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    Genetic diversity and population structure of Korean wild soybean (Glycine soja Sieb. and Zucc.) inferred from microsatellite markers
    (Pergamon-Elsevier Science Ltd, 2017) Nawaz, Muhammad Amjad; Yang, Seung Hwan; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad; Lee, Jeong Dong
    Korea is considered one of the centers of genetic diversity for cultivated as well as wild soybeans. Natural habitats of wild soybeans are distributed across the Korean mainland and the islands surrounding the Korean peninsula. In this study, the genetic diversity of 100 mainland Korean wild soybean accessions was evaluated by using 42 simple sequence repeat markers covering 17 soybean chromosomes. All analyzed loci were polymorphic and a total of 114 alleles were found. The observed average genetic diversity was low (0.4). The results showed that the 100 selected accessions did not exactly follow the geographical distribution. These results were further confirmed by the phylogeny inferred from five morphological characteristics (i.e., leaf shape, leaf area, plant shape, seed area, and 100-seed weight). Together, the genetic and morphological evaluations suggested conclusively that the selected population did not follow the geographical distribution pattern. The present study could provide useful information for the ex situ conservation and exploitation of wild soybean accessions in soybean improvement stratagems, and will aid in further understanding about the phylogeography of the species in the Korean center of diversity. (C) 2017 Elsevier Ltd. All rights reserved.
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    Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean
    (Elsevier GmbH, 2017) Nawaz, Muhammad Amjad; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad; Ijaz, Babar; Ali, Muhammad Amjad; Khan, Iqrar Ahmad; Lee, Jeong Dong
    The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages. © 2017 Elsevier GmbH
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    Isoflavone profile diversity in Korean wild soybeans (Glycine soja Sieb. & Zucc.)
    (2018) Tsukamoto, Chigen; Nawaz, Muhammad Amjad; Kurosaka, Ayaka; Le, Bao; Lee, Jeong Dong; Baloch, Faheem Shehzad
    Isoflavones prevent the incidence of cancer, reduce cardiovascular problems, and decrease menopausal symptoms. In soybean (Glycine soja Sieb. & Zucc.) seeds, the content is greatly affected by growing conditions. The variations in soy-isoflavone content were investigated by growing 346 Korean wild soybean accessions from natural habitats under the same agroclimatic conditions. Highperformance liquid chromatography was used to measure the profiles of six soy-isoflavones, i.e. glycosides (daidzin, glycitin, genistin) and malonyl glycosides (malonyl-daidzin, malonyl-glycitin, and malonyl-genistin). The soy-isoflavone content of the wild soybeans ranged from 0.5 to 5.51 mg/g with an average of 2.78 mg/g. The highest mean total soy-isoflavone was genistin (1.393 mg/g), followed by daidzin (0.939 mg/g) and glycitin (0.250 mg/g). Korean wild soybean seeds examined in this study were rich in malonyl-genistin. An increasing trend for total soy-isoflavone content was observed from the north to the southeast in the geographical distribution sites, which signifies the effect of genotype and collection site. The information generated in this report will greatly aid soybean breeding stratagems aimed at improving soy-isoflavone concentration in soybean seeds.
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    Systems identification and characterization of cell wall reassembly and degradation related genes in Glycine max (L.) Merill, a bioenergy legume
    (Nature Publishing Group, 2017) Nawaz, Muhammad Amjad; Rehman, Hafiz Mamoon; Imtiaz, Muhammad; Baloch, Faheem Shehzad; Lee, Jeong Dong
    Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.