The pangenome of an agronomically important crop plant Brassica oleracea

Golicz, Agnieszka A.; Bayer, Philipp E.; Barker, Guy C.; Edger, Patrick P.; Kim, Hye Ran; Martinez, Paula Andrea; Chan, Chon‐Kit Kenneth; Severn‐Ellis, Anita A.; McCombie, W. Richard; Parkin, Isobel A. P.; Paterson, Andrew H.; Pires, J. Chris; Sharpe, Andrew; Tang, Haibao; Teakle, Graham R.; Town, Christopher D.; Batley, Jacqueline; Edwards, David

doi:10.1038/ncomms13390

Cited by 376 publications

(402 citation statements)

References 71 publications

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“…3). Similar trends have been observed in pan-genomic analyses of seven de novo Glycine soja genome [47], ten Brassica oleracea genomes [48], as well as a pan-transcriptome analysis 503 maize accessions [49], results that together suggest higher plant pan-genomes may generally be restricted in size. The finding that 67% of Medicago ortholog groups are dispensable is likewise comparable to earlier estimates of 51% in the G. soja analysis mentioned above [47], 73% in a study of five Oryza AA genomes [50], and 83% of the representative transcript assemblies (RTAs) in the pan-transcriptome analysis of maize [49].…”

Section: Discussionsupporting

confidence: 75%

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

et al. 2017

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Background: Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome. Results: Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable -estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/ absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.

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Section: Discussionsupporting

confidence: 75%

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

et al. 2017

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“…However, the emergence of the pangenome concept (Golicz et al, 2016) makes it clear that conventional breeding results in the introduction of additional genes and alleles, as well as novel combinations of genes. It is evident that the same mechanisms of genome instability found in nature that lead to genetic diversity (Table 1) are also active during conventional breeding (Weber et al, 2012;Schnell et al, 2015).…”

Section: Conventional Plant Breeding Sources Of Genetic Variation Usementioning

confidence: 99%

“…This germplasm is adapted for breeding in Maize proteins (300-400 amino acids long) from 2 alleles differ by 3-4 amino acids Tenaillon et al (2001) Maize genome has 55 million SNPs Gore et al (2009) Green Revolution gene has 2 SNPs for dwarf wheat Peng et al (1999) One SNP caused loss of shattering in domestic rice Konishi et al (2006) Tall or short pea plants (Mendel) Ellis et al (2011) Silva et al (2013) Only 81% of Brassica genes are always present in the same number Golicz et al (2016) 2500 genes found only in either B73 or PH207 Hirsch et al (2016) G. soja genotypes can vary by 1000 to 3000 gene families from each other Li et al (2014) 1992). Nevertheless, breeders are shifting from using these random methods of introducing genetic diversity over the past couple of decades to newer, more predictable methods like genetic engineering.…”

Section: Conventional Plant Breeding Sources Of Genetic Variation Usementioning

confidence: 99%

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

et al. 2017

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Commercial‐scale plant breeding is a complex process in which new crop varieties are continuously being developed to improve yield and agronomic performance over current varieties. A wide array of naturally occurring genetic changes are sources of new characteristics available to plant breeders. During conventional plant breeding, genetic material is exchanged that has the potential to beneficially or adversely affect plant characteristics. For this reason, commercial‐scale breeders have implemented extensive plant selection practices to identify the top‐performing candidates with the desired characteristics while minimizing the advancement of unintended changes. Selection practices in maize (Zea mays L.) breeding involve phenotypic assessments of thousands of candidate lines throughout hundreds of different environmental conditions over many years. Desirable characteristics can also be introduced through genetic modification. For genetically modified (GM) crops, molecular analysis is used to select transformed plants with a single copy of an intact DNA insert and without disruption of endogenous genes. All the while, GM crops go through the same extensive phenotypic characterization as conventionally bred crops. Data from both conventional and GM maize breeding programs are presented to show the similarities between these two processes.

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“…gemmifera (Brussels sprouts), and B. oleraceae var. acephala (kale) 5,6 . Among the Brassicaceae, kale is a popular vegetable, largely consumed in tropical areas and mostly produced by small growers and urban gardeners.…”

Section: Introductionmentioning

confidence: 99%

Bio-based products control black rot (Xanthomonas campestris pv. campestris) and increase the nutraceutical and antioxidant components in kale

Núñez

Rodríguez

Monteiro

et al. 2018

Sci Rep

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Black rot of crucifers, (Xanthomonas campestris pv. campestris) is the principal yield-limiting and destructive pathogen of cruciferous crop worldwide. In order to validate a bio-based control alternative for this disease, whey, lime sulfur, biofertilizer, Bordeaux mixture or raw milk were applied to kale (Brassica oleracea var. acephala) plants. The disease control was achieved by most of the tested products. Milk-based products (raw milk and whey) and biofertilizer reduced the severity by 44 and 56% in the field. Antioxidants, crude fibber, crude protein and lipid contents and kale yield were verified in the five treatments on the leaves with and without X. campestris pv. campestris inoculation. In the absence of the pathogen (non-inoculated), lime sulfur and Bordeaux mixture improved plant nutritional value compared to organic treatments, nevertheless milk-based products and biofertilizer improved the evaluated variables more than the control. However, on leaves inoculated with X. campestris pv. campestris raw milk increased antioxidant activity, crude protein and fiber contents, whereas biofertilizer increased kale yield, lipid and antioxidant contents. Milk-based products and biofertilizer were further evaluated in greenhouse trials to determinate the activity of defense-related enzymes and lignin content. Biofertilizer treatment resulted in increased phenylalanine ammonia lyase, catalase, peroxidase activities and lignin content. Hence, the application of milk-based products and biofertilizer are promising to control black rot of crucifers and also improves food quality by boosting nutritional values and antioxidant activity.

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The pangenome of an agronomically important crop plant Brassica oleracea

Cited by 376 publications

References 71 publications

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

Bio-based products control black rot (Xanthomonas campestris pv. campestris) and increase the nutraceutical and antioxidant components in kale

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