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Multiple wheat genomes reveal global variation in modern breeding.

ABSTRACT: Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome¹, and the lack of genome-assembly data for multiple wheat lines^2,3. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses^4,5. We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1⁶, a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

SUBMITTER: Walkowiak S

PROVIDER: S-EPMC7759465 | biostudies-literature | 2020 Dec

REPOSITORIES: biostudies-literature

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Multiple wheat genomes reveal global variation in modern breeding.

Walkowiak Sean S Gao Liangliang L Monat Cecile C Haberer Georg G Kassa Mulualem T MT Brinton Jemima J Ramirez-Gonzalez Ricardo H RH Kolodziej Markus C MC Delorean Emily E Thambugala Dinushika D Klymiuk Valentyna V Byrns Brook B Gundlach Heidrun H Bandi Venkat V Siri Jorge Nunez JN Nilsen Kirby K Aquino Catharine C Himmelbach Axel A Copetti Dario D Ban Tomohiro T Venturini Luca L Bevan Michael M Clavijo Bernardo B Koo Dal-Hoe DH Ens Jennifer J Wiebe Krystalee K N'Diaye Amidou A Fritz Allen K AK Gutwin Carl C Fiebig Anne A Fosker Christine C Fu Bin Xiao BX Accinelli Gonzalo Garcia GG Gardner Keith A KA Fradgley Nick N Gutierrez-Gonzalez Juan J Halstead-Nussloch Gwyneth G Hatakeyama Masaomi M Koh Chu Shin CS Deek Jasline J Costamagna Alejandro C AC Fobert Pierre P Heavens Darren D Kanamori Hiroyuki H Kawaura Kanako K Kobayashi Fuminori F Krasileva Ksenia K Kuo Tony T McKenzie Neil N Murata Kazuki K Nabeka Yusuke Y Paape Timothy T Padmarasu Sudharsan S Percival-Alwyn Lawrence L Kagale Sateesh S Scholz Uwe U Sese Jun J Juliana Philomin P Singh Ravi R Shimizu-Inatsugi Rie R Swarbreck David D Cockram James J Budak Hikmet H Tameshige Toshiaki T Tanaka Tsuyoshi T Tsuji Hiroyuki H Wright Jonathan J Wu Jianzhong J Steuernagel Burkhard B Small Ian I Cloutier Sylvie S Keeble-Gagnère Gabriel G Muehlbauer Gary G Tibbets Josquin J Nasuda Shuhei S Melonek Joanna J Hucl Pierre J PJ Sharpe Andrew G AG Clark Matthew M Legg Erik E Bharti Arvind A Langridge Peter P Hall Anthony A Uauy Cristobal C Mascher Martin M Krattinger Simon G SG Handa Hirokazu H Shimizu Kentaro K KK Distelfeld Assaf A Chalmers Ken K Keller Beat B Mayer Klaus F X KFX Poland Jesse J Stein Nils N McCartney Curt A CA Spannagl Manuel M Wicker Thomas T Pozniak Curtis J CJ

Nature 20201125 7837

Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat (Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome<sup>1</sup>, and the lack of genome-assembly data for multiple wheat lines<sup>2,3</sup>. Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding progra ...[more]

PMID: 33239791

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Project description:BACKGROUND: A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. RESULTS: Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. CONCLUSIONS: In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.

Project description:Key messageWe evaluated genomic selection across five breeding cycles of bread wheat breeding. Bias of within-cycle cross-validation and methods for improving the prediction accuracy were assessed. The prospect of genomic selection has been frequently shown by cross-validation studies using the same genetic material across multiple environments, but studies investigating genomic selection across multiple breeding cycles in applied bread wheat breeding are lacking. We estimated the prediction accuracy of grain yield, protein content and protein yield of 659 inbred lines across five independent breeding cycles and assessed the bias of within-cycle cross-validation. We investigated the influence of outliers on the prediction accuracy and predicted protein yield by its components traits. A high average heritability was estimated for protein content, followed by grain yield and protein yield. The bias of the prediction accuracy using populations from individual cycles using fivefold cross-validation was accordingly substantial for protein yield (17-712 %) and less pronounced for protein content (8-86 %). Cross-validation using the cycles as folds aimed to avoid this bias and reached a maximum prediction accuracy of [Formula: see text] = 0.51 for protein content, [Formula: see text] = 0.38 for grain yield and [Formula: see text] = 0.16 for protein yield. Dropping outlier cycles increased the prediction accuracy of grain yield to [Formula: see text] = 0.41 as estimated by cross-validation, while dropping outlier environments did not have a significant effect on the prediction accuracy. Independent validation suggests, on the other hand, that careful consideration is necessary before an outlier correction is undertaken, which removes lines from the training population. Predicting protein yield by multiplying genomic estimated breeding values of grain yield and protein content raised the prediction accuracy to [Formula: see text] = 0.19 for this derived trait.

Project description:Background:Plant breeding requires numerous generations to be cycled and evaluated before an improved cultivar is released. This lengthy process is required to introduce and test multiple traits of interest. However, a technology for rapid generation advance named 'speed breeding' was successfully deployed in bread wheat (Triticum aestivum L.) to achieve six generations per year while imposing phenotypic selection for foliar disease resistance and grain dormancy. Here, for the first time the deployment of this methodology is presented in durum wheat (Triticum durum Desf.) by integrating selection for key traits, including above and below ground traits on the same set of plants. This involved phenotyping for seminal root angle (RA), seminal root number (RN), tolerance to crown rot (CR), resistance to leaf rust (LR) and plant height (PH). In durum wheat, these traits are desirable in environments where yield is limited by in-season rainfall with the occurrence of CR and epidemics of LR. To evaluate this multi-trait screening approach, we applied selection to a large segregating F2 population (n?=?1000) derived from a bi-parental cross (Outrob4/Caparoi). A weighted selection index (SI) was developed and applied. The gain for each trait was determined by evaluating F3 progeny derived from 100 'selected' and 100 'unselected' F2 individuals. Results:Transgressive segregation was observed for all assayed traits in the Outrob4/Caparoi F2 population. Application of the SI successfully shifted the population mean for four traits, as determined by a significant mean difference between 'selected' and 'unselected' F3 families for CR tolerance, LR resistance, RA and RN. No significant shift for PH was observed. Conclusions:The novel multi-trait phenotyping method presents a useful tool for rapid selection of early filial generations or for the characterization of fixed lines out-of-season. Further, it offers efficient use of resources by assaying multiple traits on the same set of plants. Results suggest that when performed in parallel with speed breeding in early generations, selection will enrich recombinant inbred lines with desirable alleles and will reduce the length and number of years required to combine these traits in elite breeding populations and therefore cultivars.

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Multiple wheat genomes reveal global variation in modern breeding.

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Multiple wheat genomes reveal global variation in modern breeding.

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