Loss-of-Function Alleles of Heading date 1 (Hd1) Are Associated With Adaptation of Temperate Japonica Rice Plants to the Tropical Region.

Sung-Ryul Kim,O-Young Jeong,Gideon Torollo,Mi-Ra Yoon,Kshirod K Jena,Jeom-Sig Lee,Un-Sang Yeo,Il-Ryong Choi,Jieun Kwak,Choon-Ki Lee,G D Prahalada

doi:10.3389/fpls.2018.01827

Abstract

Adaptation of temperate japonica rice varieties to tropical regions is impeded by extremely early flowering probably due to photoperiod change from long to short. However, constant breeding efforts led to development of temperate japonica varieties adapted to tropical/subtropical regions, but the genetic factor underlying this is still elusive. We analyzed the 45 diverse rice accessions and 12 tropical-adapted temperate japonica lines for the allele types of seven major flowering genes Hd1, OsPPR37, DTH8, Ghd7, Ehd1, RFT1, and Hd3a and flowering time under three different field conditions in temperate and tropical locations. The accessions originated from the tropical/subtropical regions preferred the non-functional alleles of Hd1 and not other flowering genes. The genetic effect analysis of each gene showed that only the functional Hd1 caused early flowering in the tropical location. All 12 temperate japonica breeding lines adapted to the tropics possessed the loss-of-function alleles of Hd1 with no change of other flowering genes compared to common Korean temperate japonica varieties. A phylogenetic analysis using 2,918 SNP data points revealed that the genome status of the 12 breeding lines were very similar to Korean temperate japonica varieties. These results indicate that the functional Hd1 alleles of temperate japonica varieties induced extremely early flowering in the tropics and the non-functional hd1 alleles brought about the adaptation of temperate japonica rice to tropical regions.

Highlights

Rice is a major staple food in the world especially in Asian countries
Quite early flowering of the elite temperate japonica varieties in the tropical zone is a major constraint in breeding temperate japonica rice varieties for the tropics
More than 40 flowering-related genes have been cloned in the rice genome and the process of gene identification and its functional studies were mostly done in controlled conditions like a growth chamber or room and/or at a paddy field in high-latitude locations (Lee and An, 2015a,b; Hori et al, 2016)

Summary

Introduction

Rice is a major staple food in the world especially in Asian countries. It is the most rapidly growing food source in African countries (Seck et al, 2012). Various rice genotypes are cultivated in wide ranges of geographical locations in the world (40◦ S – equator – 53◦ N). In tropical zones surrounding the equator (23.2◦ S – equator – 23.2◦ N) and in some subtropical zones, indica rice types are widely grown in a double-season rice rotation cropping system because of the mild temperature throughout the year. The adjustment or fine-tuning of the flowering time of rice varieties can bring about some advantages such as enhanced multiple rice cropping per year, precise rotation cropping systems with other profitable crops, high prices of rice for specific consumers, and the possible improvement of rice field management by avoiding a regular encounter with biotic/abiotic stresses

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Results

Conclusion