class: center, middle, title-slide background-color: wheat # Genome Plasticity of Wheat ### Junli Zhang ### Dubcovsky Lab, UC Davis ---  ---  ---  ??? 小麦是在距今4000到4500年之间传入到中国的 --- ### Importance of wheat - The 3rd most important cereals in the world: 713 million tons annually worldwide at 2013 - Provide 20% of calories and proteins in human nutritions - Grown from Norway and Russia at 65°N to Argentina at 45°S --- exclude: true ### Wheat Origin  --- ### Wheat Classification #### Based on ploidy - Common wheat (hexaploid, AABBDD) - Durum wheat (tetroploid, AABB) - Einkorn wheat (diploid, AA) #### By color, hardness and growing season - color: white vs. red - hardness: soft vs. hard - growing season: winter vs. spring ---  ---  ??? http://www.uswheat.org/wheatClasses --- ### Wheat genomes  --- ### Wheat Origin  --- **Wild einkorn** .pull-left[ Massive stands of wild einkorn wheat (*T. boeoticum*) in the Karacadag mountain range. Picture taken in early July 2004 ] .pull-right[  ] --- ### Wheat domestication - ~ 10,000 BP: domesticated einkorn in the Karacadag region of southeastern Turkey in the northern Levantine Corridor - ~ 9,500–9,000 BP: domesticated emmer first appeared in the southern Levant and in southeastern Turkey - ~ 6,500–7,500 BP: durum wheat was evolved from domesticated emmer wheat - ~ 8,500 BP: the earliest findings of free-threshing ssp. *aestivum* --- ### Wheat domestication  ??? Wheat spikes showing (A) brittle rachis, (B to D) nonbrittle rachis, (A and B) hulled grain, and (C and D) naked grain. (A) Wild emmer wheat (T. turgidum ssp. dicoccoides), (B) domesticated emmer (T. turgidum ssp. dicoccon), (C) durum (T. turgidum ssp. durum), and (D) common wheat (T. aestivum). White scale bars represent 1 cm. Letters at the lower right corner indicate the genome formula of each type of wheat. Gene symbols: Br, brittle rachis; Tg, tenacious glumes; and Q, square head. [Photos by C. Uauy] domestication syndrome shared by all domesticated wheats are increased seed size, reduced number of tillers, more erect growth, and reduced seed dormancy --- ### Wheat seeds diversity  --- exclude: true ### Advantages of hexploid wheat Compared with tetraploid wheat, hexaploid *T. aestivum* has - broader adaptability to different photoperiod and vernalization requirements - improved tolerance to salt, low pH, aluminum, and frost - better resistance to several pests and diseases - extended potential to make different food products --- ### Hexaploid wheat genomes - Big: 17 Gb (5x human, 40x rice, ...) - Three subgenomes: A, B, D - Behaves much like a diploid organism during meiosis - Genome plasitity: high buffering effect of polyploidy on gene deletions - Can tolerate aneuploidy: a large number of aneuploids, including - a complete set of monosomics - a set of 42 compensating nullisomic-tetrasomics - a complete set of 42 ditelocentrics, and - more than 400 segmental deletion lines - Polyploidy bottleneck: D-genome diversity is limited ---  ---  --- ### Wheat genome evolution - `>` 10-fold genome expansion due to transposable elements (TE)  - Rapid divergence in intergenic regions: in 1 MYA 70% of the intergenic regions are different  ??? - Fast change in regions between genes - Fast rate of gene deletions and changes in gene regulation - Wheat has a dynamic genome buffered by the redundancy of polyploidy --- ### Gene examples - Insertions of repetitive elements within regulatory regions of the wheat *VRN1* and *VRN3* vernalization genes, as well as four large independent deletions within the *VRN1* first intron, have been associated with the elimination of the vernalization requirement - A deletion upstream of the *PPD-D1* photoperiod gene is associated with the widely distributed photoperiod insensitive allele - Male sterility gene *Ms2* is an orphan gene within the *Triticinae* and expression of *Ms2* in anthers is associated with insertion of a retroelement into the promoter --- ### Sequencecd wheat genomes - The progenitor of the wheat D genome *Aegilops tauschii* (Luo et al. 2017) - Wild emmer genome (AABB) (Avni et al. 2017) - Chinese Spring hexploid wheat genome (AABBDD) (Zimin et al. 2017, no psuedomolecules; IWGSC version has psuedomolecules, but not unpublished yet) --- ### Increase wheat genetic diversity - Use collection materials - Introduce genes or genomic fragments from its relatives: 1BL.1RS translocation lines, several rust resistance genes, Xiaoyan series wheat cultivars from Dr. Zhensheng Li - Synthetic wheat: increase D genome diversity - Indcued mutations - Gene editing --- ### Example: USDA NSGC wheat core collection  --- ### *Ph1* locus on 5B - Control homologous choromsome paring - Important agronomically: help introduce novel genes into modern cultivars from wheat relatives  --- exclude: true ### Important genes in wheat - Vernalization genes: *Vrn1* - Photoperiod genes: *Ppd1* - Reduced height genes: *Rht1* --- ### Importance of reverse genetics in wheat - Common wheat is a young polyploid with duplicated or triplicated gene copies - The effects of gene mutations are more frequently masked by redundant gene copies of the other genomes - Have to use reverse genetic tools to study some gene functions --- ### Example: *VRN1* vs. *VRN2* - ***VRN1***: promotes the transition of the apical meristem between the vegetative and reproductive stages. - Natural variation in the vernalization requirement for both barley and wheat is frequently associated with deletions or mutations in the regulatory regions - ***VRN2***: acts as a flowering repressor - a spring growth habit associated with natural loss-of-function mutations or deletions of the VRN2 gene has been observed so far only in barley and diploid species of wheat -- - **.blue[Recessive mutations]** are more difficult to select in in the polyploid wheat species than in diploid wheat and barley species - The selection of .blue[dominant or semidominant] mutations is favored in the polyploid wheat species during domestication and more recent breeding efforts - Need to combine loss-of-function mutations in multiple homoeologs to reveal the hidden variations ??? The free-threshing Q allele originated from a silent mutation in the microRNA miR172 binding site in the 5A homoeolog that reduces the cleavage of this specific transcript. only 9 out of 135 rust resistance genes are characterized as recessive --- .center[  ] --- ### Wheat TILLING database - http://www.wheat-tilling.com/ - Tetraploid durum wheat cv 'Kronos' and hexaploid bread wheat cv 'Cadenza' - Exon-capture sequencing to identify mutations and predict their effects - 35 mutations per kilobase in tetraploid wheat and 40 mutations per kilobase in hexaploid wheat ---  ---  --- ### Acknowledgement - My postdoc advisor: **Dr. Jorge Dubcovsky** - My PhD advisor: **Dr. Jianli Chen** --- ### References .cite[ - Dubcovsky, J., and J. Dvorak, 2007 Genome Plasticity a Key Factor in the Success of Polyploid Wheat Under Domestication. Science 316: 1862–1866. - Uauy, C., B. B. H. Wulff, and J. Dubcovsky, 2017 Combining Traditional Mutagenesis with New High-Throughput Sequencing and Genome Editing to Reveal Hidden Variation in Polyploid Wheat. Annual Review of Genetics 51: 435–454. - Krasileva, K. V., H. A. Vasquez-Gross, T. Howell, P. Bailey, F. Paraiso et al., 2017 Uncovering hidden variation in polyploid wheat. PNAS 114: E913–E921. - Maccaferri, M., J. Zhang, P. Bulli, Z. Abate, S. Chao et al., 2015 A genome-wide association study of resistance to stripe rust (Puccinia striiformis f. sp. tritici) in a worldwide collection of hexaploid spring wheat (Triticum aestivum L.). G3 5: 449–465. - Wang, M., S. Wang, Z. Liang, W. Shi, C. Gao et al., 2018 From Genetic Stock to Genome Editing: Gene Exploitation in Wheat. Trends in Biotechnology 36: 160–172. - 年度盘点:2017年小麦研究领域的重大事件: http://blog.sciencenet.cn/blog-1094241-1092636.html - 考古 | 南稻北麦的饮食格局: http://mp.weixin.qq.com/s/tFUDimXvtucn2edjzAxomw ]