Genetic diversity and peculiarity of annual wild soybean (G. soja Sieb. et Zucc.) from various eco-regions in China

Soybean Research Institute, National Center for Soybean Improvement, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, Jiangsu 210095, People's Republic of China.
Theoretical and Applied Genetics (Impact Factor: 3.79). 06/2009; 119(2):371-81. DOI: 10.1007/s00122-009-1045-y
Source: PubMed


Annual wild soybean (Glycine soja Sieb. et Zucc.) is believed to be a potential gene source for future soybean improvement in coping with the world climate change for food security. To evaluate the wild soybean genetic diversity and differentiation, we analyzed allelic profiles at 60 simple-sequence repeat (SSR) loci and variation of eight morph-biological traits of a representative sample with 196 accessions from the natural growing area in China. For comparison, a representative sample with 200 landraces of Chinese cultivated soybean was included in this study. The SSR loci produced 1,067 alleles (17.8 per locus) with a mean gene diversity of 0.857 in the wild sample, which indicated the genetic diversity of G. soja was much higher than that of its cultivated counterpart (total 826 alleles, 13.7 per locus, mean gene diversity 0.727). After domestication, the genetic diversity of the cultigens decreased, with its 65.5% alleles inherited from the wild soybean, while 34.5% alleles newly emerged. AMOVA analysis showed that significant variance did exist among Northeast China, Huang-Huai-Hai Valleys and Southern China subpopulations. UPGMA cluster analysis indicated very significant association between the geographic grouping and genetic clustering, which demonstrated the geographic differentiation of the wild population had its relevant genetic bases. In comparison with the other two subpopulations, the Southern China subpopulation showed the highest allelic richness, diversity index and largest number of specific-present alleles, which suggests Southern China should be the major center of diversity for annual wild soybean.

Download full-text


Available from: Zixiang Wen, Mar 09, 2015
20 Reads
    • "The PCR amplification conditions and the identification of the SSR products were described by Wen et al. (2009). The admixture model and the non-origin-base model were used to evaluate the population structure matrix Q based on the 107 SSRs using the software STRUCTURE 2.2 (Pritchard et al. 2000). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Resistance and tolerance are different plant defense mechanisms against herbivores. In this study, four compensatory growth (tolerance) indexes—the ratios of treatment to control for plant height (RPH), branching number of the stem (RBN), seed number per plant (RSN), and seed weight per plant (RSW)—and three resistance indexes—larval weight (LW), pupal weight (PW), and larva-consumed leaf weight (LCL)—were used to evaluate soybean (Glycine max (L.) Merr) defense against common cutworm (CCW; Spodoptera litura Fabricius). The phenotypic variations of seven traits among 170 accessions were significant (ANOVA, P < 0.01). Five of the seven traits had a large variation (>20 %) in this population. The decay distance of linkage disequilibrium was approximately 639 kb on average in intrachromosomal regions. Approximately 80 % of the intervals between two neighboring single-nucleotide polymorphisms were less than 600 kb. The natural population was divided into two subpopulations with little population structure. The genetic relationship among the accessions was distant. Fifty-one quantitative trait loci (QTLs) were significantly associated with the seven traits: six for RPH, nine for RBN, seven for RSN/RSW, one for RBN/RSN/RSW, six for LW, nineteen for LCL, and three for PW (−Log P ≥ 2.00, P ≤ 0.01). Single QTLs contributed 2.8–11 % of the phenotypic variance. Three QTLs were co-associated with soybean resistance and compensatory growth at the 0.05 significant level. Of these three QTLs, the qSCCW18-3 located in the promoter sequence of the soybean Rubisco activase β subunit gene (GmRCAβ) and its resistance allele reduced LW and increased plant height.
    Molecular Breeding 08/2015; 35(8). DOI:10.1007/s11032-015-0360-z · 2.25 Impact Factor
  • Source
    • "Due to its better appearance, flavors, tastes, nutrition factors and easy to cook characters, the demand for vegetable soybeans keeps growing worldwide (Mebrahtu et al. 2004; Mimura et al. 2007). With the increasing emphasis on soybean germplasms collection, evaluation and utilization, a lot of works has been done to reveal the genetic structure and diversity of soybean cultivars, landraces, and/or wild soybean germplasms (Ude et al. 2003; Dong et al. 2004; Chen and Nelson 2005; Bhat et al. 2006; Liu et al. 2006; Qiu et al. 2006; Wang et al. 2006; Li et al. 2008a, b; Kuroda et al. 2009; Wen et al. 2009; Lam et al. 2010; He et al. 2012). These works provide very useful information on the exploring of soybean resources and the establishing of breeding strategies. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Vegetable soybean is a kind of value-added specialty soybean serving as vegetable or snacks. Understanding the genetic structure of vegetable soybean is a key point for further utilization in breeding programs. In the present study, the genetic structure and diversity of 100 vegetable soybean accessions planted in China was analyzed using 53 simple sequence repeat (SSR) markers. A total of 296 alleles were detected with an average of 5.6 alleles per SSR locus. The polymorphism information content (PIC) values of SSR markers ranged from 0.074 to 0.831, with an average of 0.573. Nei’s genetic distance between accessions ranged from 0 to 0.9434 with an average of 0.6286. These vegetable soybean germplasms could be divided into 8 subgroups based on STRUCTURE analysis, or 11 subgroups based on unweighted pair group method with arithmetic average (UPGMA) cluster. Further comparison showed that the UPGMA subgroups and STRUCTURE subgroups were in fact highly consistent. Germplasms in each classified groups showed great consistency with their origins, seed coat colors or pedigrees. Genetic relationships among germplasm panels that initially came from different geographical regions were also analyzed. Germplasm panels from China Mainland, Taiwan Island and Japan were highly similar to each other with the similarities of over 98 %. Molecular data and cluster analysis also showed that germplasms from China Mainland are more diverse than those from other areas. These results gave us a deep insight into the genetic structure of vegetable soybeans in China and will help us to improve the breeding strategies.
    Genetic Resources and Crop Evolution 01/2014; 61(1). DOI:10.1007/s10722-013-0024-y · 1.46 Impact Factor
  • Source
    • "Molecular markers linked to agronomic traits can increase the accuracy and veracity of selection, thereby reducing the field workload, so the selection of suitable markers has become one of the key factors in the success of molecular breeding programs. Many types of molecular markers, such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs), random amplified polymorphic DNA (RAPD), simple sequence repeats (SSRs), and single nucleotide polymorphisms (SNPs), have been used to study the genetic diversity and population structure of plants (Wen et al., 2009). Among these markers, SSRs have stood out and are considered to be the most powerful tools because of their high abundance, co-dominant inheritance, multiple alleles, reproducibility, extensive genome coverage , and ease-of-detection by polymerase chain reaction (PCR) (Moe et al., 2010). "
    [Show abstract] [Hide abstract]
    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.
    Journal of Zhejiang University SCIENCE B 04/2013; 14(4):279-88. DOI:10.1631/jzus.B1200243 · 1.28 Impact Factor
Show more