Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the MiR156, MiR5488 and MiR399 are Involved in the Regulation of Male Sterility in PTGMS Rice.

Yujun Sun,Qian Wang,Xinguo Xiong,Ying He,Hanlai Zeng,Lei Wang,Lan Zhu

doi:10.3390/ijms22052260

Yujun Sun, Qian Wang + Show 5 more

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https://doi.org/10.3390/ijms22052260

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Abstract

A photoperiod- and thermo-sensitive genic male sterile (PTGMS) line is the basic material for two-hybrid rice and is an important genetic breeding resource. Peiai64S (PA64S) is an important germplasm resource of PTGMS rice, and it has been applied to two-line hybrid rice systems in China. Pollen fertility in PA64S is regulated by the temperature and photoperiod, but the mechanism of the fertility transition is unclear. In this study, we obtained the male fertile plant PA64S(F) and the male sterile plant PA64S(S) by controlling different temperatures under long light conditions and used the male fertile and sterile plants to investigate the role of microRNAs (miRNAs) in regulating male fertility in rice. We performed the small RNA library sequencing of anthers from PA64S(S) and PA64S(F). A total of 196 miRNAs were identified—166 known miRNAs among 27 miRNA families and 30 novel miRNAs. In the transcriptome analysis, the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes revealed significant enrichment in the synthesis and metabolism of fatty acids and some secondary metabolism pathways such as fatty acid metabolism and phenylalanine metabolism. With a comprehensive analysis of miRNA, transcriptome, and degradome sequencing, we identified that 13 pairs of miRNA/target genes regulated male fertility in rice by responding to temperature change, among which the miR156, miR5488, and miR399 affect the male fertility of PA64S by influencing SPLs, the lignin synthesis of anther walls, and the flavonoid metabolism pathway. The results provide a new understanding of PTGMS rice, which will help us better understand the potential regulatory mechanisms of male sterility in the future.

Highlights

Rice is one of the main cereal crops in China and the world, providing a food source for nearly 50% of the global population
In the obtained raw data (Table S6), the reads of each library averaged 27 million (24,983,037–32,138,241), unique mappable reads were all greater than 99%, unique transcript mapped reads were stable at approximately 80%, the number of covered transcripts ranged from 52,925 to 58,864, and the results indicated that degradation group sequencing yielded a high coverage of degradation fragments
The PA64S plants used in this study were photoperiod- and thermo-sensitive genic male sterile (PTGMS) rice varieties selected by ten generations of continuous directional temperature and agronomic traits that are relatively stable in terms of growth stages and fecundity critical temperature characteristics [37]

Summary

Introduction

Rice is one of the main cereal crops in China and the world, providing a food source for nearly 50% of the global population. The three-line hybrid system is based on male sterile lines, restorer lines, and maintainer lines, which have higher requirements for germplasm resources [3,4]. The two-line hybrid system method is based on an environmentally sensitive genic male sterile line; it uses a photoperiod- and thermo-sensitive genic male sterile (PTGMS) line to produce hybrid seeds, eliminating the need for maintainer lines and strict restorer–maintainer relationship restrictions, which makes it more conducive to superior hybrid configuration and hybrid seed production [5,6,7]

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