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Rice Molecular Breeding and Genetics

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (31 October 2022) | Viewed by 20111

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Dr. Deyong Ren

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State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou 310006, China
Interests: molecular genetics; crop breeding; gene cloning; genome editing; abiotic stress tolerance
Special Issues, Collections and Topics in MDPI journals

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Dear Colleagues,

Bread is an integral food source for people all over the world, and ensuring food security and successful agricultural production is a major issue related to economic development and social stability. With the increasing global population, climate warming, environmental pollution, and farmland degradation, global food production must increase by 70% by 2050 to ensure food supply. Germplasm resources are the "chips" that ensure the security of food production. However, their key problem concerns excavating and innovating gene and germplasm resources and breaking through the limitations of conventional breeding by using biological frontier technology for accurate and efficient breeding. In view of the urgent problems regarding yield and quality, the large-scale cracking of genetic code, exploring functional genes with important breeding value, and the in-depth analyses of their molecular regulatory networks are of great significance for breeding new varieties for the rapid aggregation of excellent alleles.

Dr. Deyong Ren
Guest Editor

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Keywords

molecular genetics and breeding
cell biology
genetic resource innovation
gene cloning
genome editing
abiotic stress tolerance

Published Papers (10 papers)

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Research

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13 pages, 1920 KiB

Open AccessArticle

The Pyramiding of Elite Allelic Genes Related to Grain Number Increases Grain Number per Panicle Using the Recombinant Lines Derived from Indica–japonica Cross in Rice

by Xuhui Liu, Xiaoxiao Deng, Weilong Kong, Tong Sun and Yangsheng Li

Int. J. Mol. Sci. 2023, 24(2), 1653; https://doi.org/10.3390/ijms24021653 - 14 Jan 2023

Viewed by 1521

Abstract

Indica(xian)-japonica(geng) hybrid rice has many heterosis traits that can improve rice yield. However, the traditional hybrid technology will struggle to meet future needs for the development of higher-yield rice. Available genomics resources can be used to efficiently understand the gene-trait association trait for rice breeding. Based on the previously constructed high-density genetic map of 272 high-generation recombinant inbred lines (RILs) originating from the cross of Luohui 9 (indica, as female) and RPY geng (japonica, as male) and high-quality genomes of parents, here, we further explore the genetic basis for an important complex trait: possible causes of grain number per panicle (GNPP). A total of 20 genes related to grains number per panicle (GNPP) with the differences of protein amino acid between LH9 and RPY were used to analyze genotype combinations, and PCA results showed a combination of PLY1, LAX1, DTH8 and OSH1 from the RPY geng with PYL4, SP1, DST and GNP1 from Luohui 9 increases GNPP. In addition, we also found that the combination of LAX1-T2 and GNP1-T3 had the most significant increase in GNPP. Notably, Molecular Breeding Knowledgebase (MBK) showed a few aggregated rice cultivars, LAX1-T2 and GNP1-T3, which may be a result of the natural geographic isolation between the two gene haplotypes. Therefore, we speculate that the pyramiding of japonica-type LAX-T2 with indica-type GNP1-T3 via hybridization can significantly improve rice yield by increasing GNPP. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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16 pages, 2554 KiB

Open AccessArticle

OsMKKK70 Negatively Regulates Cold Tolerance at Booting Stage in Rice

by Enyang Mei, Jiaqi Tang, Mingliang He, Zhiqi Liu, Xiaojie Tian and Qingyun Bu

Int. J. Mol. Sci. 2022, 23(22), 14472; https://doi.org/10.3390/ijms232214472 - 21 Nov 2022

Cited by 3 | Viewed by 1471

Abstract

Cold stress at the booting stage leads to a lower seed setting rate and seriously threatens the production of rice (Oryza sativa L.), which has become a major yield-limiting factor in higher-altitude and -latitude regions. Because cold tolerance at the booting stage (CTB) is a complex trait and is controlled by multiple loci, only a few genes have been reported so far. In this study, a function of OsMKKK70 (Mitogen Activated Protein Kinase Kinase Kinase 70) in response to CTB was characterized. OsMKKK70 expression was rapidly induced by cold stress at the booting stage. OsMKKK70 overexpression (OsMKKK70-OE) plants were more sensitive to cold stress at the booting stage with a lower seed setting and pollen fertility, but there was no significant difference between the osmkkk70 mutant and WT. Considering the effect of functional redundancy, we further tested the CTB response of osmkkk62/70 and osmkkk55/62/70, the double and triple mutants of OsMKKK70 with its closest homologs OsMKKK62 and OsMKKK55, and found that osmkkk62/70 and osmkkk55/62/70 displayed significantly increased CTB with a higher seed setting and pollen fertility, indicating that OsMKKK70 negatively regulates rice CTB. Moreover, under the low-temperature (LT) condition, the osmkkk62/70 mutant had slightly higher Gibberellin (GA) contents, increased expression of GA biosynthesis genes, and lower protein level of OsSLR1 in anthers than those in WT. By contrast, OsMKKK70-OE anther had a lower GA biosynthesis than that of WT. Together, these findings suggest that OsMKKK70 negatively regulates rice CTB by fine-tuning GA levels in anthers. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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18 pages, 6498 KiB

Open AccessArticle

Improvement of Rice Agronomic Traits by Editing Type-B Response Regulators

by Chuanhong Li, Chenbo Gong, Jiemin Wu, Linfeng Yang, Lei Zhou, Bian Wu, Liang Gao, Fei Ling, Aiqing You, Changyan Li and Yongjun Lin

Int. J. Mol. Sci. 2022, 23(22), 14165; https://doi.org/10.3390/ijms232214165 - 16 Nov 2022

Cited by 4 | Viewed by 1933

Abstract

Type-B response regulator proteins in rice contain a conserved receiver domain, followed by a GARP DNA binding domain and a longer C-terminus. Some type-B response regulators such as RR21, RR22 and RR23 are involved in the development of rice leaf, root, flower and trichome. In this study, to evaluate the application potential of type-B response regulators in rice genetic improvement, thirteen type-B response regulator genes in rice were respectively knocked out by using CRISPR/Cas9 genome editing technology. Two guide RNAs (gRNAs) were simultaneously expressed on a knockout vector to mutate one gene. T₀ transformed plants were used to screen the plants with deletion of large DNA fragments through PCR with specific primers. The mutants of CRISPR/Cas9 gene editing were detected by Cas9 specific primer in the T₁ generation, and homozygous mutants without Cas9 were screened, whose target regions were confirmed by sequencing. Mutant materials of 12 OsRRs were obtained, except for RR24. Preliminary phenotypic observation revealed variations of various important traits in different mutant materials, including plant height, tiller number, tillering angle, heading date, panicle length and yield. The osrr30 mutant in the T₂ generation was then further examined. As a result, the heading date of the osrr30 mutant was delayed by about 18 d, while the yield was increased by about 30%, and the chalkiness was significantly reduced compared with those of the wild-type under field high temperature stress. These results indicated that osrr30 has great application value in rice breeding. Our findings suggest that it is feasible to perform genetic improvement of rice by editing the type-B response regulators. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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10 pages, 2018 KiB

Open AccessArticle

Introgression of a Complex Genomic Structural Variation Causes Hybrid Male Sterility in GJ Rice (Oryza sativa L.) Subspecies

by Na Xu, Hai Xu, Zhengjin Xu, Fengcheng Li and Quan Xu

Int. J. Mol. Sci. 2022, 23(21), 12804; https://doi.org/10.3390/ijms232112804 - 24 Oct 2022

Viewed by 1215

Abstract

Hybrids between different subspecies of rice Oryza sativa L. commonly show hybrid sterility. Here we show that a widely planted commercial japonica/GJ variety, DHX2, exhibited hybrid sterility when crossing with other GJ varieties. Using the high-quality genome assembly, we identified three copies of the Sc gene in DHX2, whereas Nipponbare (Nip) had only one copy of Sc. Knocking out the extra copies of Sc in DHX2 significantly improved the pollen fertility of the F₁ plant of DHX2/Nip cross. The population structure analysis revealed that a slight introgression from Basmati1 might occur in the genome of DHX2. We demonstrated that both DHX2 and Basmati1 harbored three copies of Sc. Moreover, the introgression of GS3 and BADH2/fgr from Basmati1 confers the slender and fragrance grain of DHX2. These results add to our understanding of the hybrid sterility of inter-subspecies and intra-subspecies and may provide a novel strategy for hybrid breeding. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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14 pages, 3703 KiB

Open AccessArticle

Pyramiding of gn1a, gs3, and ipa1 Exhibits Complementary and Additive Effects on Rice Yield

by Meiru Li, Xiaoping Pan and Hongqing Li

Int. J. Mol. Sci. 2022, 23(20), 12478; https://doi.org/10.3390/ijms232012478 - 18 Oct 2022

Cited by 4 | Viewed by 1918

Abstract

Pyramiding of quantitative trait loci (QTLs) is a powerful approach in breeding super-high-yield varieties. However, the performance of QTLs in improving rice yield varies with specific genetic backgrounds. In a previous study, we employed the CRISPR/Cas9 system to target three yield-related genes, gn1a, gs3, and ipa1 in japonica ‘Zhonghua 11’, mutants of which featured large panicle, big grain, few sterile tillers, and thicker culm, respectively. In this paper, four pyramided lines, including gn1a-gs3, gn1a-ipa1, gs3-ipa1, and gn1a-gs3-ipa1, were further generated by conventional cross-breeding to be tested. Agronomic traits analysis showed that: (1) the stacking lines carried large panicles with an increased spikelet number in the main panicle or panicle; (2) the grain weight of the stacking lines, especially gs3-ipa1 and gn1a-gs3-ipa1, were heavier than those in single mutants; (3) both gn1a-gs3 and gs3-ipa1 produced more grain yield per plant than single mutant lines; (4) pyramided lines were higher than single mutants and transcriptome analysis found improved expression levels of genes related to lipid, amino acid, and carbohydrate transport and metabolism in lines pyramiding three mutant alleles, possibly as a result of complementary and additive effects. Accordingly, the alteration of gene-expression patterns relating to hormone signaling, plant growth, and seed size control was characterized in pyramided lines. The present study not only investigates the effects of pyramiding genes, but also may provide an efficient strategy for breeding super-high-yield rice by reducing the time cost of developing pyramided lines. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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13 pages, 3074 KiB

Open AccessArticle

OsTBP2.1, a TATA-Binding Protein, Alters the Ratio of OsNRT2.3b to OsNRT2.3a and Improves Rice Grain Yield

by Yong Zhang, Muhammad Faseeh Iqbal, Yulong Wang, Kaiyun Qian, Jinxia Xiang, Guohua Xu and Xiaorong Fan

Int. J. Mol. Sci. 2022, 23(18), 10795; https://doi.org/10.3390/ijms231810795 - 16 Sep 2022

Cited by 2 | Viewed by 1532

Abstract

The OsNRT2.3a and OsNRT2.3b isoforms play important roles in the uptake and transport of nitrate during rice growth. However, it is unclear which cis-acting element controls the transcription of OsNRT2.3 into these specific isoforms. In this study, we used a yeast one-hybrid assay to obtain the TATA-box binding protein OsTBP2.1, which binds to the TATA-box of OsNRT2.3, and verified its important role through transient expression and RNA-seq. We found that the TATA-box of OsNRT2.3 mutants and binding protein OsTBP2.1 together increased the transcription ratio of OsNRT2.3b to OsNRT2.3a. The overexpression of OsTBP2.1 promoted nitrogen uptake and increased rice yield compared with the wild-type; however, the OsTBP2.1 T-DNA mutant lines exhibited the opposite trend. Detailed analyses demonstrated that the TATA-box was the key cis-regulatory element for OsNRT2.3 to be transcribed into OsNRT2.3a and OsNRT2.3b. Additionally, this key cis-regulatory element, together with the binding protein OsTBP2.1, promoted the development of rice and increased grain yield. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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18 pages, 3174 KiB

Open AccessArticle

OsRAD51 Plays a Vital Role in Promoting Homologous Recombination in Rice Meiosis

by Xiaofei Liu, Yiwei Cao, Guijie Du, Chao Zhang, Meng Xu, Zhukuan Cheng, Yi Shen and Hengxiu Yu

Int. J. Mol. Sci. 2022, 23(17), 9906; https://doi.org/10.3390/ijms23179906 - 31 Aug 2022

Cited by 2 | Viewed by 1713

Abstract

Meiotic recombination plays a pivotal role in achieving accurate chromosomal segregation and increasing genetic diversity. In the homologous recombination pathway, the detailed mechanisms of how OsRAD51 and OsDMC1 work in rice meiosis remain to be explored. Here, we obtained different types of mutants for Osrad51a1, Osrad51a2, Osdmc1a, and Osdmc1b through CRISPR/Cas9. Both Osrad51a1 and Osrad51a2 exhibited normal vegetative growth and fertility. Osrad51 (Osrad51a1 Osrad51a2) mutant plants show normal vegetative growth but exhibit complete sterility, indicating that OsRAD51A1 and OsRAD51A2 are functionally redundant in rice fertility. In contrast to the wild type, Osrad51 chromosomes are not paired perfectly at pachytene and synaptonemal complex (SC) formation is deficient. Moreover, univalents and multivalent associations were observed at metaphase I, chromosome fragments presented at anaphase I, and crossover formation is basically suppressed in Osrad51 pollen mother cells (PMCs). OsRAD51 foci emerge at leptotene and disappear from late pachytene and chromosome localization of OsRAD51 depends on the formation of double-strand breaks (DSBs). Most OsRAD51 foci can co-localize with OsDMC1 signals. OsRAD51 is essential for the loading of OsDMC1 onto chromosomes, and vice versa. In addition, both OsRAD51 and OsDMC1 can interact with OsFIGL1 and OsBRCA2, two important components in rice meiosis. Moreover, the Osrad51 Osdmc1 (Osrad51a1 Osrad51a2 Osdmc1a Osdmc1b) quadruple mutant PMCs exhibited similar defective phenotypes as Osrad51 in homologous pairing, synapsis, and DSB repair. Taken together, our results suggest that the recombinases DMC1 and RAD51 may functionally depend on each other and play important roles in meiotic recombination during meiosis in rice. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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15 pages, 1288 KiB

Open AccessArticle

Target Lines for in Planta Gene Stacking in Japonica Rice

by Ruyu Li, Zhiguo Han, Qian Yin, Meiru Li, Mingyong Zhang, Zhenzhen Li, Ping Wang, Li Jiang and David W. Ow

Int. J. Mol. Sci. 2022, 23(16), 9385; https://doi.org/10.3390/ijms23169385 - 20 Aug 2022

Cited by 2 | Viewed by 1317

Abstract

The clustering of transgenes at a chromosome location minimizes the number of segregating loci that needs to be introgressed to field cultivars. Transgenes could be efficiently stacked through site-specific recombination and a recombinase-mediated in planta gene stacking process was described previously in tobacco based on the Mycobacteriophage Bxb1 site-specific integration system. Since this process requires a recombination site in the genome, this work describes the generation of target sites in the Japonica rice genome. Agrobacterium-mediated gene transfer yielded ~4000 random-insertion lines. Seven lines met the criteria of being single copy, not close to a centromere, not inserted within or close to a known gene or repetitive DNA, having precise recombination site sequences on both ends, and able to express the reporter gene. Each target line tested was able to accept the site-specific integration of a new gfp-containing plasmid and in three of those lines, we regenerated fertile plants. These target lines could be used as foundation lines for stacking new traits into Japonica rice. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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20 pages, 5645 KiB

Open AccessArticle

Transcriptional Comparison of Genes Associated with Photosynthesis, Photorespiration, and Photo-Assimilate Allocation and Metabolic Profiling of Rice Species

by Jae-Yeon Joo, Me-Sun Kim, Yong-Gu Cho, Alisdair R. Fernie and Jwakyung Sung

Int. J. Mol. Sci. 2022, 23(16), 8901; https://doi.org/10.3390/ijms23168901 - 10 Aug 2022

Cited by 3 | Viewed by 1709

Abstract

The ever-increasing human population alongside environmental deterioration has presented a pressing demand for increased food production per unit area. As a consequence, considerable research effort is currently being expended in assessing approaches to enhance crop yields. One such approach is to harness the allelic variation lost in domestication. This is of particular importance since crop wild relatives often exhibit better tolerance to abiotic stresses. Here, we wanted to address the question as to why wild rice species have decreased grain production despite being characterized by enhanced rates of photosynthesis. In order to do so, we selected ten rice species on the basis of the presence of genome information, life span, the prominence of distribution, and habitat type and evaluated the expression of genes in photosynthesis, photorespiration, sucrose and starch synthesis, sucrose transport, and primary and secondary cell walls. We additionally measured the levels of a range of primary metabolites via gas chromatography–mass spectrometry. The results revealed that the wild rice species exhibited not only higher photosynthesis but also superior CO₂ recovery by photorespiration; showed greater production of photosynthates such as soluble sugars and starch and quick transportation to the sink organs with a possibility of transporting forms such as RFOs, revealing the preferential consumption of soluble sugars to develop both primary and secondary cell walls; and, finally, displayed high glutamine/glutamic acid ratios, indicating that they likely exhibited high N-use efficiency. The findings from the current study thus identify directions for future rice improvement through breeding. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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Review

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17 pages, 10991 KiB

Open AccessReview

Molecular Events of Rice AP2/ERF Transcription Factors

by Wei Xie, Chaoqing Ding, Haitao Hu, Guojun Dong, Guangheng Zhang, Qian Qian and Deyong Ren

Int. J. Mol. Sci. 2022, 23(19), 12013; https://doi.org/10.3390/ijms231912013 - 10 Oct 2022

Cited by 21 | Viewed by 4888

Abstract

APETALA2/ethylene response factor (AP2/ERF) is widely found in the plant kingdom and plays crucial roles in transcriptional regulation and defense response of plant growth and development. Based on the research progress related to AP2/ERF genes, this paper focuses on the classification and structural features of AP2/ERF transcription factors, reviews the roles of rice AP2/ERF genes in the regulation of growth, development and stress responses, and discusses rice breeding potential and challenges. Taken together; studies of rice AP2/ERF genes may help to elucidate and enrich the multiple molecular mechanisms of how AP2/ERF genes regulate spikelet determinacy and floral organ development, flowering time, grain size and quality, embryogenesis, root development, hormone balance, nutrient use efficiency, and biotic and abiotic response processes. This will contribute to breeding excellent rice varieties with high yield and high resistance in a green, organic manner. Full article

(This article belongs to the Special Issue Rice Molecular Breeding and Genetics)

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