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

Abstract

the development of rice cultivars with desirable traits is essential. the decision-making is a crucial step in rice breeding programs. Breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the accessions and cultivars in rice breeding germplasm. 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 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 such as the assessment of before organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each other to produce improved varieties to meet global challenges. Rice is one of the major crops in the world, with an annual production over 700 million metric tons 1. Half of the world population consumes rice as the staple food 2. Currently, the demand for rice is rapidly increasing due to the growth of the human population 3. However, the current rice production cannot meet the increasing demand causing severe food security issues. The biotic and abiotic stresses also exert a negative influence on rice production 4. The rice farming is also a way of living for many people, especially in numerous Asian countries 5. At present, 1.8 million Sri Lankan families engage in rice farming over 870,000 hectares 6. The annual rice production in Sri Lanka is approximately 2.3 million metric tons (MT), which is insufficient to fulfill the domestic rice demand of 3.0 million 7. Hence, the Sri Lankan government spends about USD 400 million to import rice annually 7,8. The rice production is mainly affected by drought and irregular rainfall patterns caused by climate change 9-11 , adverse soil conditions such as salinity 6,12 , and pest and disease attacks 13. The biotic and abiotic stresses in rice farming can be controlled using numerous agronomic practices such as irrigation, drainage, fertilization, and the application of pesticides. However, the rate of success of the controlling methods is limited 13 due to the unpredictable nature of climate change, soil degradation, variations in pest dynamics, and development of pest resistance 14. Therefore, breeding is considered as the most successful strategy to produce high yielding and stress-resilient rice varieties 15. The improved rice genotypes can...

How productive are rice farmers in Sri Lanka? The impact of resource accessibility, seed sources and varietal diversification

“…Given the increasing demand for rice in the country, increased rice productivity can, potentially, improve Sri Lanka's food security situation and the standard of livelihoods of a large percentage of the country's population. At present, Sri Lanka imports 0.7 million metric tons of rice (US$400 million) annually due to the growing demand for rice (Rathnayake et al, 2020).…”