Rice Genomics Research, Gene Mining and Utilization: A Themed Issue Dedicated to Academician/Prof. Yingguo Zhu

We are honored and privileged to edit this Special Issue, “Rice Genomics Research, Gene Mining and Utilization: A Themed Issue Dedicated to Academician Yingguo Zhu”.

Rice is the primary staple food for over half of the world’s population. Rice production has experienced several periods of rapid growth, referred to as green revolutions. The first such revolution was a consequence of the utilization of a semi-dwarf gene, while the second green revolution arose due to the development of hybrid rice, which has effectively and economically enhanced rice yield. In recent years, hybrid rice has come to cover 17 million hectares (ha), or 57%, of the total rice area in China, with a national average yield of 8 tons per hectare (t/ha); this is approximately 1.7 t/ha higher than the yield of conventional inbred varieties (6.3 t/ha). The annual increment in grain production in the country due to the cultivation of hybrid rice has the potential to feed an additional 70 million people per year. Therefore, hybrid rice has played, and continues to play, a crucial role in alleviating China’s food scarcity problem and in ensuring that it is the largest self-sufficient country in terms of food. Professor Zhu is an outstanding rice geneticist both in China and worldwide. Throughout his 58-year scientific career, he has contributed to enriching the diversity of cultivated rice and the development of hybrid rice. His team successfully developed a Honglian-type cytoplasmic male sterile (HL-CMS) system in 1976 by crossing wild rice and cultivar rice. In 1985, he also designed the Maxie-type cytoplasmic male sterile (MX-CMS) system, by crossing the modern rice variety with a traditional landrace. These CMS systems have been used extensively in the development of hybrid rice in China and in the expansion of hybrid rice-growing areas in tropical Asian countries. Professor Zhu isolated the HL-CMS gene and the corresponding fertility-restoration genes, and elucidated the molecular mechanism. He has contributed to numerous aspects of hybrid rice genetics, including breeding and production. Professor Zhu has published more than 150 research papers, has co-authored four monographs, and has won both a second National Invention Award and a third National Natural Science Award.

Due to the growth in the human population, the need for sufficient and nutritious food has increased significantly in recent decades, while global climate change continues to threaten food production and specific aspects of food quality. With breakthroughs in hybrid rice research, the advent of high-quality, high-yield, multi-resistant rice that has wider adaptability, higher fertilization utility, requires limited pesticide application and has a higher stress tolerance is widely anticipated. In this Special Issue, we are pleased to publish ten papers attend to various aspects of this research area, including rice genomics, gene mining, and cultivation towards the development of the ideal hybrid rice.

Cultivated rice O. sativa is divided into two subspecies, indica and japonica, which differ widely, in genomics and in their morphological, agronomical, and ecological traits. Transposons (TEs) are noted for their ability to alter gene expression and function, and are the cause of plant speciation and evolution. Professor Yuxian Zhu and his colleagues developed a method named matrix-TE, in order to comprehensively investigate the differentiation of intact and truncated LTR/TEs in indica and japonica genomes [1]. As such, six LTR/TE superfamilies were identified. They observed that the indica rice-specific TE peak is P-Gypsy and that the japonica rice-specific TE peak is P-Copia. The single TE peak P-Gypsy was observed in centromeric regions of the indica genome. By utilizing the matrix TE method, the divergence in the indica and japonica genomes, especially their centromeric regions, was discovered to primarily be a consequence of Ty3/Gypsy insertions at 0.77 Mya. Inter-subspecific hybrids between indica and japonica possess enhanced heterosis, and often produce greater yields compared to intra-subspecific hybrids. However, the sterility of inter-subspecific hybrids prevents the application of inter-subspecific heterosis. Wide compatibility varieties (WCVs) permit interspecific hybrids to achieve normal fertility. Zhao et al. reported upon the F12 gene, which affected pollen and spikelet fertility, and improved the performance of the indica–japonica hybrid [2]. The F12 gene was mapped to a region of 630 kb, and was flanked by the D1101 and D1164 markers on chromosome 12. In this region, two putative genes were predicted to be candidates for the wide compatibility genes (WCGs), and deletions/insertions within the exons of both putative genes were observed between indica and japonica rice. Identifying F12 thus provides more opportunities for the further exploitation of inter-subspecific hybrids in rice. This discovery will also aid the elucidation of the mechanism involved in the wide compatibility and development of inter-subspecific hybrid rice.

Deng et al. developed a RIL population and applied testcrosses that were derived by crossing RILs with two cytoplasmic male sterile lines; this was performed in order to dissect heterosis loci and thus report six heterosis-related QTLs of panicle numbers (PN) and five heterosis-related QTLs of tiller numbers (TN), including several known genes: MOC1, TAC1 and OsETR2 [3]. They concluded that several serine/threonine protein kinase genes may play an important role in heterosis, which encourages the production of a high yield. Chlorophyll biosynthesis and chloroplast development affect photosynthetic activity, thus regulating grain production. Lu et al. generated a yellow-green-leaf mutant named ygl9311 [4]. Compared with the wild type, the content of the photosynthetic pigment in ygl9311 leaves was significantly reduced, and chloroplast development was delayed. They mapped the mutant gene to a 430 kb region on chromosome 3. They performed transcriptome sequencing analysis and revealed that the candidate gene, OsChlC1 (BGIOSGA012976), encodes a Mg-chelatase I subunit. The CRISPR/Cas9 knockout of OsChlC1 reproduced the same yellow-green leaf phenotype, revealing that OsChlC1 is plays an essential role in maintaining chlorophyll content and in aiding chloroplast development in rice leaves.

The heading date is a fundamental factor in the determination of crop yield. Yuan et al. isolated an early-flowering gene OsHd8 on the short arm of chromosome 8 in the early-flowering rice JiaHong2B (JH2B) through map-based cloning [5]. OsHd8 encodes a putative HAP3 subunit of the CCAAT-box-binding transcription factor and regulates the expression of OsGI, OsSDG718, OsHDT1, and OsGHD7.1 in order to promote rice heading under long-day conditions. A genetic divergence analysis at the OsHd8 locus exhibited strong genetic differentiation between the indica and japonica subspecies, suggestive of artificial selection during the domestication of cultivated rice. Gibberellins (GAs) are a large group of diterpene plant hormones that play essential roles in rice development processes, such as seed germination, stem elongation, root development, pollen development, and flower induction. Gibberellin-dioxygenases (GAoxes) are involved in the biosynthesis and deactivation of gibberellins. He et al. conducted a comprehensive genome-wide investigation of GA oxidases in rice [6]. They identified 80 candidate OsGAox genes, of which 19 were further analyzed. RNA-seq data indicated that all GAox genes exhibited tissue-specific expression patterns in the leaf, shoot apical meristem, inflorescence, and seed. GA₃ treatment resulted in the differential expression of OsGAox genes. The chalkiness of rice is characterized by the opaque part of the grain, which raises the incidence of grain breakage and reduces its milling yield. Together with the white core (center), these characteristics are considered critical factors regarding rice quality and its commercial value. In the study by Shi et al., a QTL of white-core rate (WCR), qWCR4, was fine-mapped to a 35 kb region containing six annotated genes on chromosome 4, using a BC₅F₂ population [7]. Based on the relative expression levels of these genes in different endosperm developmental stages and on nucleotide diversities of the two parents, LOC_Os04g50060 and LOC_Os04g50070 in the qWCR4 region were identified as the candidate genes for WCR. Compared with NIL (BL130), which has a lower WCR, starch granules in the central endosperm of chalky grains of NIL (J23B) displayed higher WCR values; they also possessed a typical round and loosely packed morphology, as well as a higher rate of seed filling. These results pave the way for improving rice yield and grain quality.

Brown planthopper (BPH) is rice’s most devastating insect pest and is a severe threat to rice production. Exploring new resistance genes and integrating them into the rice genome is necessary for a durable BPH-resistant variety. Kim et al. identified and mapped the BPH-resistance gene Bph43 to a region of ~380 kb on chromosome 11 [8]. A gene cluster that encodes putative nucleotide-binding domain leucine-rich repeat-containing (NBS-LRR) proteins and LRR family proteins was identified in the Bph43 region. A highly resistant near-isogenic line (NILBph43-9311) was developed by introgressing Bph43 into the elite restorer line 9311 through marker-assisted selection. NIL-Bph43-9311 conferred strong antibiosis and antixenosis effects on BPH. A comparative transcriptome analysis revealed the presence of 194 upregulated and 183 downregulated genes in BPH-infested NIL-Bph43-9311.

Lodging severely reduces the grain yield and quality of rice. In order to decipher the mechanisms underlying the lodging response to temperature and solar radiation, Luo et al. analyzed the lodging resistance of 12 indica rice varieties at two eco-sites on three sowing dates for three consecutive years [9]. They demonstrated that temperature had a negative effect, while solar radiation positively affected the lodging resistance. A high temperature resulted in a low lodging resistance, since it reduced the culm’s physical strength by producing a longer and thinner basal second internode. The variety Chuanxiang 29B was most sensitive to temperature, and the lodging-resistant cultivar Jiangan was least responsive to temperature. In traditional rice production, the rice seeds are sown in a nursery to raise rice seedling rates, and then the rice seedlings are manually transplanted to the puddled field, which involves strenuous manual labor. Thus, developing an efficient and high-yielding mechanical rice establishment system is of significant value in the quest for efficient and large-scale rice production. Wang et al. conducted a two-year field experiment using the orderly mechanical rice seedling throwing system (OMST) [10]. The grain yield with the OMST system was significantly enhanced compared to the manual seedling throwing (MST) method, and was equivalent to the manual transplanting (MT) method. The final tiller number, panicle number, and total spikelet number, as well as the final yield when utilizing the OMST system, were significantly elevated compared to that of the MST method. Their study suggests that the OMST system is an efficient and high-yielding rice establishment method that possesses the potential to replace traditional manual transplanting methods in rice production. All of these excellent works contribute significantly to the development of hybrid rice. We would like to take this opportunity to thank all the contributors to this Special Issue.