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Discovery and Utilization of Germplasm Resources in Rice

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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 May 2023) | Viewed by 15869

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Special Issue Editors

Dr. Yue Feng

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Guest Editor

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Interests: identification, evaluation and innovative utilization of rice germplasm resources

Dr. Xiaodeng Zhan

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Guest Editor

State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Interests: germplasm resources; molecular breeding of rice

Special Issue Information

Dear Colleagues,

Rice is a major food crop for over half of the world’s population, its yield having experienced two quantum leaps benefitting from the introduction of semidwarf varieties and the utilization of heterosis. Germplasm resources are the most important basis for rice breeding. Germplasm resources are formed through long-term natural evolution under different ecological conditions, and contain various potentially usable genes. The discovery and utilization of germplasm resources are, therefore, very important. Every major progress in rice breeding, including the green revolution and heterosis utilization, is inseparable from the discovery and utilization of germplasm resources. As a model cereal crop, the complete genome sequence of rice laid the foundation for functional genomics research and breeding. Recent advances in quantitative trait loci (QTLs), genome-wide association studies (GWAS), CRISPR gene editing, and transgenic analysis have facilitated the identification and functional analysis of important genes from rice germplasm resources.

This Special Issue, concerning the “Discovery and Utilization of Germplasm Resources in Rice”, aims to focus on progress related to the identification and evaluation of germplasm resources, creation of novel germplasms based on the genetic effect of important QTLs/genes, utilization of germplasms for gene cloning, and breeding novel varieties for rice production.

Genetic diversity and evolution study of rice germplasm resources, including wild species, landraces, and main varieties, in different historical periods. The identification of important genetic loci (gene alleles) related to evolution, domestication, and some valuable agronomic traits.
Screen phenotyping of germplasm resources with important variations, such as the ideotype, high yield, high quality, tolerance to biological/abiotic stresses, high nutrition, etc., especially valuable traits.
The identification of valuable genes/QTLs from germplasm resources through genetic mapping, GWAS, next-generation sequencing, and other approaches. The functional validation of target genes through CRISPR gene editing. The development of novel DNA markers for marker-assisted selection (MAS) breeding.
Creation of novel germplasms through mutagenesis, the introgression of foreign DNA, or chromosome fragments.
The mechanism study of valuable traits in germplasm resources and cloning key genes, which could be used for modifying agronomic traits in future breeding.

Researchers are invited to contribute original articles, short reports, novel methods, or reviews addressing current advances in these fields.

Dr. Yue Feng
Dr. Xiaodeng Zhan
Guest Editors

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Keywords

rice
germplasm resources
breeding
discovery
utilization

Published Papers (9 papers)

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Research

21 pages, 4732 KiB

Open AccessArticle

A Plastid RNA Polymerase-Associated Protein Is Involved in Early Chloroplast Development in Rice

by Shuang Song, Ying Wang, Xin Ding, Yunlu Tian, Zewan Wu, Hang Li, Qing Li, Yunpeng Wang, Shirong Zhou, Xiaoou Dong, Jianmin Wan and Linglong Liu

Agronomy 2023, 13(5), 1424; https://doi.org/10.3390/agronomy13051424 - 21 May 2023

Cited by 2 | Viewed by 1412

Abstract

Plastid-encoded RNA polymerase (PEP) regulates the expression of chloroplast genes involved in photosynthesis and chloroplast development in rice. The PEP-associated protein (PAP) PAP7/pTAC14 is essential for the formation of the PEP complex. However, the function of PAP7 in chloroplast development in rice remains unclear. In this study, we identified a mutant, w81, which displays a yellow-green leaf symptom before the four-leaf stage. The seedlings of the w81 mutant display reduced chlorophyll content, abnormal chloroplast structure, and elevated reactive oxygen species (ROS) level. After the four-leaf stage, plant leaves of the w81 mutant gradually turn green with increased chlorophyll content. Map-based cloning reveals that the PAP7 in the w81 mutant harbors a T to A single-base substitution. This mutation blocks the normal splicing of the fifth intron and generates 74 bp longer transcripts in the mutant. The OsPAP7 protein mainly localizes to the chloroplast and directly interacts with OsPAP5. Our results highlight that OsPAP7 regulates the expression of PEP-dependent chloroplast genes and plays a key role in chloroplast development in rice. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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18 pages, 2874 KiB

Open AccessArticle

Comparative Nutritional Assessment and Metabolomics of a WRKY Rice Mutant with Enhanced Germination Rates

by Santiago Bataller, Anne J. Villacastin, Qingxi J. Shen and Christine Bergman

Agronomy 2023, 13(4), 1149; https://doi.org/10.3390/agronomy13041149 - 18 Apr 2023

Cited by 1 | Viewed by 1093

Abstract

Rice is the primary staple food for half the world’s population. Climate change challenges and food insecurity supports the need for rice with agronomically advantageous traits. We report on a transposon insertional rice mutant with enhanced germination rates. This trait is advantageous for rice growth in limited water regions and to reduce yield constraints caused by weed and bird competition. Evaluations of vital nutritional components, compositional analysis, and comparative metabolomics on threshed grain samples are performed, as these assays are those used to assess the safety of foods from genetically modified crops. Compared with the wild type (cv. Nipponbare), oswrky71 mutant grains have a similar size, shape, amount of crude fiber, crude fat, and ash content but higher crude protein. Mineral analyses reveal higher contents of phosphorus and zinc but lower calcium, potassium, sodium, and manganese in the mutant. Analysis of B vitamins reveals significantly higher riboflavin concentrations but lower choline chloride, calcium pantothenate, and thiamine. In addition, untargeted metabolomics analyses identify approximately 50 metabolites whose levels differed between the mutant and its wild type. Physical traits and compositional parameters analyzed are mostly similar and within the range or very close to being considered safe for consumption by the International Life Sciences Institute Crop Composition Database. Further agronomic evaluation and cooked rice sensory properties assessment are needed before positioning this mutant for human consumption. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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12 pages, 3166 KiB

Open AccessArticle

Removing Harmful Pericarp Character of Weedy Rice as the First Step of Domestication towards Direct-Seeding Rice Using CRISPR/Cas9-Targeted Mutagenesis

by Mengyao Kong, Xiaotong He, Zhendong Yin, Xianshu Chen, Yujie Zhang, Zhihua Shi, Xiaoling Song, Sheng Qiang and Weimin Dai

Agronomy 2023, 13(4), 1130; https://doi.org/10.3390/agronomy13041130 - 15 Apr 2023

Cited by 1 | Viewed by 1731

Abstract

With the scarcity of fresh water resources and the increase in labor prices, rice cultivation is changing from transplanting to direct seeding. Weedy rice is a malignant weed with strong drought tolerance in seed germination in direct-seeding rice fields. As the same species of cultivated rice (Oryza sativa L.), weedy rice (Oryza sativa f. spontanea) has the potential of domestication into direct-seeding rice with strong drought tolerance in seed germination by changing a few unfavorable traits. The red pericarp, one of the harmful traits of weedy rice, seriously affects the quality and commercial value of cultivated rice. The recently developed CRISPR/Cas9 (Clustered Regular Interspaced Short Palindromic Repeats) technology can accurately edit the function of genes, providing a possibility for the directed evolution. Weedy rice (WRL-162) with red pericarp was used as a mutant material. Two mutation sites, upstream and downstream of the 14 bp differential fragment of exon 6 of Rc gene, were designed using the CRISPR-Cas9 gene-editing technique. Consequently, three mutant types in T1 generation weedy rice with CRISPR-Cas9 vector changed from red to white pericarp. One mutant type in T1 generation weedy rice with CRISPR-Cas9 vector maintained red pericarp. Comparing the wild type of weedy rice and rice variety control (Nipponbare), mutant types in T3 generation weedy rice without CRISPR-Cas9 vector significantly improved the drought resistance in seed germination. In addition, there was no significant difference in panicle number, seed setting rate per plant, grain length and width between wild type and T3 generation mutant weedy rice without CRISPR-Cas9 vector. Comparing the wild type, some mutant types in T3 generation weedy rice without CRISPR-Cas9 vector significantly decreased plant height, decreased spikelet number per main panicle, decreased plump seed number per main panicle, and increased 1000-grain weight. Our results showed that the Rc gene editing using CRISPR/Cas9 technology can not only remove the harmful pericarp character of weedy rice, but also improve drought tolerance in seed germination. This study might provide new insights for the utilization of weedy rice as germplasm resources for direct-seeding rice by precisely editing genes to remove unfavorable traits. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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16 pages, 4304 KiB

Open AccessArticle

Transcriptome-Based Comparative Analysis of Transcription Factors in Response to NaCl, NaOH, and Na₂CO₃ Stresses in Roots of Autotetraploid Rice (Oryza sativa L.)

by Yingkai Wang, Yiming Zhou, Keyan Liu, Ningning Wang, Yujie Wu, Chunying Zhang and Jian Ma

Agronomy 2023, 13(4), 959; https://doi.org/10.3390/agronomy13040959 - 23 Mar 2023

Cited by 2 | Viewed by 1550

Abstract

Soil salinity is a severe constraint on crop productivity that triggers plant salt stress response pathways. The salt stress responses are controlled by transcriptional regulatory networks that enhance plant stress tolerance by manipulating the expression of transcription factor (TFs)-encoding genes. Identifying TFs associated with salt tolerance contributes to salt-tolerant crop breeding. In this study, a comparative transcriptome analysis was performed to investigate the global gene expression of entire TFs in diploid and autotetraploid rice with different salt tolerance levels, considering NaCl stress, NaOH stress, and Na₂CO₃ stress. A total of 54, 54 and 55 TF families were co-expressed in diploid and tetraploid roots under three stresses, respectively. Furthermore, we investigated differentially expressed TFs (DE-TFs) based on different comparisons, and the statistical analysis indicated that the DE-TFs derived from the three types of stress were as follows: Na₂CO₃ (53 TF families, 1356 DE-TFs) > NaCl (19 TF families, 214 DE-TFs) > NaOH (18 TF families, 152 DE-TFs). These results imply that Na₂CO₃ stress induced a more obvious biological responses in the roots than the other two stresses. GO and KEGG pathway enrichment analysis of DE-TFs revealed the importance of plant hormone signal transduction and MAPK signaling pathways that may contribute to the saline–alkaline tolerance of tetraploid rice. This study provides gene resources that are valuable for exploring the regulatory mechanism of TFs involved in the saline–alkaline tolerance of polyploid rice. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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12 pages, 2064 KiB

Open AccessArticle

Breeding of the Long-Grain Restorer of Indica-Japonica Hybrid Rice by Using the Genetic Effects of Grain Shape QTLs

by Keke Liu, Zequn Peng, Zhihao Sun, Zhengping Zhou, Yanhui Li, Ran Zhou, Dengmei He, Chenbo Huang, Daibo Chen, Shihua Cheng, Liyong Cao, Xiaodeng Zhan and Lianping Sun

Agronomy 2023, 13(1), 107; https://doi.org/10.3390/agronomy13010107 - 29 Dec 2022

Viewed by 1531

Abstract

Grain shape improvement, which determines grain yield, quality traits and commercial value, is an extremely important aspect of rice breeding. Grain size is controlled by multiple genes, and Maker Assistant Selection (MAS) breeding is effective for breeders in developing stable and efficient markers to aggregate these genes in order to speed up the selection of new lines with desirable traits during the breeding process. In this study, functional markers were developed based on the sequence differences of five grain-shaped genes (GL7, GW6a, GS6, GW5 and TGW6) between the long-grain japonica rice variety Zhendao and the indica-japonica restorer R2027. We then constructed a population of recombinant inbred lines (RILs) based on their cross. The newly designed functional markers were used to genotype grain-size genes, and a genetic effect analysis was conducted to screen high-quality long-grain restorers. Our results reveal diverse effects of different genes on grain size, and the five genotypes were distributed in the 36 selected BC₁F₈ lines. Specifically, gw5 positively regulates grain width and 1000-grain weight, gl7 and gs6 positively regulate grain length but negatively regulate grain width and 1000-grain weight, tgw6 positively regulates grain length and gw6a positively regulates 1000-grain weight. The most outstanding outcome is that 5 of the 36 lines achieved in this study showing an excellent performance of long grain and yield characters are ideal materials not only for studying the interaction and genetic effects between polygenes but also as restorers or donors for dominant genes in indica-japonica hybrid rice breeding. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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18 pages, 2203 KiB

Open AccessArticle

QTL Mapping of Mineral Element Contents in Rice Using Introgression Lines Derived from an Interspecific Cross

by Cheryl Adeva, Yeo-Tae Yun, Kyu-Chan Shim, Ngoc Ha Luong, Hyun-Sook Lee, Ju-Won Kang, Hyun-Jung Kim and Sang-Nag Ahn

Agronomy 2023, 13(1), 76; https://doi.org/10.3390/agronomy13010076 - 26 Dec 2022

Cited by 5 | Viewed by 2825

Abstract

Developing rice varieties with increased mineral element content is the most cost-effective and efficient approach for alleviating human malnutrition and nutrient deficiencies. In this study, quantitative trait loci (QTLs) were mapped for mineral element content in 96 introgression lines derived from a cross between the elite Korean Oryza sativa japonica cultivar “Hwaseong” and the wild rice Oryza rufipogon (IRGC105491). The population was grown in two locations, and Fe, Zn, Mn, and Ca contents of the brown rice were measured. Six QTLs were identified on chromosomes 6, 8, and 10, and all O. rufipogon alleles increased trait values. The positions of qFe10 and qZn10 were further defined; higher Fe and Zn contents are related to the 375-kb O. rufipogon segment between the markers RM1873 and RM25612. The combined analysis of the whole-genome sequencing data, spatiotemporal expression profile, and gene expression suggested that a transcription factor gene, namely the rice homeobox gene 9 (LOC_Os10g33960) marks as the high potential candidate associated with Fe and/or Zn regulation. This study provides valuable information on candidate genes qFe10 and qZn10 from O. rufipogon, which may be vital in developing rice varieties with increased Fe and/or Zn content without any penalty in traits of agronomic importance. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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15 pages, 6000 KiB

Open AccessArticle

Genetic Diversity and Population Differentiation of Dongxiang Wild Rice (Oryza rufipogon Griff.) Based on SNP Markers

by Yuanyuan Nie, Guihua Hou, Hui Xia, Lei Wang, Jianguo Lei, Hong Chen, Liang Chen and Lijun Luo

Agronomy 2022, 12(12), 3056; https://doi.org/10.3390/agronomy12123056 - 02 Dec 2022

Cited by 2 | Viewed by 1411

Abstract

Dongxiang wild rice (DXWR) is one of the most valuable germplasm resources of rice. It is important to conserve the genetic diversity and uncover the population differentiation of DXWR. In this study, we analyzed the genetic diversity and population differentiation of DXWR based on whole-genome resequencing of 220 DXWR lines collected from nine natural populations in an ex situ conservation nursery. Almost half of the SNPs and Indels detected in these DXWR lines were absent in cultivated rice or other common wild rice, indicating the potential and importance of DXWR in rice breeding. Based on Structure and PCA analysis, these DXWR lines could be divided into two subpopulations, in which subpopulation G1 had more specific SNPs and Indels and was genetically more genetically diverse than subpopulation G2. The average Fst of regions with low relative genetic diversity between G1 and G2 were significantly lower than whole-genomic Fst, indicating directional selection in these regions. Some functional genes and QTLs were found to locate in highly differentiated regions between G1 and G2. Moreover, the deep root ratios of G2 were significantly higher than G1. Our results would be helpful to the conservation and utilization of DXWR germplasm. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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9 pages, 2112 KiB

Open AccessCommunication

QTL Mapping of Mesocotyl Elongation and Confirmation of a QTL in Dongxiang Common Wild Rice in China

by Qian Huang, Chunyan Ju, Yibing Cheng, Di Cui, Bing Han, Zhengwu Zhao, Xiaoding Ma and Longzhi Han

Agronomy 2022, 12(8), 1800; https://doi.org/10.3390/agronomy12081800 - 29 Jul 2022

Cited by 5 | Viewed by 1324

Abstract

Direct-seeded rice (DSR) cultivation is an effective and important way to resolve agricultural labor scarcity, water scarcity and high production cost issues. Mesocotyl elongation (ME) is the main driver of the rapid emergence of rice seedlings from the soil and is an important indicator of the suitability of rice varieties for direct seeding. Hence, discovering ME-related genes is particularly important for breeding rice varieties suitable for direct seeding. In this study, a chromosome segment substitution line (CSSL) population generated from a cross between Dongxiang common wild rice and Nipponbare (Nip) was used to map quantitative trait loci (QTLs) for ME. Two QTLs for mesocotyl length were identified on chromosomes 3 and 6 with logarithm of odds (LOD) scores ranging from 5.47 to 6.04 and explaining 15.95–16.79% of the phenotypic variance. Among these QTLs, qML6 accounted for the highest phenotypic variance (16.79%). Then, to confirm the strongest QTL, we generated an F₂ segregating population via the CSL127 line harboring the qML6 locus and the recurrent parent Nip. The QTL qML6-1 associated with ME was mapped to a location between markers DX-C6-2 and DX-C6-4, which is consistent with the location of the previously mapped QTL qML6. qML6-1 had an LOD score of 8.45 and explained 30.56% of the phenotypic variance. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to develop varieties with improved ME for the cultivation of DSR. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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13 pages, 1885 KiB

Open AccessArticle

Genome-Wide Association Study of Sheath Blight Resistance within a Core Collection of Rice (Oryza sativa L.)

by Dong Fu, Kaizhen Zhong, Zhengzheng Zhong, Guocheng Hu, Peng Zhang and Hanhua Tong

Agronomy 2022, 12(7), 1493; https://doi.org/10.3390/agronomy12071493 - 22 Jun 2022

Cited by 6 | Viewed by 1813

Abstract

Sheath blight disease (ShB) is considered to be the second most important disease affecting rice, and the genetic mechanism of ShB resistance in rice is great complicated. Uncovering genetic mechanism of ShB resistance and strong resistant varieties in rice are the premise for ShB resistance improvement. A rice ShB genome-wide association study (GWAS) was performed using approximately five million SNPs within Ting’s core collection. “Early pradifice”, one typical japonica, was determined to be the most resistant variety in both 2016 and 2017. A total of 34 and four significant (p ≤ 1.93 × 10⁻⁸) SNPs were observed in 2016 and 2017, respectively. Moreover, 23 of 34 and two of four gene-based SNPs not reported in previous studies in 2016 and 2017, respectively, were identified as significantly associated with rice ShB resistance. Furthermore, we performed GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses for the genes located at a region within 10 kb of the significant SNPs. Both in 2016 and 2017, we observed that genes were uniquely enriched in the regulation of transcription and RNA processing in the category of “biological process”, plasma membrane, nucleus, integral component of membrane and cell wall in the category of “cellular component”, and ATP binding in the category of “molecular function”. The results of the present study may establish a foundation for further research investigating these elite genes and utilizing the resistant varieties in Ting’s core collection to improve rice ShB resistance. Full article

(This article belongs to the Special Issue Discovery and Utilization of Germplasm Resources in Rice)

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