Publications by authors named "Haifei Hu"

15 Publications

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The chicken pan-genome reveals gene content variation and a promoter region deletion in IGF2BP1 affecting body size.

Mol Biol Evol 2021 Jul 30. Epub 2021 Jul 30.

College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China.

Domestication and breeding have reshaped the genomic architecture of chicken, but the retention and loss of genomic elements during these evolutionary processes remain unclear. We present the first chicken pan-genome constructed using 664 individuals, which identified an additional ∼66.5 Mb sequences that are absent from the reference genome (GRCg6a). The constructed pan-genome encoded 20,491 predicated protein-coding genes, of which higher expression level are observed in conserved genes relative to dispensable genes. Presence/absence variation (PAV) analyses demonstrated that gene PAV in chicken was shaped by selection, genetic drift, and hybridization. PAV-based GWAS identified numerous candidate mutations related to growth, carcass composition, meat quality, or physiological traits. Among them, a deletion in the promoter region of IGF2BP1 affecting chicken body size is reported, which is supported by functional studies and extra samples. This is the first time to report the causal variant of chicken body size QTL located at chromosome 27 which was repeatedly reported. Therefore, the chicken pan-genome is a useful resource for biological discovery and breeding. It improves our understanding of chicken genome diversity and provides materials to unveil the evolution history of chicken domestication.
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http://dx.doi.org/10.1093/molbev/msab231DOI Listing
July 2021

Amborella gene presence/absence variation is associated with abiotic stress responses that may contribute to environmental adaptation.

New Phytol 2021 Jul 30. Epub 2021 Jul 30.

School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, 6009, Australia.

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http://dx.doi.org/10.1111/nph.17658DOI Listing
July 2021

Sequencing the USDA core soybean collection reveals gene loss during domestication and breeding.

Plant Genome 2021 Jun 24:e20109. Epub 2021 Jun 24.

Div. of Plant Sciences and National Ctr. for Soybean Biotechnology, Univ. of Missouri, Columbia, MO, USA.

The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.
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http://dx.doi.org/10.1002/tpg2.20109DOI Listing
June 2021

Genome-Wide Identification and Expansion Patterns of SULTR Gene Family in Gramineae Crops and Their Expression Profiles under Abiotic Stress in .

Genes (Basel) 2021 04 23;12(5). Epub 2021 Apr 23.

State Key Laboratory of Hybrid Rice, Key Laboratory for Research and Utilization of Heterosis in Indica Rice of Ministry of Agriculture, Engineering Research Center for Plant Biotechnology and Germplasm Utilization of Ministry of Education, College of Life Science, Wuhan University, Wuhan 430072, China.

Sulfate transporters (SULTRs), also known as H/SO symporters, play a key role in sulfate transport, plant growth and stress responses. However, the evolutionary relationships and functional differentiation of SULTRs in Gramineae crops are rarely reported. Here, 111 SULTRs were retrieved from the genomes of 10 Gramineae species, including , , , , , , , and ( ssp. indica and ssp. japonica). The SULTRs were clustered into five clades based on a phylogenetic analysis. Syntheny analysis indicates that whole-genome duplication/segmental duplication and tandem duplication events were essential in the SULTRs family expansion. We further found that different clades and orthologous groups of SULTRs were under a strong purifying selective force. Expression analysis showed that rice SULTRs with high-affinity transporters are associated with the functions of sulfate uptake and transport during rice seedling development. Furthermore, using ssp. indica as a model species, we found that was significantly upregulated under salt stress, while and showed remarkable upregulation under high temperature, low-selenium and drought stresses. and were upregulated under both low-selenium and high-selenium stresses. This study illustrates the expression and evolutionary patterns of the SULTRs family in Gramineae species, which will facilitate further studies of SULTR in other Gramineae species.
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http://dx.doi.org/10.3390/genes12050634DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8146379PMC
April 2021

Crop breeding for a changing climate: integrating phenomics and genomics with bioinformatics.

Theor Appl Genet 2021 Jun 14;134(6):1677-1690. Epub 2021 Apr 14.

School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, 6009, Australia.

Key Message: Safeguarding crop yields in a changing climate requires bioinformatics advances in harnessing data from vast phenomics and genomics datasets to translate research findings into climate smart crops in the field. Climate change and an additional 3 billion mouths to feed by 2050 raise serious concerns over global food security. Crop breeding and land management strategies will need to evolve to maximize the utilization of finite resources in coming years. High-throughput phenotyping and genomics technologies are providing researchers with the information required to guide and inform the breeding of climate smart crops adapted to the environment. Bioinformatics has a fundamental role to play in integrating and exploiting this fast accumulating wealth of data, through association studies to detect genomic targets underlying key adaptive climate-resilient traits. These data provide tools for breeders to tailor crops to their environment and can be introduced using advanced selection or genome editing methods. To effectively translate research into the field, genomic and phenomic information will need to be integrated into comprehensive clade-specific databases and platforms alongside accessible tools that can be used by breeders to inform the selection of climate adaptive traits. Here we discuss the role of bioinformatics in extracting, analysing, integrating and managing genomic and phenomic data to improve climate resilience in crops, including current, emerging and potential approaches, applications and bottlenecks in the research and breeding pipeline.
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http://dx.doi.org/10.1007/s00122-021-03820-3DOI Listing
June 2021

Geometric layout optimization of a large aperture thin elliptical mirror's axial and lateral support.

Appl Opt 2021 Apr;60(10):2861-2869

For passive support of large aperture telescopes, geometric layout optimization of the support structure is one of the most critical tasks because it determines the deformation of the mirror under gravity, which affects the wavefront aberration and image quality of the system. Due to a lack of symmetry, the optimization of an elliptical mirror support can be much more complex compared with circular mirrors. We optimize the geometric layout of axial and lateral support for the tertiary mirror of the Thirty Meter Telescope (TMT). Based on a theoretical analysis of the whiffletree principle, a parametric model of axial support is established based on the multi-point constraint equation. The mirror deformation SlopeRMS of the tertiary mirror under vertical gravity is used as the optimization target of the support points. The axial support point position is optimized by means of a simulated annealing algorithm and a mirror-deformed post-processing script written in Python. The TMT tertiary mirror lateral support also uses the whiffletree structure, and its in-plane layout affects the system's resonant modal frequency and the maximum load at each point. According to the dynamic equation and the static principle, the lateral support optimization model is established. The first-order resonant frequency and maximum load of the support point are the objective function. Through optimization of the axial and lateral support, the overall mirror distortion of the system is improved.
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http://dx.doi.org/10.1364/AO.405638DOI Listing
April 2021

Stress-induced deformation of the coating on large lightweight freeform optics.

Opt Express 2021 Feb;29(4):4755-4769

Large aperture, lightweight optics are frequently utilized in modern optical systems. However, despite the use of advanced techniques for developing their materials, fabrication, and mechanical structure, the coatings placed on the substrates induce slight lattice mismatches and increase the thin film stress on polished surfaces. This significantly distorts nano-accuracy optical surfaces, especially on lightweight freeform surfaces. In this study, we construct a finite element model (FEM) and a ray tracing model to estimate the impact of the stress-induced deformation of the coating on a 1.5m class lightweight silicon carbine (SiC) mirror with a freeform surface. Our simulation results are within 10% deviation from the experimental results, and the deformation texture map matches these results as well. We discuss several possible strategies to overcome stress-induced deformation, including fabrication pre-compensation, lightweight structure redesign, and an inverse print-through effect.
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http://dx.doi.org/10.1364/OE.414953DOI Listing
February 2021

Equivalent thin-plate method for stressed mirror polishing of an off-axis aspheric silicon carbide lightweight mirror.

Opt Express 2020 Nov;28(24):36413-36431

No physical model of stressed mirror polishing, based on the small deflection and deformation of elastic thin plates, has been applied in processing lightweight mirrors. We propose an equivalent thin-plate method for the stressed loading of lightweight mirrors for the first time. Stressed loading and polishing of an aspheric lightweight mirror are simulated using the small-deflection deformation theory of an elastic thin plate. We simulate off-axis aspheric silicon carbide (SiC) lightweight mirrors with three different structures, determining the corresponding equivalent thickness plate in a lightweight structure with a nearly uniform surface density distribution and isotropic bending properties. We then establish a residual removal model of a stressed polishing surface, design the stressed loading equipment, and propose an iterative method for stressed polishing of an off-axis aspheric SiC lightweight mirror. The results demonstrate that it is feasible to choose a lightweight structure that performs full-aperture stressed polishing on off-axis aspheric lightweight mirrors consisting of SiC or other materials.
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http://dx.doi.org/10.1364/OE.410759DOI Listing
November 2020

Comprehensive study of the rapid stressed mirror polishing method for off-axis aspheric SiC thin-plate mirrors.

Opt Express 2020 Oct;28(22):32802-32818

In this study, the stressed mirror polishing technique is used to perform off-axis aspheric silicon carbide (SiC) mirror full-aperture polishing for the first time. Mechanical and optical parameter analysis methods have been proposed. A medium-diameter off-axis aspheric SiC thin-plate mirror is used as a scaling model for an optical system mirror. A full diameter polishing simulation was completed, and a conceptual design for stress loading equipment is presented. An initial aspheric surface method for stressed mirror polishing of an off-axis aspheric SiC thin-plate mirror, providing a reference for rapid stress mirror polishing of SiC mirrors, is also proposed.
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http://dx.doi.org/10.1364/OE.405389DOI Listing
October 2020

Legume Pangenome Construction Using an Iterative Mapping and Assembly Approach.

Methods Mol Biol 2020 ;2107:35-47

School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia.

A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.
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http://dx.doi.org/10.1007/978-1-0716-0235-5_3DOI Listing
January 2021

Construction and comparison of three reference-quality genome assemblies for soybean.

Plant J 2019 12 28;100(5):1066-1082. Epub 2019 Oct 28.

Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA.

We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
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http://dx.doi.org/10.1111/tpj.14500DOI Listing
December 2019

Relay optical function and pre-construction results of a Giant Steerable Science Mirror for a thirty meter telescope.

Opt Express 2019 May;27(10):13991-14008

The Giant Steerable Science Mirror (GSSM) is the tertiary mirror system of the Thirty Meter Telescope (TMT) that relays optical beams from the secondary mirror to active instruments on Nasmyth platforms. One of the key technologies involved in GSSM functions is the error budget allocation from the system engineering of TMT. A novel approach of error analysis and allocation with strong adaptability, which is based on normalized Point Source Sensitivity (PSSn), is proposed. The relay optical function including the quality of the wavefront, the rationality of the mechanism, and the stability of the light were achieved based on the proposed method. The experiments validate the proposed method.
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http://dx.doi.org/10.1364/OE.27.013991DOI Listing
May 2019

Designing a hydraulic support system for large monolithic mirror's precise in-situ testing-polishing iteration.

Opt Express 2019 Feb;27(3):3746-3760

In order to improve the fabrication efficiency and testing accuracy of meter-scale, large monolithic mirrors, hydraulic support units (HSUs) are commonly used. However, the challenges to reduce the disparity of the HSUs' stiffness and keep the stability of the mirrors' altitude are hard to resolve, especially for large-scale mirrors. In this paper, we found the air ratio of the working fluid for HSUs is a key factor for designing the HSUs to resolve the challenges from the analytical solution that we derived for supporting large mirrors. Here we designed, tested and fabricated dozens of HSUs and used a four-meter SiC mirror, the world's largest monolithic SiC reported in public, as a study case. It shows that the stiffness values of grouped HSUs vary within ± 3%, and the mirror's reference surface PV is less than 20 μm in 10 days, producing a mirror tip/tilt angle less than 1.5″. The surface error of the supported mirror is about 20 nm, which is very close to the ideal case where uniform stiffness exists, for randomly distributed stiffness values. The repeatability of the in-situ interferometric test with 0.019 λ RMS of the mirror surface demonstrates the supporting system in a high precision. With such a supporting system, the fabrication process of this mirror was estimated to be sped up by 47% compared to the typical fabricating iteration. With minor modifications and easy extensions, such a novel supporting system could be used widely for many in-situ, high-quality fabricating-testing processes.
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http://dx.doi.org/10.1364/OE.27.003746DOI Listing
February 2019

Economic fabrication of a novel hybrid planar Grating/Fresnel lens for miniature spectrometers.

Opt Express 2018 Mar;26(5):6079-6089

We propose a new technique to fabricate a highly specialized optical element, a hybrid planar Grating/Fresnel lens (G-Fresnel), which is particularly useful to improve or enable more-affordable miniature/portable spectrometers. Both the Fresnel and the grating surface are fabricated simultaneously by sandwiching soft PDMS between a hard grating and a pre-replicated negative Fresnel surface. Several adhesion reduction techniques are also investigated that help improve both fabrication and cost efficiency (by reducing the solidification time) as well as the lifetime of the mold. Alignment errors are systematically analyzed, and their effects on the G-Fresnel lens evaluated. A compact fabrication platform was built, which is smaller than a volume of 160☓140☓106 mm to fit into a conventional vacuum drying oven, for the fabrication of a G-Fresnel lens with a diameter of 25.4 mm, an equivalent focal length of 25 mm, and a blazed grating pattern with 600 lines/mm spacing. The solidification time was reduced to 2 hours thanks to the improved adhesion reduction technique that permits a PDMS drying-temperature as high as 65 °C. The fabricated G-Fresnel lens was evaluated with regard to both geometrical fabrication precision and optical performance. The measured results, using a step gauge and atomic force microscopy, confirm that this replication technique produces high-quality replicates of the master surface-profile. Furthermore, a prototype spectrometer that uses a G-Fresnel lens was built and evaluated. The spectrometer fits within a volume of about 100 mm☓50 mm☓30 mm, and it operates across a wide wavelength spectrum (450 nm to 650 nm). Both the calculation based on the optical software ZEMAX and the experimental measurements are consistent and confirm that the spectrometer with the G-Fresnel lens can provide a spectral resolution of better than 1.2nm.
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http://dx.doi.org/10.1364/OE.26.006079DOI Listing
March 2018

Single-Cell Genomic Analysis in Plants.

Genes (Basel) 2018 Jan 22;9(1). Epub 2018 Jan 22.

School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia.

Individual cells in an organism are variable, which strongly impacts cellular processes. Advances in sequencing technologies have enabled single-cell genomic analysis to become widespread, addressing shortcomings of analyses conducted on populations of bulk cells. While the field of single-cell plant genomics is in its infancy, there is great potential to gain insights into cell lineage and functional cell types to help understand complex cellular interactions in plants. In this review, we discuss current approaches for single-cell plant genomic analysis, with a focus on single-cell isolation, DNA amplification, next-generation sequencing, and bioinformatics analysis. We outline the technical challenges of analysing material from a single plant cell, and then examine applications of single-cell genomics and the integration of this approach with genome editing. Finally, we indicate future directions we expect in the rapidly developing field of plant single-cell genomic analysis.
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http://dx.doi.org/10.3390/genes9010050DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5793201PMC
January 2018
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