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E-book The Wheat Genome
In 2018, the International Wheat Genome Sequencing Consortium published a reference genome sequence for bread wheat (Triticum aestivum L.). The landmark achievement was the culmination of a thirteen-year international effort focused on the production of a genome sequence linked to genotypic/phenotypic maps to advance understanding of traits and accelerate improvements in wheat breeding. In this mono-graph, we bring together contributions from col-leagues to highlight the advances and document the resources now available for wheat research and its relatives.This first chapter describes the challenges of developing the bread wheat reference genome sequence project, the strategies employed, how the project adapted over time to incorpo-rate technological improvements in genome sequencing and the project outcomes. The fol-lowing chapters include Chap. 2 for a com-prehensive documentation of available data repositories; Chap. 3 using chromosomes as a focus underpinning the establishment of a high-quality assembly; Chap. 4 on the challenge of the structural and functional annotation of the genome; Chap. 5 the wheat transcriptome and functional gene networks; Chap. 6 covering the genome-level diversity within cultivated wheats; Chap. 7 highlights the advances in sequenc-ing ancient wheat DNA; Chap. 8 examines the mpact of the durum wheat genome in identify-ing new germplasm for breeding; Chap. 9 dem-onstrates the use of the genome sequence to identify genes underpinning agronomic traits; Chap. 10 examines new and faster approaches to cloning disease resistance; Chap. 11 docu-ments the genome views of the CIMMYT breed-ing programme; Chap. 12 reviews the gene pools contributing to wheat genetic variation; Chap. 13 provides an overview of approaches to integrating genomics into breeding strategies; Chap. 14 explores pan-genomes for capturing new functionalities and refining wheat genom-ics; Chap. 15 provides insights into the exten-sive germplasm resources established within the wheat community. Since the early 1990s, there has been a growing realization across the world that to feed a rap-idly growing human population grain production needs to increase by an annual rate of 2% on an area of land equivalent to that already under cultivation. Wheat was one of the first domes-ticated food crops and continues to be the most important food grain source for humans today. Wheat is grown on a greater area than any other crop (approx. 255 m ha, Bonjean et al. 2016; https://www.fao.org/faostat/en/#data) and is best adapted to temperate regions of the world.By 2003, demand for wheat already regularly outstripped annual global production, and, faced with an estimated 25% annual loss due to biotic (pests) and abiotic stresses (heat, frost, drought and salinity), it was clear that a paradigm shift was needed in wheat breeding and understand-ing of wheat biology to attain a sustainable food supply. At the time, other areas of biology were benefitting from access to genome data gener-ated through high throughput DNA sequencing projects. The largest genome sequence avail-able was the human genome sequence (3 Gb), for which draft and finished versions were published in 2001 (Lander et al. 2001; Venter et al. 2001) and 2004 (International Human Genome Consortium 2004), respectively. The sequence rapidly yielded new information about the structure, organisation, genes, genetic traits and genome variation to make an imme-diate impact on human biology and medicine. The Arabidopsis thaliana genome sequence (ca.100 Mb) published in 2000 (The Arabidopsis Genome Initiative 2000) was similarly impact-ing understanding of genes and genetic traits in plants, and genome sequencing projects for rice (450 Mb) (Eckhardt 2000; International Rice Genome Sequencing Project and Sasaki 2005) and maize (ca 1 Gb) (Chandler and Brender 2002) were underway.
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