted pair group method with arithmetic averages (UPGMA) and principal component analysis (PCA) indicated that majority of the genotypes were very closely related. All the 47 genotypes showed heterorygosity for at least one of the SSR loci. We discovered 19 rare and 6 unique alleles among the tested genotypes of cotton. Fingerprint based on all the 38 loci revealed a probability of identical match by chance of 3.98x10. A set of ten SSR markers was identified which could distinguish all the 47 genotypes with a moderate probability of identical match by chance (X?_D ⁿ = 0.01).     

Identification and characterization of 43 novel polymorphic EST-SSR markers for arum lily,Zantedeschia aethiopica (Araceae)

• Premise of the study: A new set of microsatellite or simple sequence repeat (SSR) markers from expressed sequence tags (ESTs) was developed for arum lily (Zantedeschia aethiopica), which is one of the most iconic and widely recognized ornamental plants in the world. • Methods and Results: Using 2175 unigenes derived from 4283 random ESTs in arum lily, 166 primer pairs were designed and tested for amplification in 24 accessions from Asia, Europe, and Africa. A total of 43 loci were polymorphic, with the number of alleles per locus ranging from two to 10. The observed heterozygosity, expected heterozygosity, and polymorphism information content ranged from 0.2313 to 0.8480, 0.3034 to 0.8648, and 0.1015 to 0.7364, respectively. • Conclusions: These novel polymorphic EST-SSR markers will facilitate future studies of genetic variation and molecular-assisted breeding systems in arum lily.     

基于转录组数据高通量发掘扶桑绵粉蚧微卫星引物

【目的】扶桑绵粉蚧Phenacoccus solenopsis Tinsley是我国重要的检疫性害虫。简单重复序列(simple sequence repeat,SSR)研究在遗传图谱和物理图谱的构建、分子标记辅助育种、品种鉴定、基因定位、遗传多样性、动植物分类和进化等方面具有重要意义。筛选的SSR引物将为扶桑绵粉蚧遗传多样性分析、进化分析及入侵生物学等奠定基础。【方法】利用高通量搜索的方法对扶桑绵粉蚧转录组中28 120条unigenes的数据进行搜索。【结果】共找到1 781个SSR位点。扶桑绵粉蚧转录组中SSRs的主要重复类型是单核苷酸重复,占SSR总数的89.44%;其次是三核苷酸重复,占SSR总数的7.52%。单核苷酸重复里主要是A/T基序,占了总量的87.42%。基于筛选的SSRs,运用Primer 3软件进行引物的批量设计,共有481个unigenes成功设计引物,共设计出1 228对引物。【结论】研究表明利用扶桑绵粉蚧转录组数据开发SSR标记是可行的,本研究开发的引物将为扶桑绵粉蚧遗传多样性分析、进化分析及入侵生物学等奠定基础。