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Genetics and Breeding of Rice
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Genetics and Breeding of Rice

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (25 December 2024) | Viewed by 11301

Special Issue Editor

Dr. Banpu Ruan

E-Mail Website
Guest Editor
College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
Interests: rice; abiotic stress; molecular mechanisms; physiological adaptations; yield
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rice (Oryza sativa) stands as a cornerstone of sustenance for more than half of the global population, underlining the imperative of its genetic enhancement for bolstering global food security. Recent years have witnessed remarkable advancements in comprehending rice genetics and deploying pioneering breeding methodologies to amplify its productivity, quality, and resilience. Central to contemporary rice genetic breeding are approaches that tap into the natural genetic reservoir through genome-wide association studies (GWASs) and quantitative trait locus (QTL) mapping. These endeavors pinpoint advantageous alleles governing pivotal agronomic traits like yield, disease resistance, and stress tolerance. Molecular markers extrapolated from these investigations play a pivotal role in expediting breeding schemes through marker-assisted selection (MAS) and genomic selection (GS), thereby optimizing breeding efficiency.

The trajectory of rice genetic improvement is further propelled by breakthroughs in genomic technologies, epitomized by high-throughput sequencing and CRISPR-Cas9 genome editing. These innovations accelerate the introgression of desired traits, expedite gene discovery, and facilitate allele mining, thus affording precise manipulation of the rice genome for the swift generation of superior cultivars.

Concurrently, there is a concerted effort directed toward augmenting the nutritional profile of rice by elevating its essential nutrient content while mitigating antinutritional factors. This endeavor assumes critical significance in combating malnutrition and dietary deficiencies, which are particularly prevalent in developing regions.

In essence, the fusion of diverse genetic resources with cutting-edge genomic tools propels the continuum of rice genetic enhancement, accentuating the imperative of sustainable strategies to navigate global challenges while catering to the dynamic demands of consumers worldwide.

Dr. Banpu Ruan
Guest Editor

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Keywords

  • rice
  • genetics
  • yield
  • quality
  • breeding

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Published Papers (8 papers)

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Research

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17 pages, 5777 KiB  
Article
Identification and Expression Analysis of CCCH Zinc Finger Family Genes in Oryza sativa
by Zhihan Wang, Shunyuan Li, Hongkai Wu, Linzhou Huang, Liangbo Fu, Chengfang Zhan, Xueli Lu, Long Yang, Liping Dai and Dali Zeng
Genes 2025, 16(4), 429; https://doi.org/10.3390/genes16040429 - 3 Apr 2025
Viewed by 441
Abstract
Background: CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice (Oryza [...] Read more.
Background: CCCH zinc finger proteins (OsC3Hs) are a class of transcriptional regulators that play important roles in plant development and stress responses. Although their functional significance has been widely studied in model species, comprehensive genome-wide characterization of CCCH proteins in rice (Oryza sativa) remains limited. Methods: Using Arabidopsis CCCH proteins as references, we identified the CCCH gene family in rice and analyzed the physicochemical properties, subcellular localization, conserved structures, phylogeny, cis-regulatory elements, synteny analysis, spatiotemporal expression patterns, and expression patterns under drought, ABA, and MeJA treatments for the identified CCCH family members. Results: The results showed that the rice CCCH family comprises 73 members, which are unevenly distributed across the 12 chromosomes. Phylogenetic analysis classified them into 11 subfamilies. Subcellular localization indicated that most members are localized in the nucleus. The upstream regions of CCCH promoters contain a large number of cis-regulatory elements related to plant hormones and biotic stress responses. Most genes respond to drought, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments. OsC3H36 was highly expressed under drought, ABA, and MeJA treatments. Haplotype analysis of this gene revealed two major allelic variants (H1 and H2), with H1 predominantly found in japonica rice and associated with increased grain width and 1000-grain weight. Functional validation using a chromosome segment substitution line (CSSL1) confirmed these findings. Conclusions: CCCH genes play important roles in rice growth, development, and stress responses. Additionally, we validated that OsC3H36 is associated with rice grain width and 1000-grain weight. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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15 pages, 8188 KiB  
Article
Revealing Physiological Basis for Floret Opening Difference Between Indica and Japonica Rice: Based on Floral Structure, Transcriptome, and Endogenous Floret Opening Regulator
by Ruyue Deng, Zhiqiang Yan, Huihui Tang and Susong Zhu
Genes 2024, 15(11), 1396; https://doi.org/10.3390/genes15111396 - 30 Oct 2024
Viewed by 946
Abstract
Background: The differing floret opening times between subsp. indica and subsp. japonica in rice limit the potential for increased hybrid seed production. Objectives: To elucidate the physiological basis underlying the differences in floret opening time between indica and japonica rice. Materials: A comparative [...] Read more.
Background: The differing floret opening times between subsp. indica and subsp. japonica in rice limit the potential for increased hybrid seed production. Objectives: To elucidate the physiological basis underlying the differences in floret opening time between indica and japonica rice. Materials: A comparative analysis involved nine indica and ten japonica rice varieties. Methods: Using paraffin sectioning, transcriptome sequencing, RT-PCR, and endogenous substance quantification, we investigated the structural variations in floral organs, the differences in the initiation timing of floret opening regulatory pathways, and endogenous regulators. Results: The results indicated insignificant differences in lemma thickness, lodicule thickness, lodicule area, and the coupling-lodicule length between indica and japonica rice. However, japonica rice exhibited larger lodicule-lemma gaps and more vascular bundles compared to indica rice. Within the 9:00 a.m. to 10:00 a.m. interval, the expression of OsAOS1 in α-linolenic acid metabolism and OsISA3 in starch and sucrose metabolism notably increased in indica rice, with no significant change in japonica rice. Additionally, the endogenous JA and α-amylase surged more significantly in indica rice than in japonica rice. The increase in soluble carbohydrate in indica rice is greater than in japonica rice, but the difference is not significant. Conclusions: These findings suggest that in the process of the floret opening, the α-linolenic acid metabolism and starch and sucrose metabolism are initiated earlier in indica rice, accompanied by a more pronounced elevation in endogenous JA and α-amylase. Furthermore, the smaller lodicule-lemma gap in indica rice contributes to earlier floret opening compared to japonica rice. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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10 pages, 1324 KiB  
Article
Genetic Loci Mining and Candidate Gene Analysis for Determining Fatty Acid Composition in Rice
by Yiyun Ge, Yiting Wei, Xuan Li, Zhenan Zhu, Jinjin Lian, Huimin Yang, Tiantian Lu, Sanfeng Li, Jiahui Huang, Yuhan Ye, Yuexing Wang and Yuchun Rao
Genes 2024, 15(11), 1372; https://doi.org/10.3390/genes15111372 - 25 Oct 2024
Cited by 1 | Viewed by 1110
Abstract
Fatty acid composition and its proportions are critical to the nutritional value and storage quality of rice (Oryza sativa L.) as the third major nutrient component in this staple food. This study involved crossing an indica rice variety, Huazhan (HZ), as the [...] Read more.
Fatty acid composition and its proportions are critical to the nutritional value and storage quality of rice (Oryza sativa L.) as the third major nutrient component in this staple food. This study involved crossing an indica rice variety, Huazhan (HZ), as the male parent, with a japonica variety, Nekken2, as the female parent, to produce the F1 generation. Subsequently, a population of 120 recombinant inbred lines (RILs) was developed through multiple generations of self-breeding. By utilizing a high-density molecular genetic linkage map and phenotypic data of four fatty acid components, we identified a total of 14 quantitative trait loci (QTLs) related to fatty acid composition across chromosomes 1, 3, 4, 6, 8, and 9. These included two QTLs for C14 content, three for C16:0 content, six for C18:1 content, and three for C18:2 content. Notably, the QTL qCOPT4.2 exhibited a high LOD score of 5.22. Within QTL intervals, genes such as OsACX3 and SLG affecting grain length were identified. The expression of candidate genes within these intervals was assessed and further analyzed by using quantitative real-time PCR. Genes such as LOC_Os01g15000, LOC_Os04g47120, LOC_Os04g49194, LOC_Os06g22080, LOC_Os06g23870, LOC_Os06g24704, LOC_Os06g30780, LOC_Os08g44840, and LOC_Os09g36860 were found to regulate fatty acid synthesis or metabolic pathways, potentially enhancing fatty acid content in rice. These QTLs are indispensable for breeding rice varieties with improved fatty acid profiles, offering new genetic resources for enhancing the nutritional and storage qualities of rice. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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15 pages, 16488 KiB  
Article
YELLOW LEAF AND DWARF 7, Encoding a Novel Ankyrin Domain-Containing Protein, Affects Chloroplast Development in Rice
by Yongtao Cui, Jian Song, Liqun Tang and Jianjun Wang
Genes 2024, 15(10), 1267; https://doi.org/10.3390/genes15101267 - 27 Sep 2024
Viewed by 1103
Abstract
Background: The proper development of grana and stroma within chloroplasts is critical for plant vitality and crop yield in rice and other cereals. While the molecular mechanisms underpinning these processes are known, the genetic networks governing them require further exploration. Methods and Results: [...] Read more.
Background: The proper development of grana and stroma within chloroplasts is critical for plant vitality and crop yield in rice and other cereals. While the molecular mechanisms underpinning these processes are known, the genetic networks governing them require further exploration. Methods and Results: In this study, we characterize a novel rice mutant termed yellow leaf and dwarf 7 (yld7), which presents with yellow, lesion-like leaves and a dwarf growth habit. The yld7 mutant shows reduced photosynthetic activity, lower chlorophyll content, and abnormal chloroplast structure. Transmission electron microscopy (TEM) analysis revealed defective grana stacking in yld7 chloroplasts. Additionally, yld7 plants accumulate high levels of hydrogen peroxide (H2O2) and exhibit an up-regulation of senescence-associated genes, leading to accelerated cell death. Map-based cloning identified a C-to-T mutation in the LOC_Os07g33660 gene, encoding the YLD7 protein, which is a novel ankyrin domain-containing protein localized to the chloroplast. Immunoblot analysis of four LHCI proteins indicated that the YLD7 protein plays an important role in the normal biogenesis of chloroplast stroma and grana, directly affecting leaf senescence and overall plant stature. Conclusions: This study emphasizes the significance of YLD7 in the intricate molecular mechanisms that regulate the structural integrity of chloroplasts and the senescence of leaves, thus providing valuable implications for the enhancement of rice breeding strategies and cultivation. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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11 pages, 8076 KiB  
Article
Genetic Diversity and Divergence between Southern Japonica and Northern Japonica Rice Varieties in China
by Zhiqiang Yan, Ruyue Deng, Huihui Tang and Susong Zhu
Genes 2024, 15(9), 1182; https://doi.org/10.3390/genes15091182 - 9 Sep 2024
Viewed by 1097
Abstract
Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern [...] Read more.
Given the notable ecological and breeding disparities between southern and northern rice regions, delving into the genetic diversity and divergence between southern and northern japonica rice contributes to enhancing the genetic pool for japonica rice breeding. In this study, we analyzed 90 southern and 51 northern japonica rice varieties, focusing on nucleotide diversity (Pi), agronomic trait variations, population structure, genetic divergence, and a neutral test. For genetic diversity, the results demonstrated higher Pi in northern japonica rice varieties (NJRVs) on Chr2, Chr5, Chr6, Chr8, and Chr10, whereas in southern japonica rice varieties (SJRVs) on Chr7 and Chr9. In addition, SJRVs exhibited higher grain width and thickness, whereas NJRVs featured a higher grain aspect ratio, filled grain number, and grain number per panicle. Regarding genetic divergence, geographic differentiation existed between NJRVs and SJRVs, with Chr5 exhibiting numerous higher genetic differentiation windows, including cloned grain shape-controlling genes RGA1 and SFD5, stemming from intensified selection pressure on SJRVs. In summary, SJRVs and NJRVs exhibited diversity differences and genetic differentiation. Hence, it was suggested to conduct genetic introgression between NJRVs and SJRVs to broaden the genetic basis of the local japonica rice germplasm. By exploiting their heterotic advantage, new japonica rice cultivars with superior comprehensive traits could be developed. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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19 pages, 2950 KiB  
Article
Molecular Mapping and Transfer of Quantitative Trait Loci (QTL) for Sheath Blight Resistance from Wild Rice Oryza nivara to Cultivated Rice (Oryza sativa L.)
by Kumari Neelam, Sumit Kumar Aggarwal, Saundarya Kumari, Kishor Kumar, Amandeep Kaur, Ankita Babbar, Jagjeet Singh Lore, Rupinder Kaur, Renu Khanna, Yogesh Vikal and Kuldeep Singh
Genes 2024, 15(7), 919; https://doi.org/10.3390/genes15070919 - 14 Jul 2024
Cited by 1 | Viewed by 1995
Abstract
Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by the soil-borne fungus Rhizoctonia solani Kühn (R. solani). It poses a significant threat to global rice productivity, resulting in approximately 50% annual yield loss. Managing [...] Read more.
Sheath blight (ShB) is the most serious disease of rice (Oryza sativa L.), caused by the soil-borne fungus Rhizoctonia solani Kühn (R. solani). It poses a significant threat to global rice productivity, resulting in approximately 50% annual yield loss. Managing ShB is particularly challenging due to the broad host range of the pathogen, its necrotrophic nature, the emergence of new races, and the limited availability of highly resistant germplasm. In this study, we conducted QTL mapping using an F2 population derived from a cross between a partially resistant accession (IRGC81941A) of Oryza nivara and the susceptible rice cultivar Punjab rice 121 (PR121). Our analysis identified 29 QTLs for ShB resistance, collectively explaining a phenotypic variance ranging from 4.70 to 48.05%. Notably, a cluster of four QTLs (qRLH1.1, qRLH1.2, qRLH1.5, and qRLH1.8) on chromosome 1 consistently exhibit a resistant response against R. solani. These QTLs span from 0.096 to 420.1 Kb on the rice reference genome and contain several important genes, including Ser/Thr protein kinase, auxin-responsive protein, protease inhibitor/seed storage/LTP family protein, MLO domain-containing protein, disease-responsive protein, thaumatin-like protein, Avr9/Cf9-eliciting protein, and various transcription factors. Additionally, simple sequence repeats (SSR) markers RM212 and RM246 linked to these QTLs effectively distinguish resistant and susceptible rice cultivars, showing great promise for marker-assisted selection programs. Furthermore, our study identified pre-breeding lines in the advanced backcrossed population that exhibited superior agronomic traits and sheath blight resistance compared to the recurrent parent. These promising lines hold significant potential for enhancing the sheath blight resistance in elite cultivars through targeted improvement efforts. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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12 pages, 5214 KiB  
Article
Genome-Wide Identification and Bioinformatics Analysis of the FK506 Binding Protein Family in Rice
by Fanhao Nie, Minghao Wang, Linlin Liu, Xuefei Ma and Juan Zhao
Genes 2024, 15(7), 902; https://doi.org/10.3390/genes15070902 - 10 Jul 2024
Cited by 1 | Viewed by 1399
Abstract
The FK506 Binding Protein (FKBP), ubiquitously present across diverse species, is characterized by its evolutionarily conserved FK506 binding domain (FKBd). In plants, evidence suggests that this gene family plays integral roles in regulating growth, development, and responses to environmental stresses. Notably, research on [...] Read more.
The FK506 Binding Protein (FKBP), ubiquitously present across diverse species, is characterized by its evolutionarily conserved FK506 binding domain (FKBd). In plants, evidence suggests that this gene family plays integral roles in regulating growth, development, and responses to environmental stresses. Notably, research on the identification and functionality of FKBP genes in rice remains limited. Therefore, this study utilized bioinformatic tools to identify 30 FKBP-encoding genes in rice. It provides a detailed analysis of their chromosomal locations, evolutionary relationships with the Arabidopsis thaliana FKBP family, and gene structures. Further analysis of the promoter elements of these rice FKBP genes revealed a high presence of stress-responsive elements. Quantitative PCR assays under drought and heat stress conditions demonstrated that genes OsFKBP15-2, OsFKBP15-3, OsFKBP16-3, OsFKBP18, and OsFKBP42b are inducible by these adverse conditions. These findings suggest a significant role for the rice FKBP gene family in stress adaptation. This research establishes a critical foundation for deeper explorations of the functional roles of the OsFKBP genes in rice. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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Review

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27 pages, 16059 KiB  
Review
Advances in Understanding Drought Stress Responses in Rice: Molecular Mechanisms of ABA Signaling and Breeding Prospects
by Yingying Ma, Mingyue Tang, Mingyang Wang, Yanchun Yu and Banpu Ruan
Genes 2024, 15(12), 1529; https://doi.org/10.3390/genes15121529 - 27 Nov 2024
Cited by 1 | Viewed by 2103
Abstract
Drought stress is a pivotal environmental factor impacting rice production and presents a significant challenge to sustainable agriculture worldwide. This review synthesizes the latest research advancements in the regulatory mechanisms and signaling pathways that rice employs in response to drought stress. It elaborates [...] Read more.
Drought stress is a pivotal environmental factor impacting rice production and presents a significant challenge to sustainable agriculture worldwide. This review synthesizes the latest research advancements in the regulatory mechanisms and signaling pathways that rice employs in response to drought stress. It elaborates on the adaptive changes and molecular regulatory mechanisms that occur in rice under drought conditions. The review highlights the perception and initial transmission of drought signals, key downstream signaling networks such as the MAPK and Ca2+ pathways, and their roles in modulating drought responses. Furthermore, the discussion extends to hormonal signaling, especially the crucial role of abscisic acid (ABA) in drought responses, alongside the identification of drought-resistant genes and the application of gene-editing technologies in enhancing rice drought resilience. Through an in-depth analysis of these drought stress regulatory signaling pathways, this review aims to offer valuable insights and guidance for future rice drought resistance breeding and agricultural production initiatives. Full article
(This article belongs to the Special Issue Genetics and Breeding of Rice)
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