RESUMEN

Suyunuo is a valuable glutinous rice variety cultivated mainly in the Lake Taihu area of China. Historically, Suyunuo was presented to emperors as a tribute, and, still today, enjoys a great reputation in China. This study aimed to develop a unique, specific molecular marker for the identification of Suyunuo rice. Polymerase chain reaction (PCR) amplification of inter-simple sequence repeat (ISSR) molecular markers was performed on Suyunuo and 11 other glutinous rice varieties that are mainly cultivated in the Yangtze River Delta region. A Suyunuo-specific band was detected in the PCR products generated from primer ISSR-807. A sequence characterized amplified region (SCAR) primer pair targeting a Suyunuo-specific band was subsequently designed. The SCAR primers amplified a target band in all individuals of Suyunuo and in four glutinous indica varieties, whereas no bands were found in the seven glutinous japonica varieties. Subsequently, sequences amplified by the SCAR primer pair were analyzed to facilitate the design of Suyunuo allele-specific primers. The allele-specific primer pair produced target bands in all individuals of Suyunuo rice but no bands in individuals of any of the other 11 rice varieties. This study provides a theoretical guideline for rice germplasm identification and innovation of other valuable rice landraces.

Asunto(s)

Alelos , Repeticiones de Microsatélite/genética , Oryza/genética , Reacción en Cadena de la Polimerasa/métodos , Secuencia de Bases , Cartilla de ADN/metabolismo , Electroforesis en Gel de Agar , Marcadores Genéticos , Reproducibilidad de los Resultados , Alineación de Secuencia

RESUMEN

Colocasia esculenta cv. Xinmaoyu is an eddoe-type taro cultivar local to Taicang, Jiangsu Province, China; it is characterized by its pure flavor, glutinous texture, and high nutritional value. Due to its excellent qualities, the Trademark Office of the State Administration for Industry and Commerce of the People's Republic of China awarded Xinmaoyu, a geographical indication certification in 2014. Therefore, there is an urgent need to develop an efficient molecular marker for the specific identification of this cultivar, which would greatly facilitate the conservation and utilization of this unique germplasm resource. In the present study, amplifying the psbE-petL fragment from two dasheen-type and seven eddoe-type taro cultivars revealed three conserved insertions/deletions among sequences from the two taro types. Based on these sequence differences, a pair of site-specific primers was designed targeting the psbE-petL sequence from the dasheen-type taro, which specifically amplified a DNA band in all individuals from cultivars of this type, but not in those from the seven eddoe-type cultivars. To discriminate Xinmaoyu from the other eddoe-type taro cultivars, a pair of simple sequence repeat-sequence characterized amplified region (SSR-SCAR) primers was further developed to specifically amplify a DNA band from all Xinmaoyu individuals, but not from individuals of other eddoe-type taro cultivars. In conclusion, through a two-step-screening procedure using psbE-petL and SSR-SCAR markers, we developed a pair of primers that could specifically discriminate Xinmaoyu from nine taro cultivars commonly cultivated in Jiangsu Province and Fujian Province.

Asunto(s)

Colocasia/genética , Marcadores Genéticos , Repeticiones de Microsatélite , Colocasia/clasificación , Humanos

RESUMEN

Non-heading Chinese cabbage [Brassica rapa var. chinensis (Linnaeus) Kitamura] is a popular vegetable and is also used as a medicinal plant in traditional Chinese medicine. Fragrant Bok Choy is a unique accession of non-heading Chinese cabbage and a product of geographic indication certified by the Ministry of Agriculture of China, which is noted for its rich aromatic flavor. However, transitional and overlapping morphological traits can make it difficult to distinguish this accession from other non-heading Chinese cabbages. This study aimed to develop a molecular method for efficient identification of Fragrant Bok Choy. Genetic diversity analysis, based on inter-simple sequence repeat molecular markers, was conducted for 11 non-heading Chinese cabbage accessions grown in the Yangtze River Delta region. Genetic similarity coefficients between the 11 accessions ranged from 0.5455 to 0.8961, and the genetic distance ranged from 0.0755 to 0.4475. Cluster analysis divided the 11 accessions into two major groups. The primer ISSR-840 amplified a fragment specific for Fragrant Bok Choy. A pair of specific sequence-characterized amplified region (SCAR) primers based on this fragment amplified a target band in Fragrant Bok Choy individuals, but no band was detected in individuals of other accessions. In conclusion, this study has developed an efficient strategy for authentication of Fragrant Bok Choy. The SCAR marker described here will facilitate the conservation and utilization of this unique non-heading Chinese cabbage germplasm resource.

Asunto(s)

Brassica rapa/genética , Variación Genética , Repeticiones de Microsatélite/genética , Brassica rapa/crecimiento & desarrollo , China , Marcadores Genéticos , Hojas de la Planta/genética , Hojas de la Planta/crecimiento & desarrollo

RESUMEN

Brassicaceae is a large plant family of special interest; it includes many economically important crops, herbs, and ornamentals, as well as model organisms. The taxonomy of the Brassicaceae has long been controversial because of the poorly delimited generic boundaries and artificially circumscribed tribes. Despite great effort to delimitate species and reconstruct the phylogeny of Brassicaceae, little research has been carried out to investigate the applicability and effectiveness of different DNA regions as barcodes - a recent aid for taxonomic identification - to identify economically important species in Brassicaceae. In this study, we evaluated the feasibility of five intensively recommended regions [rbcL, matK, trnH-psbA, internal transcribed spacer (ITS), ITS2] as candidate DNA barcodes to discriminate economic species of Brassicaceae in China and try to establish a new digital identification method for economic plants of Brassicaceae. All sequences of 58 samples from 27 economic species (Brassicaceae) in China were assessed in the success rates of PCR amplifications, intra- and inter-specific divergence, DNA barcoding gaps, and efficiency of identification. Compared with other markers, ITS showed superiority in species discrimination with an accurate identification of 67.2% at the species level. Consequently, as one of the most popular phylogenetic markers, our study indicated that ITS was a powerful but not perfect barcode for Brassicaceae identification. We further discuss the discrimination power of different loci due to inheritance pattern, polyploidization and hybridization in species-specific evolution. Further screening of other nuclear genes related to species isolation as plant barcode candidates is also proposed.

Asunto(s)

Brassicaceae/genética , Código de Barras del ADN Taxonómico/métodos , Variación Genética , Brassicaceae/clasificación , China , ADN de Plantas/química , ADN de Plantas/genética , ADN Espaciador Ribosómico/química , ADN Espaciador Ribosómico/genética , Sitios Genéticos/genética , Marcadores Genéticos/genética , Filogenia , Proteínas de Plantas/genética , Análisis de Secuencia de ADN , Especificidad de la Especie

RESUMEN

Camellia ptilophylla, or cocoa tea, is naturally decaffeinated and its predominant catechins and purine alkaloids are trans-catechins and theobromine Regular tea [Camellia sinensis (L.) O. Ktze.] is evolutionarily close to cocoa tea and produces cis-catechins and caffeine. Here, the transcriptome of C. ptilophylla was sequenced using the 101-bp paired-end technique. The quality of the raw data was assessed to yield 70,227,953 cleaned reads totaling 7.09 Gbp, which were assembled de novo into 56,695 unique transcripts and then clustered into 44,749 unigenes. In catechin biosynthesis, leucoanthocyanidin reductase (LAR) catalyzes the transition of leucoanthocyanidin to trans-catechins, while anthocyanidin synthase (ANS) and anthocyanidin reductase (ANR) catalyze cis-catechin production. Our data demonstrate that two LAR genes (CpLAR1 and CpLAR2) by C. ptilophylla may be advantageous due to the combined effects of this quantitative trait, permitting increased leucoanthocyanidin consumption for the synthesis of trans-catechins. In contrast, the only ANS gene observed in C. sinensis (CsANS) shared high identity (99.2%) to one homolog from C. ptilophylla (CpANS1), but lower identity (~80%) to another (CpANS2). We hypothesized that the diverged CpANS2 might have lost its ability to synthesize cis-catechins. C. ptilophylla and C. sinensis each contain two copies of ANR, which share high identity and may share the same function. Transcriptomic sequencing captured two N-methyl nucleosidase genes named NMT1 and NMT2. NMT2 was highly identical to three orthologous genes TCS2, PCS2, and ICS2, which did not undergo methylation in vitro; in contrast, NMT1 was less identical to TCS, PCS and ICS, indicating that NMT1 may undergo neofunctionalization.

Asunto(s)

Camellia/genética , Regulación de la Expresión Génica de las Plantas , N-Glicosil Hidrolasas/genética , Oxidorreductasas/genética , Oxigenasas/genética , Proteínas de Plantas/genética , Transcriptoma , Antocianinas/biosíntesis , Cafeína/biosíntesis , Camellia/clasificación , Camellia/metabolismo , Camellia sinensis/clasificación , Camellia sinensis/genética , Camellia sinensis/metabolismo , Catequina/biosíntesis , Flavonoides/biosíntesis , Secuenciación de Nucleótidos de Alto Rendimiento , Isoenzimas/genética , Isoenzimas/metabolismo , N-Glicosil Hidrolasas/metabolismo , Oxidorreductasas/metabolismo , Oxigenasas/metabolismo , Filogenia , Proteínas de Plantas/metabolismo , Carácter Cuantitativo Heredable , Teobromina/biosíntesis

RESUMEN

Dioscorea bulbifera L. is widely distributed in pantropical regions along the equator. The taxonomic treatment of this species is ambiguous due to its extreme polymorphic morphological characters. In order to provide tools to facilitate the study of genetic diversity, population structure, patterns of gene flow, and the mating system of this species, and to assess intraspecific variability and relationships in D. bulbifera, 14 novel polymorphic microsatellite loci were developed using the dual-suppression PCR technique. The number of alleles per locus ranged from 4 to 17, with an average of 9.93. The mean observed heterozygosities were 0.7327 and 0.7223, and the mean Shannon-Wiener indices were 1.6431 and 1.811 in the Nanjing and Nanchong populations, respectively. All novel microsatellite loci showed high levels of polymorphism, indicating that these markers offer great potential significance and profound influence for future studies of this species.

Asunto(s)

Dioscorea/genética , Variación Genética , Repeticiones de Microsatélite/genética , Alelos , Reacción en Cadena de la Polimerasa , Polimorfismo Genético

RESUMEN

Wild Brassica juncea is a widespread weed in China with increasingly great impact on the yield of many crops. This study aimed to develop microsatellite markers for assessing the genetic diversity and population genetic structure of B. juncea, and to provide basic information for biological and chemical control of the weed. The compound microsatellite marker technique was used to develop markers for investigating population genetics of wild B. juncea. Twelve loci were obtained, each of which showed high polymorphisms when tested in two populations in Sichuan and Jiangsu Provinces. The number of alleles per locus ranged from 4 to 27, with an average of 15.2 alleles per locus. The newly developed microsatellite loci will be informative for further investigations of the population genetics and evolutionary patterns of wild B. juncea.

Asunto(s)

Brassica/genética , ADN de Plantas/genética , Repeticiones de Microsatélite

RESUMEN

Fallopia multiflora, locally known as Heshouwu, is one of the most important and widely used Chinese medicinal herbs. However, there is still considerable confusion concerning its different provenances. DNA barcoding is a recent aid to taxonomic identification and uses a short standardized DNA region to discriminate plant species. We assessed the applicability of 4 candidate DNA barcodes (matK, rbcL, psbA-trnH, and ITS2) to identify populations of F. multiflora. To our knowledge, this is the first attempt involving the plant kingdom to apply DNA barcoding at a level lower than species. Four DNA loci (matK, rbcL, psbA-trnH, and ITS2) of 105 samples, including the wild F. multiflora distributed in 17 provinces of China and 4 cultivated F. multiflora lines, were amplified by PCR and sequenced. The 4 loci were evaluated by PCR amplification for sequence quality, extent of genetic divergence, DNA barcoding gap, and the ability to discriminate between populations by BLAST1 and Nearest Distance. We found that psbA-trnH was the best barcode, with significant inter-population variability and best potential for identifying F. multiflora. The combination of loci gave better performance for distinguishing populations than a single locus. We recommend using matK + rbcL + psbA-trnH + ITS2 or psbA-trnH alone for this species. This research demonstrates the utility of DNA barcoding for geoherbalism identifications.

Asunto(s)

Código de Barras del ADN Taxonómico , Genes de Plantas , Plantas Medicinales/genética , Polygonaceae/genética , China , ADN de Plantas/genética , Sitios Genéticos , Filogeografía , Polygonaceae/clasificación , Alineación de Secuencia , Análisis de Secuencia de ADN , Especificidad de la Especie

RESUMEN

Dioscorea zingiberensis C.H. Wright (Dioscoreaceae) is an endemic species in central and southwestern China. In order to study the genetic diversity and population structure of this species, 19 novel polymorphic microsatellite loci were developed using a dual-suppression PCR technique. The number of alleles per locus ranged from 3 to 21, with an average of 9.53. All the markers showed high transferability in cross-species amplification in other species of sect. Stenophora.

Asunto(s)

Dioscorea/genética , Repeticiones de Microsatélite , Polimorfismo Genético , Alelos , ADN de Plantas/genética , Dioscorea/clasificación , Sitios Genéticos , Reacción en Cadena de la Polimerasa , Especificidad de la Especie

RESUMEN

Toll-like receptor 4 (TLR4) is potentially an important gene affecting the susceptibility to type 2 diabetes mellitus (T2DM). The objective of this study was to evaluate whether genetic polymorphisms of the TLR4 gene are associated with T2DM susceptibility. This potential association was analyzed in 668 T2DM patients and 672 healthy controls by polymerase chain reaction-restriction fragment length polymorphism and DNA sequencing methods. Two novel genetic polymorphisms (g.12375A>G and g.14367G>A) were investigated, and our data support the idea that the g.14367G>A variant significantly increased susceptibility to T2DM in homozygote comparison (AA vs GG: OR = 2.396, 95%CI = 1.682-3.413, P < 0.0001), heterozygote comparison (GA vs AA: OR = 1.322, 95%CI = 1.050-1.664, P = 0.0175), dominant model (AA/GA vs GG: OR = 1.511, 95%CI = 1.217-1.876, P = 0.0002), recessive model (AA vs GA/GG: OR = 2.093, 95%CI = 1.496-2.927, P < 0.0001), and allele contrast (A vs G: OR = 1.503, 95%CI = 1.279-1.766, P < 0.0001). The allele A of g.14367G>A variants may contribute to the susceptibility to T2DM. However, we failed to detect a similar significantly increased susceptibility to T2DM in the g.12375A>G variant. Our findings suggest that the g.14367G>A genetic polymorphism of the TLR4 gene is associated with the susceptibility to T2DM in the population studied.

Asunto(s)

Pueblo Asiatico/genética , Diabetes Mellitus Tipo 2/genética , Predisposición Genética a la Enfermedad , Polimorfismo de Nucleótido Simple , Receptor Toll-Like 4/genética , Adulto , Estudios de Casos y Controles , Femenino , Genotipo , Humanos , Modelos Logísticos , Masculino , Persona de Mediana Edad , Análisis Multivariante , Polimorfismo de Longitud del Fragmento de Restricción , Análisis de Secuencia de ADN