Translational genomics for plant breeding with the genome sequence explosion

Kang, Yang Jae; Lee, Taeyoung; Lee, Jayern; Shim, Sangrea; Jeong, Haneul; Satyawan, Dani; Kim, Moon Young; Lee, Suk-Ha

doi:10.1111/pbi.12449

Cited by 52 publications

(50 citation statements)

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“…With the development of NGS resequencing technology, we can identify all possible polymorphisms between target parental lines and select highly informative variations based on previous knowledge, such as known gene function and QTL of the corresponding species. We can also take advantage of related model species using comparative genomics approaches [9]. These technological and analytical advances can, in fact, reduce the number of molecular markers required for genotyping and increase the efficiency of marker-assisted breeding schemes, by allowing us to assign priority on each possible molecular marker.…”

Section: Discussionmentioning

confidence: 99%

“…These techniques have almost completely replaced laborious and time-consuming gel-based genotyping procedures, at least for marker development, and consequently, the majority of beneficial crop species have been sequenced and assembled into draft reference genomes, after which, the genomic resources for a given crop species are often enriched using resequencing strategies [9]. For example, after completion of the pepper ( C. annuum ) reference genome, which covers 87.9 % of the estimated genome size, two pepper cultivars (Perennial and Dempsey) and a wild species of pepper ( C. chinense PI159236) were resequenced, revealing millions of single nucleotide polymorphisms (SNPs) that may discriminate between cultivars or between species [6].…”

Section: Introductionmentioning

confidence: 99%

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Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance

et al. 2016

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BackgroundBacterial wilt (BW) is a widespread plant disease that affects a broad range of dicot and monocot hosts and is particularly harmful for solanaceous plants, such as pepper, tomato, and eggplant. The pathogen responsible for BW is the soil-borne bacterium, Ralstonia solanacearum, which can adapt to diverse temperature conditions and is found in climates ranging from tropical to temperate. Resistance to BW has been detected in some pepper plant lines; however, the genomic loci and alleles that mediate this are poorly studied in this species.ResultsWe resequenced the pepper cultivars YCM344 and Taean, which are parental recombinant inbred lines (RIL) that display differential resistance phenotypes against BW, with YCM344 being highly resistant to infection with this pathogen. We identified novel single nucleotide polymorphisms (SNPs) and insertions/deletions (Indels) that are only present in both parental lines, as compared to the reference genome and further determined variations that distinguish these two cultivars from one another. We then identified potentially informative SNPs that were found in genes related to those that have been previously associated with disease resistance, such as the R genes and stress response genes. Moreover, via comparative analysis, we identified SNPs located in genomic regions that have homology to known resistance genes in the tomato genomes.ConclusionsFrom our SNP profiling in both parental lines, we could identify SNPs that are potentially responsible for BW resistance, and practically, these may be used as markers for assisted breeding schemes using these populations. We predict that our analyses will be valuable for both better understanding the YCM334/Taean-derived populations, as well as for enhancing our knowledge of critical SNPs present in the pepper genome.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0931-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance

et al. 2016

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“…Genomics has discovered some evolutionary issues like polyploidy in wheat Borrill et al (2015) and family relation in bred and wild plants (Kang et al, 2016). These can lead us to a better understanding of plant kingdom toward plants with better potential yield or special characters in terms of agronomic traits.…”

Section: * Ingeniero Agrónomomentioning

confidence: 99%

Genomic and transcriptomic approaches toward plant selection

Jazayeri¹,

Torres

2017

JSR

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Abstract-Omics era has opened a new window to biology. Genomics and transcriptomics are two well-known fields by which plant selection and breeding are fulfilled more easily and accurately. They provide useful information about genes, transcripts, their functions those are the principal data for other subsequent approaches. Reference genomes of various plants are available and facilitate genome-based studies. The complex of genomic, transcriptomic data and the findings from variant methods like QTLs (quantitative trait loci), SNPs (single nucleotide polymorphism), CNVs (copy number variant), resequencing, GBS (genome-by-sequencing) are extremely important for plant selection in terms of price and time. The new workflows are routinely using different approaches and mixing them based on the genomic/transcriptomic information in their subsequent steps. They, however, are validated during the whole process toward screening genotypes possessing agronomically important desired trait. SNP-Seq presented hereinafter is a new approach for analyzing plants toward selection and screening by SNP sequencing in various genotypes simultaneously. It can accelerate the cycle of plant selection from genotypes to phenotypes in a reverse engineering way.Keywords:-Genomics, Omics, Plant Selection, Plant Improvement, TranscriptomicsResumen-La era Omica ha abierto una nueva ventana a la biología. La genómica y la transcriptómica son dos campos conocidos, con los cuales, la selección y el mejoramiento de plantas se cumplen con mayor facilidad y precisión. Proporcionan informaciónútil sobre los genes, las transcripciones, sus funciones y sirven como datos primordiales para otros enfoques posteriores. Los genomas de referencia de varias plantas han sido secuenciados, y están disponibles, facilitando así el acceso a informaciónómica indispensable para llevar a cabo estudios basados en estos mismos genomas. El total de datos genómicos, transcriptómicos y los hallazgos de métodos variantes que van desde QTL (rasgo cuantitativo), PSN (polimorfismo de un solo nucleótido), NCV (número de copias variante), GBS (genoma por secuencia) son extremadamente importantes para la selección y el mejoramiento de plantas en términos de precio y tiempo. Los nuevos flujos de trabajo utilizan diferentes enfoques basados en la información genómica / transcriptómica en pasos posteriores mezclándolos y se validan durante todo el proceso para seleccionar genotipos que posean un rasgo deseado agronómicamente importante. SNP-Seq, que se presenta en este artículo, es un nuevo enfoque para analizar las plantas hacia la selección y la detección mediante secuenciación de SNP en varios genotipos simultáneamente. Este proceso puede acelerar el ciclo de selección de plantas desde los genotipos a los fenotipos en una forma de ingeniería inversa.

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“…Although this strategy will not hold true for all of the quantitative traits but will work for many of the legume specific traits. Further, the newly generated reference sequences of unstudied legume species can be annotated by the knowledge of soybean via translational genomics approaches (Kang et al, 2015). …”

Section: Soybean As Model Crop For Translation Genomics and Breeding mentioning

confidence: 99%

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

et al. 2016

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Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported. For their effective use in breeding programme it is imperative to narrow down the confidence interval of QTLs, to identify the underlying genes, and most importantly allelic characterization of these genes for identifying superior variants. In the field of functional genomics, especially in the identification and characterization of gene responsible for quantitative traits, soybean is far ahead from other legume crops. The availability of genic information about quantitative traits is more significant because it is easy and effective to identify homologs than identifying shared syntenic regions in other crop species. In soybean, genes underlying QTLs have been identified and functionally characterized for phosphorous efficiency, flowering and maturity, pod dehiscence, hard-seededness, α-Tocopherol content, soybean cyst nematode, sudden death syndrome, and salt tolerance. Candidate genes have also been identified for many other quantitative traits for which functional validation is required. Using the sequence information of identified genes from soybean, comparative genomic analysis of homologs in other legume crops could discover novel structural variants and useful alleles for functional marker development. The functional markers may be very useful for molecular breeding in soybean and harnessing benefit of translational research from soybean to other leguminous crops. Thus, soybean crop can act as a model crop for translational genomics and breeding of quantitative traits in legume crops. In this review, we summarize current status of identification and characterization of genes underlying QTLs for various quantitative traits in soybean and their significance in translational genomics and breeding of other legume crops.

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Translational genomics for plant breeding with the genome sequence explosion

Cited by 52 publications

References 82 publications

Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance

Resequencing of Capsicum annuum parental lines (YCM334 and Taean) for the genetic analysis of bacterial wilt resistance

Genomic and transcriptomic approaches toward plant selection

QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding

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