Plant Science Today, ISSN 2348-1900 (online) OPEN ACCESS ARTICLE HISTORY Received: 01 May 2022 Accepted: 29 October 2022 Available online Version 1.0 : 22 January 2023 Additional information Peer review: Publisher thanks Sectional Editor and the other anonymous reviewers for their contribution to the peer review of this work. Reprints & permissions information is avail- able at https://horizonepublishing.com/ journals/index.php/PST/open_access_policy Publisher’s Note: Horizon e-Publishing Group remains neutral with regard to jurisdic- tional claims in published maps and institu- tional afiliations. Indexing: Plant Science Today, published by Horizon e-Publishing Group, is covered by Scopus, Web of Science, BIOSIS Previews, Clarivate Analytics, NAAS etc. See https://horizonepublishing.com/journals/ index.php/PST/indexing_abstracting Copyright: © The Author(s). This is an open- access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited (https://creativecommons.org/licenses/ by/4.0/) CITE THIS ARTICLE Pohan S D, Sukiran N L, Jamsari J, Shamsudin N A A. Morpho-physiological screenings and molecular analysis of West Sumatra rice genotypes under submergence stress. Plant Science Today (Early Access). https://doi.org/10.14719/pst.1869 Abstract This study investigates the submergence tolerance level of 14 rice geno- types by morpho-physiological and molecular analyses of Sub1 alleles. IR64- Sub1 was used as a submergence tolerant check. The submergence screen- ings were conducted by submerging 14-days-old seedlings in water tanks for 14 days while molecular analysis was conducted using 14 Sub1 linked markers. The results showed that 5 tested genotypes, namely Inpari 48 Blas, Mundam Putiah, Batang Piaman, Banang Pulau and Pulau Sijunjung, rec- orded high survival rates (SR) of 80% to 100% under submergence stress. PCR-based identification of the Sub1 alleles confirmed that several tested genotypes carry Sub1A and Sub1C, but not all were expressed in their phe- notypic performance towards submergence. IR64-Sub1 and Batang Piaman not only showed well-adaptation towards submergence by maintaining lower elongation (<20%) and less chlorophyll content change (TCC) (<30%) but were also equipped with the Sub1A allele. These genotypes potentially provide good phenotypic and genotypic performance under submergence stress conditions. Additionally, based on population structure analysis, these genotypes were grouped into 3 clusters, of which 35.71% are pure accessions, while the remaining 64.29% have admixture ancestry between populations 1, 2 and 3. The data in model -based population structure and UPGMA dendrogram supported that rice genotypes in this study have 3 well - diferentiated genetic populations and admixtures. Most genotypes have a close genetic relationship with Nei’s similarity index ranging from 0.571 to 0.893. Keywords Morpho-physiological, molecular analysis, rice, submergence, West Sumatra Introduction West Sumatra is located at 0°54’ N-3°30’S altitude and 98°36’-101°53’E longi- tude in the middle of the western coast of Sumatra, with an area of 42,130.82 km 2 . West Sumatra is one of the centers of rice diversity, which might serve as valuable genetic resources for future rice improvement and provide society’s demand for food. Several lowland rice landraces from West Sumatra, such as Anak Daro, Pulau Batu, Cantik Manis, Mundam Putiah, Kuriak and Pulau Sijunjung, are preferred by local consumers due to their good taste and high amylose content (>20%) (1). Therefore, most rice farmers in this region prefer to cultivate these landraces although they are usually low-yielding and long maturity. Socially, local rice varieties are pre- cious. Economically, attempting local rice will increase farmers' income. RESEARCH ARTICLE PLANT SCIENCE TODAY ISSN 2348-1900 (online) Vol x(x): xx–xx https://doi.org/10.14719/pst.1869 HORIZON e-Publishing Group Morpho-physiological screenings and molecular analysis of West Sumatra rice genotypes under submergence stress Selvia Dewi Pohan 1* , Noor Liyana Sukiran 1 , Jamsari Jamsari 2 & Noraziyah Abd Aziz Shamsudin 1 1 Department of Biological Sciences and Biotechnology, Faculty of Sciences and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia 2 Department of Agrotechnology, Faculty of Agriculture, Andalas University, Padang, West Sumatra 25163, Indonesia *Email: nora_aziz@ukm.edu.my