How the pan-genome is changing crop genomics and improvement

Coletta, Rafael Della; Qiu, Yefeng; Ou, Shujun; Hufford, Matthew B.; Hirsch, Candice N.

doi:10.1186/s13059-020-02224-8

Cited by 157 publications

(102 citation statements)

References 176 publications

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“…However, our knowledge of the complete gene set of F. graminearum still remains incomplete, because a single reference genome does not reflect the genetic variability within a species. Genetic variants, new haplotypes, change total genetic content and thus expand the number of unique gene models to the pangenome concept [31][32][33][34]. Hence, the pangenome includes (i) the core genome, i.e., genes conserved in all isolates or strains, and (ii) the dispensable or accessory genome, i.e., genes shared by only a subset of isolates or strains, or even specific to a single genome [35].…”

Section: Introductionmentioning

confidence: 99%

Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures

Alouane

Rimbert

Bormann

et al. 2021

IJMS

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Fusarium graminearum, the primary cause of Fusarium head blight (FHB) in small-grain cereals, demonstrates remarkably variable levels of aggressiveness in its host, producing different infection dynamics and contrasted symptom severity. While the secreted proteins, including effectors, are thought to be one of the essential components of aggressiveness, our knowledge of the intra-species genomic diversity of F. graminearum is still limited. In this work, we sequenced eight European F. graminearum strains of contrasting aggressiveness to characterize their respective genome structure, their gene content and to delineate their specificities. By combining the available sequences of 12 other F. graminearum strains, we outlined a reference pangenome that expands the repertoire of the known genes in the reference PH-1 genome by 32%, including nearly 21,000 non-redundant sequences and gathering a common base of 9250 conserved core-genes. More than 1000 genes with high non-synonymous mutation rates may be under diverse selection, especially regarding the trichothecene biosynthesis gene cluster. About 900 secreted protein clusters (SPCs) have been described. Mostly localized in the fast sub-genome of F. graminearum supposed to evolve rapidly to promote adaptation and rapid responses to the host’s infection, these SPCs gather a range of putative proteinaceous effectors systematically found in the core secretome, with the chloroplast and the plant nucleus as the main predicted targets in the host cell. This work describes new knowledge on the intra-species diversity in F. graminearum and emphasizes putative determinants of aggressiveness, providing a wealth of new candidate genes potentially involved in the Fusarium head blight disease.

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Section: Introductionmentioning

confidence: 99%

Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures

Alouane

Rimbert

Bormann

et al. 2021

IJMS

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“…In that regard, presence of the Tsn1 gene in Millewa but absent from the corresponding region in Chinese spring exemplify limitations when using a single reference sequence to identify genes controlling trait variation within QTL intervals in breeding lines and cultivars. Therefore, research efforts are moving from relying on a single reference genome in crop species to resequencing multiple accessions in an attempt to capture a wider repertoire of gene diversity as a pan-genome [ 36 , 39 ]. A complete genome sequence for EGA Blanco and Millewa will add to the wheat pan-genome [ 31 , 32 ] and further contribute towards identifying the entire functional gene complement controlling SNB response on 1BS and 5BL.…”

Section: Discussionmentioning

confidence: 99%

Genes Associated with Foliar Resistance to Septoria Nodorum Blotch of Hexaploid Wheat (Triticum aestivum L.)

Walker

Francki

2021

IJMS

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The genetic control of host response to the fungal necrotrophic disease Septoria nodorum blotch (SNB) in bread wheat is complex, involving many minor genes. Quantitative trait loci (QTL) controlling SNB response were previously identified on chromosomes 1BS and 5BL. The aim of this study, therefore, was to align and compare the genetic map representing QTL interval on 1BS and 5BS with the reference sequence of wheat and identify resistance genes (R-genes) associated with SNB response. Alignment of QTL intervals identified significant genome rearrangements on 1BS between parents of the DH population EGA Blanco, Millewa and the reference sequence of Chinese Spring with subtle rearrangements on 5BL. Nevertheless, annotation of genomic intervals in the reference sequence were able to identify and map 13 and 12 R-genes on 1BS and 5BL, respectively. R-genes discriminated co-located QTL on 1BS into two distinct but linked loci. NRC1a and TFIID mapped in one QTL on 1BS whereas RGA and Snn1 mapped in the linked locus and all were associated with SNB resistance but in one environment only. Similarly, Tsn1 and WK35 were mapped in one QTL on 5BL with NETWORKED 1A and RGA genes mapped in the linked QTL interval. This study provided new insights on possible biochemical, cellular and molecular mechanisms responding to SNB infection in different environments and also addressed limitations of using the reference sequence to identify the full complement of functional R-genes in modern varieties.

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“…These two assemblies place elephant grass in a unique position among the TFGs. Current research trends indicate the benefits of having not only one but multiple genome assemblies for a species of interest (Della Coletta et al, 2021). Large sequencing projects now target pan-genomes, instead of a single reference that does not capture the full diversity of a species (Zhao et al, 2018).…”

Section: Genomic Resources and Genomementioning

confidence: 99%

Genomic Selection in Tropical Forage Grasses: Current Status and Future Applications

et al. 2021

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The world population is expected to be larger and wealthier over the next few decades and will require more animal products, such as milk and beef. Tropical regions have great potential to meet this growing global demand, where pasturelands play a major role in supporting increased animal production. Better forage is required in consonance with improved sustainability as the planted area should not increase and larger areas cultivated with one or a few forage species should be avoided. Although, conventional tropical forage breeding has successfully released well-adapted and high-yielding cultivars over the last few decades, genetic gains from these programs have been low in view of the growing food demand worldwide. To guarantee their future impact on livestock production, breeding programs should leverage genotyping, phenotyping, and envirotyping strategies to increase genetic gains. Genomic selection (GS) and genome-wide association studies play a primary role in this process, with the advantage of increasing genetic gain due to greater selection accuracy, reduced cycle time, and increased number of individuals that can be evaluated. This strategy provides solutions to bottlenecks faced by conventional breeding methods, including long breeding cycles and difficulties to evaluate complex traits. Initial results from implementing GS in tropical forage grasses (TFGs) are promising with notable improvements over phenotypic selection alone. However, the practical impact of GS in TFG breeding programs remains unclear. The development of appropriately sized training populations is essential for the evaluation and validation of selection markers based on estimated breeding values. Large panels of single-nucleotide polymorphism markers in different tropical forage species are required for multiple application targets at a reduced cost. In this context, this review highlights the current challenges, achievements, availability, and development of genomic resources and statistical methods for the implementation of GS in TFGs. Additionally, the prediction accuracies from recent experiments and the potential to harness diversity from genebanks are discussed. Although, GS in TFGs is still incipient, the advances in genomic tools and statistical models will speed up its implementation in the foreseeable future. All TFG breeding programs should be prepared for these changes.

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How the pan-genome is changing crop genomics and improvement

Cited by 157 publications

References 176 publications

Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures

Comparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures

Genes Associated with Foliar Resistance to Septoria Nodorum Blotch of Hexaploid Wheat (Triticum aestivum L.)

Genomic Selection in Tropical Forage Grasses: Current Status and Future Applications

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