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Molecular Breeding and Germplasm Improvement of Rice
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Molecular Breeding and Germplasm Improvement of Rice

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 October 2023) | Viewed by 14517

Special Issue Editors

Dr. Xiangjin Wei

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Guest Editor
China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
Interests: genetic improvement of rice quality; genetic improvement of rice quality; developmental biology of rice
Special Issues, Collections and Topics in MDPI journals
Dr. Yingxin Zhang

E-Mail Website
Guest Editor
China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice; yield; quantitative trait locus
Special Issues, Collections and Topics in MDPI journals
Dr. Weixun Wu

E-Mail Website
Guest Editor
China National Center for Rice Improvement and State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice; heading date; photoperiod sensitivity; quantitative trait locus; map-based cloning; functional analysis
Special Issues, Collections and Topics in MDPI journals
Dr. Guiai Jiao

E-Mail
Guest Editor
China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
Interests: rice quality; rice genetics and breeding; physical and chemical properties of rice
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In recent years, gene editing, whole genome selection, synthetic biology frontier biotechnology, and information technology such as artificial intelligence and big data have merged and combined with conventional breeding techniques, breeding technology, and intelligent design system, which continuously drives the modern breeding technology change iterations and has a significant influence on the crops of rice breeding. In addition, germplasm resources are the chip of crop breeding, and every breakthrough in crop breeding is inseparable from the innovation of important germplasm.

In order to promote academic exchange on the latest trends and achievements of molecular breeding and germplasm improvement of rice, this Special Issue will focus on molecular breeding and germplasm improvement of rice to promote the joint discussion of the latest research dynamics and directions and find opportunities for collaboration in this field. All original research papers and reviews are welcome for submission to this Special Issue.

Contributions in this Special Issue may include but are not limited to research and development of new technologies for rice molecular breeding and germplasm innovation. Particularly welcome is research on rice molecular breeding technologies such as gene editing, whole genome selection, synthetic biology, intelligent design breeding, and advances in the innovation of new rice germplasm with high yield, high quality, multiresistance, safety, and high efficiency.

Dr. Xiangjin Wei
Dr. Yingxin Zhang
Dr. Weixun Wu
Dr. Guiai Jiao
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 molecular breeding
  • innovation of rice germplasm
  • gene editing
  • whole genome selection
  • synthetic biology
  • intelligent design breeding

Related Special Issue

Published Papers (11 papers)

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Research

13 pages, 7254 KiB  
Article
G1 Interacts with OsMADS1 to Regulate the Development of the Sterile Lemma in Rice
by Huimin Fang, Hualan Chen, Jianing Wang, Ning Li, Long Zhang and Cunxu Wei
Plants 2024, 13(4), 505; https://doi.org/10.3390/plants13040505 - 11 Feb 2024
Viewed by 710
Abstract
Flower development, as the basis for plant seed development, is principally conserved in angiosperms. At present, a number of genes regulating flower organ differentiation have been identified, and an ABCDE model has also been proposed. In contrast, the mechanism that regulates the development [...] Read more.
Flower development, as the basis for plant seed development, is principally conserved in angiosperms. At present, a number of genes regulating flower organ differentiation have been identified, and an ABCDE model has also been proposed. In contrast, the mechanism that regulates the development of the sterile lemma remains unclear. In this study, we identified and characterized a rice floral organ mutant, M15, in which the sterile lemma transformed into a lemma-like organ. Positional cloning combined with a complementary experiment demonstrated that the mutant phenotype was restored by LONG STERILE LEMMA1/(G1). G1 was expressed constitutively in various tissues, with the highest expression levels detected in the sterile lemma and young panicle. G1 is a nucleus-localized protein and functions as a homomer. Biochemical assays showed that G1 physically interacted with OsMADS1 both in vitro and in vivo. Interestingly, the expression of G1 in M15 decreased, while the expression level of OsMADS1 increased compared with the wild type. We demonstrate that G1 plays a key role in sterile lemma development through cooperating with OsMADS1. The above results have implications for further research on the molecular mechanisms underlying flower development and may have potential applications in crop improvement strategies. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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19 pages, 3641 KiB  
Article
Identification of the CNGC Gene Family in Rice and Mining of Alleles for Application in Rice Improvement
by Xinchen Wang, Fengcai Wu, Jinguo Zhang, Yaling Bao, Nansheng Wang, Guohui Dou, Dezhuang Meng, Xingmeng Wang, Jianfeng Li and Yingyao Shi
Plants 2023, 12(24), 4089; https://doi.org/10.3390/plants12244089 - 6 Dec 2023
Viewed by 885
Abstract
Cyclic nucleotide-gated ion channel (CNGC) gene regulation plays important roles in plant immune and abiotic stress response. Here, we identified 16 CNGC genes in rice (Oryza sativa). Then, we analyzed their chromosomal location, physicochemical properties, subcellular localization, gene functional interaction network, cis-acting elements, [...] Read more.
Cyclic nucleotide-gated ion channel (CNGC) gene regulation plays important roles in plant immune and abiotic stress response. Here, we identified 16 CNGC genes in rice (Oryza sativa). Then, we analyzed their chromosomal location, physicochemical properties, subcellular localization, gene functional interaction network, cis-acting elements, phylogenetic relationships, collinearity, expression in tissues under normal conditions and abiotic stresses, and geng-cds-haplotype (gcHap) diversity in 3010 gcHaps. As a result, OsCNGC3 (Os06g0527300) was identified as a gene different from previous report, and OsCNGC genes were found to play important roles in rice population differentiation and rice improvement. Our results revealed their very strong differentiation between subspecies and populations, important roles in response to abiotic stresses, as well as strong genetic bottleneck effects and artificial selection of gcHap diversity in the modern breeding process of Xian (indica) and Geng (japonica) populations. The results also suggested that natural variations in most rice CNGC loci are potentially valuable for improving rice productivity and tolerance to abiotic stresses. The favorable alleles at the CNGC loci should be explored to facilitate their application in future rice improvement. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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15 pages, 8515 KiB  
Article
OsLEA1b Modulates Starch Biosynthesis at High Temperatures in Rice
by Gang Li, Ruijie Cao, Liuyang Ma, Guiai Jiao, Pengfei Chen, Nannan Dong, Xinwei Li, Yingqing Duan, Xiaoxue Li, Mingdong Zhu, Gaoneng Shao, Zhonghua Sheng, Shikai Hu, Shaoqing Tang, Xiangjin Wei, Yinghong Yu and Peisong Hu
Plants 2023, 12(23), 4070; https://doi.org/10.3390/plants12234070 - 4 Dec 2023
Viewed by 981
Abstract
High temperatures accelerate the accumulation of storage material in seeds, often leading to defects in grain filling. However, the mechanisms regulating grain filling at high temperatures remain unknown. Here, we want to explore the quality factors influenced by the environment and have identified [...] Read more.
High temperatures accelerate the accumulation of storage material in seeds, often leading to defects in grain filling. However, the mechanisms regulating grain filling at high temperatures remain unknown. Here, we want to explore the quality factors influenced by the environment and have identified a LATE EMBROYGENESIS ABUNDANT gene, OsLEA1b, a heat-stress-responsive gene in rice grain filling. OsLEA1b is highly expressed in the endosperm, and its coding protein localizes to the nucleus and cytoplasm. Knock-out mutants of OsLEA1b had abnormal compound starch granules in endosperm cells and chalky endosperm with significantly decreased grain weight and grain number per panicle. The oslea1b mutants exhibited a lower proportion of short starch chains with degrees of polymerization values from 6 to 13 and a higher proportion of chains with degrees from 14 to 48, as well as significantly lower contents of starch, protein, and lipid compared to the wild type. The difference was exacerbated under high temperature conditions. Moreover, OsLEA1b was induced by drought stress. The survival rate of oslea1b mutants decreased significantly under drought stress treatment, with significant increase in ROS levels. These results indicate that OsLEA1b regulates starch biosynthesis and influences rice grain quality, especially under high temperatures. This provides a valuable resource for genetic improvement in rice grain quality. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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12 pages, 3824 KiB  
Article
OsCIPK9 Interacts with OsSOS3 and Affects Salt-Related Transport to Improve Salt Tolerance
by Zhenling Zhou, Weijie Tang, Zhiguang Sun, Jingfang Li, Bo Yang, Yan Liu, Baoxiang Wang, Dayong Xu, Jianchang Yang and Yunhui Zhang
Plants 2023, 12(21), 3723; https://doi.org/10.3390/plants12213723 - 30 Oct 2023
Viewed by 860
Abstract
Salt is harmful to crop production. Therefore, it is important to understand the mechanism of salt tolerance in rice. CIPK genes have various functions, including regulating salt tolerance and other types of stress and nitrogen use efficiency. In rice, OsCIPK24 is known to [...] Read more.
Salt is harmful to crop production. Therefore, it is important to understand the mechanism of salt tolerance in rice. CIPK genes have various functions, including regulating salt tolerance and other types of stress and nitrogen use efficiency. In rice, OsCIPK24 is known to regulate salt tolerance, but other OsCIPKs could also function in salt tolerance. In this study, we identified another OsCIPK—OsCIPK9—that can regulate salt tolerance. Knockout of OsCIPK9 in rice could improve salt tolerance. Through expression analyses, OsCIPK9 was found to be mainly expressed in the roots and less expressed in mature leaves. Meanwhile, OsCIPK9 had the highest expression 6 h after salt treatment. In addition, we proved the interaction between OsCIPK9 and OsSOS3. The RNA-seq data showed that OsCIPK9 strongly responded to salt treatment, and the transporters related to salt tolerance may be downstream genes of OsCIPK9. Finally, haplotype analyses revealed that Hap6 and Hap8 mainly exist in indica, potentially providing a higher salt tolerance. Overall, a negative regulator of salt tolerance, OsCIPK9, which interacted with OsSOS3 similarly to OsCIPK24 and influenced salt-related transporters, was identified, and editing OsCIPK9 potentially could be helpful for breeding salt-tolerant rice. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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18 pages, 2797 KiB  
Article
Creation of Rice Doubled Haploids Resistant to Prolonged Flooding Using Anther Culture
by Pavel Kostylev, Nataliya Kalinina, Nataliya Vozhzhova, Valentina Golubova and Natalya Chertkova
Plants 2023, 12(21), 3681; https://doi.org/10.3390/plants12213681 - 25 Oct 2023
Viewed by 878
Abstract
Flood resistance in rice is very important in weed control, as weeds cannot overcome deep water. At present, there are no released varieties in Russia that would meet these requirements. The creation of such varieties will reduce production costs and pesticide load on [...] Read more.
Flood resistance in rice is very important in weed control, as weeds cannot overcome deep water. At present, there are no released varieties in Russia that would meet these requirements. The creation of such varieties will reduce production costs and pesticide load on the ecosystem. The object of the study was second-generation rice hybrids obtained by crossing the best varieties for economically valuable traits with samples carrying genes for resistance to prolonged flooding with water. To create double rice haploids resistant to prolonged flooding, the anther culture method was used, followed by molecular genetic evaluation of dihaploids for the presence of genes for resistance to prolonged flooding. An estimate of the growth energy under deep flooding was carried out according to our own method. As a result of the cultivation of anthers, 130 androgenic regenerated plants were obtained in 14 hybrid combinations. In terms of responsiveness to neoplasms, 60% of the panicles showed a positive result, while the rest 40% did not demonstrate callus formation. In total, 30 green regenerative lines were obtained from four rice hybrids, differing in visual morphological assessment. Large genotypic differences between the samples were revealed. These lines carry long-term flood resistance genes and can be used in rice breeding programs using dihaploids. As a result of the assessment of the growth energy in a number of obtained samples, the potential for rapid elongation of the first leaves, overcoming a large layer of water and accumulation of vegetative mass, was revealed. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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13 pages, 1912 KiB  
Article
Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations
by Fangjun Feng, Xiaosong Ma, Ming Yan, Hong Zhang, Daoliang Mei, Peiqing Fan, Xiaoyan Xu, Chunlong Wei, Qiaojun Lou, Tianfei Li, Hongyan Liu, Lijun Luo and Hanwei Mei
Plants 2023, 12(14), 2743; https://doi.org/10.3390/plants12142743 - 24 Jul 2023
Cited by 1 | Viewed by 1048
Abstract
Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population [...] Read more.
Mesocotyl elongation of rice seedlings is a key trait for deep sowing tolerance and well seedling establishment in dry direct sowing rice (DDSR) production. Subsets of the Rice Diversity Panel 1 (RDP1, 294 accessions) and Hanyou 73 (HY73) recombinant inbred line (RIL) population (312 lines) were screened for mesocotyl length (ML) via dark germination. Six RDP1 accessions (Phudugey, Kasalath, CA902B21, Surjamkuhi, Djimoron, and Goria) had an ML longer than 10 cm, with the other 19 accessions being over 4 cm. A GWAS in RDP1 detected 118 associated SNPs on all 12 chromosomes using a threshold of FDR-adjusted p < 0.05, including 11 SNPs on chromosomes 1, 4, 5, 7, 10, and 12 declared by −log10(P) > 5.868 as the Bonferroni-corrected threshold. Using phenotypic data of three successive trials and a high-density bin map from resequencing genotypic data, four to six QTLs were detected on chromosomes 1, 2, 5, 6, and 10, including three loci repeatedly mapped for ML from two or three replicated trials. Candidate genes were predicted from the chromosomal regions covered by the associated LD blocks and the confidence intervals (CIs) of QTLs and partially validated by the dynamic RNA-seq data in the mesocotyl along different periods of light exposure. Potential strategies of donor parent selection for seedling establishment in DDSR breeding were discussed. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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15 pages, 8628 KiB  
Article
Genetic Diversity and Association Mapping of Grain-Size Traits in Rice Landraces from the Honghe Hani Rice Terraces System in Yunnan Province
by Mengli Ma, En Lei, Tiantao Wang, Hengling Meng, Wei Zhang and Bingyue Lu
Plants 2023, 12(8), 1678; https://doi.org/10.3390/plants12081678 - 17 Apr 2023
Cited by 2 | Viewed by 1216
Abstract
The Honghe Hani Rice Terraces System (HHRTS) of Yunnan Province is an important agricultural and cultural heritage landscape. Until now, a large number of local rice landraces have been planted. Mining excellent genes contained in these landraces provides a reference for variety improvement [...] Read more.
The Honghe Hani Rice Terraces System (HHRTS) of Yunnan Province is an important agricultural and cultural heritage landscape. Until now, a large number of local rice landraces have been planted. Mining excellent genes contained in these landraces provides a reference for variety improvement and new variety breeding. In this study, 96 rice landraces collected from the Hani terraces were planted in Honghe Mengzi, Yunnan Province, in 2013, 2014, 2015, and 2021, and five major grain traits were measured and analyzed. The genomic variation of 96 rice landraces was scanned by 201 simple sequence repeat (SSR) markers. The genetic diversity, population structure, and genetic relationships of the natural population were analyzed. The mixed linear model (MLM) method of the TASSEL software was used to analyze the associations between markers and traits. A total of 936 alleles were amplified by 201 pairs of SSR primers. The average number of observed alleles (Na), the effective number of alleles (Ne), Shannon’s information index (I), heterozygosity (H), and the polymorphism information content (PIC) per marker were 4.66, 2.71, 1.08, 0.15, and 0.55, respectively. Ninety-six landraces were divided into two groups by population structure, clustering, and principal component analysis, and indica rice was the main group. The coefficients of variation of the five traits ranged from 6.80 to 15.24%, and their broad heritabilities were more than 70%. In addition, there were positive correlations among the same grain traits between different years. Through MLM analysis, 2, 36, 7, 7, and 4 SSR markers were significantly associated with grain length (GL), grain width (GW), grain thickness (GT), grain length–width ratio (LWR), and thousand-grain weight (TGW), respectively. The explanation rates of phenotypic variation were 16.31 (RM449, Chr. 1)—23.51% (RM316, Chr. 9), 10.84 (RM523, Chr. 3; RM161/RM305, Chr. 5)—43.01% (RM5496, Chr. 1), 11.98 (RM161/RM305, Chr. 5)—24.72% (RM275, Chr. 6), 12.68 (RM126, Chr. 8)—36.96% (RM5496, Chr. 1), and 17.65 (RM4499, Chr. 2)—26.32% (RM25, Chr. 8), respectively. The associated markers were distributed on 12 chromosomes of the genome. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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12 pages, 1963 KiB  
Article
Pyramiding of Multiple Genes to Improve Rice Blast Resistance of Photo-Thermo Sensitive Male Sterile Line, without Yield Penalty in Hybrid Rice Production
by Pei Peng, Haoyu Jiang, Lihua Luo, Changrong Ye and Yinghui Xiao
Plants 2023, 12(6), 1389; https://doi.org/10.3390/plants12061389 - 21 Mar 2023
Cited by 2 | Viewed by 1515
Abstract
Rice blast caused by pathogenic fungus Magnaporthe oryzae is one of the most serious diseases in rice. The pyramiding of effective resistance genes into rice varieties is a potential approach to reduce the damage of blast disease. In this study, combinations of three [...] Read more.
Rice blast caused by pathogenic fungus Magnaporthe oryzae is one of the most serious diseases in rice. The pyramiding of effective resistance genes into rice varieties is a potential approach to reduce the damage of blast disease. In this study, combinations of three resistance genes, Pigm, Pi48 and Pi49, were introduced into a thermo-sensitive genic male sterile (PTGMS) line Chuang5S through marker-assisted selection. The results showed that the blast resistance of improved lines increased significantly compared with Chuang5S, and the three gene pyramiding lines (Pigm + Pi48 + Pi49) had higher rice blast resistance level than monogenic line and digenic lines (Pigm +Pi48, Pigm + Pi49). The genetic backgrounds of the improved lines were highly similar (>90%) to the recurrent parent Chuang5S by using the RICE10K SNP chip. In addition, agronomic traits evaluation also showed pyramiding lines with two or three genes similar to Chuang5S. The yields of the hybrids developed from improved PTGMS lines and Chuang5S are not significantly different. The newly developed PTGMS lines can be practically used for the breeding of parental lines and hybrid varieties with broad spectrum blast resistance. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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28 pages, 7900 KiB  
Article
Isolation and Characterization of SPOTTED LEAF42 Encoding a Porphobilinogen Deaminase in Rice
by Lin Liu, Yunpeng Wang, Yunlu Tian, Shuang Song, Zewan Wu, Xin Ding, Hai Zheng, Yunshuai Huang, Shijia Liu, Xiaoou Dong, Jianmin Wan and Linglong Liu
Plants 2023, 12(2), 403; https://doi.org/10.3390/plants12020403 - 15 Jan 2023
Viewed by 1619
Abstract
The formation and development of chloroplasts play a vital role in the breeding of high-yield rice (Oryza sativa L.). Porphobilinogen deaminases (PBGDs) act in the early stage of chlorophyll and heme biosynthesis. However, the role of PBGDs in chloroplast development and chlorophyll [...] Read more.
The formation and development of chloroplasts play a vital role in the breeding of high-yield rice (Oryza sativa L.). Porphobilinogen deaminases (PBGDs) act in the early stage of chlorophyll and heme biosynthesis. However, the role of PBGDs in chloroplast development and chlorophyll production remains elusive in rice. Here, we identified the spotted leaf 42 (spl42) mutant, which exhibited a reddish-brown spotted leaf phenotype. The mutant showed a significantly lower chlorophyll content, abnormal thylakoid morphology, and elevated activities of reactive oxygen species (ROS)-scavenging enzymes. Consistently, multiple genes related to chloroplast development and chlorophyll biosynthesis were significantly down-regulated, whereas many genes involved in leaf senescence, ROS production, and defense responses were upregulated in the spl42 mutant. Map-based cloning revealed that SPL42 encodes a PBGD. A C-to-T base substitution occurred in spl42, resulting in an amino acid change and significantly reduced PBGD enzyme activity. SPL42 targets to the chloroplast and interacts with the multiple organelle RNA editing factors (MORFs) OsMORF8-1 and OsMORF8-2 to affect RNA editing. The identification and characterization of spl42 helps in elucidating the molecular mechanisms associated with chlorophyll synthesis and RNA editing in rice. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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15 pages, 2263 KiB  
Article
Mapping and Validation of qHD7b: Major Heading-Date QTL Functions Mainly under Long-Day Conditions
by Amir Sohail, Liaqat Shah, Ling Liu, Anowerul Islam, Zhengfu Yang, Qinqin Yang, Galal Bakr Anis, Peng Xu, Riaz Muhammad Khan, Jiaxin Li, Xihong Shen, Shihua Cheng, Liyong Cao, Yingxin Zhang and Weixun Wu
Plants 2022, 11(17), 2288; https://doi.org/10.3390/plants11172288 - 1 Sep 2022
Cited by 3 | Viewed by 1583
Abstract
Heading date (HD) is one of the agronomic traits that influence maturity, regional adaptability, and grain yield. The present study was a follow-up of a previous quantitative trait loci (QTL) mapping study conducted on three populations, which uncovered a total of 62 QTLs [...] Read more.
Heading date (HD) is one of the agronomic traits that influence maturity, regional adaptability, and grain yield. The present study was a follow-up of a previous quantitative trait loci (QTL) mapping study conducted on three populations, which uncovered a total of 62 QTLs associated with 10 agronomic traits. Two of the QTLs for HD on chromosome 7 (qHD7a and qHD7b) had a common flanking marker (RM3670) that may be due to tight linkage, and/or weakness of the statistical method. The objectives of the present study were to map QTLs associated with HD in a set of 76 chromosome segment substitution lines (CSSLs), fine map and validate one of the QTLs (qHD7b) using 2997 BC5F2:3 plants, and identify candidate genes using sequencing and expression analysis. Using the CSSLs genotyped with 120 markers and evaluated under two short-day and two long-day growing conditions, we uncovered a total of fourteen QTLs (qHD2a, qHD4a, qHD4b, qHD5a, qHD6a, qHD6b, qHD7b, qHD7c, qHD8a, qHD10a, qHD10b, qHD11a, qHD12a, and qHD12b). However, only qHD6a and qHD7b were consistently detected in all four environments. The phenotypic variance explained by qHD6a and qHD7b varied from 10.1% to 36.1% (mean 23.1%) and from 8.1% to 32.8% (mean 20.5%), respectively. One of the CSSL lines (CSSL52), which harbored a segment from the early heading XieqingzaoB (XQZB) parent at the qHD7b locus, was then used to develop a BC5F2:3 population for fine mapping and validation. Using a backcross population evaluated for four seasons under different day lengths and temperatures, the qHD7b interval was delimited to a 912.7-kb region, which is located between RM5436 and RM5499. Sequencing and expression analysis revealed a total of 29 candidate genes, of which Ghd7 (Os07g0261200) is a well-known gene that affects heading date, plant height, and grain yield in rice. The ghd7 mutants generated through CRISPR/Cas9 gene editing exhibited early heading. Taken together, the results from both the previous and present study revealed a consistent QTL for heading date on chromosome 7, which coincided not only with the physical position of a known gene, but also with two major effect QTLs that controlled the stigma exertion rate and the number of spikelets in rice. The results provide contributions to the broader adaptability of marker-assisted breeding to develop high-yield rice varieties. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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15 pages, 1813 KiB  
Article
YTH Domain Proteins Play an Essential Role in Rice Growth and Stress Response
by Weiwei Ma, Song Cui, Zhenfei Lu, Xiaofeng Yan, Long Cai, Yongfa Lu, Kefeng Cai, Huacheng Zhou, Rongrong Ma, Shirong Zhou and Xiaole Wang
Plants 2022, 11(17), 2206; https://doi.org/10.3390/plants11172206 - 25 Aug 2022
Cited by 6 | Viewed by 2197
Abstract
As the most prevalent epi-transcriptional modification, m6A modifications play essential roles in regulating RNA fate. The molecular functions of YTH521-B homology (YTH) domain proteins, the most known READER proteins of m6A modifications, have been well-studied in animals. Although plants [...] Read more.
As the most prevalent epi-transcriptional modification, m6A modifications play essential roles in regulating RNA fate. The molecular functions of YTH521-B homology (YTH) domain proteins, the most known READER proteins of m6A modifications, have been well-studied in animals. Although plants contain more YTH domain proteins than other eukaryotes, little is known about their biological importance. In dicot species Arabidopsis thaliana, the YTHDFA clade members ECT2/3/4 and CPSF30-L are well-studied and important for cell proliferation, plant organogenesis, and nitrate transport. More emphasis is needed on the biological functions of plant YTH proteins, especially monocot YTHs. Here we presented a detailed phylogenetic relationship of eukaryotic YTH proteins and clustered plant YTHDFC clade into three subclades. To determine the importance of monocot YTH proteins, YTH knockout mutants and RNAi-induced knockdown plants were constructed and used for phenotyping, transcriptomic analysis, and stress treatments. Knocking out or knocking down OsYTHs led to the downregulation of multicellular organismal regulation genes and resulted in growth defects. In addition, loss-of-function ythdfa mutants led to better salinity tolerance whereas ythdfc mutants were more sensitive to abiotic stress. Overall, our study establishes the functional relevance of rice YTH genes in plant growth regulation and stress response. Full article
(This article belongs to the Special Issue Molecular Breeding and Germplasm Improvement of Rice)
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