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Advances in Rice Genetics and Breeding
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Advances in Rice Genetics and Breeding

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

Deadline for manuscript submissions: closed (15 September 2021) | Viewed by 19864

Special Issue Editor

Dr. Joohyun Lee

E-Mail Website
Guest Editor
Departmen of Crop Science, Konkuk University, Seoul, Korea
Interests: abiotic stresses; rice; breeding, general genetics, GWAS, proteomics, and gene-editing

Special Issue Information

Dear Colleagues,

Rice is one of the important crops in the world as the main staple food for more than half of the world’s population. Recently, a lot of progress were archived in rice genetic research especially with accumulation of genomic data. The benefit of the accumulated knowledge from the genomic study will accelerate the rate of genetic gain through applying modern breeding approaches assisted by genomic database. Innovative breeding strategies with various tools such as genomics molecular biology have begun to emerge in rice breeding program to boost rice breeding efficiency.

Here, it is proper time to organize the achievement and future prospective in rice genetic study including genomics and innovate breeding methods in rice.

This Special Issue is a collection of articles presenting novel and international research in rice genetics, breeding, and genomics including transcriptomics and proteomics. Manuscripts on the following topics will be considered for publication and are encouraged: GWAS, developing rand evaluation of rice lines, MAS and related strategies applied in rice breeding, developing genetic markers for agronomic trats, evaluating various traits and genetic structure with rice germplasm, and biotechnology for creating variation on agronomic traits.

Dr. Joohyun Lee
Guest Editor

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

  • Rice 
  • Genetics 
  • Genomics 
  • Breeding

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Published Papers (5 papers)

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Research

14 pages, 2964 KiB  
Article
Identification and Validation of a QTL for Bacterial Leaf Streak Resistance in Rice (Oryza sativa L.) against Thai Xoc Strains
by Tripop Thianthavon, Wanchana Aesomnuk, Mutiara K. Pitaloka, Wannapa Sattayachiti, Yupin Sonsom, Phakchana Nubankoh, Srihunsa Malichan, Kanamon Riangwong, Vinitchan Ruanjaichon, Theerayut Toojinda, Samart Wanchana and Siwaret Arikit
Genes 2021, 12(10), 1587; https://doi.org/10.3390/genes12101587 - 9 Oct 2021
Cited by 7 | Viewed by 3044
Abstract
Rice is one of the most important food crops in the world and is of vital importance to many countries. Various diseases caused by fungi, bacteria and viruses constantly threaten rice plants and cause yield losses. Bacterial leaf streak disease (BLS) caused by [...] Read more.
Rice is one of the most important food crops in the world and is of vital importance to many countries. Various diseases caused by fungi, bacteria and viruses constantly threaten rice plants and cause yield losses. Bacterial leaf streak disease (BLS) caused by Xanthomonas oryzae pv. oryzicola (Xoc) is one of the most devastating rice diseases. However, most modern rice varieties are susceptible to BLS. In this study, we applied the QTL-seq approach using an F2 population derived from the cross between IR62266 and Homcholasit (HSC) to rapidly identify the quantitative trait loci (QTL) that confers resistance to BLS caused by a Thai Xoc isolate, SP7-5. The results showed that a single genomic region at the beginning of chromosome 5 was highly associated with resistance to BLS. The gene xa5 was considered a potential candidate gene in this region since most associated single nucleotide polymorphisms (SNPs) were within this gene. A Kompetitive Allele-Specific PCR (KASP) marker was developed based on two consecutive functional SNPs in xa5 and validated in six F2 populations inoculated with another Thai Xoc isolate, 2NY2-2. The phenotypic variance explained by this marker (PVE) ranged from 59.04% to 70.84% in the six populations. These findings indicate that xa5 is a viable candidate gene for BLS resistance and may help in breeding programs for BLS resistance. Full article
(This article belongs to the Special Issue Advances in Rice Genetics and Breeding)
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17 pages, 1686 KiB  
Article
Molecular Breeding for Improving Productivity of Oryza sativa L. cv. Pusa 44 under Reproductive Stage Drought Stress through Introgression of a Major QTL, qDTY12.1
by Kyaw Swar Oo, Subbaiyan Gopala Krishnan, Kunnummal Kurungara Vinod, Gaurav Dhawan, Priyanka Dwivedi, Pankaj Kumar, Prolay Kumar Bhowmick, Madan Pal, Viswanathan Chinnuswamy, Mariappan Nagarajan, Haritha Bollinedi, Ranjith Kumar Ellur and Ashok Kumar Singh
Genes 2021, 12(7), 967; https://doi.org/10.3390/genes12070967 - 24 Jun 2021
Cited by 7 | Viewed by 2443
Abstract
Increasing rice production is quintessential to the task of sustaining global food security, as a majority of the global population is dependent on rice as its staple dietary cereal. Among the various constraints affecting rice production, reproductive stage drought stress (RSDS) is a [...] Read more.
Increasing rice production is quintessential to the task of sustaining global food security, as a majority of the global population is dependent on rice as its staple dietary cereal. Among the various constraints affecting rice production, reproductive stage drought stress (RSDS) is a major challenge, due to its direct impact on grain yield. Several quantitative trait loci (QTLs) conferring RSDS tolerance have been identified in rice, and qDTY12.1 is one of the major QTLs reported. We report the successful introgression of qDTY12.1 into Pusa 44, a drought sensitive mega rice variety of the northwestern Indian plains. Marker-assisted backcross breeding (MABB) was adopted to transfer qDTY12.1 into Pusa 44 in three backcrosses followed by four generations of pedigree selection, leading to development of improved near isogenic lines (NILs). Having a recurrent parent genome (RPG) recovery ranging from 94.7–98.7%, the improved NILs performed 6.5 times better than Pusa 44 under RSDS, coupled with high yield under normal irrigated conditions. The MABB program has been modified so as to defer background selection until BC3F4 to accelerate generational advancements. Deploying phenotypic selection alone in the early backcross generations could help in the successful recovery of RPG. In addition, the grain quality could be recovered in the improved NILs, leading to superior selections. Owing to their improved adaptation to drought, the release of improved NILs for regions prone to intermittent drought can help enhance rice productivity and production. Full article
(This article belongs to the Special Issue Advances in Rice Genetics and Breeding)
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21 pages, 8548 KiB  
Article
Genome-Wide Analysis of Potassium Channel Genes in Rice: Expression of the OsAKT and OsKAT Genes under Salt Stress
by Zahra Musavizadeh, Hamid Najafi-Zarrini, Seyed Kamal Kazemitabar, Seyed Hamidreza Hashemi, Sahar Faraji, Gianni Barcaccia and Parviz Heidari
Genes 2021, 12(5), 784; https://doi.org/10.3390/genes12050784 - 20 May 2021
Cited by 57 | Viewed by 6572
Abstract
Potassium (K+), as a vital element, is involved in regulating important cellular processes such as enzyme activity, cell turgor, and nutrient movement in plant cells, which affects plant growth and production. Potassium channels are involved in the transport and release of potassium in [...] Read more.
Potassium (K+), as a vital element, is involved in regulating important cellular processes such as enzyme activity, cell turgor, and nutrient movement in plant cells, which affects plant growth and production. Potassium channels are involved in the transport and release of potassium in plant cells. In the current study, three OsKAT genes and two OsAKT genes, along with 11 nonredundant putative potassium channel genes in the rice genome, were characterized based on their physiochemical properties, protein structure, evolution, duplication, in silico gene expression, and protein–protein interactions. In addition, the expression patterns of OsAKTs and OsKATs were studied in root and shoot tissues under salt stress using real-time PCR in three rice cultivars. K+ channel genes were found to have diverse functions and structures, and OsKATs showed high genetic divergence from other K+ channel genes. Furthermore, the Ka/Ks ratios of duplicated gene pairs from the K+ channel gene family in rice suggested that these genes underwent purifying selection. Among the studied K+ channel proteins, OsKAT1 and OsAKT1 were identified as proteins with high potential N-glycosylation and phosphorylation sites, and LEU, VAL, SER, PRO, HIS, GLY, LYS, TYR, CYC, and ARG amino acids were predicted as the binding residues in the ligand-binding sites of K+ channel proteins. Regarding the coexpression network and KEGG ontology results, several metabolic pathways, including sugar metabolism, purine metabolism, carbon metabolism, glycerophospholipid metabolism, monoterpenoid biosynthesis, and folate biosynthesis, were recognized in the coexpression network of K+ channel proteins. Based on the available RNA-seq data, the K+ channel genes showed differential expression levels in rice tissues in response to biotic and abiotic stresses. In addition, the real-time PCR results revealed that OsAKTs and OsKATs are induced by salt stress in root and shoot tissues of rice cultivars, and OsKAT1 was identified as a key gene involved in the rice response to salt stress. In the present study, we found that the repression of OsAKTs, OsKAT2, and OsKAT2 in roots was related to salinity tolerance in rice. Our findings provide valuable insights for further structural and functional assays of K+ channel genes in rice. Full article
(This article belongs to the Special Issue Advances in Rice Genetics and Breeding)
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13 pages, 2156 KiB  
Article
Genome-Wide Association Study Identified Novel Candidate Loci/Genes Affecting Lodging Resistance in Rice
by Bingxin Meng, Tao Wang, Yi Luo, Deze Xu, Lanzhi Li, Ying Diao, Zhiyong Gao, Zhongli Hu and Xingfei Zheng
Genes 2021, 12(5), 718; https://doi.org/10.3390/genes12050718 - 11 May 2021
Cited by 11 | Viewed by 3034
Abstract
Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce [...] Read more.
Lodging reduces rice yield, but increasing lodging resistance (LR) usually limits yield potential. Stem strength and leaf type are major traits related to LR and yield, respectively. Hence, understanding the genetic basis of stem strength and leaf type is of help to reduce lodging and increase yield in LR breeding. Here, we carried out an association analysis to identify quantitative trait locus (QTLs) affecting stem strength-related traits (internode length/IL, stem wall thickness/SWT, stem outer diameter/SOD, and stem inner diameter/SID) and leaf type-associated traits (Flag leaf length/FLL, Flag leaf angle/FLA, Flag leaf width/FLW, leaf-rolling/LFR and SPAD/Soil, and plant analyzer development) using a diverse panel of 550 accessions and evaluated over two years. Genome-wide association study (GWAS) using 4,076,837 high-quality single-nucleotide polymorphisms (SNPs) identified 89 QTLs for the nine traits. Next, through “gene-based association analysis, haplotype analysis, and functional annotation”, the scope was narrowed down step by step. Finally, we identified 21 candidate genes in 9 important QTLs that included four reported genes (TUT1, OsCCC1, CFL1, and ACL-D), and seventeen novel candidate genes. Introgression of alleles, which are beneficial for both stem strength and leaf type, or pyramiding stem strength alleles and leaf type alleles, can be employed for LR breeding. All in all, the experimental data and the identified candidate genes in this study provide a useful reference for the genetic improvement of rice LR. Full article
(This article belongs to the Special Issue Advances in Rice Genetics and Breeding)
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24 pages, 4101 KiB  
Article
Computational and Transcriptomic Analysis Unraveled OsMATE34 as a Putative Anthocyanin Transporter in Black Rice (Oryza sativa L.) Caryopsis
by Enerand Mackon, Yafei Ma, Guibeline Charlie Jeazet Dongho Epse Mackon, Babar Usman, Yitong Zhao, Qiufeng Li and Piqing Liu
Genes 2021, 12(4), 583; https://doi.org/10.3390/genes12040583 - 16 Apr 2021
Cited by 15 | Viewed by 3495
Abstract
Anthocyanin is a flavonoid compound with potential antioxidant properties beneficial to human health and sustains plant growth and development under different environmental stresses. In black rice, anthocyanin can be found in the stems, leaves, stigmas, and caryopsis. Although the anthocyanin biosynthesis in rice [...] Read more.
Anthocyanin is a flavonoid compound with potential antioxidant properties beneficial to human health and sustains plant growth and development under different environmental stresses. In black rice, anthocyanin can be found in the stems, leaves, stigmas, and caryopsis. Although the anthocyanin biosynthesis in rice has been extensively studied, limited knowledge underlying the storage mechanism and transporters is available. This study undertook the complementation of computational and transcriptome analysis to decipher a potential multidrug and toxic compound extrusion (MATE) gene candidate for anthocyanin transportation in black rice caryopsis. The phylogenetic analysis showed that OsMATE34 has the same evolutionary history and high similarities with VvAM1, VvAM3, MtMATE2, SlMATE/MTP77, RsMATE8, AtFFT, and AtTT12 involved in anthocyanin transportation. RNA sequencing analysis in black caryopsis (Bc; Bc11, Bc18, Bc25) and white caryopsis (Wc; Wc11, Wc18, Wc25), respectively, at 11 days after flowering (DAF), 18 DAF, and 25 DAF revealed a total of 36,079 expressed genes, including 33,157 known genes and 2922 new genes. The differentially expressed genes (DEGs) showed 15,573 genes commonly expressed, with 1804 and 1412 genes uniquely expressed in Bc and Wc, respectively. Pairwise comparisons showed 821 uniquely expressed genes out of 15,272 DEGs for Wc11 vs. Bc11, 201 uniquely expressed genes out of 16,240 DEGs for Wc18 vs. Bc18, and 2263 uniquely expressed genes out of 16,240 DEGs for Wc25 vs. Bc25. Along with anthocyanin biosynthesis genes (OsPAL, OsCHS, OsCHI, OsF3H, OsDFR, OsANS, and OsUFGT/Os3GT), OsMATE34 expression was significantly upregulated in all Bc but not in Wc. OsMATE34 expression was similar to OsGSTU34, a transporter of anthocyanin in rice leaves. Taken together, our results highlighted OsMATE34 (Os08g0562800) as a candidate anthocyanin transporter in rice caryopsis. This study provides a new finding and a clue to enhance the accumulation of anthocyanin in rice caryopsis. Full article
(This article belongs to the Special Issue Advances in Rice Genetics and Breeding)
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