Microsatellite primers in red bayberry, <i>Myrica rubra</i> (Myricaceae)

Xie, Xiaonan; Yingying, Qiu; Ke, Liping; Zheng, Xiaodong; Guan-ting, WU; Chen, Jinqing; Qi, Xin; Ahn, Sang-Nag

doi:10.3732/ajb.1000271

Cited by 9 publications

(6 citation statements)

References 6 publications

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“…The fruit is not only eaten fresh, dried and canned, but is also widely used for making wine and juice [ 22 ]. It also exhibits a wide range of pharmacological properties due to the high content of anthocyanins, which are reported to have anti-inflammatory, anti-tumor and anti-oxidative properties [ 23 ]. According to the literature, Chinese bayberry has been cultivated for more than 2000 years in southern China, and the cultivated area is currently 340,000 ha, with an annual yield of 1.1 million tons valued at 1.5 billion dollars [ 24 ].…”

Section: Introductionmentioning

confidence: 99%

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

et al. 2015

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Phylogenetic relationships among Chinese species of Morella (Myricaceae) are unresolved. Here, we use restriction site-associated DNA sequencing (RAD-seq) to identify candidate loci that will help in determining phylogenetic relationships among Morella rubra, M. adenophora, M. nana and M. esculenta. Three methods for inferring phylogeny, maximum parsimony (MP), maximum likelihood (ML) and Bayesian concordance, were applied to data sets including as many as 4253 RAD loci with 8360 parsimony informative variable sites. All three methods significantly favored the topology of (((M. rubra, M. adenophora), M. nana), M. esculenta). Two species from North America (M. cerifera and M. pensylvanica) were placed as sister to the four Chinese species. According to BEAST analysis, we deduced speciation of M. rubra to be at about the Miocene-Pliocene boundary (5.28 Ma). Intraspecific divergence in M. rubra occurred in the late Pliocene (3.39 Ma). From pooled data, we assembled 29378, 21902 and 23552 de novo contigs with an average length of 229, 234 and 234 bp for M. rubra, M. nana and M. esculenta respectively. The contigs were used to investigate functional classification of RAD tags in a BLASTX search. Additionally, we identified 3808 unlinked SNP sites across the four populations of M. rubra and discovered genes associated with fruit ripening and senescence, fruit quality and disease/defense metabolism based on KEGG database.

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Section: Introductionmentioning

confidence: 99%

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

et al. 2015

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“…Molecular marker technology is a popular tool for breeding and genetic research, and with the construction of a genomic library, 13 polymorphic microsatellite loci have been developed in M. rubra [3] and 11 from an expressed sequence tag library [4]. Recently, 12 primer pairs have been temporarily developed by ISSR-suppression PCR [5] with GSG (GT) 6 as the primer for enriching microsatellite sequences. Reports on the genetic diversity in Chinese bayberry using SSR markers have also recently been published [6,7], but the number of markers for Chinese bayberry is limited.…”

Section: Introductionmentioning

confidence: 99%

Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra)

et al. 2012

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BackgroundChinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical evergreen tree originating in China. It has been cultivated in southern China for several thousand years, and annual production has reached 1.1 million tons. The taste and high level of health promoting characters identified in the fruit in recent years has stimulated its extension in China and introduction to Australia. A limited number of co-dominant markers have been developed and applied in genetic diversity and identity studies. Here we report, for the first time, a survey of whole genome shotgun data to develop a large number of simple sequence repeat (SSR) markers to analyse the genetic diversity of the common cultivated Chinese bayberry and the relationship with three other Myrica species.ResultsThe whole genome shotgun survey of Chinese bayberry produced 9.01Gb of sequence data, about 26x coverage of the estimated genome size of 323 Mb. The genome sequences were highly heterozygous, but with little duplication. From the initial assembled scaffold covering 255 Mb sequence data, 28,602 SSRs (≥5 repeats) were identified. Dinucleotide was the most common repeat motif with a frequency of 84.73%, followed by 13.78% trinucleotide, 1.34% tetranucleotide, 0.12% pentanucleotide and 0.04% hexanucleotide. From 600 primer pairs, 186 polymorphic SSRs were developed. Of these, 158 were used to screen 29 Chinese bayberry accessions and three other Myrica species: 91.14%, 89.87% and 46.84% SSRs could be used in Myrica adenophora, Myrica nana and Myrica cerifera, respectively. The UPGMA dendrogram tree showed that cultivated Myrica rubra is closely related to Myrica adenophora and Myrica nana, originating in southwest China, and very distantly related to Myrica cerifera, originating in America. These markers can be used in the construction of a linkage map and for genetic diversity studies in Myrica species.ConclusionMyrica rubra has a small genome of about 323 Mb with a high level of heterozygosity. A large number of SSRs were identified, and 158 polymorphic SSR markers developed, 91% of which can be transferred to other Myrica species.

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“…The genetic diversity of Chinese bayberry germplasm has been analyzed with different molecular markers, initially using random amplified polymorphic DNA (Lin et al, 1999;Xie et al, 2008), inter simple sequence repeat (Pan et al, 2008;Qian et al, 2006;Qiu et al, 2002;Xie et al, 2008), and amplified fragment length polymorphism (AFLP) (Zheng et al, 2006;Zhang et al, 2009a) as well as simple sequence repeat (SSR) (Jia et al, 2015;Jiao et al, 2012;Terakawa et al, 2006;Xie et al, 2011aXie et al, , 2011bZhang et al, 2015b;Zhang et al, 2012;Zhang et al, 2009b) recently. Occasionally, some other molecular markers such as sequence-related amplified polymorphism (Lin et al, 2013), inter primer binding site, and start codon targeted polymorphism (Chen and Liu, 2014) are used.…”

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Development of Highly Polymorphic Expressed Sequence Tags-Simple Sequence Repeat Markers and Their Application in Analysis of Genetic Diversity of Chinese Bayberry (Morella rubra)

Wang¹,

Feng²,

Zhang³

et al. 2016

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Chinese bayberry (Morella rubra) is an economically important subtropical evergreen fruit crop native to China and other Asian countries. For facilitating cultivar discrimination and genetic diversity analysis, a total of 38 high-quality and highly polymorphic expressed sequence tags-simple sequence repeat (EST-SSR) markers, with little or no polymerase chain reaction (PCR) stutter bands, including 21 screened from those obtained previously and 17 newly developed markers, were developed. The average number of alleles (Na) per locus was 5.6, and polymorphism information content varied from 0.34 to 0.86, with a mean value of 0.57. With these markers, all 42 Chinese bayberry accessions analyzed were successfully discriminated and the phylogenetic relationship between accessions was revealed. The accessions can be separated into two groups with six subgroups. The grouping of four main cultivars in three subgroups and 12 white-fruited accessions, each with little or no anthocyanin accumulation in ripe fruit, into five subgroups suggested the preservation of broad diversity among cultivated populations. These EST-SSR markers and the findings obtained in this study can assist the discrimination of cultivars and lines and contribute to genetic and breeding studies in Chinese bayberry.

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Microsatellite primers in red bayberry, Myrica rubra (Myricaceae)

Cited by 9 publications

References 6 publications

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

Phylogeny of Morella rubra and Its Relatives (Myricaceae) and Genetic Resources of Chinese Bayberry Using RAD Sequencing

Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra)

Development of Highly Polymorphic Expressed Sequence Tags-Simple Sequence Repeat Markers and Their Application in Analysis of Genetic Diversity of Chinese Bayberry (Morella rubra)

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