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Plants
Special Issues
Germplasm Enhancement and Breeding for Rice Quality Improvement
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Germplasm Enhancement and Breeding for Rice Quality Improvement

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (20 December 2022) | Viewed by 6510

Special Issue Editors

Prof. Dr. Xiangqian Zhao

E-Mail Website
Guest Editor
College of Advanced Agricultural Sciences, Zhejiang A&F University, No.666 Wusu Street, Lin'an District, Hangzhou 311300, China
Interests: grain quality; germplasm enhancement; molecular breeding; hybrid rice
Prof. Dr. Jinsong Bao

E-Mail Website
Guest Editor
College of Agricultural and Biotechnology, Zhejiang University, Hangzhou 310058, China
Interests: rice grain quality
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Dali Zeng

E-Mail Website
Guest Editor
College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: molecular breeding; gene regulation; plant genetics and genomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rice is the most important cereal crop for human caloric needs, feeding more than half of the world’s population. With continuous economic development and rising standards of living, demands for high-quality grain are gradually increasing. Grain quality is a combination of the physical and chemical characteristics required for a specific use by a specific customer class. Consumers prefer eating high-quality rice with an aroma, uniform shape, and translucent endosperm. For the rice industry, a high milling quality is very important, since the market value of head rice is higher than that of broken grains. Low chalkiness yield, which is associated with more translucent rice, along with head rice yield, also determines the price of rice in almost all markets. In addition, chalkiness, including the percentage of grains with chalkiness and the degree of chalky grains, influences consumer acceptability as well as cooking quality. Overall, most traits that are genetically controlled by many loci are quantitative. Therefore, rice grain quality formation is very complex.

The mining of desirable genes or alleles is the most economical and effective method to improve grain quality, and molecular breeding is another powerful method for improving quality in rice. Skills have been developed for the utilization of specific germplasms to identify functional genes, molecular-assisted marker selections, gene pyramiding, and the manipulation of genes, such as the gene transferring and genome editing of targeted traits. GS3, chalk5, Wx, and badh2 have been extensively used in rice breeding. Therefore, more molecular studies on the mechanisms of grain quality formation are necessary for high-quality rice breeding.

This Special Issue aims to provide a forum on the most recent advances in the field of applications of molecular tools to create or breed new rice germplasms, prebreeding materials, or varieties with high grain quality. We welcome any papers that focus on the subject of germplasm enhancement and breeding for the improvement of rice quality, with topics including, but not limited to, the application of molecular tools in rice grain quality improvement, understanding the mechanisms of rice grain quality formation, new genes or germplasm discoveries, and integrated techniques to develop high-quality varieties or new germplasms of rice.

Prof. Dr. Xiangqian Zhao
Prof. Dr. Jinsong Bao
Prof. Dr. Dali Zeng
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • Oryza sativa L.
  • rice grain quality
  • germplasm
  • GAWS
  • eating quality
  • milling quality
  • chalkiness
  • grain shapes
  • low GI
  • Aroma (BADH2, 2-AP)
  • gene editing
  • molecular breeding

Published Papers (4 papers)

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Research

19 pages, 5717 KiB  
Article
Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions
by Nansheng Wang, Huguang Chen, Yingzhi Qian, Zhaojie Liang, Guiqiang Zheng, Jun Xiang, Ting Feng, Min Li, Wei Zeng, Yaling Bao, Erbao Liu, Chaopu Zhang, Jianlong Xu and Yingyao Shi
Plants 2023, 12(3), 419; https://doi.org/10.3390/plants12030419 - 17 Jan 2023
Cited by 3 | Viewed by 2331
Abstract
Rice (Oryza sativa L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic [...] Read more.
Rice (Oryza sativa L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (qTGW4.1, qTGW4.2, qGL4.1, qGL12.1, qGL12.2, qGW2.1, qGW4.1, qGW6.1, qGW8.1, qGW8.2, qGW9.1, qGW11.1, qGLWR2.1, qGLWR2.2, qGLWR4.2, qPGWC5.1 and qDEC6.1) were identified for haplotype analysis. Among these QTLs, two (qTGW4.2 and qGW6.1), were overlapped with FLO19 and OsbZIP47, respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction. Full article
(This article belongs to the Special Issue Germplasm Enhancement and Breeding for Rice Quality Improvement)
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10 pages, 3364 KiB  
Article
Transcriptome and Metabolome Analyses Reveal New Insights into the Regulatory Mechanism of Head Milled Rice Rate
by Wu Yang, Xianya Jiang, Yuelan Xie, Luo Chen, Junliang Zhao, Bin Liu, Shaohong Zhang and Dilin Liu
Plants 2022, 11(21), 2838; https://doi.org/10.3390/plants11212838 - 25 Oct 2022
Cited by 1 | Viewed by 1096
Abstract
The head milled rice rate (HMRR) is the most important trait of milling quality, which affects the final yield and quality of rice. However, few genes related to HMRR have been identified and the regulatory mechanism of HMRR remains elusive. In this study, [...] Read more.
The head milled rice rate (HMRR) is the most important trait of milling quality, which affects the final yield and quality of rice. However, few genes related to HMRR have been identified and the regulatory mechanism of HMRR remains elusive. In this study, we performed a comparative analysis integrating the transcriptome sequencing of developing seeds at the grain-filling stage and a metabolome analysis of brown rice between two groups of accessions with contrasting performances in HMRR. A total of 768 differentially expressed genes (DEGs) were identified between the transcriptome profiles of low-HMRR and high-HMRR accessions. In comparison to the high-HMRR accessions, 655 DEGs were up-regulated in the low-HMRR accessions, which was 4.79 folds higher than the number of down-regulated genes. These up-regulated DEGs were enriched in various metabolic and biosynthetic processes, oxidation reduction, phosphorylation, ion transport and ATP-related processes. However, the 113 down-regulated DEGs in the low-HMRR accessions were concentrated in carbohydrate metabolic processes, cell-death-related processes and defense response. Among the 30 differential metabolites, 20 and 10 metabolites were down-/up-regulated, respectively, in the accessions with low HMRR. In addition, 10 differential metabolites, including five metabolites of the shikimate pathway and five metabolites of the pyruvate pathway, were integrated into two separate pathways, starting from sucrose. Our global analysis of HMRR provides an invaluable resource for a better understanding of the molecular mechanism underlying the genetic regulation of HMRR. Full article
(This article belongs to the Special Issue Germplasm Enhancement and Breeding for Rice Quality Improvement)
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12 pages, 1039 KiB  
Article
Control of Grain Shape and Size in Rice by Two Functional Alleles of OsPUB3 in Varied Genetic Background
by Zhu-Hao Li, Shi-Lin Wang, Yu-Jun Zhu, Ye-Yang Fan, De-Run Huang, Ai-Ke Zhu, Jie-Yun Zhuang, Yan Liang and Zhen-Hua Zhang
Plants 2022, 11(19), 2530; https://doi.org/10.3390/plants11192530 - 27 Sep 2022
Cited by 2 | Viewed by 1198
Abstract
Grain shape and size are key determinants of grain appearance quality and yield in rice. In our previous study, a grain shape QTL, qGS1-35.2, was fine-mapped using near-isogenic lines (NILs) derived from a cross between Zhenshan 97 (ZS97) and Milyang 46 (MY46). [...] Read more.
Grain shape and size are key determinants of grain appearance quality and yield in rice. In our previous study, a grain shape QTL, qGS1-35.2, was fine-mapped using near-isogenic lines (NILs) derived from a cross between Zhenshan 97 (ZS97) and Milyang 46 (MY46). One annotated gene, OsPUB3, was found to be the most likely candidate gene. Here, knockout and overexpression experiments were performed to investigate the effects of OsPUB3 on grain shape and size. Four traits were tested, including grain length, grain width, grain weight, and the ratio of grain length to width. Knockout of OsPUB3 in NILZS97, NILMY46, and another rice cultivar carrying the OsPUB3MY46 allele all caused decreases in grain width and weight and increases in the ratio of grain length to width. Results also showed that the magnitude of the mutational effects varied depending on the target allele and the genetic background. Moreover, it was found that NILZS97 and NILMY46 carried different functional alleles of OsPUB3, causing differences in grain shape rather than grain weight. In the overexpression experiment, significant differences between transgenic-positive and transgenic-negative plants were detected in all four traits. These results indicate that OsPUB3 regulates grain shape and size through a complex mechanism and is a good target for deciphering the regulatory network of grain shape. This gene could be used to improve grain appearance quality through molecular breeding as well. Full article
(This article belongs to the Special Issue Germplasm Enhancement and Breeding for Rice Quality Improvement)
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14 pages, 2122 KiB  
Article
Combined Effects of Different Alleles of FLO2, Wx and SSIIa on the Cooking and Eating Quality of Rice
by Yu Zhang, Jiajia Zhao, Yaqi Hu, Yanni Zhang, Yining Ying, Feifei Xu and Jinsong Bao
Plants 2022, 11(17), 2249; https://doi.org/10.3390/plants11172249 - 30 Aug 2022
Cited by 3 | Viewed by 1387
Abstract
The improvement of the cooking and eating quality (CEQ) of rice is one of the major objectives of current rice-breeding programs. A few major genes such as Waxy (Wx) and starch synthase IIa (SSIIa) have been successfully applied in [...] Read more.
The improvement of the cooking and eating quality (CEQ) of rice is one of the major objectives of current rice-breeding programs. A few major genes such as Waxy (Wx) and starch synthase IIa (SSIIa) have been successfully applied in molecular breeding. However, their interactive effects on CEQ have not been fully understood. In this study, a recombinant inbred line (RIL) population was constructed by crossing the white-core mutant GM645 with the transparent phenotype of the japonica rice variety Tainung 67 (TN67). GM645 and TN67 contain different alleles of FLOURY ENDOSPERM2 (FLO2), Wx, and SSIIa. The effects of different allele combinations of FLO2, Wx, and SSIIa on the CEQ of rice were investigated. The inbred lines with the mutation allele flo2 had a significantly lower apparent amylose content (AAC), viscosity characteristics except for setback (SB), and gel texture properties compared to those lines with the FLO2 allele. The allelic combination of FLO2 and Wx significantly affected the AAC, breakdown (BD), and gel textural properties, which could explain most of the variations in those rice quality traits that were correlated with AAC. The allelic combination of FLO2 and SSIIa significantly affected the hot paste viscosity (HPV) and pasting temperature (PT). The Wx × SSIIa interaction had a significant effect on the PT. The interaction of FLO2, Wx and SSIIa significantly affected the AAC, cold paste viscosity (CPV), PT, and consistency viscosity (CS). These results highlight the important roles of these quality-related genes in regulating the CEQ of rice and provide new clues for rice-quality improvement by marker-assisted selection. Full article
(This article belongs to the Special Issue Germplasm Enhancement and Breeding for Rice Quality Improvement)
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