Transcriptome characterization and development of functional polymorphic SSR marker resource for Himalayan endangered species, Taxus contorta (Griff)

Majeed, Aasim; Singh, Amandeep; Choudhary, Sonal; Bhardwaj, Pradeep

doi:10.1016/j.indcrop.2019.111600

Cited by 14 publications

(10 citation statements)

References 52 publications

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“…This higher UTR to CDS ratio is maintained by the selection pressure to avoid Open reading frame (ORF) change within the CDS region, which can cause frameshift mutations. A similar lower CDS to the UTR ratio was also observed by Majeed et al (2019) and Qu and Liu (2013).…”

Section: Discussionsupporting

confidence: 80%

“…The N 50 value of 1820 obtained in this study was better than that of Majeed et al . (2019), which also aimed at SSR screening in Taxus contorta . A total of 12,884 SSRs were identified from 72.139 Mb transcriptome with an average of 5.5 SSRs/Mb of the sequence.…”

Section: Discussionmentioning

confidence: 99%

“…A similar lower CDS to the UTR ratio was also observed by Majeed et al . (2019) and Qu and Liu (2013).…”

Section: Discussionmentioning

confidence: 99%

“…(2014) and Majeed et al . (2019). The mean PIC value of 0.57 revealed that the SSRs are efficient and substantially polymorphic.…”

Section: Discussionmentioning

confidence: 99%

“…A similar perfect transferability was also achieved between the rubber species, which decreased to only 73% in cross genera experiments (Feng et al ., 2009). A comparatively lesser percentage (75%) of cross transferability was observed for T. contorta and Taxus baccata (Majeed et al ., 2019).…”

Section: Discussionmentioning

confidence: 99%

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Elucidation of genetic diversity base in Calotropis procera – a potentially emerging new fibre resource

Majeed

Goel

Mishra

et al. 2020

Plant Genet. Resour.

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Calotropis procera is emerging as a new, yet undomesticated, resource of fibre comparable to cotton and kapok. Screening of efficient genotypes from its wild populations would be a useful pre-domestication process. The desired genotypes can then be improved through conventional breeding programmes to develop a domesticated variety. Molecular markers play a major role in modern breeding systems. Thus, an efficient marker resource for C. procera would prove useful in germplasm selection during breeding programmes. In this study, we undertook an initial step of Simple sequence repeats (SSR) marker development for C. procera, which could be applied for germplasm selection. Furthermore, using the developed markers, we assessed the genetic diversity base within its wild populations which could be useful to identify the hotspot areas of germplasm collection. Out of 94,636 de novo assembled transcripts, 9148 sequences were found to contain 12,884 SSRs at a density of 5.5 SSRs/Mb. Twelve SSRs were found as polymorphic with a mean polymorphic information content of 0.575. We observed a moderate level of genetic diversity (Na = 3.625, Ho = 0.58) in the studied populations. Mantel's test showed significant correlation between the geographic distance and the genetic distance (r = 0.147, P = 0.010). Sirsa was found as a genetically most diverse population followed by Barnala while Gurdaspur was found with the least genetic diversity. These genetically diverse populations can serve as an important resource for effective germplasm collection for breeding programmes.

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Section: Discussionsupporting

confidence: 80%

Section: Discussionmentioning

confidence: 99%

“…A similar lower CDS to the UTR ratio was also observed by Majeed et al . (2019) and Qu and Liu (2013).…”

Section: Discussionmentioning

confidence: 99%

“…(2014) and Majeed et al . (2019). The mean PIC value of 0.57 revealed that the SSRs are efficient and substantially polymorphic.…”

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning