title: SNP typing for germplasm identification of Amomum villosum Lour. Based on DNA barcoding markers.
abstract: Amomum villosum Lour., produced from Yangchun, Guangdong Province, China, is a Daodi medicinal material of Amomi Fructus in traditional Chinese medicine. This herb germplasm should be accurately identified and collected to ensure its quality and safety in medication. In the present study, single nucleotide polymorphism typing method was evaluated on the basis of DNA barcoding markers to identify the germplasm of Amomi Fructus. Genomic DNA was extracted from the leaves of 29 landraces representing three Amomum species (A. villosum Lour., A. xanthioides Wall. ex Baker and A. longiligulare T. L. Wu) by using the CTAB method. Six barcoding markers (ITS, ITS2, LSU D1-D3, matK, rbcL and trnH-psbA) were PCR amplified and sequenced; SNP typing and phylogenetic analysis were performed to differentiate the landraces. Results showed that high-quality bidirectional sequences were acquired for five candidate regions (ITS, ITS2, LSU D1-D3, matK, and rbcL) except trnH-psbA. Three ribosomal regions, namely, ITS, ITS2, and LSU D1-D3, contained more SNP genotypes (STs) than the plastid genes rbcL and matK. In the 29 specimens, 19 STs were detected from the combination of four regions (ITS, LSU D1-D3, rbcL, and matK). Phylogenetic analysis results further revealed two clades. Minimum-spanning tree demonstrated the existence of two main groups: group I was consisting of 9 STs (ST1-8 and ST11) of A. villosum Lour., and group II was composed of 3 STs (ST16-18) of A. longiligulare T.L. Wu. Our results suggested that ITS and LSU D1-D3 should be incorporated with the core barcodes rbcL and matK. The four combined regions could be used as a multiregional DNA barcode to precisely differentiate the Amomi Fructus landraces in different producing areas.
authors.affiliation: Research Center of Chinese Medicinal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China; Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou, Guangdong Province, China.
authors.forename: Qionglin
authors.initials: Q
authors.lastname: Huang
authors.affiliation: Life Science Department, Huizhou University, Huizhou, Guangdong Province, China.
authors.forename: Zhonggang
authors.initials: Z
authors.lastname: Duan
authors.affiliation: Research Center of Chinese Medicinal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China; Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou, Guangdong Province, China.
authors.forename: Jinfen
authors.initials: J
authors.lastname: Yang
authors.affiliation: Research Center of Chinese Medicinal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China; Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou, Guangdong Province, China.
authors.forename: Xinye
authors.initials: X
authors.lastname: Ma
authors.affiliation: Research Center of Chinese Medicinal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China; Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou, Guangdong Province, China.
authors.forename: Ruoting
authors.initials: R
authors.lastname: Zhan
authors.affiliation: Research Center of Chinese Medicinal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China; Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou, Guangdong Province, China.
authors.forename: Hui
authors.initials: H
authors.lastname: Xu
authors.affiliation: Research Center of Chinese Medicinal Resource Science and Engineering, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong Province, China; Key Laboratory of Chinese Medicinal Resource from Lingnan, Ministry of Education, Guangzhou, Guangdong Province, China.
authors.forename: Weiwen
authors.initials: W
authors.lastname: Chen
mesh_terms: D035801:Amomum / Q000235:genetics*; D001483:Base Sequence; D003593:Cytoplasm / Q000378:metabolism; D058893:DNA Barcoding, Taxonomic; D018744:DNA, Plant / Q000378:metabolism; D016002:Discriminant Analysis; D005819:Genetic Markers; D005838:Genotype; D010802:Phylogeny; D010940:Plant Proteins / Q000145:classification / Q000235:genetics; D020641:Polymorphism, Single Nucleotide
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers; D010940:Plant Proteins