A robust 1K-core marker set for wild germplasm management and targeted pre-breeding of rice: development and applications

Debashree Dalai, Dipti Ranjan Pani, Swayamsiddha Aswita Dhal, Motilal Behera, Tapan Kumar Mondal, Muhammad Azaharudheen TP, Joshitha Vijayan, Deepa Sarkar, Pallavi Ghose, Abhijeet Roy, Kutubuddin A Molla, Anilkumar C, Lotan Kumar Bose, Trilochan Mohapatra, Soham Ray, Meera Kumari Kar & Mridul Chakraborti

TAG; January 3 2026; vol. 139; article 23

Figure: Oryza rufipogon in Tràm Chim (BCB photo)

Key message

A core set of sequence tagged microsatellite sites (STMS) markers for Oryza sativa complex were developed, validated and utilized for pre-breding and characterization of Oryza germplasm from different taxa.  

Abstract

Development of genome-wide distributed cross-transferable molecular markers applicable to different species can enhance pre-breeding efficiency. Screening of 23.5K primer pairs across nine reference genomes identified 1,008 cross-amplifiable sequence-tagged microsatellite site (STMS) markers, including 520 genic ones, for the Oryza sativa complex. Predicted amplicon lengths of the markers were validated using polymerase chain reaction (PCR). Additionally, 3,628–13,280 markers were identified for individual species. Most cross-amplifiable markers were syntenic across the A-genome. However, substantial intra- and inter-chromosomal translocations were detected in O. longistaminata, O. nivara, and O. meridionalis compared to other A-genome species and subspecies. Notably, four markers exhibited contrasting inter-chromosomal translocations between the three Asiatic A-genome species and the five other species from Africa, South America, and Australia. Among the 1K cross-amplifiable core markers, 629 syntenic STMS loci were considered cross-transferable across the A-genome, within which three markers showed distinct species-specific amplicon lengths. Additionally, 42 markers were predicted to be cross-amplifiable among O. sativa complex, O. punctata, and O. coarctata. PCR-based cross-amplification of the markers in 21 Oryza species revealed hyper-variable amplicon lengths, though their synteny could not be confirmed. The A-genome core markers, along with the species combination-wise markers, provide a reliable genomic resource for developing chromosome segment substitution lines (CSSLs), molecular mapping, and transferring diverse traits from multiple wild species to all types of cultivated rice, including O. sativa, O. glaberrima, and New Rice for Africa (NERICA). Selected cross-transferable markers were used to develop CSSLs by introgressing O. rufipogon genomic segments into the O. sativa background.

See https://link.springer.com/article/10.1007/s00122-025-05133-1