Large germplasm collections may have several duplicates which need to be removed from the set. DUS characterization based on morphological traits are the best way to differentiate them. But it is very tough to DUS characters in large germplasm lines. Is there any method in molecular breeding to identify the duplicates in huge germplasm collections of rice? Kindly give your opinion and suggestions.
Different methods were applied:
Look in:
Virk PS, Zhu J, Newbury HJ, Bryan GJ, Jackson MT, Ford-Lloyd BV. Effectiveness of different classes of molecular marker for classifying and revealing variation in rice (Oryza sativa) germplasm. Euphytica. 2000 Apr;112(3):275-84.
McClung AM, Edwards JD, Jia MH, Huggins TD, Bockelman HE, Ali ML, Eizenga GC. Enhancing the searchability, breeding utility, and efficient management of germplasm accessions in the USDA− ARS rice collection. Crop Science. 2020 Nov;60(6):3191-211.
Singh N, Wu S, Raupp WJ, Sehgal S, Arora S, Tiwari V, Vikram P, Singh S, Chhuneja P, Gill BS, Poland J. Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions. Scientific reports. 2019 Jan 24;9(1):1-0.
Widyayanti S. Digital object identifier (DOI) application for rice germplasm collection at Yogyakarta AIAT. InIOP Conference Series: Earth and Environmental Science 2020 Mar 1 (Vol. 482, No. 1, p. 012011). IOP Publishing.
Ferrer MC, Duldulao MD, Caguiat XG, Mananghaya TE, Newingham MC, Nombrere JM, Castro JR, Alfonso DO, Regalario JB, Alvarino JB, Pacada IG. PhilRice Genebank: recent developments in managing and sharing the Philippine rice germplasm. InIOP Conference Series: Earth and Environmental Science 2020 Mar 1 (Vol. 482, No. 1, p. 012010). IOP Publishing.
You could use SNP, PCR, molecular markers, and other molecular methods to differentiate the DUS Characteristics in large germplasm lines.
Please follow the link below:
https://cropgenebank.sgrp.cgiar.org/index.php/procedures-mainmenu-242/characterization-mainmenu-205
For this purpose, the large number of the germplasm can first be divided into smaller groups (sub-sets) based on the major phenotypical traits like maturity, plant height, etc. Than using molecular methods like GWAS/ SNP genotyping, the similar individuals can be identified and can be used as desired. You can further refer to the matter as suggested by Alex Ignatov and Mohammod Hossain
Dear Parmeshwar K. Sahu, The conservation and analysis of large amounts of germplasm is always a challenge because of the investment of time and money. In this global context (climate change) it is important to search for new gene sources for plant breeding programs. Sometimes the same landrace has many different names and is widely dispersed so it is easy to incorporate duplicates in collections, I know that well from experience. The approach proposed by Dr. Satyendra (SNPs) is very adequate. I would like to mention that the selection of highly polymorphic molecular markers is crucial to identify possible duplicates in case that you adopt other methods.
High density SNP chips are the fastest method for quantification of genetic diversity and redundancy in germplasm collections.
See:
Singh, N., Jayaswal, P., Panda, K. et al. Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice. Sci Rep 5, 11600 (2015). https://doi.org/10.1038/srep11600
Shikari, A.B., Najeeb, S., Khan, G. et al. KASP™ based markers reveal a population sub-structure in temperate rice (Oryza sativa L.) germplasm and local landraces grown in the Kashmir valley, north-western Himalayas. Genet Resour Crop Evol 68, 821–834 (2021). https://doi.org/10.1007/s10722-020-01025-z
You can generate marker based kinship/relationship matrix. Any lines having 0.9 or above values may be considered duplicates.
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