Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice

Yuliang Zhou,Guiquan Zhang,Shaokui Wang,Guiyuan Cao,Ruizhen Zeng,Heng Ye,Haitao Zhu,Bin Tan,Rongqi Zheng,Zhaoyuan Pan,Wei Cao,Guangmiao Zhao,Guifu Liu,Meng Liu

doi:10.1186/s12284-021-00544-2

Abstract

Low-temperature germinability (LTG) is an important agronomic trait that can affect the planting time, planting area, and grain yield of staple crops, such as rice. However, the genetic mechanism of LTG is still unclear. In this study, a multi-parental permanent population with 208 single segment substitution lines (SSSLs) was used to conduct a genetic dissection for LTG across four cropping seasons. LTG was a typical quantitative trait with a high combined broad-sense heritability of 0.71. By comparison with the recipient parent, Huajingxian74, 24 SSSLs were identified as carrying LTG QTLs, which were further merged into integrated QTLs with shorter genetic distances by substitution mapping. Finally, 14 LTG QTLs were mapped on ten chromosomes, including seven positive-effect and seven negative-effect QTLs, with additive effect contributions ranging from 19.2 to 39.9%. qLTG3a, a main-effect and novel QTL, was confirmed by bulk segregant analysis using an F2 segregating population, and five key recombinants were selected to develop F3 populations for progeny testing. Marker-trait association analysis fine mapped qLTG3a to a 332.7-kb physical region between markers M6026 and M6341. Within this interval, 40 annotated genes were revealed, and three genes (Os03g0213300, Os03g0214400, and Os03g0214600) were considered as pivotal candidate genes for qLTG3a based on their sequence variations and expression patterns. Besides low temperature, qLTG3a can also enhance seed germination under standard temperature and osmotic stress. In summary, this study identified some genetic factors regulating LTG and opened a new window for breeding elite direct-seeded rice varieties. It will help reduce the climate risk in the production process of rice, which is of great significance to ensuring food security.

Highlights

Seed germination, a critical step in the plant life cycle, is a complex process coordinately regulated by internal genetic factors and external environmental cues (Ma et al 2017; Rajjou et al 2012)
Phenotypic Variation of lowtemperature germinability (LTG) in Single segment substitution line (SSSL) The germination percentages at 15 °C of Huajingxian 74 (HJX74) and 208 SSSLs were investigated to evaluate the phenotypic variation of LTG in four growing seasons from 2015 to 2016
The mean LTG values of HJX74 in different blocks of each cropping season were analyzed by one-way ANOVA in 2015 and 2016

Summary

Introduction

A critical step in the plant life cycle, is a complex process coordinately regulated by internal genetic factors and external environmental cues (Ma et al 2017; Rajjou et al 2012). Low temperature is one of the principal restriction factors that limit crop growth and development (Ding et al 2020). Rice (Oryza sativa L.) is sensitive to chilling stress through its life cycle, especially during the germination stage. Pan et al Rice (2021) 14:103 below 15 °C in high-latitude and high-altitude rice cultivation regions or early spring seasons, causing a severe rice yield reduction due to low germination rates, delayed seedling emergence, and abnormal seedlings (Liu et al 2018). High lowtemperature germinability (LTG) of rice varieties can extend rice planting areas and growing season to meet the expanding food demand. It is of considerable significance to fully understand the genetic basis of LTG in rice

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Conclusion