Pangenomics in crop improvement—from coding structural variations to finding regulatory variants with pangenome graphs

The Brassica genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of Brassica genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for B. rapa, B. oleracea and B. napus. Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important Brassica genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible individuals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA diversity characterised in the limited number of Brassica assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA diversity, greatly expanding breeding resources that can be utilised for crop improvement.

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CicerSpTEdb: A web-based database for high-resolution genome-wide identification of transposable elements in Cicer species

PLoS ONE ◽

10.1371/journal.pone.0259540 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0259540

Author(s):

Morad M. Mokhtar ◽

Alsamman M. Alsamman ◽

Haytham M. Abd-Elhalim ◽

Achraf El Allali

Keyword(s):

Transposable Elements ◽

Crop Improvement ◽

Draft Genome ◽

Structural Variations ◽

Web Based ◽

Cicer Echinospermum ◽

Genome Wide ◽

Cicer Species ◽

Trait Improvement ◽

Made In

Recently, Cicer species have experienced increased research interest due to their economic importance, especially in genetics, genomics, and crop improvement. The Cicer arietinum, Cicer reticulatum, and Cicer echinospermum genomes have been sequenced and provide valuable resources for trait improvement. Since the publication of the chickpea draft genome, progress has been made in genome assembly, functional annotation, and identification of polymorphic markers. However, work is still needed to identify transposable elements (TEs) and make them available for researchers. In this paper, we present CicerSpTEdb, a comprehensive TE database for Cicer species that aims to improve our understanding of the organization and structural variations of the chickpea genome. Using structure and homology-based methods, 3942 C. echinospermum, 3579 C. reticulatum, and 2240 C. arietinum TEs were identified. Comparisons between Cicer species indicate that C. echinospermum has the highest number of LTR-RT and hAT TEs. C. reticulatum has more Mutator, PIF Harbinger, Tc1 Mariner, and CACTA TEs, while C. arietinum has the highest number of Helitron. CicerSpTEdb enables users to search and visualize TEs by location and download their results. The database will provide a powerful resource that can assist in developing TE target markers for molecular breeding and answer related biological questions. Database URL: http://cicersptedb.easyomics.org/index.php

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High-quality genome assembly and resequencing of modern cotton cultivars provide resources for crop improvement

Nature Genetics ◽

10.1038/s41588-021-00910-2 ◽

2021 ◽

Author(s):

Zhiying Ma ◽

Yan Zhang ◽

Liqiang Wu ◽

Guiyin Zhang ◽

Zhengwen Sun ◽

...

Keyword(s):

Textile Industry ◽

Large Scale ◽

Natural Fiber ◽

Agronomic Traits ◽

Fiber Quality ◽

Crop Improvement ◽

Structural Variations ◽

High Quality ◽

Species Formation

AbstractCotton produces natural fiber for the textile industry. The genetic effects of genomic structural variations underlying agronomic traits remain unclear. Here, we generate two high-quality genomes of Gossypium hirsutum cv. NDM8 and Gossypium barbadense acc. Pima90, and identify large-scale structural variations in the two species and 1,081 G. hirsutum accessions. The density of structural variations is higher in the D-subgenome than in the A-subgenome, indicating that the D-subgenome undergoes stronger selection during species formation and variety development. Many structural variations in genes and/or regulatory regions potentially influencing agronomic traits were discovered. Of 446 significantly associated structural variations, those for fiber quality and Verticillium wilt resistance are located mainly in the D-subgenome and those for yield mainly in the A-subgenome. Our research provides insight into the role of structural variations in genotype-to-phenotype relationships and their potential utility in crop improvement.

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Crystalloid Inclusions in Hepatocyte Mitochondria and Their Similarity to Cytoplasmic Crystalloids

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100051001 ◽

1974 ◽

Vol 32 ◽

pp. 198-199

Author(s):

Odell T. Minick ◽

Hidejiro Yokoo

Keyword(s):

Liver Disease ◽

Alcoholic Liver Disease ◽

Special Interest ◽

Structural Variations ◽

Mitochondrial Alterations ◽

The Matrix ◽

Crystalloid Inclusions ◽

Liver Biopsies

Mitochondrial alterations were studied in 25 liver biopsies from patients with alcoholic liver disease. Of special interest were the morphologic resemblance of certain fine structural variations in mitochondria and crystalloid inclusions. Four types of alterations within mitochondria were found that seemed to relate to cytoplasmic crystalloids.Type 1 alteration consisted of localized groups of cristae, usually oriented in the long direction of the organelle (Fig. 1A). In this plane they appeared serrated at the periphery with blind endings in the matrix. Other sections revealed a system of equally-spaced diagonal lines lengthwise in the mitochondrion with cristae protruding from both ends (Fig. 1B). Profiles of this inclusion were not unlike tangential cuts of a crystalloid structure frequently seen in enlarged mitochondria described below.

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Molecular Biology and Crop Improvement

10.1017/cbo9780511753411 ◽

1986 ◽

Cited By ~ 11

Author(s):

R. B. Austin ◽

R. B. Flavell ◽

I. E. Henson ◽

H. J. B. Lowe

Keyword(s):

Molecular Biology ◽

Crop Improvement

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Evaluation of Gloriosa superba for Yield Attributing Characters and Quantification of Colchicine Originated from Different Agro Climatic Zones of Tamil Nadu and Andhra Pradesh

International Journal of Pharmaceutical and Clinical Research ◽

10.25258/ijpcr.v9i3.8315 ◽

2017 ◽

Vol 9 (3) ◽

Author(s):

Arun Kumar P. ◽

Elangaimannan R.

Keyword(s):

Seed Yield ◽

Tamil Nadu ◽

High Performance ◽

Andhra Pradesh ◽

Crop Improvement ◽

Mean Value ◽

Hplc Method ◽

Gloriosa Superba ◽

Climatic Zones ◽

Colchicine Alkaloid

The study was conducted to evolve Gloriosa superba for yield characters and alkalodi content for selecting elite genotypes for comercial exploitatio n. The genotypes were sowm in Variyankaval village, Udayarpalayam taluk of Ariyalur district, Tamil Nadu. The highest mean value for fresh and dry seed yield was observed in Chittor local. The genotype Mulanur local has recorded the highest mean value for number of pods per plant and number of seeds per pod and Arupukotai local excelled the general mean for the traits seeds per pod, fresh and dry seed yield and also for tuber characters. An investigation was carried out to quantify the colchicine (alkaloid) present in tubers by High Performance Liquid Chromatography (HPLC) method. The genotypes collected from Arupukotai recorded the highest colchicine content (0.760 mg/g) followed by Chittoor (0.578 mg/g) and Mulanur (0.496 mg/g) and there by these three genotypes were utilized for further crop improvement.

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Direct Read and Quantify Damage Nucleotide from an Oligonucleotide Using a Single Molecule Interface

10.26434/chemrxiv.10080638.v2 ◽

2019 ◽

Author(s):

Jiajun Wang ◽

Meng-Yin Li ◽

Jie Yang ◽

Ya-Qian Wang ◽

Xue-Yuan Wu ◽

...

Keyword(s):

Dna Sequencing ◽

Single Molecule ◽

Genetic Diseases ◽

High Sensitivity ◽

Dna Lesions ◽

Lesion Detection ◽

The Novel ◽

Structural Variations ◽

Dna Lesion ◽

Base Lesion

DNA lesion such as metholcytosine(mC), 8-OXO-guanine(OG), inosine(I) etc could cause the genetic diseases. Identification of the varieties of lesion bases are usually beyond the capability of conventional DNA sequencing which is mainly designed to discriminate four bases only. Therefore, lesion detection remain challenge due to the massive varieties and less distinguishable readouts for minor structural variations. Moreover, standard amplification and labelling hardly works in DNA lesions detection. Herein, we designed a single molecule interface from the mutant K238Q Aerolysin, whose confined sensing region shows the high compatible to capture and then directly convert each base lesion into distinguishable current readouts. Compared with previous single molecule sensing interface, the resolution of the K238Q Aerolysin nanopore is enhanced by 2-order. The novel K238Q could direct discriminate at least 3 types (mC, OG, I) lesions without lableing and quantify modification sites under mixed hetero-composition condition of oligonucleotide. Such nanopore could be further applied to diagnose genetic diseases at high sensitivity.

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