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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.


Frequencies length distribution of Illumina read sequences.
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pone.0131939.g001: Frequencies length distribution of Illumina read sequences.

Mentions: A total of 54.79 and 57.24 million paired-end raw reads were obtained for the ‘Jingnong2’ and ‘Zhonghong5’ varieties, respectively. After removal of the low-quality reads, 52.11 and 54.30 million clean reads with GC content of 45.9% and 46.3% were obtained for the ‘Jingnong2’ and ‘Jinghong5’ varieties, respectively. The sequence quality, based upon the clean reads of both adzuki bean varieties, was 98.4% of Q20. The combined sequences of these reads were assembled into 65,950 unigenes by Trinity. The average length of the unigene is 1,213 bp (N50 = 1,889 bp). The lengths of the unigenes ranged from 200 to 19,090 bp. Of these unigenes, 22,188 (33.6%) were 201 to 500 bp; 13,444 (20.4%) were 501 to 1,000 bp; 10,421 (15.8%) were 1,001 to 1,500 bp; 7,682 (11.7%) were 1,501 to 2,000 bp; 4,956 (7.5%) were 2,001 to 2,500 bp; 2,871 (4.4%) were 2,501 to 3,000 bp; and 4,388 (6.7%) were more than 3,000 bp in length (Fig 1).


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)

Frequencies length distribution of Illumina read sequences.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131939.g001: Frequencies length distribution of Illumina read sequences.
Mentions: A total of 54.79 and 57.24 million paired-end raw reads were obtained for the ‘Jingnong2’ and ‘Zhonghong5’ varieties, respectively. After removal of the low-quality reads, 52.11 and 54.30 million clean reads with GC content of 45.9% and 46.3% were obtained for the ‘Jingnong2’ and ‘Jinghong5’ varieties, respectively. The sequence quality, based upon the clean reads of both adzuki bean varieties, was 98.4% of Q20. The combined sequences of these reads were assembled into 65,950 unigenes by Trinity. The average length of the unigene is 1,213 bp (N50 = 1,889 bp). The lengths of the unigenes ranged from 200 to 19,090 bp. Of these unigenes, 22,188 (33.6%) were 201 to 500 bp; 13,444 (20.4%) were 501 to 1,000 bp; 10,421 (15.8%) were 1,001 to 1,500 bp; 7,682 (11.7%) were 1,501 to 2,000 bp; 4,956 (7.5%) were 2,001 to 2,500 bp; 2,871 (4.4%) were 2,501 to 3,000 bp; and 4,388 (6.7%) were more than 3,000 bp in length (Fig 1).

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.