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bioRxiv · 10.1101/2020.01.20.912477

Application of Pedimap -- a pedigree visualization tool -- to facilitate the decisioning of rice breeding in Sri Lanka

Rathnayake, P.·Sahibdeen, S.·Udawela, U.·Weebadde, C.·Weerakoon, W.·Sooriyapathirana, S.
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Abstract

The development of rice cultivars with desirable traits is essential. The decision-making is a crucial step in rice breeding programs. The breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the material of the rice breeding germplasm. The staple food in Sri Lanka is rice, and there is a great demand for improved varieties with high yield and other promising traits. In the present study, the available data of all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The Identity by Descent (IBD) probabilities were calculated using FlexQTL software and included in the Pedimap database. The parentage selection based on the variations of phenotypic traits, selection of marker alleles for molecular breeding, and detection of the founders of genetic effects can be swiftly conducted using Pedimap. However, the power of harnessing the value of Pedimap for making breeding decisions relies on the availability of data for the traits, markers, and genomic sequences. Thus, it is imperative to characterize the breeding germplasms using standard phenomic and genomic characterization procedures before organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each other to produce improved varieties to meet global challenges.

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Rathnayake, P., Sahibdeen, S., Udawela, U., Weebadde, C., Weerakoon, W., Sooriyapathirana, S.. 2020-01-20. Application of Pedimap -- a pedigree visualization tool -- to facilitate the decisioning of rice breeding in Sri Lanka. https://doi.org/10.1101/2020.01.20.912477

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