Determination of the genetic diversity of vegetable soybean [Glycine max (L.) Merr.] using EST-SSR markers

Abstract

The development of expressed sequence tag-derived simple sequence repeats (EST-SSRs) provided a useful tool for investigating plant genetic diversity. In the present study, 22 polymorphic EST-SSRs from grain soybean were identified and used to assess the genetic diversity in 48 vegetable soybean accessions. Among the 22 EST-SSR loci, tri-nucleotides were the most abundant repeats, accounting for 50.00% of the total motifs. GAA was the most common motif among tri-nucleotide repeats, with a frequency of 18.18%. Polymorphic analysis identified a total of 71 alleles, with an average of 3.23 per locus. The polymorphism information content (PIC) values ranged from 0.144 to 0.630, with a mean of 0.386. Observed heterozygosity (Ho) values varied from 0.0196 to 1.0000, with an average of 0.6092, while the expected heterozygosity (He) values ranged from 0.1502 to 0.6840, with a mean value of 0.4616. Principal coordinate analysis and phylogenetic tree analysis indicated that the accessions could be assigned to different groups based to a large extent on their geographic distribution, and most accessions from China were clustered into the same groups. These results suggest that Chinese vegetable soybean accessions have a narrow genetic base. The results of this study indicate that EST-SSRs from grain soybean have high transferability to vegetable soybean, and that these new markers would be helpful in taxonomy, molecular breeding, and comparative mapping studies of vegetable soybean in the future.

Development of genic SSR markers from transcriptome sequencing of pear buds

“…By virtue of their reproducibility, multi-allelic nature, co-dominant inheritance, relative abundance, and good genome coverage (Powell et al, 1996), SSR markers have been largely applied to genetic diversity studies (Gupta and Varshney, 2000;Chen et al, 2011;Zhang et al, 2013) and used in a variety of applications related to pears, demonstrating their adaptability for Pyrus (Yamamoto et al, 2002;Bao et al, 2007;Katayama et al, 2007;Yao et al, 2010;Cao et al, 2012). SSR loci consist of randomly repeated DNA regions with motif lengths of one to six base pairs (bp) and are spread throughout the genome (Tóth et al, 2000).…”

Analisis Keragaman Genetik Kedelai Introduksi Menggunakan Marka Mikrosatelit

“…Selaras dengan jumlah alel yang tinggi, nilai PIC mencerminkan tingkat polimorfisme (Tasliah et al, 2013). Diversitas gen total kedelai introduksi yang berasal dari negara subtropik (Amerika Serikat, Jepang, Swedia, Rusia, dan Kanada) juga lebih tinggi daripada diversitas gen koleksi kedelai gabungan dari negara di Asia maupun Amerika (Zhang et al, 2013;Kumawat et al, 2015).…”

“…Terdapat lima marka SSR yang mampu mendiskriminasi genotipe heterozigot dengan nilai heterozigositas berkisar antara 0,41 (SoyF3H) hingga 0,82 (Satt333). Sebegai tanaman yang menyerbuk sendiri, kedelai cenderung memiliki heterisigositas rendah, namun koleksi kedelai yang berasal dari berbagai negara ini, termasuk kedelai lokal Jepang dan Amerika Serikat, sangat mungkin memiliki tingkat heterozigositas yang tinggi secara fenotipik tetapi tidak terlihat akibat pengaruh lingkungan (Zhang et al, 2013).…”

Improving Seed Quality of Soybean Suitable for Growing in Europe

“…This process, which Harlan [19] called genetic erosion, appears because of the replacement of diverse indigenous populations with modern, new, uniform cultivars and hybrids, and it causes a considerable threat to the production of food and hence the survival of humans. A narrow genetic base has been identified in most soybean germplasm studies [20,21]. However, Hahn and Würschum [22] noted that the genetic base of middle European genotypes was not as narrow as expected because of the unsystematic phenotype selection.…”