Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.1
3.5
Journals
Genes
Special Issues
Genetics and Genomics of Rice
share announcement

Genetics and Genomics 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: 20 June 2024 | Viewed by 3900

Special Issue Editors

Dr. Yu-Jun Zhu

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou, China
Interests: molecular breeding; yield-related trait; flowering time; map-based cloning; QTL; genome editing; genetic interaction
Special Issues, Collections and Topics in MDPI journals
Dr. Zhen-Hua Zhang

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou, China
Interests: gene identification; genome editing; molecular breeding; rice
Special Issues, Collections and Topics in MDPI journals
Dr. Chaolei Liu

E-Mail Website
Guest Editor
China National Rice Research Institute, Hangzhou, China
Interests: rice; synthetic apomixis; haploid breeding; QTL; genome editing
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Rice is one of the most important food crops worldwide, and more than half of the global population uses rice as the main food source. Rice is also an excellent model species in plant biology, especially for studies on monocotyledonous plants, because of its small genome size and completed genome sequence, in addition to the efficient genetic transformation technology and vast genetic resources that have been developed. The intensive development and application of biotechnologies such as genome assembly, germplasm characterization, transformation and genome editing have greatly facilitated genetic and genomic analyses in rice. Genomes have been constructed for hundreds of rice accessions, and genetic variation and diversity have been analyzed among thousands of varieties. A large number of QTLs/genes for important agricultural traits have been identified and their functions have been mined.

This Special Issue aims to provide a forum for presenting the most recent advances in genetic and genomic research in rice. We seek original research articles and reviews covering all related topics, including genome assembly, germplasm resource mining, genetic diversity analysis, genome-wide association studies (GWAS), quantitative trait loci (QTL) mapping, map-based cloning, functional marker-assisted selection, etc., in the context of genetic and genomic research in rice.

Dr. Yu-Jun Zhu
Dr. Zhen-Hua Zhang
Dr. Chaolei Liu
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. Genes 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

  • genome-wide association studies
  • QTL mapping
  • map-based cloning
  • germplasm resource mining
  • genetic diversity analysis
  • genome editing

Published Papers (3 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

12 pages, 2072 KiB  
Article
Genome-Wide Association Study of Arsenic Accumulation in Polished Rice
by Zheng Dong, Liang Guo, Xiaoxiang Li, Yongchao Li, Wenqiang Liu, Zuwu Chen, Licheng Liu, Zhixi Liu, Yujing Guo and Xiaowu Pan
Genes 2023, 14(12), 2186; https://doi.org/10.3390/genes14122186 - 07 Dec 2023
Viewed by 764
Abstract
The accumulation of arsenic (As) in rice poses a significant threat to food safety and human health. Breeding rice varieties with low As accumulation is an effective strategy for mitigating the health risks associated with arsenic-contaminated rice. However, the genetic mechanisms underlying As [...] Read more.
The accumulation of arsenic (As) in rice poses a significant threat to food safety and human health. Breeding rice varieties with low As accumulation is an effective strategy for mitigating the health risks associated with arsenic-contaminated rice. However, the genetic mechanisms underlying As accumulation in rice grains remain incompletely understood. We evaluated the As accumulation capacity of 313 diverse rice accessions grown in As-contaminated soils with varying As concentrations. Six rice lines with low As accumulation were identified. Additionally, a genome-wide association studies (GWAS) analysis identified 5 QTLs significantly associated with As accumulation, with qAs4 being detected in both of the experimental years. Expression analysis demonstrated that the expression of LOC_Os04g50680, which encodes an MYB transcription factor, was up-regulated in the low-As-accumulation accessions compared to the high-As-accumulation accessions after As treatment. Therefore, LOC_Os04g50680 was selected as a candidate gene for qAs4. These findings provide insights for exploiting new functional genes associated with As accumulation and facilitating the development of low-As-accumulation rice varieties through marker-assisted breeding. Full article
(This article belongs to the Special Issue Genetics and Genomics of Rice)
►▼ Show Figures

Figure 1

13 pages, 1292 KiB  
Article
Unveiling the Genetic Basis Underlying Rice Anther Culturability via Segregation Distortion Analysis in Doubled Haploid Population
by Bin Sun, Xiaorui Ding, Junhua Ye, Yuting Dai, Can Cheng, Jihua Zhou, Fuan Niu, Rongjian Tu, Qiyan Hu, Kaizhen Xie, Yue Qiu, Hongyu Li, Zhizun Feng, Chenbing Shao, Liming Cao, Anpeng Zhang and Huangwei Chu
Genes 2023, 14(11), 2086; https://doi.org/10.3390/genes14112086 - 17 Nov 2023
Viewed by 920
Abstract
Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation [...] Read more.
Anther culture (AC) is a valuable technique in rice breeding. However, the genetic mechanisms underlying anther culturability remain elusive, which has hindered its widespread adoption in rice breeding programs. During AC, microspores carrying favorable alleles for AC are selectively regenerated, leading to segregation distortion (SD) of chromosomal regions linked to these alleles in the doubled haploid (DH) population. Using the AC method, a DH population was generated from the japonica hybrid rice Shenyou 26. A genetic map consisting of 470 SNPs was constructed using this DH population, and SD analysis was performed at both the single- and two-locus levels to dissect the genetic basis underlying anther culturability. Five segregation distortion loci (SDLs) potentially linked to anther culturability were identified. Among these, SDL5 exhibited an overrepresentation of alleles from the female parent, while SDL1.1, SDL1.2, SDL2, and SDL7 displayed an overrepresentation of alleles from the male parent. Furthermore, six pairs of epistatic interactions (EPIs) that influenced two-locus SDs in the DH population were discovered. A cluster of genetic loci, associated with EPI-1, EPI-3, EPI-4, and EPI-5, overlapped with SDL1.1, indicating that the SDL1.1 locus may play a role in regulating anther culturability via both additive and epistatic mechanisms. These findings provide valuable insights into the genetic control of anther culturability in rice and lay the foundation for future research focused on identifying the causal genes associated with anther culturability. Full article
(This article belongs to the Special Issue Genetics and Genomics of Rice)
►▼ Show Figures

Figure 1

27 pages, 4164 KiB  
Article
Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice
by Shakti Prakash Mohanty, Deepak Kumar Nayak, Priyadarsini Sanghamitra, Saumya Ranjan Barik, Elssa Pandit, Abhisarika Behera, Dipti Ranjan Pani, Shibani Mohapatra, Reshmi Raj K. R., Kartik Chandra Pradhan, Chita Ranjan Sahoo, Mihir Ranjan Mohanty, Chinmayee Behera, Alok Kumar Panda, Binod Kumar Jena, Lambodar Behera, Prasanta K. Dash and Sharat Kumar Pradhan
Genes 2023, 14(4), 902; https://doi.org/10.3390/genes14040902 - 12 Apr 2023
Cited by 2 | Viewed by 1668
Abstract
Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in [...] Read more.
Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker–trait association analysis detected eight novel QTLs, namely qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice. Full article
(This article belongs to the Special Issue Genetics and Genomics of Rice)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-3
Back to TopTop