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A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017)

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A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 19785

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Special Issue Editors

Prof. Dr. Yuxian Zhu

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Guest Editor

1. Institute for Advanced Studies, Wuhan University, Wuhan 430072, China
2. College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: mechanism of cotton fiber cell elongation; functional mechanism of plant hormones; regulation mechanism of gene expression
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Shaoqing Li

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Guest Editor

College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: functional genomics and epigenetics of rice; nucleic-cytoplasmic interaction and regulation of photosynthesis of rice

Prof. Dr. Guangcun He

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Guest Editor

College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: rice genetics and functional genomics; molecular and genetic engineering

Special Issue Information

Dear Colleagues,

Professor Yingguo Zhu, Academician of the Chinese Academy of Engineering, devoted his whole life (1939–2017) with tremendous enthusiasm to the breeding of hybrid rice. He studied and worked in Wuhan University for 58 years, and contributed to enriching the diversity of hybrid rice, such as Maxie-type and Honglian-type hybrid rice. To remember his great contributions to hybrid rice, especially Honglian-type male sterility, we are organizing this Special Issue in his honor. We invite researchers, including his former students, to submit manuscripts focused on male sterility, rice breeding and, in particular, the breeding of hybrid rice, functional genomics research, gene mining and utilization, transposons, the creation of germplasm, and so on. In addition, new technology and cutting-edge research studies are also welcome. We believe that this Special Issue will be helpful to the research on rice and to the improvement of hybrid rice breeding in future.

Prof. Dr. Yuxian Zhu
Prof. Dr. Shaoqing Li
Prof. Dr. Guangcun He
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Agronomy is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

honglian-type male sterility, hybrid rice
gene function
transposons
genomics

Published Papers (12 papers)

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Editorial

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4 pages, 180 KiB

Open AccessEditorial

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

by Guangcun He, Shaoqing Li and Yuxian Zhu

Agronomy 2023, 13(4), 1015; https://doi.org/10.3390/agronomy13041015 - 30 Mar 2023

Viewed by 854

Abstract

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” [...] Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

Research

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12 pages, 4529 KiB

Open AccessArticle

OsChlC1, a Novel Gene Encoding Magnesium-Chelating Enzyme, Affects the Content of Chlorophyll in Rice

by Wei Lu, Yantong Teng, Fushou He, Xue Wang, Yonghua Qin, Gang Cheng, Xin Xu, Chuntai Wang and Yanping Tan

Agronomy 2023, 13(1), 129; https://doi.org/10.3390/agronomy13010129 - 30 Dec 2022

Cited by 1 | Viewed by 1196

Abstract

Leaf-color mutants in rice (Oryza sativa L.) are excellent models for studying chlorophyll biosynthesis and chloroplast development. In this study, a yellow-green-leaf mutant generated by ⁶⁰Co irradiation, ygl9311, was isolated: it displayed a yellow-green leaf phenotype during the complete growth cycle. Compared with the wild type, the photosynthetic pigment contents of leaves in ygl9311 were significantly reduced, and chloroplast development was retarded. Genetic analysis indicated that the ygl9311 phenotype was controlled by a single recessive nuclear gene. Map-based cloning and transcriptome sequencing analysis suggested that the candidate gene was OsChlC1 (BGIOSGA012976), which encodes a Mg-chelatase I subunit. The results of CRISPR/Cas9 system and RNAi knockout tests show that mutation of OsChlC1 could reproduce the phenotype of yellow-green leaves of the mutant ygl9311. In conclusion, the novel rice leaf-color gene OsChlC1 affects the content of chlorophyll in rice, showing a relatively conserved function in indica and japonica rice cultivars. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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12 pages, 2564 KiB

Open AccessArticle

Identification of a New Wide-Compatibility Locus in Inter-Subspecific Hybrids of Rice (Oryza sativa L.)

by Weibo Zhao, Wei Zhou, Han Geng, Jinmei Fu, Zhiwu Dan, Yafei Zeng, Wuwu Xu, Zhongli Hu and Wenchao Huang

Agronomy 2022, 12(11), 2851; https://doi.org/10.3390/agronomy12112851 - 15 Nov 2022

Cited by 1 | Viewed by 1389

Abstract

As a special class of rice germplasm, wide-compatibility varieties (WCVs) guarantee the fertility of hybrids when there is cross-fertilization between two subspecies. In this study, Chenghui9348 was identified as a new member of the WCV family that improves pollen fertility in an inter-subspecific hybrid. Cytological analysis showed that the abnormal mitosis of microspores resulted in the sterility of pollens at the early bicellular stage in the inter-subspecific hybrid. Furthermore, the new F12 locus, corresponding to improvements in fertility of the indica-japonica hybrid, was found to co-segregate with the RM1047 marker and associated with a region of approximately 630 kb flanked by the D1101 and D1164 markers on chromosome 12. In this region, two putative genes were predicted as the candidates for wide-compatibility genes (WCGs). Sequence analysis revealed that, compared with indica/japonica alleles, deletion/insertion occurred within exons of both putative genes. Together, the present study identified another new WC locus, F12, and offers more opportunities for further exploitation of inter-subspecific hybrids in rice. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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13 pages, 3614 KiB

Open AccessArticle

Orderly Mechanical Seedling-Throwing: An Efficient and High Yielding Establishment Method for Rice Production

by Weiqin Wang, Li Xiang, Huabin Zheng and Qiyuan Tang

Agronomy 2022, 12(11), 2837; https://doi.org/10.3390/agronomy12112837 - 13 Nov 2022

Cited by 3 | Viewed by 1485

Abstract

Developing an efficient and high-yielding mechanical rice establishment system is one of the most important approaches for intensive and large-scale rice production. Recently, an orderly mechanical rice seedling throwing system (OMST) was successfully developed; however, the performance of this system is unknown. In the present study, a two-year field experiment was carried out in a split-plot design with three establishment methods arranged in the main plots, and two elite rice cultivars arranged in the sub-plots. The grain yield and growth-related traits were then determined. The results showed that the grain yield of OMST was significantly higher than manual seedling throwing, and was equivalent to that of manual transplanting, which was mainly due to the variances in panicle number and total spikelet number. Further analysis suggested that the orderly mechanical seedling throwing takes advantage of higher biomass accumulation after heading, increased leaf area index and decreased leaf senescence rate against manual seedling throwing, and more tillers and biomass accumulation at vegetative growth stage as compared to manual transplanting. The present study showed that the OMST is an efficient and high-yielding rice establishment method that may be a promising option to replace traditional manual seedling throwing in rice production. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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18 pages, 4297 KiB

Open AccessArticle

Responses of the Lodging Resistance of Indica Rice Cultivars to Temperature and Solar Radiation under Field Conditions

by Xiaoyun Luo, Zefang Wu, Lu Fu, Zhiwu Dan, Weixiong Long, Zhengqing Yuan, Ting Liang, Renshan Zhu, Zhongli Hu and Xianting Wu

Agronomy 2022, 12(11), 2603; https://doi.org/10.3390/agronomy12112603 - 23 Oct 2022

Cited by 3 | Viewed by 1270

Abstract

Much attention has shifted to the effects of temperature and solar radiation on rice production and grain quality due to global climate change. Meanwhile, lodging is a major cause of rice yield and quality losses. However, responses of the lodging resistance of rice to temperature and solar radiation are still unclear. To decipher the mechanisms through which the lodging resistance might be affected by temperature and solar radiation, 32 rice cultivars with different lodging resistance were grown at two eco-sites on three sowing dates over a period of three years. Based on the field observation, 12 indica rice cultivars which did not lodge were selected for analysis. Significant differences were found in the lodging resistance of the indica rice cultivars at different temperature and solar radiation treatments. The results showed that temperature was the main factor that affected the lodging resistance of indica rice cultivars under the conditions of this study. With the increased average daily temperature, the lodging resistance decreased rapidly, primarily due to the significant reduction in physical strength of the culm, which was attributed to the longer and thinner basal second internode. Among the 12 indica rice cultivars, the lodging-moderate cultivar Chuanxiang 29B was most sensitive to temperature, and the lodging-resistant cultivar Jiangan was least responsive to temperature. These results suggested that rice breeders could set the shorter and thicker basal internode as the main selection criteria to cultivate lodging-resistant indica cultivars to ensure a high yield at a higher ambient temperature. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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16 pages, 5802 KiB

Open AccessArticle

Natural Variation of OsHd8 Regulates Heading Date in Rice

by Huanran Yuan, Ruihua Wang, Mingxing Cheng, Xiao Wei, Wei Wang, Fengfeng Fan, Licheng Zhang, Zhikai Wang, Zhihong Tian and Shaoqing Li

Agronomy 2022, 12(10), 2260; https://doi.org/10.3390/agronomy12102260 - 21 Sep 2022

Cited by 4 | Viewed by 1639

Abstract

Heading date, as one of the most important agronomic traits, is a fundamental factor determining crop yield. Although diverse genes related to heading date have already been reported in rice, the key gene that regulates heading date is still poorly understood. Here, we identified a heading date regulator, heading date 8 (OsHd8), which promoted the heading date under long-day conditions and encoded a putative HAP3 subunit of the CCAAT-box-binding transcription factor. It is localized in the nucleus and expressed in various tissues. Sequence analysis revealed that there were four SNPs and one InDel in the promoter region of OsHd8, which was involved in the regulation of some floral regulators including GHD7.1, SDG718, OsGI and HDT1. Further evolutionary analysis showed that OsHd8 presents divergence between indica and japonica, showing natural selection during the domestication of cultivated rice. These results indicate that OsHd8 plays an important role in the regulation of heading date, and may be an important target for rice breeding programs. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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12 pages, 1602 KiB

Open AccessArticle

QTL Analysis and Heterosis Loci of Effective Tiller Using Three Genetic Populations Derived from Indica-Japonica Crosses in Rice

by Xiaoxiao Deng, Jingzhang Wang, Xuhui Liu, Jian Yang, Mingao Zhou, Weilong Kong, Yifei Jiang, Shiming Ke, Tong Sun and Yangsheng Li

Agronomy 2022, 12(9), 2171; https://doi.org/10.3390/agronomy12092171 - 13 Sep 2022

Cited by 4 | Viewed by 1537

Abstract

Effective panicle numbers (PNs) and Tiller numbers (TNs) are important traits affecting rice (Oryza sativa L.) architecture and grain yield. However, the molecular mechanisms underlying PN and TN heterosis remain unknown in rice. In addition, new PN- or TN-related genes need to be detected and discovered. In this study, in order to detect rice quantitative trait loci (QTLs) and the heterosis-related loci of PN or TN in rice, we developed a high generation recombinant inbred line (RIL) population from a cross of two elite cultivars, Luohui9 (Xian/Indica) and RPY geng (Geng/Japonica), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines, YTA (Xian/Indica) and Z7A (Geng/Japonica). Finally, nine QTLs of PN across four seasons were identified, and two QTLs of TN in 191HB were mapped. Besides this, six heterosis-related QTLs of PN and five heterosis-related QTLs of TN were located. We found that heterosis-related QTLs of PN or TN covered multiple known genes, such as MOC1, TAC1 and OsETR2. Furthermore, homologous gene analysis identified one candidate gene of PN (LOC_10g25720). Together, these findings uncover multiple heterosis-related loci, and provide a new insight into the heterosis mechanism of PN and TN in rice. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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12 pages, 2226 KiB

Open AccessArticle

Genome-Wide Analysis of the Rice Gibberellin Dioxygenases Family Genes

by Yurong He, Wei Liu, Zhihao Huang, Jishuai Huang, Yanghong Xu, Qiannan Zhang and Jun Hu

Agronomy 2022, 12(7), 1627; https://doi.org/10.3390/agronomy12071627 - 7 Jul 2022

Cited by 5 | Viewed by 1628

Abstract

Gibberellins (GAs), a pivotal plant hormone, play fundamental roles in plant development, growth, and stress response. In rice, gibberellin-dioxygenases (GAoxes) are involved in the biosynthesis and deactivation of gibberellins. However, a comprehensive genome-wide analysis of GA oxidases in rice was not uncovered. Here, a total of 80 candidate OsGAox genes were identified and 19 OsGAox genes were further analyzed. Studies on those 19 OsGAox genes, including phylogenetic tree construction, analysis of gene structure, exploration of conserved motifs and expression patterns, were conducted. Results showed that the GAox genes in Arabidopsis and rice were divided into four subgroups and shared some common features. Analysis of gene structure and conserved motifs revealed that splicing phase and motifs were well conserved during the evolution of GAox genes in Arabidopsis and rice, but some special conserved motifs possessed unknown functions need to be further studied. Exploration of expression profiles from RNA-seq data indicated that each GAox gene had tissue-specific expression patterns, although they varied greatly. The expression patterns of these genes under GA₃ treatment revealed that some genes, such as OsGA2ox1, OsGA2ox3, OsGA2ox4, OsGA2ox7, OsGA20ox1, and OsGA20ox4, may play a major role in regulating the level of bioactive GA. Taken together, our study provides a comprehensive analysis of the GAox gene family and will facilitate further studies on their roles in rice growth and development so that these genes can be better exploited. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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11 pages, 1549 KiB

Open AccessArticle

Genome-Wide Comparative Analysis of Transposable Elements by Matrix-TE Method Revealed Indica and Japonica Rice Evolution

by Zhiguo Wu, Wei Xi, Zixuan Han, Yanhua Wu, Yongzhuo Guan and Yuxian Zhu

Agronomy 2022, 12(7), 1490; https://doi.org/10.3390/agronomy12071490 - 22 Jun 2022

Cited by 1 | Viewed by 1782

Abstract

Transposons (TEs) are known to change the gene expression and function, and subsequently cause plant speciation and evolution. Nevertheless, efficient and new approaches are required to investigate the role of TEs in the plant genome structural variations. Here, we reported the method named matrix-TE to investigate the differentiation of intact and truncated LTR/TEs comprehensively in Indica and Japonica rice throughout whole genomes with a special eye on centromeric regions. Six LTR/TE super-families were identified in both Indica and Japonica rice genomes, and the TE ORF references were extracted by phylogenetic analysis. Indica rice specific TE peak P-Gypsy and Japonica rice specific TE peak P-Copia were observed, and were further analyzed by Gaussian probability density function (GPDF) fit. The individual TE peak P-Gypsy was observed in centromeric regions of the Indica genome. By the matrix-TE method, the divergence of Indica and Japonica genomes, especially their centromeric regions, mainly resulted from the Ty3/Gypsy insertion events at 0.77 Mya. Our data indicate that the optimized matrix-TE approach may be used to specifically analyze the TE content, family evolution, and time of the TE insertions. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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13 pages, 1606 KiB

Open AccessArticle

Molecular Mapping of a New Brown Planthopper Resistance Gene Bph43 in Rice (Oryza sativa L.)

by JangChol Kim, Xin An, Ke Yang, Si Miao, Yushi Qin, Yinxia Hu, Bo Du, Lili Zhu, Guangcun He and Rongzhi Chen

Agronomy 2022, 12(4), 808; https://doi.org/10.3390/agronomy12040808 - 27 Mar 2022

Cited by 10 | Viewed by 2646

Abstract

Brown planthopper (BPH) has become the most devastating insect pests of rice and a serious threat to rice production. To combat newly occurring virulent BPH populations, it is still urgent to explore more new broad-spectrum BPH resistance genes and integrate them into rice cultivars. In the present study, we explored the genetic basis of BPH resistance in IRGC 8678. We identified and mapped a new resistance gene Bph43 to a region of ~380 kb on chromosome 11. Genes encoding nucleotide-binding domain leucine-rich repeat-containing (NBS-LRR)-type disease resistance proteins or Leucine Rich Repeat family proteins annotated in this region were predicted as the possible candidates for Bph43. Meanwhile, we developed near isogenic lines of Bph43 (NIL-Bph43-9311) in an elite restorer line 9311 background using marker-assisted selection (MAS). The further characterization of NIL-Bph43-9311 demonstrated that Bph43 confers strong antibiosis and antixenosis effects on BPH. Comparative transcriptome analysis revealed that genes related to the defense response and resistance gene-dependent signaling pathway were significantly and uniquely enriched in BPH-infested NIL-Bph43-9311. Our work demonstrated that Bph43 can be deployed as a valuable donor in BPH resistance breeding programs. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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13 pages, 2315 KiB

Open AccessArticle

Fine Mapping of qWCR4, a Rice Chalkiness QTL Affecting Yield and Quality

by Huan Shi, Yun Zhu, Peng Yun, Guangming Lou, Lu Wang, Yipei Wang, Guanjun Gao, Qinglu Zhang, Xianghua Li and Yuqing He

Agronomy 2022, 12(3), 706; https://doi.org/10.3390/agronomy12030706 - 14 Mar 2022

Cited by 3 | Viewed by 1954

Abstract

Rice (Oryza sativa L.) chalkiness greatly reduces the rice quality and the commercial value. In this study, qWCR4, a previously reported quantitative trait locus (QTL) of white-core rate (WCR), was confirmed by a BC₅F₂ segregation population and further fine mapped to a 35.26 kb region. In the qWCR4 region, LOC_Os04g50060 and LOC_Os04g50070 showed significant differences in expression level in endosperm between two NILs, whereas four other genes had no expression. Starch granules in the central endosperm of chalky grains from NIL(J23B) with higher WCR exhibited a typically round and loosely packed morphology. NIL(J23B) with higher WCR accompanied a higher seed filling speed. Moreover, qWCR4^J23B (qWCR4 allele in J23B) increased WCR, grain numbers per plant, seed setting rate, grain width, and thousand-grain weight, contributing to a superior yield per plant. All in all, our research results not only lay a foundation for map-based cloning of qWCR4 but also provide new genetic resources for rice yield and quality breeding. Full article

(This article belongs to the Special Issue A Themed Issue in Memory of Academician Zhu Yingguo (1939–2017))

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