Characterization of a deletion in theHsp70cluster in the bovine reference genome

Abstract Wheat black point, which occurs in most wheat growing regions of the world, is detrimental to grain appearance, processing and nutrient quality. Mining and characterization of genetic loci for black point resistance is helpful for breeding resistant wheat cultivars. We previously identified a major QTL QBp.caas-3BL in a recombinant inbred line (RIL) population of Linmai 2/Zhong 892 across five environments. Here we confirmed the QTL in two additional environments. The genetic region of QBp.caas-3BL was enriched with newly developed markers. Using four sets of near isogenic lines QBp.caas-3BL was narrowed down to a physical interval of approximately 1.7 Mb, including five annotated genes according to IWGSC reference genome. TraesCS3B02G404300, TraesCS3B02G404600 and TraesCS3B02G404700 were predicted as candidate genes based on the analyses of sequence polymorphisms and differential expression. We also converted a SNP of TraesCS3B02G404700 into a breeding-applicable KASP marker and verified its efficacy for marker-assisted breeding in a panel of germplasm. The findings not only lay a foundation for map-based cloning of QBp.caas-3BL but also provide a useful marker for selection of resistant cultivars genotypes in wheat breeding.

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The First High-Quality Reference Genome of Sika Deer Provides Insights for High-Tannin Adaptation

10.1101/2021.05.13.443962 ◽

2021 ◽

Author(s):

Xiumei Xing ◽

Cheng Ai ◽

Tianjiao Wang ◽

Yang LI ◽

Huitao Liu ◽

...

Keyword(s):

Sika Deer ◽

Reference Genome ◽

Gene Families ◽

High Quality ◽

Genetic Mechanisms ◽

Essential Resource ◽

Genome Analyses ◽

Oak Leaves ◽

Chromosome Level

Sika deer are known to prefer oak leaves, which are rich in tannins and toxic to most mammals; however, the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear. In identifying the mechanism responsible for the tolerance of a highly toxic diet, we have made a major advancement in the elucidation of the genomics of sika deer. We generated the first high-quality, chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments. Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food, especially the expansion of UGT genes in a subfamily. The first chromosome-level assembly and genetic characterization of the tolerance toa highly toxic diet suggest that the sika deer genome will serve as an essential resource for understanding evolutionary events and tannin adaptation. Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.

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Characterization of the Resistance to Powdery Mildew and Leaf Rust Carried by the Bread Wheat Cultivar Victo

International Journal of Molecular Sciences ◽

10.3390/ijms22063109 ◽

2021 ◽

Vol 22 (6) ◽

pp. 3109

Author(s):

Francesca Desiderio ◽

Salim Bourras ◽

Elisabetta Mazzucotelli ◽

Diego Rubiales ◽

Beat Keller ◽

...

Keyword(s):

Powdery Mildew ◽

Leaf Rust ◽

Bread Wheat ◽

Gene Expression Analysis ◽

Reference Genome ◽

Gene Annotation ◽

Major Gene ◽

Puccinia Triticina ◽

A Minor

Leaf rust and powdery mildew are two important foliar diseases in wheat. A recombinant inbred line (RIL) population, obtained by crossing two bread wheat cultivars (‘Victo’ and ‘Spada’), was evaluated for resistance to the two pathogens at seedling stage. Upon developing a genetic map of 8726 SNP loci, linkage analysis identified three resistance Quantitative Trait Loci (QTLs), with ‘Victo’ contributing the resistant alleles to all loci. One major QTL (QPm.gb-7A) was detected in response to Blumeria graminis on chromosome 7A, which explained 90% of phenotypic variation (PV). The co-positional relationship with known powdery mildew (Pm) resistance loci suggested that a new source of resistance was identified in T. aestivum. Two QTLs were detected in response to Puccinia triticina: a major gene on chromosome 5D (QLr.gb-5D), explaining a total PV of about 59%, and a minor QTL on chromosome 2B (QLr.gb-2B). A positional relationship was observed between the QLr.gb-5D with the known Lr1 gene, but polymorphisms were found between the cloned Lr1 and the corresponding ‘Victo’ allele, suggesting that QLr.gb-5D could represent a new functional Lr1 allele. Lastly, upon anchoring the QTL on the T. aestivum reference genome, candidate genes were hypothesized on the basis of gene annotation and in silico gene expression analysis.

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The haplotype-resolved reference genome of lemon (Citrus limon L. Burm f.)

10.1101/2021.07.14.452308 ◽

2021 ◽

Author(s):

Mario Di Guardo ◽

Marco Moretto ◽

Mirko Moser ◽

Chiara Catalano ◽

Michela Troggio ◽

...

Keyword(s):

Reference Genome ◽

Perfect Match ◽

In Silico Analysis ◽

Mature Mirnas ◽

Citrus Limon ◽

Oxford Nanopore ◽

A Genome ◽

Set Up ◽

Definition Of

Lemon (Citrus limon (L.) Burm. f.) is an evergreen tree belonging to the genus Citrus. The fruits are particularly prized for their organoleptic and nutraceutical properties of the juice. Herein we report, for the first time, the release of a high-quality reference genome of the two haplotypes of lemon. The sequencing has been carried out coupling Illumina short reads and Oxford Nanopore data leading to the definition of a primary and an alternative assembly characterized by a genome size of 312.8 Mb and 324.74 Mb respectively. The analysis of the long terminal repeat (LTR) allowed the identification of 1921 regions on the primary and 1911 on the alternative assembly distributed across the nine chromosomes. Furthermore, an in-silico analysis of the microRNA genes was carried out using 246 mature miRNA and the respective pre-miRNA hairpin sequences of C. sinensis. Such analysis highlighted a high conservation between the two species with 233 mature miRNAs and 51 pre-miRNA stem-loops aligning with perfect match on the lemon genome. In parallel, total RNA was extracted from fruit, flower, leaf and root enabling the detection of 38,205 and 37,753 predicted transcripts on primary and alternative assemblies respectively. Among those, the highest and lowest number of tissue-specific transcripts were detected in flower (2.73% and 2.71% in primary and alternative assemblies respectively) and leaf (0.7% and 0.68%) while gene ontology analysis enables a more precise characterization of the expressed genes based on their function. The availability of a reference genome is an important prerequisite both for the set-up of high-throughput genotyping analysis and for functional genomic approaches toward the characterization of the genetic determinism of traits of agronomic interest.

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Complete Genome Sequences and Genome-Wide Characterization of Trichoderma Biocontrol Agents Provide New Insights into their Evolution and Variation in Genome Organization, Sexual Development, and Fungal-Plant Interactions

Microbiology Spectrum ◽

10.1128/spectrum.00663-21 ◽

2021 ◽

Author(s):

Wan-Chen Li ◽

Ting-Chan Lin ◽

Chia-Ling Chen ◽

Hou-Cheng Liu ◽

Hisn-Nan Lin ◽

...

Keyword(s):

Reference Genome ◽

Gene Clusters ◽

Biocontrol Agents ◽

Trichoderma Virens ◽

Plant Interactions ◽

Genome Sequences ◽

Sequencing Technologies ◽

Genome Wide ◽

Genome Assemblies

Telomere-to-telomere and gapless reference genome assemblies are necessary to ensure that all genomic variants are studied and discovered, including centromeres, telomeres, AT-rich blocks, mating type loci, biosynthetic, and metabolic gene clusters. Here, we applied long-range sequencing technologies to determine the near-completed genome sequences of four widely used biocontrol agents or biofertilizers: Trichoderma virens Gv29-8 and FT-333, Trichoderma asperellum FT101, and Trichoderma atroviride P1.

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Platinum-grade soybean reference genome facilitates characterization of genetic underpinnings of traits

10.21203/rs.3.rs-57915/v1 ◽

2020 ◽

Author(s):

Xinxin Yi ◽

Jing Liu ◽

Shengcai Chen ◽

Hao Wu ◽

Min Liu ◽

...

Keyword(s):

Reference Genome ◽

De Novo ◽

Agronomic Traits ◽

Genomic Analysis ◽

Comparative Genomic ◽

High Quality ◽

Wide Range ◽

Breeding Research ◽

High Quality Genome

Abstract BackgroundCultivated soybean (Glycine max) is an important source for protein and oil. Each soybean strain has its own genetic diversity, and the availability of more soybean genomes may enhance comparative genomic analysis of soybean.ResultsIn this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with high contiguity, completeness, and accuracy. We annotated 59,629 gene models and reconstructed 235,109 high-quality full-length transcripts. We have molecularly characterized the genotypes of some important agronomic traits of JD17 by taking advantage of these newly established genomic resources.ConclusionsWe reported a high-quality genome and annotations of a wide range of cultivars, and used them to analyze the genotypes of genes related to important agronomic traits of soybean in JD17. We have demonstrated that high-quality genome assembly can serve as a valuable reference for soybean genomics and breeding research community.

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Species-Specific Duplication Event Associated with Elevated Levels of Nonstructural Carbohydrates in Sorghum bicolor

G3 Genes|Genome|Genetics ◽

10.1534/g3.119.400921 ◽

2020 ◽

Vol 10 (5) ◽

pp. 1511-1520 ◽

Cited By ~ 1

Author(s):

Zachary W. Brenton ◽

Brendon T. Juengst ◽

Elizabeth A. Cooper ◽

Matthew T. Myers ◽

Kathleen E. Jordan ◽

...

Keyword(s):

Sorghum Bicolor ◽

Reference Genome ◽

Carbon Allocation ◽

Phenotypic Diversity ◽

Sugar Content ◽

Duplication Event ◽

Sugar Accumulation ◽

Evolutionary Mechanisms ◽

Species Specific

Simple sugars are the essential foundation to plant life, and thus, their production, utilization, and storage are highly regulated processes with many complex genetic controls. Despite their importance, many of the genetic and biochemical mechanisms remain unknown or uncharacterized. Sorghum, a highly productive, diverse C4 grass important for both industrial and subsistence agricultural systems, has considerable phenotypic diversity in the accumulation of nonstructural sugars in the stem. We use this crop species to examine the genetic controls of high levels of sugar accumulation, identify genetic mechanisms for the accumulation of nonstructural sugars, and link carbon allocation with iron transport. We identify a species-specific tandem duplication event controlling sugar accumulation using genome-wide association analysis, characterize multiple allelic variants causing increased sugar content, and provide further evidence of a putative neofunctionalization event conferring adaptability in Sorghum bicolor. Comparative genomics indicate that this event is unique to sorghum which may further elucidate evolutionary mechanisms for adaptation and divergence within the Poaceae. Furthermore, the identification and characterization of this event was only possible with the continued advancement and improvement of the reference genome. The characterization of this region and the process in which it was discovered serve as a reminder that any reference genome is imperfect and is in need of continual improvement.

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Improved maize reference genome with single molecule technologies

10.1101/079004 ◽

2016 ◽

Cited By ~ 10

Author(s):

Yinping Jiao ◽

Paul Peluso ◽

Jinghua Shi ◽

Tiffany Liang ◽

Michelle C. Stitzer ◽

...

Keyword(s):

Single Molecule ◽

Reference Genome ◽

Optical Mapping ◽

Fold Increase ◽

Smrt Sequencing ◽

Functional Variation ◽

Density Region ◽

Assembly Features ◽

Reference Genomes

ABSTRACTComplete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation. These resources facilitate elucidation of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions. Here, we report the assembly and annotation of maize, a genetic and agricultural model species, using Single Molecule Real-Time (SMRT) sequencing and high-resolution optical mapping. Relative to the previous reference genome, our assembly features a 52-fold increase in contig length and significant improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed over 130,000 intact transposable elements (TEs), allowing us to identify TE lineage expansions unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by SMRT sequencing. In addition, comparative optical mapping of two other inbreds revealed a prevalence of deletions in the low gene density region and maize lineage-specific genes.

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HiC-TE: a computational pipeline for Hi-C data analysis shows a possible role of repeat family interactions in the genome 3D organization

10.1101/2021.12.18.473300 ◽

2021 ◽

Author(s):

Matej Lexa ◽

Monika Cechova ◽

Son Hoang Nguyen ◽

Pavel Jedlicka ◽

Viktor Tokan ◽

...

Keyword(s):

Reference Genome ◽

Family Interactions ◽

Computational Pipeline ◽

Intensive Study ◽

Repeat Family ◽

Chromosome Conformation ◽

Genome Data ◽

Genomic Repeats

The role of repetitive DNA in the 3D organization of the interphase nucleus in plant cells is a subject of intensive study. High-throughput chromosome conformation capture (Hi-C) is a sequencing-based method detecting the proximity of DNA segments in nuclei. We combined Hi-C data, plant reference genome data and tools for the characterization of genomic repeats to build a Nextflow pipeline identifying and quantifying the contacts of specific repeats revealing the preferential homotypic interactions of ribosomal DNA, DNA transposons and some LTR retrotransposon families. We provide a novel way to analyze the organization of repetitive elements in the 3D nucleus.

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FaRCa1 Confers Moderate Resistance to the Root Necrosis Form of Strawberry Anthracnose Caused by Colletotrichum acutatum

HortScience ◽

10.21273/hortsci14807-20 ◽

2020 ◽

Vol 55 (5) ◽

pp. 693-698 ◽

Cited By ~ 2

Author(s):

Natalia Salinas ◽

Zhen Fan ◽

Natalia Peres ◽

Seonghee Lee ◽

Vance M. Whitaker

Keyword(s):

Reference Genome ◽

Dna Marker ◽

Screening Method ◽

Fruit Rot ◽

Colletotrichum Acutatum ◽

Dna Test ◽

Root Necrosis ◽

Strawberry Anthracnose ◽

Moderate Resistance

FaRCa1 is a major locus conferring resistance to anthracnose fruit rot (AFR) caused by Colletotrichum acutatum, an important pathogen of strawberry (Fragaria ×ananassa). The objective of this study was to characterize the effects of FaRCa1 on anthracnose root necrosis (ARN) via root inoculations and DNA marker characterization of the locus. A subgenome-specific high-resolution melting (HRM) marker for an insertion/deletion (InDel) near FaRCa1 was designed using the ‘Camarosa’ octoploid reference genome. The marker was used to genotype cultivars and advanced selections studied in two seasons. A root disease screening method was developed in which roots were cut and dipped in a spore suspension before planting, using a mixture of three local isolates of the C. acutatum species complex. ARN was indirectly scored by calculating image-based leaf area differences among inoculated and noninoculated plants. The allele of FaRCa1 conferring resistance to AFR also conferred a significant reduction in ARN. Thus, a robust and easily scored DNA test is now available to breeders for selecting for resistance to both the fruit and root forms of strawberry anthracnose.

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