Progress in plant genome sequencing: research directions

Bragina, M. K.; Afonnikov, D. A.; Салина, Е. А.

doi:10.18699/vj19.459

Cited by 5 publications

(4 citation statements)

References 88 publications

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“…The genome sequence is the basis for a chromosome structure studying, a distribution of repetitive and coding sequences, and genes identification and annotation (Bragina et al, 2019). The different species genomes information allows a comparative phylogenetic analysis to study relationships among species, their origins, and evolutionary features (Marchant et al, 2016;Wendel et al, 2016).…”

Section: Introductionmentioning

confidence: 99%

“…A single organism chromosome sequences serve as the basis ("reference" genome) for studying other genomes of the same species. The number of sequenced, assembled and annotated plant reference genomes increases every year (Bragina et al, 2019). The Ensembl Plants database version 48 (September 2020) contains 93 assembled and annotated plant genomes (Howe et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

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Crop pangenomes

2021

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Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specif ic for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants’ pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Crop pangenomes

2021

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“…Over the past few years, the efficiency of target enrichment has been proven for the study of the nucleotide diversity of polyploid species with a large, repetitive and heterozygous genome (Bragina et al, 2019). This method has been used in various crops, including in the study of ecological adaptation in barley (Russell et al, 2016), the identification of wheat disease resistance genes (Steuernagel et al, 2016), the cataloging of mutations in rice (Henry et al, 2014).…”

Section: Resultsmentioning

confidence: 99%

Study of a region on wheat chromosome 5BS by targeted sequencing

2019

Plant Genetic Resources for Breeding and Producing Functional Nutraceutical Food

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Despite the increasing use of high-throughput sequencing resulting from reduced cost and effort, large and complex genomes still pose a challenge in crop genomics. Bread wheat has a genome size of over 17 Gb, which makes targeted capture an invaluable tool for a wide range of studies. To capture and sequence the 26.6-Mb wheat chromosome 5BS region associated to leaf rust resistant genes, custom hybridization probes was created using information from the reference wheat genome ('Chinese Spring'). We show that this chromosomal region of leaf rust resistance and susceptible wheat lines were efficiently captured with sufficient coverage.

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“…Bragina et al (2019) [3] concluded in his experiment that the cost of sequencing is continuously falling, thanks to continual advancements in DNA sequencing technologies. Plant genome sequencing is becoming increasingly commonplace and more efficient.…”

Section: Key Role Of Advancing Genomics Toolsmentioning

confidence: 99%

Innovations in plant genetics adapting agriculture to climate change

Birla,

Pandey,

Johare

et al. 2024

Int. J. Adv. Biochem. Res.

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Creating new plant genotypes is one of the main ways that agriculture can adjust to the changing climate. It may be necessary for plants to offer resilience in climate change or to provide support in agriculture's expansion into new areas. It might be necessary for very distinct genotypes to function in the altered conditions of protected agriculture. Notwithstanding the increasing obstacles posed by climate change in the future, consumers will still seek food that is convenient, tastes good, is safe, and is produced sustainably and ethically. It will be difficult to increase food's nutritional content in reaction to climate change. This innovation will be supported by genomic sequences of pertinent germplasm and knowledge of the functional role of alleles governing important features.

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Progress in plant genome sequencing: research directions

Cited by 5 publications

References 88 publications

Crop pangenomes

Crop pangenomes

Study of a region on wheat chromosome 5BS by targeted sequencing

Innovations in plant genetics adapting agriculture to climate change

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