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Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis).

Chen H, Liu L, Wang L, Wang S, Somta P, Cheng X - PLoS ONE (2015)

Bottom Line: Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR.A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%).The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.

View Article: PubMed Central - PubMed

Affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

ABSTRACT
The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%). A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.

No MeSH data available.


NJ dendrogram based on share allele distance showing genetic relationships among 32 adzuki bean accessions.
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pone.0131939.g003: NJ dendrogram based on share allele distance showing genetic relationships among 32 adzuki bean accessions.

Mentions: NJ tree analysis, based on shared allele distance, grouped the 32 adzuki bean accessions into four main clusters (Fig 3). Both clusters I and II were composed of accessions from northern China, including Jilin, Heilongjiang, Liaoning, Shan’anxi, Shanxi, Shandong, Henan, Beijing, Tianjing, and Inner Mongolia. Clusters III and IV were mostly composed of accessions from southern China, including Yunnan, Sichuan, Jiangsu, Guangxi, Hubei, and Anhui provinces. These results showed an association between genetic relationship of the adzuki bean and geographical origin.


Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis).

Chen H, Liu L, Wang L, Wang S, Somta P, Cheng X - PLoS ONE (2015)

NJ dendrogram based on share allele distance showing genetic relationships among 32 adzuki bean accessions.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4492930&req=5

pone.0131939.g003: NJ dendrogram based on share allele distance showing genetic relationships among 32 adzuki bean accessions.
Mentions: NJ tree analysis, based on shared allele distance, grouped the 32 adzuki bean accessions into four main clusters (Fig 3). Both clusters I and II were composed of accessions from northern China, including Jilin, Heilongjiang, Liaoning, Shan’anxi, Shanxi, Shandong, Henan, Beijing, Tianjing, and Inner Mongolia. Clusters III and IV were mostly composed of accessions from southern China, including Yunnan, Sichuan, Jiangsu, Guangxi, Hubei, and Anhui provinces. These results showed an association between genetic relationship of the adzuki bean and geographical origin.

Bottom Line: Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR.A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%).The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.

View Article: PubMed Central - PubMed

Affiliation: The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

ABSTRACT
The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%). A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.

No MeSH data available.