A novel discovery of a long terminal repeat retrotransposon-induced hybrid weakness in rice

Nadir, Sadia; Li, Wei; Zhu, Qian; Khan, Sehroon; Zhang, Hui; Wei, Zhen-Fei; Li, Meng-Ting; Zhou, Li; Li, Chengyun; Chen, Lijuan; Lee, Dong‐Sun

doi:10.1093/jxb/ery442

Cited by 8 publications

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References 49 publications

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“…A total of 5,722 F 2 plants were used for fine mapping, and the region of hwj1 and hwj2 were narrowed down to 65-kb on chromosome 1 ( Figure 5 ) and 145-kb on chromosome 11 ( Figure 6 ), respectively. In the 65-kb candidate region of hwj1 , 11 genes were predicted, and some of these are retrotransposon-like genes ( Nadir et al, 2019 ). On the other hand, the candidate region of hwj2 contains two disease resistance-related genes, thus these two genes were primary candidates for hwj2 .…”

Section: Discussionmentioning

confidence: 99%

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A Novel Combination of Genes Causing Temperature-Sensitive Hybrid Weakness in Rice

et al. 2022

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Reproductive isolation is an obstacle for plant breeding when a distant cross is demanded. It can be divided into two main types based on different growth stages: prezygotic isolation and postzygotic isolation. The hybrid weakness, which is a type of postzygotic isolation, can become a problem in crop breeding. In order to overcome reproductive isolation, it is necessary to elucidate its mechanism. In this study, genetic analysis for low temperature-dependent hybrid weakness was conducted in a rice F2 population derived from Taichung 65 (T65, Japonica) and Lijiangxintuanheigu (LTH, Japonica). The weak and severe weak plants in F2 showed shorter culm length, late heading, reduced panicle number, decreased grain numbers per panicle, and impaired root development in the field. Our result also showed that hybrid weakness was affected by temperature. It was observed that 24°C enhanced hybrid weakness, whereas 34°C showed recovery from hybrid weakness. In terms of the morphology of embryos, no difference was observed. Therefore, hybrid weakness affects postembryonic development and is independent of embryogenesis. The genotypes of 126 F2 plants were determined through genotyping-by-sequencing and a linkage map consisting of 862 single nucleotide polymorphism markers was obtained. Two major quantitative trait loci (QTLs) were detected on chromosomes 1 [hybrid weakness j 1 (hwj1)] and 11 [hybrid weakness j 2 (hwj2)]. Further genotyping indicated that the hybrid weakness was due to an incompatible interaction between the T65 allele of hwj1 and the LTH allele of hwj2. A large F2 populations consisting of 5,722 plants were used for fine mapping of hwj1 and hwj2. The two loci, hwj1 and hwj2, were mapped in regions of 65-kb on chromosome 1 and 145-kb on chromosome 11, respectively. For hwj1, the 65-kb region contained 11 predicted genes, while in the hwj2 region, 22 predicted genes were identified, two of which are disease resistance-related genes. The identified genes along these regions serve as preliminary information on the molecular networks associated with hybrid weakness in rice.

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Section: Discussionmentioning

confidence: 99%

“…A high temperature mostly inhibits disease resistance (e.g., Dropkin, 1969 ). Only a few genes for hybrid weakness in rice have been cloned ( Yamamoto et al, 2010 ; Chen et al, 2014 ; Nadir et al, 2019 ). Therefore, the molecular mechanism of hybrid weakness in rice still needs to be elucidated.…”

Section: Introductionmentioning

confidence: 99%

A Novel Combination of Genes Causing Temperature-Sensitive Hybrid Weakness in Rice

et al. 2022

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“…Duplicate recessive genes such as hwb1/hwb2 (Oka, 1957), hwd1/hwd2 (Fukuoka, Namai and Okuno, 1998) and hwe1/hwe2 (Kubo and Yoshimura, 2002) are known as causal genes for F2 hybrid weakness. Further analyses of Hbd2/Hbd3 (Yamamoto et al, 2007;, Hwi1/Hwi2 (Chen et al, 2014) and Hwc3 (Nadir et al, 2019) revealed that deleterious interactions between these genes cause an autoimmune response.…”

Section: Genetic Factors Affecting Sterility and Weakness In Hybridis...mentioning

confidence: 99%

Biology of Safflower (Carthamus tinctorius)

2022

Safety Assessment of Transgenic Organisms in the Environment, Volume 9

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From their first commercialisation in the mid-1990s, genetically engineered crops (also known as "transgenic" or "genetically modified" plants) have been approved for commercial release in an increasing number of countries, for planting, entering in the composition of foods and feeds, or use in industrial processing. The majority of these productions are for soybean, maize, cotton and rapeseed (canola) bearing pest resistance and herbicide tolerance traits, aiming to improve yields and reduce the costs of production. Other transgenic crops that are increasingly grown to date comprise lucerne (alfalfa), sugar beet, sugarcane, papaya, safflower, potato, eggplant, as well as pumpkin, apple and pineapple in smaller areas. Other traits are increasingly introduced in engineered plants, adapting them to biotic or abiotic stress, such as resistance to drought or tolerance to salt in the growing environment, or changing a characteristic, e.g. modified oil content, reduced lignin content, non-browning or nutritional quality (biofortification). Thus, transgenic crops, where adopted and available on the market, enlarge possibilities for farmers, industry and consumers. They can play a part in addressing global concerns such as the rising need for food and feed in the growing population context or the necessary adaptation of agriculture for better resilience to climate change.Modern biotechnologies are applied to plants (crops, flowers and trees) but also animals and micro-organisms. The safety of the resulting genetically engineered organisms, when released in the environment for their use in agriculture, forestry, fishery, the food and feed industry, biofuel production or other applications, represents a challenging issue. A scientifically sound approach to their risk assessment should inform biosafety regulators and support national decisions regarding their possible market release. Genetically engineered products are rigorously assessed by their developers during their elaboration and by governments when ready for commercial use, to ensure high safety standards for the environment, human food and animal feed. Such assessments are considered essential for healthy and sustainable agriculture, industry and trade.In 2019, according to the annual report of the International Service for the Acquisition of Agri-biotech Applications, the five main producers of genetically engineered crops were the United States, Brazil, Argentina, Canada and India (listed by decreasing area) covering a combined 170 million hectares representing more than 90% of the global transgenic crop area. Among the 29 countries having grown genetically engineered crops in that year, 9 of them were OECD countries, listed by decreasing area as follows: the

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“…The identification of non-additive expression (NAE) and allele-specific expression (ASE) patterns at the gene-level is usually used to reveal the molecular mechanism of heterosis [ 9 , 10 , 11 ]. Some hybrid-weakness-associated genes have been mapped in rice [ 13 , 14 , 15 , 16 , 17 ], but there are still no reports on the study of molecular mechanisms of hybrid weakness from the perspectives of NAE and ASE. To study the molecular mechanisms underlying hybrid weakness, we performed RNA-seq with three biological replicates of the panicles at the grain-filling stage of all the hybrid and parental lines collected in E3, where four hybrids (H2, H5, H6, and H8) displayed MPHW in GYPP ( Figure 1 c).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (Oryza sativa L.)

Wang

Xia

Huang

et al. 2022

Life

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The heterosis in hybrid rice is highly affected by the environment and hybrid weakness occurs frequently depending on the genotypes of the hybrid and its parents. Hybrid weakness was also observed in our field experiments on nine rice hybrids produced by 3 × 3 incomplete diallel crosses. Among the nine hybrids, five displayed mid-parent heterosis (MPH) for grain yield per plant, while four showed mid-parent hybrid weakness (MPHW). A sequencing analysis of transcriptomes in panicles at the seed-filling stage revealed a significant association between enhanced non-additive gene expression (NAE) and allele-specific gene expression (ASE) with hybrid weakness. High proportions of ASE genes, with most being of mono-allele expression, were detected in the four MPHW hybrids, ranging from 22.65% to 45.97%; whereas only 4.80% to 5.69% of ASE genes were found in the five MPH hybrids. Moreover, an independence test indicated that the enhancements of NAE and ASE in the MPHW hybrids were significantly correlated. Based on the results of our study, we speculated that an unfavorable environment might cause hybrid weakness by enhancing ASE and NAE at the transcriptome level.

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A novel discovery of a long terminal repeat retrotransposon-induced hybrid weakness in rice

Abstract: Gene activation caused by long terminal repeat retrotransposon insertion in the promoter of a newly discovered gene, Hwc3 , leads to hybrid weakness in intrasubspecific japonica rice hybrids.

Cited by 8 publications

References 49 publications

A Novel Combination of Genes Causing Temperature-Sensitive Hybrid Weakness in Rice

A Novel Combination of Genes Causing Temperature-Sensitive Hybrid Weakness in Rice

Biology of Safflower (Carthamus tinctorius)

Transcriptome Analyses Indicate Significant Association of Increased Non-Additive and Allele-Specific Gene Expression with Hybrid Weakness in Rice (Oryza sativa L.)

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