Diploid A genome wheat species harbor immense genetic variability which has been targeted and proven useful in wheat improvement. Development and deployment of sequence-based markers has opened avenues for comparative analysis, gene transfer and marker assisted selection (MAS) using high throughput cost effective genotyping techniques. Chromosome 2A of wheat is known to harbor several economically important genes. The present study aimed at identification of genic sequences corresponding to full length cDNAs and mining of SSRs and ISBPs from 2A draft sequence assembly of hexaploid wheat cv. Chinese Spring for marker development. In total, 1029 primer pairs including 478 gene derived, 501 SSRs and 50 ISBPs were amplified in diploid A genome species Triticum monococcum and T. boeoticum identifying 221 polymorphic loci. Out of these, 119 markers were mapped onto a pre-existing chromosome 2A genetic map consisting of 42 mapped markers. The enriched genetic map constituted 161 mapped markers with final map length of 549.6 cM. Further, 2A genetic map of T. monococcum was anchored to the physical map of 2A of cv. Chinese Spring which revealed several rearrangements between the two species. The present study generated a highly saturated genetic map of 2A and physical anchoring of genetically mapped markers revealed a complex genetic architecture of chromosome 2A that needs to be investigated further.
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Contribution of all members of International Wheat Genome Sequencing Consortium (IWGSC) is highly acknowledged. Authors are grateful to the Director, School of Agricultural Biotechnology, PAU, Ludhiana, India for providing facilities. Funding provided by INSPIRE (Innovation in Scientific Pursuit for Inspired Research) Fellowship by Department of Science and Technology (DST), Government of India, India to Parampreet Kaur (Inspire fellow, IF 110226) for pursuing her Ph.D. is highly acknowledged. We thank Dr. Marie Kubaláková for assistance with chromosome flow sorting. Authors also thank other members of our research groups and collaborators for technical assistance and discussions.
The core funding for the work was provided by Department of Biotechnology, New Delhi, India under grant No. BT/IWGSC/03/TF/2008. J.V., H.Š and J.D. were supported by the ERDF project "Plants as a tool for sustainable global development" (No. CZ.02.1.01/0.0/0.0/16_019/0000827).
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Sequence Submission: 513 genic sequences (partial sequences) of T. monococcum and T. boeoticum submitted to GenBank (KP240087-KP240600).
Electronic supplementary material
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Electronic supplementary material 1—Gene derived, SSRs and ISBP primer sequences designed for chromosome 2A; details of Size based-, presence/absence based- SNPs based-, SSRs and ISBPs markers identified between T. boeoticum and T. monococcum; and SNPs observed by sequencing the RIL population through Sanger sequencing for 2 gene derived markers (XLS 368 kb)
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Kaur, P., Jindal, S., Yadav, B. et al. Comparative analysis of chromosome 2A molecular organization in diploid and hexaploid wheat. Mol Biol Rep 47, 1991–2003 (2020). https://doi.org/10.1007/s11033-020-05295-9
- Genetic map
- Chromosome 2A
- Diploid wheat
- Linkage map
- Physical map