Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice

Kyaw Myo Aung; Win Htet Oo; Thant Zin Maung; Myeong-Hyeon Min; Aueangporn Somsri; Jungrye Nam; Kyu-Won Kim; Bhagwat Nawade; Chang-Yong Lee; Sang-Ho Chu; Yong-Jin Park

doi:10.3389/fpls.2023.1225445

Genomic landscape of the OsTPP7 gene in its haplotype diversity and association with anaerobic germination tolerance in rice

Front Plant Sci. 2023 Jul 25:14:1225445. doi: 10.3389/fpls.2023.1225445. eCollection 2023.

Authors

Affiliations

¹ Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, Republic of Korea.
² Center for Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan, Republic of Korea.
³ Department of Industrial and Systems Engineering, College of Engineering, Kongju National University, Cheonan, Republic of Korea.

Abstract

Early season flooding is a major constraint in direct-seeded rice, as rice genotypes vary in their coleoptile length during anoxia. Trehalose-6-phosphate phosphatase 7 (OsTPP7, Os09g0369400) has been identified as the genetic determinant for anaerobic germination (AG) and coleoptile elongation during flooding. We evaluated the coleoptile length of a diverse rice panel under normal and flooded conditions and investigated the Korean rice collection of 475 accessions to understand its genetic variation, population genetics, evolutionary relationships, and haplotypes in the OsTPP7 gene. Most accessions displayed enhanced flooded coleoptile lengths, with the temperate japonica ecotype exhibiting the highest average values for normal and flooded conditions. Positive Tajima's D values in indica, admixture, and tropical japonica ecotypes suggested balancing selection or population expansion. Haplotype analysis revealed 18 haplotypes, with three in cultivated accessions, 13 in the wild type, and two in both. Hap_1 was found mostly in japonica, while Hap-2 and Hap_3 were more prevalent in indica accessions. Further phenotypic performance of major haplotypes showed significant differences in flooded coleoptile length, flooding tolerance index, and shoot length between Hap_1 and Hap_2/3. These findings could be valuable for future selective rice breeding and the development of efficient haplotype-based breeding strategies for improving flood tolerance.

Keywords: anaerobic germination; genetics; haplotype diversity; haplotype-based breeding; rice; trehalose-6-phosphate phosphatase 7.

Grants and funding

This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (No. NRF-2022R1A4A1030348 and 2023R1A2C1004432) and Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry (IPET) through Digital Breeding Transformation Technology Development Program, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA)(322060031HD020), and “Cooperative Research Program for Agriculture Science and Technology Development (RS-2023-00222739)” Rural Development Administration, Republic of Korea.