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Genome-wide SNP Discovery for Variety Identification in a Collection of Cultivated Peach
Jeyun Yeon,Sung-Chur Sim 한국원예학회 2021 한국원예학회 학술발표요지 Vol.2021 No.10
Peach (Prunus persica L.) is a major fruit crop species in the Rosaceae family including apple, pear, and strawberry. With its nutritional and economic value, breeders have made many efforts to develop new cultivars. Molecular markers can facilitate variety identification to protect breeder’s intellectual property rights. In this study, we conducted genotyping by sequencing to identify genome-wide single nucleotide polymorphisms (SNPs) in 48 peach cultivars. This peach collection consisted of 36 cultivars from the Republic of Korea (ROK), eight from Japan, and four from the United State. The illumine HiSeq X sequencing of GBS library generated 72.6 Gb of trimmed read sequences representing 273x coverage for a peach reference genome assembly (227 Mb). A total of 38,616 confident SNPs was identified from GBS and these SNP were unevenly distributed on eight chromosomes. The number of SNPs per chromosome ranged from 2,840 (chromosome 5) to 6,836 (chromosome 2). Of these, a subset of 344 SNPs was filtered based on ≤ 15% of heterozygote rate, ≥ 0.3 of polymorphism information content, and physical map position on each chromosome. In this subset, 83 and 261 SNPs were derived from coding and non-coding sequences, respectively. The Nei’s genetic distances were calculated among 48 peach cultivars using these SNP markers. The resulting dendrogram showed that all of these cultivars were distinguished, suggesting that the 344 markers are a useful resource to develop molecular tools for variety identification in peach.
Ahn, Soo-Yeon,Jo, Mun Seok,Lee, Dahae,Baek, Seon-Eun,Baek, Jiwon,Yu, Jae Sik,Jo, Jeyun,Yun, Hwayoung,Kang, Ki Sung,Yoo, Jeong-Eun,Kim, Ki Hyun Elsevier 2019 Bioorganic chemistry Vol.83 No.-
<P><B>Abstract</B></P> <P> <I>Pueraria lobata</I> root (PLR), well known as Kudzu root, has recently become commercially available in Western dietary supplements for menopausal symptoms. The scientific basis for its action has been attributed to the action of phytoestrogens. This study aimed to investigate the estrogen-like activity of isoflavonoids isolated from <I>P. lobata</I> root and their safety with respect to their effect on breast cancer cell proliferation. In an E-screen assay, crude MeOH extract of PLR significantly increased the proliferation of MCF-7 cells in a concentration-dependent manner. Among the four fractions obtained by solvent fractionation of MeOH extract, the <I>n</I>-BuOH fraction had significant estrogen-like activities at all concentrations tested. Phytochemical analysis of the <I>n</I>-BuOH fraction led to the isolation of 10 isoflavones (<B>1</B>–<B>10</B>), among which genistein (<B>10</B>) had significant estrogen-like activities at all concentrations tested. These activities were significantly enhanced by treatment with genistein and 17β-estradiol compared with 17β-estradiol alone, and this effect was mediated by decreased expression of estrogen receptor (ER)α and phospho-ERα in MCF-7 cells. In a cell cytotoxicity assay, genistein (<B>10</B>) exhibited significant cytotoxicity in both ER-positive MCF-7 and ER-negative MDA-MB-231 breast cancer cells. This cytotoxicity was characterized by the induction of apoptotic cells stained with annexin V conjugated with Alexa Fluor 488 and involved activation of mitochondria-independent and -dependent apoptosis pathways in MCF-7 cells. Our results demonstrated that genistein (<B>10</B>) has estrogen-like effects dependent on ER pathway activation and anti-proliferative effects mediated by the apoptosis pathway rather than the ER pathway in MCF-7 breast cancer cells.</P> <P><B>Highlights</B></P> <P> <UL> <LI> MeOH extract of <I>Pueraria lobata</I> root had significant estrogen-like activities<I>.</I> </LI> <LI> Phytochemical analysis of the <I>n</I>-BuOH fraction led to the isolation of 10 isoflavones (1–10). </LI> <LI> Genistein (10) had significant estrogen-like activities. </LI> <LI> Genistein (10) also exhibited significant cytotoxicity against breast cancer cells. </LI> <LI> The cytotoxicity was characterized by the induction of apoptotic cells. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>