Using Precision Phenotyping to Inform de novo Domestication

Abstract To test the hypothesis that the cultivated peanut species possesses almost no molecular variability, we sequenced a diverse panel of 22 Arachis accessions representing Arachis hypogaea botanical classes, A-, B-, and K- genome diploids, a synthetic amphidiploid, and a tetraploid wild species. RNASeq was performed on pools of three tissues, and de novo assembly was performed. Realignment of individual accession reads to transcripts of the cultivar OLin identified 306,820 biallelic SNPs. Among 10 naturally occurring tetraploid accessions, 40,382 unique homozygous SNPs were identified in 14,719 contigs. In eight diploid accessions, 291,115 unique SNPs were identified in 26,320 contigs. The average SNP rate among the 10 cultivated tetraploids was 0.5, and among eight diploids was 9.2 per 1000 bp. Diversity analysis indicated grouping of diploids according to genome classification, and cultivated tetraploids by subspecies. Cluster analysis of variants indicated that sequences of B genome species were the most similar to the tetraploids, and the next closest diploid accession belonged to the A genome species. A subset of 66 SNPs selected from the dataset was validated; of 782 SNP calls, 636 (81.32%) were confirmed using an allele-specific discrimination assay. We conclude that substantial genetic variability exists among wild species. Additionally, significant but lesser variability at the molecular level occurs among accessions of the cultivated species. This survey is the first to report significant SNP level diversity among transcripts, and may explain some of the phenotypic differences observed in germplasm surveys. Understanding SNP variants in the Arachis accessions will benefit in developing markers for selection.

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NLR Genes Related Transcript Sets in Potato Cultivars Bearing Genetic Material of Wild Mexican Solanum Species

Agronomy ◽

10.3390/agronomy11122426 ◽

2021 ◽

Vol 11 (12) ◽

pp. 2426

Author(s):

Alex V. Kochetov ◽

Dmitry A. Afonnikov ◽

Nikolay Shmakov ◽

Gennady V. Vasiliev ◽

Olga Y. Antonova ◽

...

Keyword(s):

Potato Breeding ◽

Reference Genome ◽

De Novo ◽

Genetic Material ◽

Solanum Species ◽

Potato Cultivars ◽

R Genes ◽

Genes Expression ◽

History Of ◽

Cultivated Species

The long history of potato breeding includes the numerous introgressions of resistance genes from many wild species of South and Central America as well as from cultivated species into the breeding genepool. Most R genes belong to the NLR family with nucleotide-binding site–leucine-rich repeat. The aim of this research concerns an evaluation of NLR genes expression in transcriptomes of three potato cultivars (Evraziya, Siverskij, Sudarynya), which combine genetic material from wild and cultivated potato species, and each bears intragenic markers of RB/Rpi-blb1/Rpi-sto1 genes conferring broad-range resistance to late blight. The transcriptomes of the cultivars were compared before and 24 h after the Phytophthora infestans inoculation. The induction of RB/Rpi-blb1/Rpi-sto1 transcript after 24 h of inoculation was detected in the resistant cultivars Siverskij and Sudarynya but not in susceptible cv. Evraziya. This demonstrates the importance of transcriptomic assay for understanding the results of marker-assisted selection and phenotyping. Interestingly, assembling the transcriptomes de novo and analysis with NLR-parser tool revealed significant fractions of novel NLR genes with no homology to the reference genome (from 103 (cv. Siverskij) to 160 (S. stoloniferum, 30514/15). Comparison of novel NLRs demonstrated a relatively small intersection between the genotypes that coincided with their complex pedigrees with several interspecific hybridization events. These novel NLRs may facilitate the discovery of new efficient R genes.

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A de novo genome assembly of the dwarfing pear rootstock Zhongai 1

Scientific Data ◽

10.1038/s41597-019-0291-3 ◽

2019 ◽

Vol 6 (1) ◽

Cited By ~ 1

Author(s):

Chunqing Ou ◽

Fei Wang ◽

Jiahong Wang ◽

Song Li ◽

Yanjie Zhang ◽

...

Keyword(s):

De Novo ◽

Repetitive Sequences ◽

Draft Genome ◽

Genome Sequences ◽

Fruit Characteristics ◽

De Novo Genome Assembly ◽

Protein Coding ◽

Protein Coding Genes ◽

Long Reads ◽

Cultivated Species

Abstract‘Zhongai 1’ [(Pyrus ussuriensis × communis) × spp.] is an excellent pear dwarfing rootstock common in China. It is dwarf itself and has high dwarfing efficiency on most of main Pyrus cultivated species when used as inter-stock. Here we describe the draft genome sequences of ‘Zhongai 1’ which was assembled using PacBio long reads, Illumina short reads and Hi-C technology. We estimated the genome size is approximately 511.33 Mb by K-mer analysis and obtained a final genome of 510.59 Mb with a contig N50 size of 1.28 Mb. Next, 506.31 Mb (99.16%) of contigs were clustered into 17 chromosomes with a scaffold N50 size of 23.45 Mb. We further predicted 309.86 Mb (60.68%) of repetitive sequences and 43,120 protein-coding genes. The assembled genome will be a valuable resource and reference for future pear breeding, genetic improvement, and comparative genomics among related species. Moreover, it will help identify genes involved in dwarfism, early flowering, stress tolerance, and commercially desirable fruit characteristics.

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De novo genetic variation revealed in somatic sectors of single Arabidopsis plants

F1000Research ◽

10.12688/f1000research.2-5.v2 ◽

2013 ◽

Vol 2 ◽

pp. 5 ◽

Cited By ~ 5

Author(s):

Marianne T Hopkins ◽

Aaron M Khalid ◽

Pei-Chun Chang ◽

Karen C Vanderhoek ◽

Dulcie Lai ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Variation ◽

Reproductive Strategies ◽

De Novo ◽

Genomic Information ◽

Single Nucleotide ◽

Evolutionary Advantage ◽

Quantitative Analyses ◽

Cultivated Species ◽

Genomic Insertions

Concern over the tremendous loss of genetic diversity among many of our most important crops has prompted major efforts to preserve seed stocks derived from cultivated species and their wild relatives. Arabidopsis thaliana propagates mainly by self-fertilizing, and therefore, like many crop plants, theoretically has a limited potential for producing genetically diverse offspring. Despite this, inbreeding has persisted in Arabidopsis for over a million years suggesting that some underlying adaptive mechanism buffers the deleterious consequences of this reproductive strategy. Using presence-absence molecular markers we demonstrate that single Arabidopsis plants can have multiple genotypes. Sequence analyses reveal single nucleotide changes, loss of sequences and, surprisingly, acquisition of unique genomic insertions. Estimates based on quantitative analyses suggest that these genetically discordant sectors are very small but can have a complex genetic makeup. In ruling out more trivial explanations for these data, our findings raise the possibility that intrinsic drivers of genetic variation are responsible for the targeted sequence changes we detect. Given the evolutionary advantage afforded to populations with greater genetic diversity, we hypothesize that organisms that primarily self-fertilize or propagate clonally counteract the genetic cost of such reproductive strategies by leveraging a cryptic reserve of extra-genomic information.

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The Morphology of the Rat Kidney Following Folic Acid Administration

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100067996 ◽

1970 ◽

Vol 28 ◽

pp. 200-201

Author(s):

Aline Byrnes ◽

Elsa E. Ramos ◽

Minoru Suzuki ◽

E.D. Mayfield

Keyword(s):

Folic Acid ◽

De Novo ◽

Specific Activity ◽

Rat Kidney ◽

Present Report ◽

Intracellular Localization ◽

Male Rats ◽

Renal Hypertrophy ◽

Electron Microscopic ◽

Biochemical Alterations

Renal hypertrophy was induced in 100 g male rats by the injection of 250 mg folic acid (FA) dissolved in 0.3 M NaHCO3/kg body weight (i.v.). Preliminary studies of the biochemical alterations in ribonucleic acid (RNA) metabolism of the renal tissue have been reported recently (1). They are: RNA content and concentration, orotic acid-c14 incorporation into RNA and acid soluble nucleotide pool, intracellular localization of the newly synthesized RNA, and the specific activity of enzymes of the de novo pyrimidine biosynthesis pathway. The present report describes the light and electron microscopic observations in these animals. For light microscopy, kidney slices were fixed in formalin, embedded, sectioned, and stained with H & E and PAS.

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Early ossicle growth in the regenerating disc of a brittle star

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100169559 ◽

1994 ◽

Vol 52 ◽

pp. 364-365

Author(s):

M. Shlepr ◽

R. L. Turner

Keyword(s):

Cell Membrane ◽

Light Microscopy ◽

De Novo ◽

Current Model ◽

Syncytium Formation ◽

Brittle Star ◽

Intracellular Location ◽

Limited Volume ◽

Tissue Calcification

Calcification in the echinoderms occurs within a limited-volume cavity enclosed by cytoplasmic extensions of the mineral depositing cells, the sclerocytes. The current model of this process maintains that the sheath formed from these cytoplasmic extensions is syncytial. Prior studies indicate that syncytium formation might be dependent on sclerocyte density and not required for calcification. This model further envisions that ossicles formed de novo nucleate and grow intracellularly until the ossicle effectively outgrows the vacuole. Continued ossicle growth occurs within the sheath but external to the cell membrane. The initial intracellular location has been confirmed only for elements of the echinoid tooth.The regenerating aboral disc integument of ophiophragmus filograneus was used to test the current echinoderm calcification model. This tissue is free of calcite fragments, thus avoiding questions of cellular engulfment, and ossicles are formed de novo. The tissue calcification pattern was followed by light microscopy in both living and fixed preparations.

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Arabidopsis 4-COUMAROYL-COA LIGASE 8 contributes to the biosynthesis of the benzenoid ring of coenzyme Q in peroxisomes

Biochemical Journal ◽

10.1042/bcj20190688 ◽

2019 ◽

Vol 476 (22) ◽

pp. 3521-3532

Author(s):

Eric Soubeyrand ◽

Megan Kelly ◽

Shea A. Keene ◽

Ann C. Bernert ◽

Scott Latimer ◽

...

Keyword(s):

Oxidative Metabolism ◽

Time Course ◽

Reverse Genetics ◽

De Novo ◽

Coenzyme Q ◽

Control Level ◽

Wild Type ◽

Fluorescent Reporters ◽

Coa Ligase ◽

Peroxisomal Targeting

Plants have evolved the ability to derive the benzenoid moiety of the respiratory cofactor and antioxidant, ubiquinone (coenzyme Q), either from the β-oxidative metabolism of p-coumarate or from the peroxidative cleavage of kaempferol. Here, isotopic feeding assays, gene co-expression analysis and reverse genetics identified Arabidopsis 4-COUMARATE-COA LIGASE 8 (4-CL8; At5g38120) as a contributor to the β-oxidation of p-coumarate for ubiquinone biosynthesis. The enzyme is part of the same clade (V) of acyl-activating enzymes than At4g19010, a p-coumarate CoA ligase known to play a central role in the conversion of p-coumarate into 4-hydroxybenzoate. A 4-cl8 T-DNA knockout displayed a 20% decrease in ubiquinone content compared with wild-type plants, while 4-CL8 overexpression boosted ubiquinone content up to 150% of the control level. Similarly, the isotopic enrichment of ubiquinone's ring was decreased by 28% in the 4-cl8 knockout as compared with wild-type controls when Phe-[Ring-13C6] was fed to the plants. This metabolic blockage could be bypassed via the exogenous supply of 4-hydroxybenzoate, the product of p-coumarate β-oxidation. Arabidopsis 4-CL8 displays a canonical peroxisomal targeting sequence type 1, and confocal microscopy experiments using fused fluorescent reporters demonstrated that this enzyme is imported into peroxisomes. Time course feeding assays using Phe-[Ring-13C6] in a series of Arabidopsis single and double knockouts blocked in the β-oxidative metabolism of p-coumarate (4-cl8; at4g19010; at4g19010 × 4-cl8), flavonol biosynthesis (flavanone-3-hydroxylase), or both (at4g19010 × flavanone-3-hydroxylase) indicated that continuous high light treatments (500 µE m−2 s−1; 24 h) markedly stimulated the de novo biosynthesis of ubiquinone independently of kaempferol catabolism.

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