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Genomics, Genetics, and Breeding for Rice Crop Improvement
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Genomics, Genetics, and Breeding for Rice Crop 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 (31 March 2021) | Viewed by 21274

Special Issue Editors

Dr. Sung-Ryul Kim

E-Mail Website
Guest Editor
Trait and Genome Engineering Cluster, Strategic Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna 4031, Philippines
Interests: rice molecular genetics; genetic potentials of wild rice species for rice improvement; rice genome engineering; rice molecular breeding
Dr. Chih-Wei Tung

E-Mail Website
Guest Editor
Department of Agronomy, National Taiwan University, Taipei City 10617, Taiwan
Interests: rice genetics and genomics; rice QTL mapping; genetics and breeding of rice tolerant to abiotic stress; rice traits discovery

Special Issue Information

Dear Colleagues,

Rice (Oryza sativa L.) is the most important cereal crop, feeding more than half of the world’s population as well as being important in science as a model plant of monocots. Since the release of whole genome sequences of the rice reference genome, O. sativa spp. japonica cv. Nipponbare and release of a set of genome-wide simple sequence repeats (SSR) markers and large numbers of rice T-DNA/transposon tagging lines in early 2000’s, genomics and genetics of rice have been remarkably advanced. In addition, next generation sequencing (NGS) technologies with bioinformatics produced a huge amount of sequence information from diverse germplasm, including cultivars, landraces, and wild rice species. NGS techniques and advanced high-throughput genotyping technologies enabled genome-wide association study (GWAS) for rapid identification of novel genes associated with the phenotypes. Recently, new genome engineering tools such as CRISPR/Cas9 and sequence-specific DNA binding protein-based nuclease are well adapted in rice for functional study and direct trait improvement of rice. As a consequence, for the last two decades rice research has been remarkable in terms of many scientific aspects including completion of high quality reference genomes sequences, gene identification, gene functional studies, DNA mark technologies, marker-assisted breeding, and genome engineering.

Despite the tremendous achievements in rice science using advanced resources and technologies, their contributions to rice crop improvement are not highly correlated and there are still big gaps between rice science and rice crop improvement. To date, more than 2,800 genes out of the 39,045 annotated protein-coding genes in rice genome are functionally characterized and some portions of them are well studied at the molecular mechanisms level. However, the identified genes controlling useful agronomic traits are fewer, and the favorable alleles of the genes are already present in many elite rice cultivars, making them inapplicable for breeding modern elite varieties. Most of all, the products of genomics and genetics were not well extended to rice crop improvement.   

Therefore, this Special Issue will focus on rice crop improvement by genomics, genetics, and breeding and related topics (original research papers, perspectives, opinions, reviews, modeling approaches and methods) covering genes/QTLs, novel/superior alleles, grain yield, grain quality and nutrition, biotic/abiotic stress, current and emerging problems (direct seeding, rice cultivation in harsh environments such as saline area and iron/aluminum toxicity soils, and mitigation of methane gas emission in rice field), hybrid rice, utilization of wild rice species, genome engineering, and breeding scheme/strategies are most welcome.

Dr. Sung-Ryul Kim
Dr. Chih-Wei Tung
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

  • Rice genomics
  • Rice genetics
  • Rice breeding
  • Rice yield
  • Rice nutrition
  • Genome engineering
  • CRISPR/Cas
  • Wild rice species
  • Biotic stress
  • Abiotic stress

Published Papers (6 papers)

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Research

15 pages, 5312 KiB  
Article
Starch Synthesis-Related Genes (SSRG) Evolution in the Genus Oryza
by Karine E. Janner de Freitas, Railson Schreinert dos Santos, Carlos Busanello, Filipe de Carvalho Victoria, Jennifer Luz Lopes, Rod A. Wing and Antonio Costa de Oliveira
Plants 2021, 10(6), 1057; https://doi.org/10.3390/plants10061057 - 25 May 2021
Viewed by 2830
Abstract
Cooking quality is an important attribute in Common/Asian rice (Oryzasativa L.) varieties, being highly dependent on grain starch composition. This composition is known to be highly dependent on a cultivar’s genetics, but the way in which their genes express different phenotypes [...] Read more.
Cooking quality is an important attribute in Common/Asian rice (Oryzasativa L.) varieties, being highly dependent on grain starch composition. This composition is known to be highly dependent on a cultivar’s genetics, but the way in which their genes express different phenotypes is not well understood. Further analysis of variation of grain quality genes using new information obtained from the wild relatives of rice should provide important insights into the evolution and potential use of these genetic resources. All analyses were conducted using bioinformatics approaches. The analysis of the protein sequences of grain quality genes across the Oryza suggest that the deletion/mutation of amino acids in active sites result in variations that can negatively affect specific steps of starch biosynthesis in the endosperm. On the other hand, the complete deletion of some genes in the wild species may not affect the amylose content. Here we present new insights for Starch Synthesis-Related Genes (SSRGs) evolution from starch-specific rice phenotypes. Full article
(This article belongs to the Special Issue Genomics, Genetics, and Breeding for Rice Crop Improvement)
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15 pages, 3819 KiB  
Article
Marker-Assisted Introgression and Stacking of Major QTLs Controlling Grain Number (Gn1a) and Number of Primary Branching (WFP) to NERICA Cultivars
by Vincent P. Reyes, Rosalyn B. Angeles-Shim, Merlyn S. Mendioro, Ma. Carmina C. Manuel, Ruby S. Lapis, Junghyun Shim, Hidehiko Sunohara, Shunsaku Nishiuchi, Mayumi Kikuta, Daigo Makihara, Kshirod K. Jena, Motoyuki Ashikari and Kazuyuki Doi
Plants 2021, 10(5), 844; https://doi.org/10.3390/plants10050844 - 22 Apr 2021
Cited by 30 | Viewed by 4703
Abstract
The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of [...] Read more.
The era of the green revolution has significantly improved rice yield productivity. However, with the growing population and decreasing arable land, rice scientists must find new ways to improve rice productivity. Although hundreds of rice yield-related QTLs were already mapped and some of them were cloned, only a few were utilized for actual systematic introgression breeding programs. In this study, the major yield QTLs Grain Number 1a (Gn1a) and Wealthy Farmer’s Panicle (WFP) were introgressed and stacked in selected NERICA cultivars by marker-assisted backcross breeding (MABB). The DNA markers RM3360, RM3452, and RM5493 were used for foreground selection. At BC3F4 and BC3F5 generation, a combination of marker-assisted selection and phenotypic evaluation were carried out to select lines with target alleles and traits. Further, genotyping-by-sequencing (GBS) was conducted to validate the introgression and determine the recurrent parent genome recovery (RPGR) of the selected lines. The Gn1a and/or WFP introgression lines showed significantly higher numbers of spikelets per panicle and primary branching compared to the recurrent parents. In addition, lines with Gn1a and/or WFP alleles were comparatively similar to the recurrent parents (RP) in most yield-related traits. This study demonstrates the success of utilizing yield QTLs and marker-assisted selection to develop and improve rice cultivars. Full article
(This article belongs to the Special Issue Genomics, Genetics, and Breeding for Rice Crop Improvement)
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18 pages, 3445 KiB  
Article
Genome-Wide Association Study of Local Thai Indica Rice Seedlings Exposed to Excessive Iron
by Reunreudee Kaewcheenchai, Phanchita Vejchasarn, Kousuke Hanada, Kazumasa Shirai, Chatchawan Jantasuriyarat and Piyada Juntawong
Plants 2021, 10(4), 798; https://doi.org/10.3390/plants10040798 - 19 Apr 2021
Cited by 2 | Viewed by 3294
Abstract
Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity (FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study [...] Read more.
Excess soluble iron in acidic soil is an unfavorable environment that can reduce rice production. To better understand the tolerance mechanism and identify genetic loci associated with iron toxicity (FT) tolerance in a highly diverse indica Thai rice population, a genome-wide association study (GWAS) was performed using genotyping by sequencing and six phenotypic data (leaf bronzing score (LBS), chlorophyll content, shoot height, root length, shoot biomass, and root dry weight) under both normal and FT conditions. LBS showed a high negative correlation with the ratio of chlorophyll content and shoot biomass, indicating the FT-tolerant accessions can regulate cellular homeostasis when encountering stress. Sixteen significant single nucleotide polymorphisms (SNPs) were identified by association mapping. Validation of candidate SNP using other FT-tolerant accessions revealed that SNP:2_21262165 might be associated with tolerance to FT; therefore, it could be used for SNP marker development. Among the candidate genes controlling FT tolerance, RAR1 encodes an innate immune responsive protein that links to cellular redox homeostasis via interacting with abiotic stress-responsive Hsp90. Future research may apply the knowledge obtained from this study in the molecular breeding program to develop FT-tolerant rice varieties. Full article
(This article belongs to the Special Issue Genomics, Genetics, and Breeding for Rice Crop Improvement)
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12 pages, 864 KiB  
Article
Genetic Mapping by Sequencing More Precisely Detects Loci Responsible for Anaerobic Germination Tolerance in Rice
by John Carlos I. Ignacio, Maricris Zaidem, Carlos Casal, Jr., Shalabh Dixit, Tobias Kretzschmar, Jaime M. Samaniego, Merlyn S. Mendioro, Detlef Weigel and Endang M. Septiningsih
Plants 2021, 10(4), 705; https://doi.org/10.3390/plants10040705 - 06 Apr 2021
Cited by 7 | Viewed by 3191
Abstract
Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, [...] Read more.
Direct seeded rice (DSR) is a mainstay for planting rice in the Americas, and it is rapidly becoming more popular in Asia. It is essential to develop rice varieties that are suitable for this type of production system. ASD1, a landrace from India, possesses several traits desirable for direct-seeded fields, including tolerance to anaerobic germination (AG). To map the genetic basis of its tolerance, we examined a population of 200 F2:3 families derived from a cross between IR64 and ASD1 using the restriction site-associated DNA sequencing (RAD-seq) technology. This genotyping platform enabled the identification of 1921 single nucleotide polymorphism (SNP) markers to construct a high-resolution genetic linkage map with an average interval of 0.9 cM. Two significant quantitative trait loci (QTLs) were detected on chromosomes 7 and 9, qAG7 and qAG9, with LOD scores of 7.1 and 15.0 and R2 values of 15.1 and 29.4, respectively. Here, we obtained more precise locations of the QTLs than traditional simple sequence repeat and low-density SNP genotyping methods and may help further dissect the genetic factors of these QTLs. Full article
(This article belongs to the Special Issue Genomics, Genetics, and Breeding for Rice Crop Improvement)
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12 pages, 4960 KiB  
Article
Mapping of a Major QTL, qBK1Z, for Bakanae Disease Resistance in Rice
by Sais-Beul Lee, Namgyu Kim, Sumin Jo, Yeon-Jae Hur, Ji-Youn Lee, Jun-Hyeon Cho, Jong-Hee Lee, Ju-Won Kang, You-Chun Song, Maurene Bombay, Sung-Ryul Kim, Jungkwan Lee, Young-Su Seo, Jong-Min Ko and Dong-Soo Park
Plants 2021, 10(3), 434; https://doi.org/10.3390/plants10030434 - 25 Feb 2021
Cited by 15 | Viewed by 2946
Abstract
Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). This study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed [...] Read more.
Bakanae disease is a fungal disease of rice (Oryza sativa L.) caused by the pathogen Gibberella fujikuroi (also known as Fusarium fujikuroi). This study was carried out to identify novel quantitative trait loci (QTLs) from an indica variety Zenith. We performed a QTL mapping using 180 F2:9 recombinant inbred lines (RILs) derived from a cross between the resistant variety, Zenith, and the susceptible variety, Ilpum. A primary QTL study using the genotypes and phenotypes of the RILs indicated that the locus qBK1z conferring bakanae disease resistance from the Zenith was located in a 2.8 Mb region bordered by the two RM (Rice Microsatellite) markers, RM1331 and RM3530 on chromosome 1. The log of odds (LOD) score of qBK1z was 13.43, accounting for 30.9% of the total phenotypic variation. A finer localization of qBK1z was delimited at an approximate 730 kb interval in the physical map between Chr01_1435908 (1.43 Mbp) and RM10116 (2.16 Mbp). Introducing qBK1z or pyramiding with other previously identified QTLs could provide effective genetic control of bakanae disease in rice. Full article
(This article belongs to the Special Issue Genomics, Genetics, and Breeding for Rice Crop Improvement)
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18 pages, 1954 KiB  
Article
Incorporating Drought and Submergence Tolerance QTL in Rice (Oryza sativa L.)—The Effects under Reproductive Stage Drought and Vegetative Stage Submergence Stresses
by Asmuni Mohd Ikmal, Abd Aziz Shamsudin Noraziyah and Ratnam Wickneswari
Plants 2021, 10(2), 225; https://doi.org/10.3390/plants10020225 - 24 Jan 2021
Cited by 14 | Viewed by 3128
Abstract
Drought and submergence have been the major constraint in rice production. The present study was conducted to develop high-yielding rice lines with tolerance to drought and submergence by introgressing Sub1 into a rice line with drought yield QTL (qDTY; QTL = [...] Read more.
Drought and submergence have been the major constraint in rice production. The present study was conducted to develop high-yielding rice lines with tolerance to drought and submergence by introgressing Sub1 into a rice line with drought yield QTL (qDTY; QTL = quantitative trait loci) viz. qDTY3.1 and qDTY12.1 using marker-assisted breeding. We report here the effect of different combinations of Sub1 and qDTY on morpho-physiological, agronomical traits and yield under reproductive stage drought stress (RS) and non-stress (NS) conditions. Lines with outstanding performance in RS and NS trials were also evaluated in vegetative stage submergence stress (VS) trial to assess the tolerance level. The QTL class analysis revealed Sub1 + qDTY3.1 as the best QTL combination affecting the measured traits in RS trial followed by Sub1 + qDTY12.1. The effects of single Sub1, qDTY3.1 and qDTY12.1 were not as superior as when the QTLs are combined, suggesting the positive interaction of Sub1 and qDTY. Best performing lines selected from the RS and NS trials recorded yield advantage up to 4453.69 kg ha−1 and 6954 kg ha−1 over the parents, respectively. The lines were also found having great tolerance to submergence ranging from 80% to 100%, contributed by a lower percentage of shoot elongation and reduction of chlorophyll content after 14 days of VS. These lines could provide yield sustainability to farmers in regions impacted with drought and submergence while serving as important genetic materials for future breeding programs. Full article
(This article belongs to the Special Issue Genomics, Genetics, and Breeding for Rice Crop Improvement)
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