Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

Rabanus‐Wallace, M. Timothy; Hackauf, Bernd; Mascher, Martin; Lux, Thomas; Wicker, Thomas; Gundlach, Heidrun; Báez, Mariana; Houben, Andreas; Mayer, Klaus; Guo, Liangliang; Poland, Jesse; Pozniak, Curtis; Walkowiak, Sean; Melonek, Joanna; Praz, Coraline R.; Schreiber, Mona; Budak, Hikmet; Heuberger, Matthias; Steuernagel, Burkhard; Wulff, Brande B. H.; Börner, Andreas; Byrns, Brook; Čížková, Jana; Fowler, D. B.; Fritz, Allan K.; Himmelbach, Axel; Kaithakottil, Gemy; Keilwagen, Jens; Keller, Beat; Konkin, David; Larsen, Julie S.; Li, Qiang; Myśków, Beata; Padmarasu, Sudharsan; Rawat, Nidhi; Sesiz, Uğur; Biyiklioglu, Sezgi; Sharpe, Andy; Šimková, Hana; Small, Ian; Swarbreck, David; Tsvetkova, Natalia; Voylokov, A. V.; Vrána, Jan; Bauer, Eva; Bolibok-Brągoszewska, Hanna; Doležel, Jaroslav; Hall, Anthony; Jia, Jizeng; Korzun, Viktor; Laroche, André; Ma, Xuefeng; Ordon, Frank; Özkan, Hakan; Rakoczy-Trojanowska, Monika; Scholz, Uwe; Schulman, Alan H.; Siekmann, Dörthe; Stojałowski, Stefan; Tiwari, Vijay K.; Spannagl, Manuel; Stein, Nils

doi:10.1101/2019.12.11.869693

Cited by 31 publications

(54 citation statements)

References 136 publications

(167 reference statements)

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“…Considering the plethora of diversity preserved in genetic resources it is the emphasis of this study to pursue a marker-assisted broadening of the NRG&CMS population to address the strong population structure and narrow genetic profile. Furthermore, the novel rye reference genome by Rabanus-Wallace et al [21] facilitates physical mapping and annotation of the 5K-set and 600K-set markers for combined linkage study and large-scale functional analysis to further unravel the genetic features of the hybrid rye elite breeding germplasm.…”

Section: Resultsmentioning

confidence: 99%

“…The 'Gülzow' Rfg1 and 'C' type Rfc1 Rf major genes have likewise been mapped to the distal region of the 4RL chromosome and been proposed allelic to the P-type [68,71]. The novel rye reference genome by Rabanus-Wallace et al [21], however, constitutes a milestone in large-scale functional analysis, de novo annotating the near-full complement of 34.441 gene models in the rye genome.…”

Section: Plos Onementioning

confidence: 99%

“…In 2011 Haseneyer et al [20] published a 5K single nucleotide polymorphism (SNP) array for rye, succeeded by the 600K array by Bauer et al [1]. Recently Rabanus-Wallace et al [21] published the first chromosome-scale assembly of the 7.9 Gbp rye genome. In conjunction, these genomic resources represent significant milestones, providing indispensable tools for elucidating genes underlying important agronomic traits, implementation of genomic-based breeding techniques and dissecting population genetics in rye [22].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

Vendelbo

Sarup²,

Orabi³

et al. 2020

PLoS ONE

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Rye (Secale cereale L.) responds strongly to changes in heterozygosity with hybrids portraying strong heterosis effect on all developmental and yielding characteristics. In order to achieve the highest potential heterosis effect parental lines must originate from genetically distinct gene pools. Here we report the first comprehensive SNP-based population study of an elite germplasm using fertilization control system for hybrid breeding in rye that is genetically different to the predominating P-type. In total 376 inbred lines from Nordic Seed Germany GmbH were genotyped for 4419 polymorphic SNPs. The aim of this study was to confirm and quantify the genetic separation of parental populations, unveil their genetic characteristics and investigate underlying population structures. Through a palette of complimenting analysis, we confirmed a strong genetic differentiation (F ST = 0.332) of parental populations validating the germplasms suitability for hybrid breeding. These were, furthermore, found to diverge considerably in several features with the maternal population portraying a strong population structure characterized by a narrow genetic profile, small effective population size and high genome-wise linkage disequilibrium. We propose that the employed male-sterility system putatively constitutes a population determining parameter by influencing the rate of introducing novel genetic variation to the parental populations. Functional analysis of linkage blocks led to identification of a conserved segment on the distal 4RL chromosomal region annotated to the Rfp3 male-fertility restoration 'Pampa' type gene. Findings of our study emphasized the immediate value of comprehensive population studies on elite breeding germplasms as a prerequisite for application of genomic-based breeding techniques, introgression of novel material and to support breeder decisionmaking.

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Section: Resultsmentioning

confidence: 99%

Section: Plos Onementioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

Vendelbo

Sarup²,

Orabi³

et al. 2020

PLoS ONE

View full text Add to dashboard Cite

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“…There is a rich history in wheat breeding of impactful translocations coming from distant species and wild relatives. For example, the wheat-rye 1RS translocations in wheat is frequently associated with higher yield and stress tolerance and was brought into hundreds of wheat cultivars worldwide (Lukaszewski 2015;Graybosch et al 2019;Rabanus-Wallace et al 2019). The T7DL•7Ag translocation in wheat from Thinopyrum elongatum (syn.…”

Section: Discussionmentioning

confidence: 99%

The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding

et al. 2020

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Key message The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. Abstract The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, ‘Jagger’ and ‘CDC Stanley,’ and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.

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“…Unfortunately, we have not succeeded in the indisputable targeting of the gene of interest. Recently released new data on the wheat genome sequence [ 95 ], and the more advanced version of rye genome sequence [ 96 ], opened new opportunities in candidate gene identification. Indication of the ScGA2ox12 gene as a candidate for determinant of the dominant type of dwarfing named Ddw1 in rye [ 97 ] can be showed as a case in point.…”

Section: Discussionmentioning

confidence: 99%

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

Góralska

Bińkowski

Lenarczyk

et al. 2020

IJMS

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The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F2 population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.0) and three ML algorithms: logistic regression (LR), random forest and extreme gradient boosted trees (XGBoost), were used to select markers closely linked to the gene encoding wax layer. The allele conditioning the nonglaucous appearance of plants, derived from the cultivar Karlikovaja Zelenostebelnaja, was mapped at the chromosome 2R, which is the first report on this localization. The DNA sequence of DArT-Silico 3585843, closely linked to wax segregation detected by using ML methods, was indicated as one of the candidates controlling the studied trait. The putative gene encodes the ABCG11 transporter.

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Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential

Cited by 31 publications

References 136 publications

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

Genetic structure of a germplasm for hybrid breeding in rye (Secale cereale L.)

The Aegilops ventricosa 2NvS segment in bread wheat: cytology, genomics and breeding

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data

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