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14 pages, 2215 KiB

Open AccessArticle

Mapping of QTLs for Brown Rice Traits Based on Chromosome Segment Substitution Line in Rice (Oryza sativa L.)

by Yujia Leng, Lianmin Hong, Tao Tao, Qianqian Guo, Qingqing Yang, Mingqiu Zhang, Xinzhe Ren, Sukui Jin, Xiuling Cai and Jiping Gao

Agriculture 2023, 13(5), 928; https://doi.org/10.3390/agriculture13050928 - 24 Apr 2023

Viewed by 1175

Abstract

Brown rice traits are critical to both grain yield and quality. In the present study, the chromosome segment substitution lines (CSSLs) population derived from a cross between japonica Koshihikari and indica Nona Bokra was used to analyze the brown rice length (BRL), brown [...] Read more.

Brown rice traits are critical to both grain yield and quality. In the present study, the chromosome segment substitution lines (CSSLs) population derived from a cross between japonica Koshihikari and indica Nona Bokra was used to analyze the brown rice length (BRL), brown rice width (BRW), length–width ratio of brown rice (BLWR), brown rice thickness (BRT), brown rice perimeter (BRP), brown rice area (BRA), thousand-grain weight of brown rice (BRGW), brown rice ratio (BRR), taste value of brown rice (BTV), and water content of brown rice (BWC). Correlations analysis showed that most of the brown rice traits had significant correlations with each other, except for BRR, BTV, and BWC. A total of sixty-one QTLs for these traits were identified under three environments, which mapped to chromosomes 1, 2, 3, 5, 6, 7, 8, 10, 11, and 12, with the LOD ranging from 2.52 to 16.68 and accounting for 2.60 to 25.38% of the total phenotypic variations. Moreover, thirty pairs of epistatic interactions for BRL, BRW, BLWR, BRP, and BRA were estimated and distributed on all chromosomes except 10. These findings will provide a further understanding of the genetic basis of brown rice traits and facilitate the genetic improvement of rice yield and quality through breeding. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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18 pages, 3701 KiB

Open AccessArticle

Identification of Thermo-Sensitive Chloroplast Development Gene TSCD5 Required for Rice Chloroplast Development under High Temperature

by Shenglong Yang, Guonan Fang, Banpu Ruan, Anpeng Zhang, Yun Zhou, Guangji Ye, Wang Su, Heng Guo, Jian Wang and Zhenyu Gao

Agriculture 2023, 13(3), 563; https://doi.org/10.3390/agriculture13030563 - 26 Feb 2023

Viewed by 1457

Abstract

Chloroplasts are critical organelles for photosynthesis and play significant roles in plant growth and metabolism. High temperature is one of abiotic stresses affecting the growth and development of plants, involving chlorophyll biosynthesis and chloroplast development. It is well known that the methyl erythritol [...] Read more.

Chloroplasts are critical organelles for photosynthesis and play significant roles in plant growth and metabolism. High temperature is one of abiotic stresses affecting the growth and development of plants, involving chlorophyll biosynthesis and chloroplast development. It is well known that the methyl erythritol 4-phosphate (MEP) pathway is vital to photosynthesis and plant growth, and 1-deoxy-D-xylulose-5-phosphate synthase (DXS) is the enzyme that catalyze the first step of the MEP pathway. Although DXS has been widely studied in microbes and plants, no DXS gene has been identified in rice. Here, a novel thermo-sensitive chlorophyll-deficient 5 (tscd5) mutant was isolated in rice with decreased chlorophyll contents, impaired chloroplasts, and albino leaves at high temperature (35 °C). Fine mapping and DNA sequencing of TSCD5 found a missense mutation (G to A) in the sixth exon of LOC_Os05g33840 in tscd5. The TSCD5 gene encodes a 1-deoxy-D-xylulose-5-phosphate synthase 1 (OsDXS1) localized in chloroplast. Complementation tests and overexpression assay demonstrated that the mutation in LOC_Os05g33840 caused the tscd5 phenotype. qRT-PCR of TSCD5 showed it was constitutively expressed in all tissues, and its transcript amounts were reduced in tscd5 under high temperature. Here, TSCD5 is verified to be crucial to chloroplast development under high temperature in rice, which may facilitate the elucidation of the molecular mechanisms which underlie acclimation to high temperature stress in plants. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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14 pages, 3266 KiB

Open AccessArticle

Comparative Biochemical and Transcriptome Analyses Reveal Potential Candidate Genes Related to Pericarp Browning in Red Rice

by Gileung Lee, Jae Wan Park, Jisu Park, Ah-Reum Han, Min Jeong Hong, Yeong Deuk Jo, Jin-Baek Kim, Sang Hoon Kim and Hong-Il Choi

Agriculture 2023, 13(1), 183; https://doi.org/10.3390/agriculture13010183 - 11 Jan 2023

Viewed by 1478

Abstract

Proanthocyanidins (PAs) are major phytochemicals in rice, and accumulate abundantly in red pericarp (RP) rice. Consumers and rice breeders are increasingly showing interest in PAs because of their beneficial health effects; however, PA biosynthesis in rice is not well-understood. Therefore, to gain insights [...] Read more.

Proanthocyanidins (PAs) are major phytochemicals in rice, and accumulate abundantly in red pericarp (RP) rice. Consumers and rice breeders are increasingly showing interest in PAs because of their beneficial health effects; however, PA biosynthesis in rice is not well-understood. Therefore, to gain insights into this process, we performed comparative transcriptome analysis of grains harvested at 14 days after flowering (DAF; i.e., the stage at which active PA biosynthesis occurs without pericarp color change) and 28 DAF (the stage of late seed development with pericarp color change) from RP and white pericarp rice. In RP rice at 14 DAF, the expression levels of six structural genes (OsCHS, OsF3H, OsF3′H, OsDFR, OsANS, and OsLAR), one modification gene (OsUGT), and one transport gene (OsGSTU34) were significantly upregulated, along with the activation of Rc, the key regulator of PA accumulation in the pericarp. Functional enrichment analysis of 56 differentially expressed genes specifically upregulated in RP rice at 28 DAF revealed the presence of three laccase genes known to cause the browning reaction through oxidation. These results expand our understanding of PA biosynthesis in rice, and provide a genetic basis that will lead to further studies on the genes and underlying molecular mechanisms associated with this process. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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12 pages, 5792 KiB

Open AccessArticle

Drought Stress-Related Gene Identification in Rice by Random Walk with Restart on Multiplex Biological Networks

by Liu Zhu, Hongyan Zhang, Dan Cao, Yalan Xu, Lanzhi Li, Zilan Ning and Lei Zhu

Agriculture 2023, 13(1), 53; https://doi.org/10.3390/agriculture13010053 - 24 Dec 2022

Viewed by 1428

Abstract

Drought stress-related gene identification is vital in revealing the drought resistance mechanisms underlying rice and for cultivating rice-resistant varieties. Traditional methods, such as Genome-Wide Association Studies (GWAS), usually identify hundreds of candidate stress genes, and further validation by biological experiements is then time-consuming [...] Read more.

Drought stress-related gene identification is vital in revealing the drought resistance mechanisms underlying rice and for cultivating rice-resistant varieties. Traditional methods, such as Genome-Wide Association Studies (GWAS), usually identify hundreds of candidate stress genes, and further validation by biological experiements is then time-consuming and laborious. However, computational and prioritization methods can effectively reduce the number of candidate stress genes. This study introduces a random walk with restart algorithm (RWR), a state-of-the-art guilt-by-association method, to operate on rice multiplex biological networks. It explores the physical and functional interactions between biological molecules at different levels and prioritizes a set of potential genes. Firstly, we integrated a Protein–Protein Interaction (PPI) network, constructed by multiple protein interaction data, with a gene coexpression network into a multiplex network. Then, we implemented the RWR on multiplex networks (RWR-M) with known drought stress genes as seed nodes to identify potential drought stress-related genes. Finally, we conducted association analysis between the potential genes and the known drought stress genes. Thirteen genes were identified as rice drought stress-related genes, five of which have been reported in the recent literature to be involved in drought stress resistance mechanisms. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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13 pages, 4295 KiB

Open AccessArticle

Disruption of the Expression of the Cinnamoyl–CoA Reductase (CCR) Gene OsCCR18 Causes Male Sterility in Rice (Oryza sativa L. japonica)

by Xiangjian Pan, Xiaoyue Jiang, Junli Wen, Menghan Huang, Yanqing Wang, Mei Wang, Hui Dong and Qingpo Liu

Agriculture 2022, 12(10), 1685; https://doi.org/10.3390/agriculture12101685 - 13 Oct 2022

Viewed by 1490

Abstract

The biological process of anther development is very complex. It remains largely unclear how the cinnamoyl–CoA reductase (CCR) encoding genes function in the regulation of anther development in plants. Here, we establish that the CCR family gene OsCCR18 is essential for maintaining male [...] Read more.

The biological process of anther development is very complex. It remains largely unclear how the cinnamoyl–CoA reductase (CCR) encoding genes function in the regulation of anther development in plants. Here, we establish that the CCR family gene OsCCR18 is essential for maintaining male fertility in rice. The OsCCR18 transcripts were greatly abundant in the panicles at the S4 and S5 developmental stages in rice. The subcellular localization of OsCCR18 proteins was in the nucleus of the rice. The knockout of the OsCCR18 gene resulted in a severely abnormal degradation of the tapetum as well as the abnormal development of granular Ubisch bodies, leading to the inability to form normal pollen in the mutants. Compared with the wild–type (WT) rice, the osccr18 mutants had no visible pollen grains and had entirely male sterility. Furthermore, several anther development–related genes, including OsPDA1, OsDTD, OsC6, OsACOS12, OsTDR, OsWDA1, OsDPW, OsCYP703A3, and OsNOP, were significantly lower expressed in the panicles at the stages from S5 to S8 in the osccr18 mutants than in the WT plants. Additionally, hundreds of genes involved in phenylpropanoid biosynthesis, fatty acid synthesis and metabolism exhibited distinct expression patterns between the WT and mutants, which may be crucial for controlling anther development in rice. These findings add a new regulatory role to CCR family gene–mediated male fertility in rice. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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9 pages, 2304 KiB

Open AccessArticle

Development of Multiple-Heading-Date mtl Haploid Inducer Lines in Rice

by Jian Wang, Yuexuan Cao, Kejian Wang and Chaolei Liu

Agriculture 2022, 12(6), 806; https://doi.org/10.3390/agriculture12060806 - 2 Jun 2022

Cited by 3 | Viewed by 1938

Abstract

In vivo doubled haploid (DH) production based on crossing heterozygous germplasm with mtl haploid inducer lines promises to transform modern rice (Oryza sativa) breeding. However, this technology is limited, as haploid inducers and pollen acceptors have asynchronous heading dates. To address [...] Read more.

In vivo doubled haploid (DH) production based on crossing heterozygous germplasm with mtl haploid inducer lines promises to transform modern rice (Oryza sativa) breeding. However, this technology is limited, as haploid inducers and pollen acceptors have asynchronous heading dates. To address this obstacle, we developed a panel of multiple-heading-date mtl haploid inducer lines that produce pollen for more than 35 days. We edited the MTL gene in a hybrid rice with the CRISPR-Cas9 system. We then selected transgene-free homozygous mutants in the T₁ generation and reproduced to T₄ generation by single-seed descent method. We obtained 547 mtl haploid inducers with diverse heading dates (from 73 to 110 days) and selected 16 lines comprising a core population with continuous flowering. The seed-setting rate and haploid induction rate (HIR) of the core panel were 4.0–12.7% and 2.8–12.0%, respectively. Thus, our strategy of using multiple-heading-date mtl haploid inducers could accelerate the use of in vivo DH technology in rice breeding. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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13 pages, 2233 KiB

Open AccessArticle

Effects of Carbon and Nitrogen Fertilisers on Rice Quality of the OsNRT2.3b-Overexpressing Line

by Yong Zhang, Pulin Kong, Fan Wang, Limei Zhao, Kaiyun Qian, Yadong Zhang and Xiaorong Fan

Agriculture 2022, 12(6), 802; https://doi.org/10.3390/agriculture12060802 - 1 Jun 2022

Viewed by 1721

Abstract

Excessive nitrogen fertiliser use reduces nitrogen use efficiency and causes significant damage to the environment. Carbon fertilisers have the advantage of improving soil fertility; however, the effects of carbon and nitrogen fertilisers on rice yield and quality are not clear. In this study, [...] Read more.

Excessive nitrogen fertiliser use reduces nitrogen use efficiency and causes significant damage to the environment. Carbon fertilisers have the advantage of improving soil fertility; however, the effects of carbon and nitrogen fertilisers on rice yield and quality are not clear. In this study, the nitrogen-efficient line (OsNRT2.3b-overexpressing [O8]) and wild type (WT) were treated with different levels of nitrogen and carbon fertilisers under field conditions to study the effects of different fertilisation treatments on rice quality. The results showed that the appearance, nutrition, and taste qualities of O8 were generally high compared with WT under various fertilisation treatment conditions in 2019 and 2020. Compared with 90 kg/ha and 270 kg/ha nitrogen fertiliser, a single application of 90 kg/ha and 270 kg/ha carbon fertiliser significantly reduced the protein content of O8 by approximately 37.08% and 35.50% in 2019 and 2020, respectively, compared with WT, and improved the eating quality of O8 and WT. However, the replacement of nitrogen fertiliser with 20% carbon fertiliser did not improve the eating quality of O8 and WT compared with a single application of nitrogen fertiliser. This study identifies a high-quality gene, OsNRT2.3b, for breeding high-quality rice and provides a theoretical basis for obtaining high-quality rice and molecular breeding. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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12 pages, 3931 KiB

Open AccessArticle

Modulation of Growth Duration, Grain Yield and Nitrogen Recovery Efficiency by EMS Mutagenesis under OsNRT2.3b Overexpression Background in Rice

by Jingguang Chen, Fan Wang, Biqi Lei, Kaiyun Qian, Jia Wei and Xiaorong Fan

Agriculture 2022, 12(6), 799; https://doi.org/10.3390/agriculture12060799 - 31 May 2022

Viewed by 1692

Abstract

Growth duration is an important agronomic trait that determines the season and area of crop growth. Previous experiments showed that overexpression of nitrate transporter OsNRT2.3b significantly increased rice yield, nitrogen use efficiency, and growth duration. Through screening, we obtained four ethyl methanesulfonate (EMS)-mutagenized [...] Read more.

Growth duration is an important agronomic trait that determines the season and area of crop growth. Previous experiments showed that overexpression of nitrate transporter OsNRT2.3b significantly increased rice yield, nitrogen use efficiency, and growth duration. Through screening, we obtained four ethyl methanesulfonate (EMS)-mutagenized mutants with shorter growth duration compared with O8 of OsNRT2.3b overexpression line. The nitrogen translocation efficiency and physiological nitrogen use efficiency of the mutants were not significantly different from O8, which were increased by 24.4% and 14.2%, respectively compared with WT, but the growth duration of the mutant was significantly lower than O8. Analysis of O8 and mutants showed that the growth duration positively correlated with grain weight per panicle, grain yield, and nitrogen recovery efficiency. In conclusion, our results provide a new idea for balancing rice yield and growth duration. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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Review

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17 pages, 1718 KiB

Open AccessReview

Advances in the Biological Functions of Auxin Transporters in Rice

by Yaning Feng, Enhe Bayaer and Yanhua Qi

Agriculture 2022, 12(7), 989; https://doi.org/10.3390/agriculture12070989 - 9 Jul 2022

Cited by 5 | Viewed by 3914

Abstract

Auxin is the earliest discovered plant hormone, which plays important roles in each aspect of plant growth and development. There are two main pathways for auxin to be transported from the synthetic site (such as young leaves and terminal buds) to the active [...] Read more.

Auxin is the earliest discovered plant hormone, which plays important roles in each aspect of plant growth and development. There are two main pathways for auxin to be transported from the synthetic site (such as young leaves and terminal buds) to the active site. First, auxin is transported over long distances through phloem in an unfixed direction throughout the whole plant. Second, short-distance polar transport between cells requires the participation of auxin carriers, including unidirectional transport from stem tip to root and local unidirectional transport between tissues. Polar transport is critical to the establishment and maintenance of the auxin concentration gradient, which specifically regulates plant growth and development and responds to environmental changes. In this article, we reviewed the research progress of auxin transporters AUX1/LAX, PIN, and ABCB families, and some potential auxin transporters in rice growth and development, which provide information for the interpretation of biological functions of polar auxin transport families and lay a foundation for the genetic improvement of important agronomic traits in rice. Full article

(This article belongs to the Special Issue Genetics, Genomics and Breeding of Rice)

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