Development and utility of PCR-based intron polymorphism markers in sorghum [Sorghum bicolor (L.) Moench]

Jaikishan, I.; Rajendrakumar, P.; Madhusudhana, R.; Elangovan, M.; Patil, J. V.

doi:10.1007/s12892-015-0015-y

Cited by 9 publications

(1 citation statement)

References 41 publications

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“…Among the simple PCR-based markers, ILP is gene-specific, often hypervariable, neutral to the environment, and co-dominant, which has a high transferability rate in related species 12 . Previously, genome-wide intron-derived polymorphic markers in rice 14 , foxtail millet 15 sorghum 26 , chickpea 27 , and Macrotyloma spp 28 were reported. In the present study, we developed a large number of CsILP markers (4192) from the two sequenced genomes of tea harnessing the intron derived marker development tool 12 .…”

Section: Discussionmentioning

confidence: 99%

Genome-wide identification and development of miniature inverted-repeat transposable elements and intron length polymorphic markers in tea plant (Camellia sinensis)

Rohilla

Mazumder

Saha

et al. 2022

Sci Rep

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Marker-assisted breeding and tagging of important quantitative trait loci for beneficial traits are two important strategies for the genetic improvement of plants. However, the scarcity of diverse and informative genetic markers covering the entire tea genome limits our ability to achieve such goals. In the present study, we used a comparative genomic approach to mine the tea genomes of Camellia sinensis var. assamica (CSA) and C. sinensis var. sinensis (CSS) to identify the markers to differentiate tea genotypes. In our study, 43 and 60 Camellia sinensis miniature inverted-repeat transposable element (CsMITE) families were identified in these two sequenced tea genomes, with 23,170 and 37,958 putative CsMITE sequences, respectively. In addition, we identified 4912 non-redundant, Camellia sinensis intron length polymorphic (CsILP) markers, 85.8% of which were shared by both the CSS and CSA genomes. To validate, a subset of randomly chosen 10 CsMITE markers and 15 CsILP markers were tested and found to be polymorphic among the 36 highly diverse tea genotypes. These genome-wide markers, which were identified for the first time in tea plants, will be a valuable resource for genetic diversity analysis as well as marker-assisted breeding of tea genotypes for quality improvement.

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