Development, characterization, functional annotation and validation of genomic and genic-SSR markers using de novo next generation sequencing in Melia dubia Cav.

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

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Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants

Molecules ◽

10.3390/molecules23020399 ◽

2018 ◽

Vol 23 (2) ◽

pp. 399 ◽

Cited By ~ 41

Author(s):

Sima Taheri ◽

Thohirah Lee Abdullah ◽

Mohd Yusop ◽

Mohamed Hanafi ◽

Mahbod Sahebi ◽

...

Keyword(s):

Next Generation Sequencing ◽

Ssr Markers ◽

Next Generation ◽

Next Generation Sequencing Ngs ◽

Ngs Data ◽

Generation Sequencing

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Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides

Molecules ◽

10.3390/molecules23112963 ◽

2018 ◽

Vol 23 (11) ◽

pp. 2963 ◽

Cited By ~ 3

Author(s):

Jing Tan ◽

Jun-Jie Guo ◽

Ming-Yu Yin ◽

Huan Wang ◽

Wen-Pan Dong ◽

...

Keyword(s):

Next Generation Sequencing ◽

Molecular Marker ◽

Ssr Markers ◽

Southern China ◽

Diversity Index ◽

Next Generation ◽

Wiener Diversity Index ◽

Nucleotide Repeats ◽

Betula Alnoides ◽

Generation Sequencing

Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96–84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.

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