Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Qin, Peng; Lu, Hongwei; Du, Huilong; Wang, Hao; Chen, Weilan; Chen, Zhuo; He, Qiang; Ou, Shujun; Zhang, Hongyu; Li, Xuanzhao; Li, Xiuxiu; Li, Yan; Liao, Yi; Gao, Qiang; Tu, Bin; Yuan, Hua; Ma, Bo; Wang, Yuping; Qian, Yangwen; Fan, Shijun; Li, Weitao; Wang, Jing; He, Min; Yin, Junjie; Li, Ting; Jiang, Ning; Liang, Chengzhi; Li, Shigui

doi:10.1016/j.cell.2021.04.046

Cited by 298 publications

(332 citation statements)

References 93 publications

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“…Data reported in one study showed that nearly half of examined convalescent plasma samples (21 of 44; 48%) had no detectable neutralization activity against the B.1.351 variant 58 . Other experiments with pseudotyped viruses showed that the B.1.351 variant was also resistant to the neutralizing activity of some mAbs (12 of 17; 70%) 67 . Similarly, a study showed that the neutralizing effect of convalescent plasma collected from 14 individuals was strongly reduced against a live (authentic) B.1.351 virus (with IC 50 reduced by 3.2-fold to 41.9-fold relative to the first-wave virus) 68 .…”

Section: Variants Of Interest or Concernmentioning

confidence: 96%

SARS-CoV-2 variants, spike mutations and immune escape

et al. 2021

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Although most mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome are expected to be either deleterious and swiftly purged or relatively neutral, a small proportion will affect functional properties and may alter infectivity, disease severity or interactions with host immunity. The emergence of SARS-CoV-2 in late 2019 was followed by a period of relative evolutionary stasis lasting about 11 months. Since late 2020, however, SARS-CoV-2 evolution has been characterized by the emergence of sets of mutations, in the context of ‘variants of concern’, that impact virus characteristics, including transmissibility and antigenicity, probably in response to the changing immune profile of the human population. There is emerging evidence of reduced neutralization of some SARS-CoV-2 variants by postvaccination serum; however, a greater understanding of correlates of protection is required to evaluate how this may impact vaccine effectiveness. Nonetheless, manufacturers are preparing platforms for a possible update of vaccine sequences, and it is crucial that surveillance of genetic and antigenic changes in the global virus population is done alongside experiments to elucidate the phenotypic impacts of mutations. In this Review, we summarize the literature on mutations of the SARS-CoV-2 spike protein, the primary antigen, focusing on their impacts on antigenicity and contextualizing them in the protein structure, and discuss them in the context of observed mutation frequencies in global sequence datasets.

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Section: Variants Of Interest or Concernmentioning

confidence: 96%

SARS-CoV-2 variants, spike mutations and immune escape

et al. 2021

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“…With the development of high-throughput sequencing, molecular marker development has become feasible and convenient for various crops. Both small InDels and SVs have become powerful marker systems for genotyping, SV-GWAS, and map-based cloning analyses ( Qin et al, 2021 ). Previous studies on molecular marker development in Setaria have focused on SSR markers ( Jia et al, 2007 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1

et al. 2021

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Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the “Yugu1” variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, “SSR41”, which is morphologically similar to, and readily cross-pollinates with, “Yugu1”. High-throughput resequencing of “SSR41” identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used “SSR41” and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.

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“…The optimized grain development process should meet the best carbon and nitrogen nutrient flow from sink to source. Recently a new pan-genome analysis of 33 genetically diverse rice accessions revealed multiple structural variations and gene copy number variations information ( Qin et al, 2021 ). To utilize this variation information as well as phenotypical messages, researchers should accelerate molecular breeding work on these important traits.…”

Section: Conclusion and Perspectivementioning

confidence: 99%

Genetic and Molecular Factors Determining Grain Weight in Rice

et al. 2021

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Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.

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Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

Cited by 298 publications

References 93 publications

SARS-CoV-2 variants, spike mutations and immune escape

SARS-CoV-2 variants, spike mutations and immune escape

Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1

Genetic and Molecular Factors Determining Grain Weight in Rice

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