High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

Winfield, Mark; Allen, Alexandra M.; Burridge, Amanda J.; Barker, G. L.; Benbow, Harriet R.; Wilkinson, Paul; Coghill, Jane A.; Waterfall, Christy; Davassi, Alessandro; Scopes, Geoff; Pirani, Ali; Webster, Teresa A.; Brew, Fiona; Bloor, Claire; King, Julie; West, Claire; Griffiths, Simon; King, Ian P.; Bentley, Alison R.; Edwards, Keith J.

doi:10.1111/pbi.12485

Cited by 344 publications

(297 citation statements)

References 46 publications

(59 reference statements)

Supporting

Mentioning

288

Contrasting

Unclassified

Order By: Relevance

“…However, most of these QTLs could not be physically mapped, and individual results are not typically comparable because studies used different mapping populations and different sets of markers. To address this deficiency, we mapped all available markers, including 735 firstgeneration restriction-fragment length polymorphisms (RFLPs) 40 , 3,536 second-generation marker SSRs 41 and millions of third-generation SNPs (90 K 42 , 820 K 43 and 660 K used in our laboratory) to the Ae. tauschii genome, and generated a high-resolution integrated genetic map corresponding to the genome sequences (Fig.…”

Section: Integrated Genetic Map and Key Agronomic Genes/qtls Mapmentioning

confidence: 99%

The Aegilops tauschii genome reveals multiple impacts of transposons

Zhao¹,

Zou²,

et al. 2017

Nature Plants

148

100

View full text Add to dashboard Cite

Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/ quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time. NaTuRe PLaNTs

show abstract

“…A high number of genome-wide, segmental Am. muticum introgressions into wheat could be detected by using a subset of a previously developed array of single nucleotide polymorphism (SNP) markers (SNPs), showing polymorphism between ten wild wheat relatives and wheat genotypes [87].…”

Section: The Way Forwardmentioning

confidence: 99%

Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities

et al. 2017

View full text Add to dashboard Cite

Wild species are extremely rich resources of useful genes not available in the cultivated gene pool. For species providing staple food to mankind, such as the cultivated Triticum species, including hexaploid bread wheat (Triticum aestivum, 6x) and tetraploid durum wheat (T. durum, 4x), widening the genetic base is a priority and primary target to cope with the many challenges that the crop has to face. These include recent climate changes, as well as actual and projected demographic growth, contrasting with reduction of arable land and water reserves. All of these environmental and societal modifications pose major constraints to the required production increase in the wheat crop. A sustainable approach to address this task implies resorting to non-conventional breeding strategies, such as "chromosome engineering". This is based on cytogenetic methodologies, which ultimately allow for the incorporation into wheat chromosomes of targeted, and ideally small, chromosomal segments from the genome of wild relatives, containing the gene(s) of interest. Chromosome engineering has been successfully applied to introduce into wheat genes/QTL for resistance to biotic and abiotic stresses, quality attributes, and even yield-related traits. In recent years, a substantial upsurge in effective alien gene exploitation for wheat improvement has come from modern technologies, including use of molecular markers, molecular cytogenetic techniques, and sequencing, which have greatly expanded our knowledge and ability to finely manipulate wheat and alien genomes. Examples will be provided of various types of stable introgressions, including pyramiding of different alien genes/QTL, into the background of bread and durum wheat genotypes, representing valuable materials for both species to respond to the needed novelty in current and future breeding programs. Challenging contexts, such as that inherent to the 4x nature of durum wheat when compared to 6x bread wheat, or created by presence of alien genes affecting segregation of wheat-alien recombinant chromosomes, will also be illustrated.

show abstract

“…Examples of the former include alfalfa (Li et al, 2014b), chrysanthemum (van Geest et al, 2017c, potato (Hamilton et al, 2011;Felcher et al, 2012;Vos et al, 2015), rose and sour cherry (Peace et al, 2012). Examples of allopolyploid SNP arrays include cotton (Hulse-Kemp et al, 2015), oat (Tinker et al, 2014), oilseed rape (Dalton- Morgan et al, 2014;Clarke et al, 2016), peanut (Pandey et al, 2017), strawberry (Bassil et al, 2015) and wheat (Akhunov et al, 2009;Cavanagh et al, 2013;Wang et al, 2014b;Winfield et al, 2016). Untargeted approaches such as genotyping-by-sequencing have also been applied, for example in autopolyploids such as alfalfa Yu et al, 2017), blueberry (McCallum et al, 2016), bluestem prairie grass (Andropogon gerardii) (McAllister and Miller, 2016), cocksfoot (Dactylis glomerata) (Bushman et al, 2016), potato (Uitdewilligen et al, 2013;Sverrisdóttir et al, 2017), sugarcane (Balsalobre et al, 2017;Yang et al, 2017b) and sweet potato (Shirasawa et al, 2017), and in allopolyploids such as coffee (Moncada et al, 2016), cotton (Islam et al, 2015;Reddy et al, 2017), intermediate wheatgrass (Thinopyrum intermedium) (Kantarski et al, 2017), oat (Chaffin et al, 2016), prairie cordgrass (Spartina pectinata) (Crawford et al, 2016), shepherd's purse (Capsella bursa-pastoris) (Cornille et al, 2016), wheat (Poland et al, 2012;Edae et al, 2...…”

Section: Genotyping Technologiesmentioning

confidence: 99%

Genetic mapping in polyploids

Bourke¹

View full text Add to dashboard Cite

“…A total of 7652 high quality polymorphic markers were retained for downstream analysis having frequency of minor allele higher than 5%, frequency of heterozygotes less than 10%. These were aligned via BLAST to the available Bread Wheat Reference Genome [16] with a matching identity cut-off of 99%. As described in Kabbaj et al [15], a selection of 500 hihgly informative and evenly spaced markers with PIC value superior to 0.2 was used to determine that this panel is constituted of 10 sub-populations, of which 4 are landraces: T. abyssinicum type, Central and South Asian, Mediterranean trades, and Middle East.…”

Section: Population Sub-structurementioning

confidence: 99%

Durum Wheat Breeding: In the Heat of the Senegal River

Sall

Bassi²,

Cissé

et al. 2018

Agriculture

View full text Add to dashboard Cite

Global warming may cause +4 • C temperature increases before the end of this century. Heat tolerant bred-germplasm remains the most promising method to ensure farm productivity under this scenario. A global set of 384 durum wheat accessions were exposed to very high temperatures occurring along the Senegal River at two sites for two years. The goal was to identify germplasm with enhanced tolerance to heat. There was significant variation for all traits. The genetic (G) effect accounted for >15% of the total variation, while the genotype by environment interaction (G × E) reached 25%. A selection index that combines G and a G × E wide adaptation index was used to identify stable high yielding germplasm. Forty-eight accessions had a stable grain yield above the average (2.7 t ha −1 ), with the three top lines above 3.5 t ha −1 . Flowering time, spike fertility and harvest index were the most critical traits for heat tolerance, while 1000-kernel weight and spike density only had environment-specific effects. Testing of six subpopulations for grain yield across heat-prone sites revealed an even distribution among clusters, thus showing the potential of this panel for dissecting heat tolerance via association genetics.

show abstract

“…Modern molecular breeding tools apply single nucleotide polymorphism (SNP) molecular genetic markers, and numerous studies have discovered and validated large numbers of SNP markers across the wheat genome (Winfield et al, 2015, Lai et al, 2012c.…”

Section: Introductionmentioning

confidence: 99%

The wheat pangenome: assembly and analysis

Cabrera¹,

Daniel²

View full text Add to dashboard Cite

Wheat is one of the most important food crops in the world and its continued breeding is essential to achieve the production goals set by FAO in 2050. Breeding programs benefit from the development of genomic resources that reduce time and costs of selection of suitable varieties. Recent evidence has suggested that an important fraction of crop plant genomes exhibits presence-absence variation and cannot be exploited following the single reference paradigm. Pangenomic studies aim to fill this vacuum by creating a complete catalogue of genes in a species and characterizing them. With the release of the first wheat draft genome for cultivar Chinese Spring, we are able to explore the wheat pangenome. In the first chapter I performed a review of the current status of wheat genomics and pangenomic studies. In the second chapter the public wheat reference is assessed for its suitability as the basis of a pangenomic study. Extensive uncollapsed duplicated sequences and the absence of support for some gene models prompted us to reassemble the genome. Both assemblies were then compared and the new assembly was selected for further study. In the third chapter, eighteen wheat cultivars were used to extend the Chinese Spring reference. A metagenomics assembly approach was employed and 350 Mbp of additional sequence absent from the Chinese Spring reference were assembled. These sequences contained over 20,000 additional genes which were classified into core and variable genes and later characterized. The pangenome size was modelled as a function of the number of genomes and functional enrichment of the variable genes showed that these were enriched with genes involved in response to biotic and abiotic stress. In chapter 4, we use the new pangenome to identify over 34.6 million SNPs and further use these SNPs to characterize core and variable genes, to construct a high density genetic map and to assess the relatedness of the cultivars used in this study. We show that the variable genes have a higher SNP density particularly for non-synonymous SNPs. The results show that the synthetic cultivar W7984 is the most divergent accession alongside Chinese Spring. Finally, in chapter 5, the future of pangenomic studies is evaluated with a critique and suggestions to improve the current wheat pangenome.

show abstract

High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool

Cited by 344 publications

References 46 publications

The Aegilops tauschii genome reveals multiple impacts of transposons

Harnessing Genetic Diversity of Wild Gene Pools to Enhance Wheat Crop Production and Sustainability: Challenges and Opportunities

Genetic mapping in polyploids

Durum Wheat Breeding: In the Heat of the Senegal River

The wheat pangenome: assembly and analysis

Contact Info

Product

Resources

About