Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice

Jia, Xianqing; Yu, Luyao; Tang, Menglu; Tian, Dacheng; Yang, Sihai; Zhang, Xiaohui; Traw, M. Brian

doi:10.1016/j.jplph.2020.153141

Cited by 13 publications

(7 citation statements)

References 68 publications

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“…Liang-You-Pei-Jiu (LYP9) (F 1 ) plants were obtained from the cross of 2 commercially important and well-studied semidwarf rice varieties, namely PA64s (female) and 93-11 (male) [95]. To meet the need for a large number of LYP9 seeds, PA64s, a sterile line of PA64, was used to process a large-scale cross with 93-11, which is photoperiod and thermosensitive genic male sterile.…”

Section: Rice Materials and Samplingmentioning

confidence: 99%

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

et al. 2021

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In contrast to common meiotic gene conversion, mitotic gene conversion, because it is so rare, is often ignored as a process influencing allelic diversity. We show that if there is a large enough number of premeiotic cell divisions, as seen in many organisms without early germline sequestration, such as plants, this is an unsafe position. From examination of 1.1 million rice plants, we determined that the rate of mitotic gene conversion events, per mitosis, is 2 orders of magnitude lower than the meiotic rate. However, owing to the large number of mitoses between zygote and gamete and because of long mitotic tract lengths, meiotic and mitotic gene conversion can be of approximately equivalent importance in terms of numbers of markers converted from zygote to gamete. This holds even if we assume a low number of premeiotic cell divisions (approximately 40) as witnessed in Arabidopsis. A low mitotic rate associated with long tracts is also seen in yeast, suggesting generality of results. For species with many mitoses between each meiotic event, mitotic gene conversion should not be overlooked.

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Section: Rice Materials and Samplingmentioning

confidence: 99%

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

et al. 2021

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“…Library construction of RNA and sequencing were carried out by BGI-Shenzhen, with paired-end (2 9 150 bp) sequencing on an Illumina HiSeq 4000 platform. RNA-seq analysis was performed by the pipelines described previously (Jia et al, 2020). Briefly, the paired-end reads were mapped against a rice reference genome (IRGSP1.0) using HISAT2 (version 2.1.0) (Kim et al, 2015).…”

Section: Expression Profiles Of Dof Genesmentioning

confidence: 99%

“…Field experiments with the edited and control lines were conducted in the experimental field of Nanjing University, Nanjing, China, in 2017 and 2018. The cultivation method and field management were as described previously (Jia et al, 2020). Measurement of plant height and tiller number was performed at 14 days after WT lines heading, and an average of six plants were measured for each Dof gene (Table 2).…”

Section: Phenotypic Measurement Of Crispr/cas9 Edited Linesmentioning

confidence: 99%

Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication

Zhang

et al. 2021

The Plant Journal

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Whole genome duplication (WGD) in plants is typically followed by genomic downsizing, where large portions of the new genome are lost. Whether this downsizing is accompanied by increased or decreased evolutionary rates of the remaining genes is poorly known, not least because homeolog pairings are often obscured by chromosomal rearrangement. Here, we use the newly published genome from a sedge, namely Kobresia littledalei, and CRISPR/Cas-9 editing to investigate how the Rho WGD event 70 million years ago (MYA) affected transcription factor evolutionary rates, fates, and function in rice (Oryza sativa) and sorghum (Sorghum bicolor). We focus on the 30-member DNA-binding with one zinc finger (Dof) transcription factor family in both crops due to their agronomic importance. Using the known speciation dates of rice from Kobresia (97 MYA) and sorghum (50 MYA), we find that rates of amino acid substitution in the critical Dof domain region were over twofold higher during the 20-million-year period following the WGD than before or afterward. Through comparison of synteny blocks, we report that at least 11% of Dof genes were purged from 70 to 50 MYA, while only 6% have been lost in the most recent 50-million-year interval. CRISPR/Cas9 editing revealed widespread fitness-related defects in flowering and lack of redundancy of paired members, as well as significant differences in expression between gene pairs. Together these findings demonstrate the strength of Dof genes as a model for deep evolutionary study and offer one of the most detailed portraits yet of the Rho WGD impact on a gene lineage.

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“…In addition to the widely used GA-insensitive dwarfing genes Rht-B1 and Rht-D1 , there is a wide spectrum of loci that can be used to modulate plant height [ 50 ]. Rice sd1 was initially defined as a semi-dwarfism gene encoding a defective enzyme in the GA biosynthetic pathway [ 41 , 51 , 52 , 53 , 54 ], and pleiotropic changes were revealed by the recovery of the wild-type cultivar following restoration of the sd1 mutant protein to wild-type in rice [ 54 ].…”

Section: The Green Revolution and Its Genesmentioning

confidence: 99%

Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population?

Buzdin

Патрушев

2021

Plants

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Growing scientific evidence demonstrates unprecedented planetary-scale human impacts on the Earth’s system with a predicted threat to the existence of the terrestrial biosphere due to population increase, resource depletion, and pollution. Food systems account for 21–34% of global carbon dioxide (CO2) emissions. Over the past half-century, water and land-use changes have significantly impacted ecosystems, biogeochemical cycles, biodiversity, and climate. At the same time, food production is falling behind consumption, and global grain reserves are shrinking. Some predictions suggest that crop yields must approximately double by 2050 to adequately feed an increasing global population without a large expansion of crop area. To achieve this, “quantum-leap” improvements in crop cultivar productivity are needed within very narrow planetary boundaries of permissible environmental perturbations. Strategies for such a “quantum-leap” include mutation breeding and genetic engineering of known crop genome sequences. Synthetic biology makes it possible to synthesize DNA fragments of any desired sequence, and modern bioinformatics tools may hopefully provide an efficient way to identify targets for directed modification of selected genes responsible for known important agronomic traits. CRISPR/Cas9 is a new technology for incorporating seamless directed modifications into genomes; it is being widely investigated for its potential to enhance the efficiency of crop production. We consider the optimism associated with the new genetic technologies in terms of the complexity of most agronomic traits, especially crop yield potential (Yp) limits. We also discuss the possible directions of overcoming these limits and alternative ways of providing humanity with food without transgressing planetary boundaries. In conclusion, we support the long-debated idea that new technologies are unlikely to provide a rapidly growing population with significantly increased crop yield. Instead, we suggest that delicately balanced humane measures to limit its growth and the amount of food consumed per capita are highly desirable for the foreseeable future.

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Pleiotropic changes revealed by in situ recovery of the semi-dwarf gene sd1 in rice

Cited by 13 publications

References 68 publications

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

Mitotic gene conversion can be as important as meiotic conversion in driving genetic variability in plants and other species without early germline segregation

Ancient rapid functional differentiation and fixation of the duplicated members in rice Dof genes after whole genome duplication

Will Plant Genome Editing Play a Decisive Role in “Quantum-Leap” Improvements in Crop Yield to Feed an Increasing Global Human Population?

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