Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Sansaloni, Carolina; Franco, Jorge; Santos, Bruno; Percival‐Alwyn, Lawrence; Singh, Sukhwinder; Petroli, César; Campos, Jaime; Dreher, Kate; Payne, Thomas; Marshall, David; Kilian, Benjamin; Milne, Iain; Raubach, Sebastian; Shaw, Paul; Stephen, Gordon; Carling, Jason; Pierre, Carolina Saint; Burgueño, Juan; Crosa, José; Li, HuiHui; Guzmán, Carlos; Kehel, Zakaria; Amri, Ahmed; Kilian, Andrzej; Wenzl, Peter; Uauy, Cristóbal; Bänziger, Marianne; Cáccamo, Mario; Pixley, K.V.

doi:10.1038/s41467-020-18404-w

Cited by 145 publications

(90 citation statements)

References 70 publications

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“…This would permit more efficient utilization of the germplasm and lower the barrier to mobilizing novel genetic variation into breeding programs. Such a curation effort has been undertaken by the Seeds of Discovery project (CIMMYT, Mexico), wherein 80 000 wheat accessions have been genotyped and core lines representing the genetic diversity of wheat have been identified (Sansaloni et al, 2020).…”

Section: Building Diversity Panelsmentioning

confidence: 99%

Creation and judicious application of a wheat resistance gene atlas

et al. 2021

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Disease-resistance (R) gene cloning in wheat (Triticum aestivum) has been accelerated by the recent surge of genomic resources, facilitated by advances in sequencing technologies and bioinformatics. However, with the challenges of population growth and climate change, it is vital not only to clone and functionally characterize a few handfuls of R genes, but also to do so at a scale that would facilitate the breeding and deployment of crops that can recognize the wide range of pathogen effectors that threaten agroecosystems. Pathogen populations are continually changing, and breeders must have tools and resources available to rapidly respond to those changes if we are to safeguard our daily bread. To meet this challenge, we propose the creation of a wheat R-gene atlas by an international community of researchers and breeders. The atlas would consist of an online directory from which sources of resistance could be identified and deployed to achieve more durable resistance to the major wheat pathogens, such as wheat rusts, blotch diseases, powdery mildew, and wheat blast. We present a costed proposal detailing how the interacting molecular components governing disease resistance could be captured from both the host and the pathogen through biparental mapping, mutational genomics, and whole-genome association genetics. We explore options for the configuration and genotyping of diversity panels of hexaploid and tetraploid wheat, as well as their wild relatives and major pathogens, and discuss how the atlas could inform a dynamic, durable approach to R-gene deployment. Set against the current magnitude of wheat yield losses worldwide, recently estimated at 21%, this endeavor presents one route for bringing R genes from the lab to the field at a considerable speed and quantity.

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Section: Building Diversity Panelsmentioning

confidence: 99%

Creation and judicious application of a wheat resistance gene atlas

et al. 2021

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“…Bread wheat ( Triticum aestivum L.) is an allohexaploid species originating from successive rounds of hybridization in the Fertile Crescent during the Neolithic time, ∼8,000 to 10,000 years ago ( Sansaloni et al, 2020 ). Wheat is the largest contributor to world grain production, with nearly 30% of total grain production and 50% of the world grain trade ( Akter & Rafiqul Islam, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

Tomar

Dhillon

Singh

et al. 2021

PeerJ

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Genetic diversity and population structure information are crucial for enhancing traits of interest and the development of superlative varieties for commercialization. The present study elucidated the population structure and genetic diversity of 141 advanced wheat breeding lines using single nucleotide polymorphism markers. A total of 14,563 high-quality identified genotyping-by-sequencing (GBS) markers were distributed covering 13.9 GB wheat genome, with a minimum of 1,026 SNPs on the homoeologous group four and a maximum of 2,838 SNPs on group seven. The average minor allele frequency was found 0.233, although the average polymorphism information content (PIC) and heterozygosity were 0.201 and 0.015, respectively. Principal component analyses (PCA) and population structure identified two major groups (sub-populations) based on SNPs information. The results indicated a substantial gene flow/exchange with many migrants (Nm = 86.428) and a considerable genetic diversity (number of different alleles, Na = 1.977; the number of effective alleles, Ne = 1.519; and Shannon’s information index, I = 0.477) within the population, illustrating a good source for wheat improvement. The average PIC of 0.201 demonstrates moderate genetic diversity of the present evaluated advanced breeding panel. Analysis of molecular variance (AMOVA) detected 1% and 99% variance between and within subgroups. It is indicative of excessive gene traffic (less genetic differentiation) among the populations. These conclusions deliver important information with the potential to contribute new beneficial alleles using genome-wide association studies (GWAS) and marker-assisted selection to enhance genetic gain in South Asian wheat breeding programs.

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“…Seven SNP arrays that are now available in wheat (Wheat 9K, 15K, 35K, 55K, 90K, 660K, and 820K SNP array) have been widely used mainly to detect trait-related genetic loci by QTL mapping and GWAS [ 14 ]. Among GBS technologies, Diversity Arrays Technology sequencing (DArTseq TM ), which starts from a smart reduction of the complexity of the genome to produce both sequence data and SNP markers, was recently applied to a diversity analysis of 80,000 wheat accessions by Sansaloni et al [ 15 ].…”

Section: Introductionmentioning

confidence: 99%

Digital PCR for Genotype Quantification: A Case Study in a Pasta Production Chain

Morcia¹,

Terzi²,

Ghizzoni³

et al. 2021

Biology

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Digital polymerase chain reaction (dPCR) is a breakthrough technology based on the partitioning of the analytical sample and detection of individual end-point amplifications into the separate compartments. Among the numerous applications of this technology, its suitability in mutation detection is relevant and characterized by unprecedented levels of precision. The actual applicability of this analytical technique to quantify the presence of a specific plant genotype, in both raw materials and transformed products, by exploiting a point polymorphism has been evaluated. As proof of concept, an Italian premium pasta production chain was considered and a dPCR assay based on a durum wheat target variety private point mutation was designed and evaluated in supply-chain samples. From the results obtained, the assay can be applied to confirm the presence of a target variety and to quantify it in raw materials and transformed products, such as commercial grain lots and pasta. The performance, costs, and applicability of the assay has been compared to analytical alternatives, namely simple sequence repeats (SSRs) and genotype-by-sequencing based on Diversity Arrays Technology sequencing (DArTseqTM).

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Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints

Cited by 145 publications

References 70 publications

Creation and judicious application of a wheat resistance gene atlas

Creation and judicious application of a wheat resistance gene atlas

Elucidating SNP-based genetic diversity and population structure of advanced breeding lines of bread wheat (Triticum aestivum L.)

Digital PCR for Genotype Quantification: A Case Study in a Pasta Production Chain

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