Abstract
Cereal crops are members of the Poaceae family that are grown primarily for their seed, many of which are staple foods around the globe. Together, maize, rice, wheat, barley, sorghum, millet, oat, rye, and triticale make up more than half of the agricultural production globally. Since diverging from a common ancestor 50–70 Mya, the genomes of cereal crops have been subject to evolutionary forces giving rise to changes in genome size, composition, and complexity. Over the past two decades, efforts to sequence the genomes of the main cereal crops have resulted in highly contiguous, chromosome-scale genome assemblies. Rice has the smallest genome size (420 megabases (Mb)), which led to it being the first assembled cereal genome. However, the immense genome size and complexity for some cereal crops, such as wheat (17 gigabases (Gb)) and oat (12 Gb), have hindered genome sequencing progress. Recently, the reduction in sequencing costs coupled with new technological advances including ultra-long-read sequencing and advanced genome assembly algorithms has now made it possible to achieve chromosome-scale assemblies in all cereals. As a result, we have now entered a new era of genomics for cereal crops. Researchers now face the daunting task of unravelling the function of all genes and non-genic regions of the genomes in cereals, particularly in crops like wheat and oat where little is known about the genetic basis for most economically important traits. Recent advances in high-throughput phenotyping, metabolomics, proteomics, and CRISPR/CAS9 technologies will facilitate this process and pave the way for exciting discoveries in functional genomics of cereals.
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Wang N, Yuan Y, Wang H, Yu D, Liu Y, Zhang A, Gowda M, Nair SK, Hao Z, Lu Y, San Vicente F, Prasanna BM, Li X, Zhang X (2020) Applications of genotyping-by-sequencing (GBS) in maize genetics and breeding. Sci Rep 10(1):16308. https://doi.org/10.1038/s41598-020-73321-8
Goff SA, Ricke D, Lan T-H, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun W-L, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296(5565):92. https://doi.org/10.1126/science.1068275
Paterson AH, Freeling M, Sasaki T (2005) Grains of knowledge: genomics of model cereals. Genome Res 15(12):1643–1650. https://doi.org/10.1101/gr.3725905
Zhao T, Schranz ME (2019) Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes. Proc Natl Acad Sci 116(6):2165. https://doi.org/10.1073/pnas.1801757116
Hu H, Scheben A, Edwards D (2018) Advances in integrating genomics and bioinformatics in the plant breeding pipeline. Agriculture 8:6. https://doi.org/10.3390/agriculture8060075
International Wheat Genome Sequencing Consortium (IWGSC) (2014) A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345(6194):1251788. https://doi.org/10.1126/science.1251788
Zhang M, Zhang Y, Scheuring CF, Wu C-C, Dong JJ, Zhang H-B (2012) Preparation of megabase-sized DNA from a variety of organisms using the nuclei method for advanced genomics research. Nat Protoc 7(3):467–478. https://doi.org/10.1038/nprot.2011.455
Krasileva KV, Vasquez-Gross HA, Howell T, Bailey P, Paraiso F, Clissold L, Simmonds J, Ramirez-Gonzalez RH, Wang X, Borrill P, Fosker C, Ayling S, Phillips AL, Uauy C, Dubcovsky J (2017) Uncovering hidden variation in polyploid wheat. PNAS 114(6):E913–E921. https://doi.org/10.1073/pnas.1619268114
Arora S, Steuernagel B, Gaurav K, Chandramohan S, Long Y, Matny O, Johnson R, Enk J, Periyannan S, Singh N, Asyraf Md Hatta M, Athiyannan N, Cheema J, Yu G, Kangara N, Ghosh S, Szabo LJ, Poland J, Bariana H, Jones JDG, Bentley AR, Ayliffe M, Olson E, Xu SS, Steffenson BJ, Lagudah E, Wulff BBH (2019) Resistance gene cloning from a wild crop relative by sequence capture and association genetics. Nat Biotechnol 37(2):139–143. https://doi.org/10.1038/s41587-018-0007-9
Steuernagel B, Witek K, Jones JDG, Wulff BBH (2017) MutRenSeq: a method for rapid cloning of plant disease resistance genes. Methods Mol Biol 1659:215–229. https://doi.org/10.1007/978-1-4939-7249-4_19
Jouanin A, Borm T, Boyd LA, Cockram J, Leigh F, Santos BACM, Visser RGF, Smulders MJM (2019) Development of the GlutEnSeq capture system for sequencing gluten gene families in hexaploid bread wheat with deletions or mutations induced by γ-irradiation or CRISPR/Cas9. J Cereal Sci 88:157–166. https://doi.org/10.1016/j.jcs.2019.04.008
Miga KH, Koren S, Rhie A, Vollger MR, Gershman A, Bzikadze A, Brooks S, Howe E, Porubsky D, Logsdon GA, Schneider VA, Potapova T, Wood J, Chow W, Armstrong J, Fredrickson J, Pak E, Tigyi K, Kremitzki M, Markovic C, Maduro V, Dutra A, Bouffard GG, Chang AM, Hansen NF, Wilfert AB, Thibaud-Nissen F, Schmitt AD, Belton J-M, Selvaraj S, Dennis MY, Soto DC, Sahasrabudhe R, Kaya G, Quick J, Loman NJ, Holmes N, Loose M, Surti U, Ra R, Graves Lindsay TA, Fulton R, Hall I, Paten B, Howe K, Timp W, Young A, Mullikin JC, Pevzner PA, Gerton JL, Sullivan BA, Eichler EE, Phillippy AM (2020) Telomere-to-telomere assembly of a complete human X chromosome. Nature 585(7823):79–84. https://doi.org/10.1038/s41586-020-2547-7
Nilsen KT, Walkowiak S, Xiang D, Gao P, Quilichini TD, Willick IR, Byrns B, N’Diaye A, Ens J, Wiebe KJPotNAoS (2020) Copy number variation of TdDof controls solid-stemmed architecture in wheat. Proc Natl Acad Sci U S A 117(46):28708–28718
Kovaka S, Fan Y, Ni B, Timp W, Schatz MC (2020) Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED. Nat Biotechnol. https://doi.org/10.1038/s41587-020-0731-9
Maccaferri M, Harris NS, Twardziok SO, Pasam RK, Gundlach H, Spannagl M, Ormanbekova D, Lux T, Prade VM, Milner SG, Himmelbach A, Mascher M, Bagnaresi P, Faccioli P, Cozzi P, Lauria M, Lazzari B, Stella A, Manconi A, Gnocchi M, Moscatelli M, Avni R, Deek J, Biyiklioglu S, Frascaroli E, Corneti S, Salvi S, Sonnante G, Desiderio F, Marè C, Crosatti C, Mica E, Özkan H, Kilian B, De Vita P, Marone D, Joukhadar R, Mazzucotelli E, Nigro D, Gadaleta A, Chao S, Faris JD, Melo ATO, Pumphrey M, Pecchioni N, Milanesi L, Wiebe K, Ens J, MacLachlan RP, Clarke JM, Sharpe AG, Koh CS, Liang KYH, Taylor GJ, Knox R, Budak H, Mastrangelo AM, Xu SS, Stein N, Hale I, Distelfeld A, Hayden MJ, Tuberosa R, Walkowiak S, Mayer KFX, Ceriotti A, Pozniak CJ, Cattivelli L (2019) Durum wheat genome highlights past domestication signatures and future improvement targets. Nat Genet 51(5):885–895. https://doi.org/10.1038/s41588-019-0381-3
Avni R, Nave M, Barad O, Baruch K, Twardziok SO, Gundlach H, Hale I, Mascher M, Spannagl M, Wiebe K, Jordan KW, Golan G, Deek J, Ben-Zvi B, Ben-Zvi G, Himmelbach A, MacLachlan RP, Sharpe AG, Fritz A, Ben-David R, Budak H, Fahima T, Korol A, Faris JD, Hernandez A, Mikel MA, Levy AA, Steffenson B, Maccaferri M, Tuberosa R, Cattivelli L, Faccioli P, Ceriotti A, Kashkush K, Pourkheirandish M, Komatsuda T, Eilam T, Sela H, Sharon A, Ohad N, Chamovitz DA, Mayer KFX, Stein N, Ronen G, Peleg Z, Pozniak CJ, Akhunov ED, Distelfeld A (2017) Wild emmer genome architecture and diversity elucidate wheat evolution and domestication. Science 357(6346):93. https://doi.org/10.1126/science.aan0032
The International Wheat Genome Sequencing Consortium (IWGSC), Appels R, Eversole K, Feuillet C, Keller B, Rogers J, Stein N, Pozniak CJ, Choulet F, Distelfeld A, Poland JJS (2018) Shifting the limits in wheat research and breeding using a fully annotated reference genome. Science 361(6403):eaar7191
Walkowiak S, Gao L, Monat C, Haberer G, Kassa MT, Brinton J, Ramirez-Gonzalez RH, Kolodziej MC, Delorean E, Thambugala DJN (2020) Multiple wheat genomes reveal global variation in modern breeding. Nature 588:1–7
Clavijo BJ, Garcia Accinelli G, Wright J, Heavens D, Barr K, Yanes L, Di-Palma F (2017) W2RAP: a pipeline for high quality, robust assemblies of large complex genomes from short read data. bioRxiv:110999. https://doi.org/10.1101/110999
Monat C, Padmarasu S, Lux T, Wicker T, Gundlach H, Himmelbach A, Ens J, Li C, Muehlbauer GJ, Schulman AH, Waugh R, Braumann I, Pozniak C, Scholz U, Mayer KFX, Spannagl M, Stein N, Mascher M (2019) TRITEX: chromosome-scale sequence assembly of Triticeae genomes with open-source tools. Genome Biol 20(1):284. https://doi.org/10.1186/s13059-019-1899-5
Jayakodi M, Padmarasu S, Haberer G, Bonthala VS, Gundlach H, Monat C, Lux T, Kamal N, Lang D, Himmelbach A, Ens J, Zhang X-Q, Angessa TT, Zhou G, Tan C, Hill C, Wang P, Schreiber M, Boston LB, Plott C, Jenkins J, Guo Y, Fiebig A, Budak H, Xu D, Zhang J, Wang C, Grimwood J, Schmutz J, Guo G, Zhang G, Mochida K, Hirayama T, Sato K, Chalmers KJ, Langridge P, Waugh R, Pozniak CJ, Scholz U, Mayer KFX, Spannagl M, Li C, Mascher M, Stein N (2020) The barley pan-genome reveals the hidden legacy of mutation breeding. Nature 588(7837):284–289. https://doi.org/10.1038/s41586-020-2947-8
Zimin AV, Puiu D, Luo MC, Zhu T, Koren S, Marçais G, Yorke JA, Dvořák J, Salzberg SL (2017) Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm. Genome Res 27(5):787–792. https://doi.org/10.1101/gr.213405.116
Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KFX, Scholz U, Poland JA, Stein N, Waugh R (2013) Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J 76(4):718–727. https://doi.org/10.1111/tpj.12319
Zhu T, Wang L, Rodriguez JC, Deal KR, Avni R, Distelfeld A, McGuire PE, Dvorak J, Luo M-C (2019) Improved genome sequence of wild emmer wheat Zavitan with the aid of optical maps. G3 (Bethesda) 9(3):619–624. https://doi.org/10.1534/g3.118.200902
Li H (2018) Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 34(18):3094–3100. https://doi.org/10.1093/bioinformatics/bty191
Kim D, Langmead B, Salzberg SL (2015) HISAT: a fast spliced aligner with low memory requirements. Nat Methods 12(4):357–360. https://doi.org/10.1038/nmeth.3317
Kim D, Paggi JM, Park C, Bennett C, Salzberg SL (2019) Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol 37(8):907–915. https://doi.org/10.1038/s41587-019-0201-4
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2012) STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635
Stein N (2007) Triticeae genomics: advances in sequence analysis of large genome cereal crops. Chromosom Res 15(1):21–31. https://doi.org/10.1007/s10577-006-1107-9
Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown. Nat Protoc 11:1650. https://doi.org/10.1038/nprot.2016.095
Ma J, Bennetzen JL (2004) Rapid recent growth and divergence of rice nuclear genomes. Proc Natl Acad Sci U S A 101(34):12404. https://doi.org/10.1073/pnas.0403715101
Yu J, Hu S, Wang J, Wong GK-S, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296(5565):79. https://doi.org/10.1126/science.1068037
Sasaki T, Matsumoto T, Yamamoto K, Sakata K, Baba T, Katayose Y, Wu J, Niimura Y, Cheng Z, Nagamura Y, Antonio BA, Kanamori H, Hosokawa S, Masukawa M, Arikawa K, Chiden Y, Hayashi M, Okamoto M, Ando T, Aoki H, Arita K, Hamada M, Harada C, Hijishita S, Honda M, Ichikawa Y, Idonuma A, Iijima M, Ikeda M, Ikeno M, Ito S, Ito T, Ito Y, Ito Y, Iwabuchi A, Kamiya K, Karasawa W, Katagiri S, Kikuta A, Kobayashi N, Kono I, Machita K, Maehara T, Mizuno H, Mizubayashi T, Mukai Y, Nagasaki H, Nakashima M, Nakama Y, Nakamichi Y, Nakamura M, Namiki N, Negishi M, Ohta I, Ono N, Saji S, Sakai K, Shibata M, Shimokawa T, Shomura A, Song J, Takazaki Y, Terasawa K, Tsuji K, Waki K, Yamagata H, Yamane H, Yoshiki S, Yoshihara R, Yukawa K, Zhong H, Iwama H, Endo T, Ito H, Hahn JH, Kim H-I, Eun M-Y, Yano M, Jiang J, Gojobori T (2002) The genome sequence and structure of rice chromosome 1. Nature 420(6913):312–316. https://doi.org/10.1038/nature01184
Feng Q, Zhang Y, Hao P, Wang S, Fu G, Huang Y, Li Y, Zhu J, Liu Y, Hu X, Jia P, Zhang Y, Zhao Q, Ying K, Yu S, Tang Y, Weng Q, Zhang L, Lu Y, Mu J, Lu Y, Zhang LS, Yu Z, Fan D, Liu X, Lu T, Li C, Wu Y, Sun T, Lei H, Li T, Hu H, Guan J, Wu M, Zhang R, Zhou B, Chen Z, Chen L, Jin Z, Wang R, Yin H, Cai Z, Ren S, Lv G, Gu W, Zhu G, Tu Y, Jia J, Zhang Y, Chen J, Kang H, Chen X, Shao C, Sun Y, Hu Q, Zhang X, Zhang W, Wang L, Ding C, Sheng H, Gu J, Chen S, Ni L, Zhu F, Chen W, Lan L, Lai Y, Cheng Z, Gu M, Jiang J, Li J, Hong G, Xue Y, Han B (2002) Sequence and analysis of rice chromosome 4. Nature 420(6913):316–320. https://doi.org/10.1038/nature01183
Consortium TRCS (2003) In-depth view of structure, activity, and evolution of rice chromosome 10. Science 300(5625):1566. https://doi.org/10.1126/science.1083523
Sasaki T, International Rice Genome Sequencing P (2005) The map-based sequence of the rice genome. Nature 436(7052):793–800. https://doi.org/10.1038/nature03895
Kawahara Y, de la Bastide M, Hamilton JP, Kanamori H, McCombie WR, Ouyang S, Schwartz DC, Tanaka T, Wu J, Zhou S, Childs KL, Davidson RM, Lin H, Quesada-Ocampo L, Vaillancourt B, Sakai H, Lee SS, Kim J, Numa H, Itoh T, Buell CR, Matsumoto T (2013) Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data. Rice 6(1):4. https://doi.org/10.1186/1939-8433-6-4
Choi JY, Lye ZN, Groen SC, Dai X, Rughani P, Zaaijer S, Harrington ED, Juul S, Purugganan MD (2020) Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice. Genome Biol 21(1):21. https://doi.org/10.1186/s13059-020-1938-2
Du H, Yu Y, Ma Y, Gao Q, Cao Y, Chen Z, Ma B, Qi M, Li Y, Zhao X, Wang J, Liu K, Qin P, Yang X, Zhu L, Li S, Liang C (2017) Sequencing and de novo assembly of a near complete indica rice genome. Nat Commun 8(1):15324. https://doi.org/10.1038/ncomms15324
Tanaka T, Nishijima R, Teramoto S, Kitomi Y, Hayashi T, Uga Y, Kawakatsu T (2020) De novo genome assembly of the indica rice variety IR64 using linked-read sequencing and nanopore sequencing. G3: Genes|Genomes|Genetics 10(5):1495. https://doi.org/10.1534/g3.119.400871
Brozynska M, Copetti D, Furtado A, Wing RA, Crayn D, Fox G, Ishikawa R, Henry RJ (2017) Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice. Plant Biotechnol J 15(6):765–774. https://doi.org/10.1111/pbi.12674
Song S, Tian D, Zhang Z, Hu S, Yu J (2018) Rice genomics: over the past two decades and into the future. Genomics Proteomics Bioinformatics 16(6):397–404. https://doi.org/10.1016/j.gpb.2019.01.001
Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, Zhang J, Zhang Y, Li R, Xu Z, Li S, Li X, Zheng H, Cong L, Lin L, Yin J, Geng J, Li G, Shi J, Liu J, Lv H, Li J, Wang J, Deng Y, Ran L, Shi X, Wang X, Wu Q, Li C, Ren X, Wang J, Wang X, Li D, Liu D, Zhang X, Ji Z, Zhao W, Sun Y, Zhang Z, Bao J, Han Y, Dong L, Ji J, Chen P, Wu S, Liu J, Xiao Y, Bu D, Tan J, Yang L, Ye C, Zhang J, Xu J, Zhou Y, Yu Y, Zhang B, Zhuang S, Wei H, Liu B, Lei M, Yu H, Li Y, Xu H, Wei S, He X, Fang L, Zhang Z, Zhang Y, Huang X, Su Z, Tong W, Li J, Tong Z, Li S, Ye J, Wang L, Fang L, Lei T, Chen C, Chen H, Xu Z, Li H, Huang H, Zhang F, Xu H, Li N, Zhao C, Li S, Dong L, Huang Y, Li L, Xi Y, Qi Q, Li W, Zhang B, Hu W, Zhang Y, Tian X, Jiao Y, Liang X, Jin J, Gao L, Zheng W, Hao B, Liu S, Wang W, Yuan L, Cao M, McDermott J, Samudrala R, Wang J, Wong GK-S, Yang H (2005) The genomes of Oryza sativa: a history of duplications. PLoS Biol 3(2):e38. https://doi.org/10.1371/journal.pbio.0030038
Chandler VL, Brendel V (2002) The maize genome sequencing project. Plant Physiol 130(4):1594. https://doi.org/10.1104/pp.015594
Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW, Ying K, Yeh C-T, Emrich SJ, Jia Y, Kalyanaraman A, Hsia A-P, Barbazuk WB, Baucom RS, Brutnell TP, Carpita NC, Chaparro C, Chia J-M, Deragon J-M, Estill JC, Fu Y, Jeddeloh JA, Han Y, Lee H, Li P, Lisch DR, Liu S, Liu Z, Nagel DH, McCann MC, SanMiguel P, Myers AM, Nettleton D, Nguyen J, Penning BW, Ponnala L, Schneider KL, Schwartz DC, Sharma A, Soderlund C, Springer NM, Sun Q, Wang H, Waterman M, Westerman R, Wolfgruber TK, Yang L, Yu Y, Zhang L, Zhou S, Zhu Q, Bennetzen JL, Dawe RK, Jiang J, Jiang N, Presting GG, Wessler SR, Aluru S, Martienssen RA, Clifton SW, McCombie WR, Wing RA, Wilson RK (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326(5956):1112. https://doi.org/10.1126/science.1178534
Sun S, Zhou Y, Chen J, Shi J, Zhao H, Zhao H, Song W, Zhang M, Cui Y, Dong X, Liu H, Ma X, Jiao Y, Wang B, Wei X, Stein JC, Glaubitz JC, Lu F, Yu G, Liang C, Fengler K, Li B, Rafalski A, Schnable PS, Ware DH, Buckler ES, Lai J (2018) Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes. Nat Genet 50(9):1289–1295. https://doi.org/10.1038/s41588-018-0182-0
Yang N, Xu X-W, Wang R-R, Peng W-L, Cai L, Song J-M, Li W, Luo X, Niu L, Wang Y, Jin M, Chen L, Luo J, Deng M, Wang L, Pan Q, Liu F, Jackson D, Yang X, Chen L-L, Yan J (2017) Contributions of Zea mays subspecies mexicana haplotypes to modern maize. Nat Commun 8(1):1874. https://doi.org/10.1038/s41467-017-02063-5
Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan J-C, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP (2018) The maize W22 genome provides a foundation for functional genomics and transposon biology. Nat Genet 50(9):1282–1288. https://doi.org/10.1038/s41588-018-0158-0
Yang N, Liu J, Gao Q, Gui S, Chen L, Yang L, Huang J, Deng T, Luo J, He L, Wang Y, Xu P, Peng Y, Shi Z, Lan L, Ma Z, Yang X, Zhang Q, Bai M, Li S, Li W, Liu L, Jackson D, Yan J (2019) Genome assembly of a tropical maize inbred line provides insights into structural variation and crop improvement. Nat Genet 51(6):1052–1059. https://doi.org/10.1038/s41588-019-0427-6
Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA (2016) Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize. Plant Cell 28(11):2700. https://doi.org/10.1105/tpc.16.00353
Li C, Song W, Luo Y, Gao S, Zhang R, Shi Z, Wang X, Wang R, Wang F, Wang J, Zhao Y, Su A, Wang S, Li X, Luo M, Wang S, Zhang Y, Ge J, Tan X, Yuan Y, Bi X, He H, Yan J, Wang Y, Hu S, Zhao J (2019) The HuangZaoSi maize genome provides insights into genomic variation and improvement history of maize. Mol Plant 12(3):402–409. https://doi.org/10.1016/j.molp.2019.02.009
Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin C-S, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D (2017) Improved maize reference genome with single-molecule technologies. Nature 546(7659):524–527. https://doi.org/10.1038/nature22971
Ling H-Q, Ma B, Shi X, Liu H, Dong L, Sun H, Cao Y, Gao Q, Zheng S, Li Y, Yu Y, Du H, Qi M, Li Y, Lu H, Yu H, Cui Y, Wang N, Chen C, Wu H, Zhao Y, Zhang J, Li Y, Zhou W, Zhang B, Hu W, van Eijk MJT, Tang J, Witsenboer HMA, Zhao S, Li Z, Zhang A, Wang D, Liang C (2018) Genome sequence of the progenitor of wheat a subgenome Triticum urartu. Nature 557(7705):424–428. https://doi.org/10.1038/s41586-018-0108-0
Luo M-C, Gu YQ, Puiu D, Wang H, Twardziok SO, Deal KR, Huo N, Zhu T, Wang L, Wang Y, McGuire PE, Liu S, Long H, Ramasamy RK, Rodriguez JC, Van SL, Yuan L, Wang Z, Xia Z, Xiao L, Anderson OD, Ouyang S, Liang Y, Zimin AV, Pertea G, Qi P, Bennetzen JL, Dai X, Dawson MW, Müller H-G, Kugler K, Rivarola-Duarte L, Spannagl M, Mayer KFX, Lu F-H, Bevan MW, Leroy P, Li P, You FM, Sun Q, Liu Z, Lyons E, Wicker T, Salzberg SL, Devos KM, Dvořák J (2017) Genome sequence of the progenitor of the wheat D genome Aegilops tauschii. Nature 551(7681):498–502. https://doi.org/10.1038/nature24486
Wang H, Sun S, Ge W, Zhao L, Hou B, Wang K, Lyu Z, Chen L, Xu S, Guo J, Li M, Su P, Li X, Wang G, Bo C, Fang X, Zhuang W, Cheng X, Wu J, Dong L, Chen W, Li W, Xiao G, Zhao J, Hao Y, Xu Y, Gao Y, Liu W, Liu Y, Yin H, Li J, Li X, Zhao Y, Wang X, Ni F, Ma X, Li A, Xu SS, Bai G, Nevo E, Gao C, Ohm H, Kong L (2020) Horizontal gene transfer of Fhb7 from fungus underlies Fusarium head blight resistance in wheat. Science 368(6493):eaba5435. https://doi.org/10.1126/science.aba5435
Purugganan MD, Fuller DQ (2009) The nature of selection during plant domestication. Nature 457(7231):843–848. https://doi.org/10.1038/nature07895
Sato K (2020) History and future perspectives of barley genomics. DNA Res 27:4. https://doi.org/10.1093/dnares/dsaa023
Blake T, Blake V, Bowman J, Abdel-Haleem H (2011) Barley: production, improvement and uses. In: Ullrich SE (ed) Barley: production, improvement and uses. Wiley-Blackwell, pp 522–531
Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N (2009) The international barley sequencing consortium--at the threshold of efficient access to the barley genome. Plant Physiol 149(1):142–147. https://doi.org/10.1104/pp.108.128967
The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491(7426):711–716. https://doi.org/10.1038/nature11543
Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang X-Q, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544:427. https://doi.org/10.1038/nature22043
Rabanus-Wallace MT, Hackauf B, Mascher M, Lux T, Wicker T, Gundlach H, Báez M, Houben A, Mayer KFX, Guo L, Poland J, Pozniak CJ, Walkowiak S, Melonek J, Praz C, Schreiber M, Budak H, Heuberger M, Steuernagel B, Wulff B, Börner A, Byrns B, Čížková J, Fowler DB, Fritz A, Himmelbach A, Kaithakottil G, Keilwagen J, Keller B, Konkin D, Larsen J, Li Q, Myśków B, Padmarasu S, Rawat N, Sesiz U, Sezgi B, Sharpe A, Šimková H, Small I, Swarbreck D, Toegelová H, Tsvetkova N, Voylokov AV, Vrána J, Bauer E, Bolibok-Bragoszewska H, Doležel J, Hall A, Jia J, Korzun V, Laroche A, Ma X-F, Ordon F, Özkan H, Rakoczy-Trojanowska M, Scholz U, Schulman AH, Siekmann D, Stojałowski S, Tiwari V, Spannagl M, Stein N (2019) Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential. bioRxiv:2019.2012.2011.869693. https://doi.org/10.1101/2019.12.11.869693
Evtushenko EV, Lipikhina YA, Stepochkin PI, Vershinin AV (2019) Cytogenetic and molecular characteristics of rye genome in octoploid triticale (× Triticosecale Wittmack). Comp Cytogenet 13(4):423–434
Ryöppy PH (1997) Haploidy in triticale. In: Jain SM, Sopory SK, Veilleux RE (eds) In vitro haploid production in higher plants. Current plant science and biotechnology in agriculture, vol 26. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-1862-2_5
Bennett MD, Leitch IJ (1995) Nuclear DNA amounts in angiosperms. Ann Bot 76(2):113–176. https://doi.org/10.1006/anbo.1995.1085
Sanz MJ, Jellen EN, Loarce Y, Irigoyen ML, Ferrer E, Fominaya A (2010) A new chromosome nomenclature system for oat (Avena sativa L. and A. byzantina C. Koch) based on FISH analysis of monosomic lines. Theor Appl Genet 121(8):1541–1552. https://doi.org/10.1007/s00122-010-1409-3
Maughan PJ, Lee R, Walstead R, Vickerstaff RJ, Fogarty MC, Brouwer CR, Reid RR, Jay JJ, Bekele WA, Jackson EW, Tinker NA, Langdon T, Schlueter JA, Jellen EN (2019) Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species. BMC Biol 17(1):92. https://doi.org/10.1186/s12915-019-0712-y
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A, Schmutz J, Spannagl M, Tang H, Wang X, Wicker T, Bharti AK, Chapman J, Feltus FA, Gowik U, Grigoriev IV, Lyons E, Maher CA, Martis M, Narechania A, Otillar RP, Penning BW, Salamov AA, Wang Y, Zhang L, Carpita NC, Freeling M, Gingle AR, Hash CT, Keller B, Klein P, Kresovich S, McCann MC, Ming R, Peterson DG, Mehboobur R, Ware D, Westhoff P, KFX M, Messing J, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457(7229):551–556. https://doi.org/10.1038/nature07723
Abrouk M, Ahmed HI, Cubry P, Šimoníková D, Cauet S, Pailles Y, Bettgenhaeuser J, Gapa L, Scarcelli N, Couderc M, Zekraoui L, Kathiresan N, Čížková J, Hřibová E, Doležel J, Arribat S, Bergès H, Wieringa JJ, Gueye M, Kane NA, Leclerc C, Causse S, Vancoppenolle S, Billot C, Wicker T, Vigouroux Y, Barnaud A, Krattinger SG (2020) Fonio millet genome unlocks African orphan crop diversity for agriculture in a changing climate. Nat Commun 11(1):4488. https://doi.org/10.1038/s41467-020-18329-4
Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava RK, Chitikineni A, Fan G, Bajaj P, Punnuri S, Gupta SK, Wang H, Jiang Y, Couderc M, Katta MAVSK, Paudel DR, Mungra KD, Chen W, Harris-Shultz KR, Garg V, Desai N, Doddamani D, Kane NA, Conner JA, Ghatak A, Chaturvedi P, Subramaniam S, Yadav OP, Berthouly-Salazar C, Hamidou F, Wang J, Liang X, Clotault J, Upadhyaya HD, Cubry P, Rhoné B, Gueye MC, Sunkar R, Dupuy C, Sparvoli F, Cheng S, Mahala RS, Singh B, Yadav RS, Lyons E, Datta SK, Hash CT, Devos KM, Buckler E, Bennetzen JL, Paterson AH, Ozias-Akins P, Grando S, Wang J, Mohapatra T, Weckwerth W, Reif JC, Liu X, Vigouroux Y, Xu X (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol 35(10):969–976. https://doi.org/10.1038/nbt.3943
Kang S-H, Kim B, Choi B-S, Lee HO, Kim N-H, Lee SJ, Kim HS, Shin MJ, Kim H-W, Nam K, Kang KD, Kwon S-J, Oh T-J, Lee S-C, Kim C-K (2020) Genome assembly and annotation of soft-shelled Adlay (Coix lacryma-jobi variety ma-yuen), a cereal and medicinal crop in the Poaceae Family. Front Plant Sci 11:630–630. https://doi.org/10.3389/fpls.2020.00630
Gardiner L-J, Wingen LU, Bailey P, Joynson R, Brabbs T, Wright J, Higgins JD, Hall N, Griffiths S, Clavijo BJ, Hall A (2019) Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency. Genome Biol 20(1):69. https://doi.org/10.1186/s13059-019-1675-6
Röder MS, Korzun V, Wendehake K, Plaschke J, Tixier M-H, Leroy P, Ganal MW (1998) A microsatellite map of wheat. Genetics 149(4):2007
Somers DJ, Isaac P, Edwards K (2004) A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet 109(6):1105–1114. https://doi.org/10.1007/s00122-004-1740-7
Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, da Silva ML, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci U S A 110(20):8057–8062. https://doi.org/10.1073/pnas.1217133110
Allen AM, Winfield MO, Burridge AJ, Downie RC, Benbow HR, Barker GLA, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, Griffiths S, Bentley AR, Alda M, Jack P, Phillips AL, Edwards KJ (2017) Characterization of a wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum). Plant Biotechnol J 15(3):390–401. https://doi.org/10.1111/pbi.12635
Wang SC, Wong DB, Forrest K, Allen A, Chao SM, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E, Sequencing IWG (2014) Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array. Plant Biotechnol J 12(6):787–796. https://doi.org/10.1111/pbi.12183
Sun C, Dong Z, Zhao L, Ren Y, Zhang N, Chen F (2020) The wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat. Plant Biotechnol J 18(6):1354–1360. https://doi.org/10.1111/pbi.13361
Winfield MO, Allen AM, Burridge AJ, Barker GLA, Benbow HR, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, King J, West C, Griffiths S, King I, Bentley AR, Edwards KJ (2016) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool. Plant Biotechnol J 14(5):1195–1206. https://doi.org/10.1111/pbi.12485
Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R (2015) A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. Plant Biotechnol J 13(5):648–663. https://doi.org/10.1111/pbi.12288
Robertsen CD, Hjortshøj RL, Janss LL (2019) Genomic selection in cereal breeding. Agronomy 9:2. https://doi.org/10.3390/agronomy9020095
Bettgenhaeuser J, Krattinger SG (2019) Rapid gene cloning in cereals. Theor Appl Genet 132(3):699–711. https://doi.org/10.1007/s00122-018-3210-7
Klymiuk V, Yaniv E, Huang L, Raats D, Fatiukha A, Chen S, Feng L, Frenkel Z, Krugman T, Lidzbarsky G, Chang W, Jääskeläinen MJ, Schudoma C, Paulin L, Laine P, Bariana H, Sela H, Saleem K, Sørensen CK, Hovmøller MS, Distelfeld A, Chalhoub B, Dubcovsky J, Korol AB, Schulman AH, Fahima T (2018) Cloning of the wheat Yr15 resistance gene sheds light on the plant tandem kinase-pseudokinase family. Nat Commun 9(1):3735. https://doi.org/10.1038/s41467-018-06138-9
Chen S, Rouse MN, Zhang W, Zhang X, Guo Y, Briggs J, Dubcovsky J (2020) Wheat gene Sr60 encodes a protein with two putative kinase domains that confers resistance to stem rust. New Phytol 225(2):948–959. https://doi.org/10.1111/nph.16169
Hiebert CW, Moscou MJ, Hewitt T, Steuernagel B, Hernández-Pinzón I, Green P, Pujol V, Zhang P, Rouse MN, Jin Y, McIntosh RA, Upadhyaya N, Zhang J, Bhavani S, Vrána J, Karafiátová M, Huang L, Fetch T, Doležel J, Wulff BBH, Lagudah E, Spielmeyer W (2020) Stem rust resistance in wheat is suppressed by a subunit of the mediator complex. Nat Commun 11(1):1123. https://doi.org/10.1038/s41467-020-14937-2
Doudna JA, Charpentier E (2014) The new frontier of genome engineering with CRISPR-Cas9. Science 346(6213):1258096. https://doi.org/10.1126/science.1258096
Hou Z, Zhang Y (2019) Inserting DNA with CRISPR. Science 365(6448):25–26. https://doi.org/10.1126/science.aay2056
Heigwer F, Kerr G, Boutros M (2014) E-CRISP: fast CRISPR target site identification. Nat Methods 11(2):122–123. https://doi.org/10.1038/nmeth.2812
Naito Y, Hino K, Bono H, Ui-Tei K (2015) CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites. Bioinformatics 31(7):1120–1123. https://doi.org/10.1093/bioinformatics/btu743
Cram D, Kulkarni M, Buchwaldt M, Rajagopalan N, Bhowmik P, Rozwadowski K, Parkin IAP, Sharpe AG, Kagale S (2019) WheatCRISPR: a web-based guide RNA design tool for CRISPR/Cas9-mediated genome editing in wheat. BMC Plant Biol 19(1):474. https://doi.org/10.1186/s12870-019-2097-z
Hu X, Cui Y, Dong G, Feng A, Wang D, Zhao C, Zhang Y, Hu J, Zeng D, Guo L, Qian Q (2019) Using CRISPR-Cas9 to generate semi-dwarf rice lines in elite landraces. Sci Rep 9(1):19096. https://doi.org/10.1038/s41598-019-55757-9
Meng X, Yu H, Zhang Y, Zhuang F, Song X, Gao S, Gao C, Li J (2017) Construction of a genome-wide mutant library in rice using CRISPR/Cas9. Mol Plant 10(9):1238–1241. https://doi.org/10.1016/j.molp.2017.06.006
Liu H-J, Jian L, Xu J, Zhang Q, Zhang M, Jin M, Peng Y, Yan J, Han B, Liu J, Gao F, Liu X, Huang L, Wei W, Ding Y, Yang X, Li Z, Zhang M, Sun J, Bai M, Song W, Chen H, Xa S, Li W, Lu Y, Liu Y, Zhao J, Qian Y, Jackson D, Fernie AR, Yan J (2020) High-throughput CRISPR/Cas9 mutagenesis streamlines trait gene identification in maize. Plant Cell 32(5):1397–1413. https://doi.org/10.1105/tpc.19.00934
Zhao Q, Feng Q, Lu H, Li Y, Wang A, Tian Q, Zhan Q, Lu Y, Zhang L, Huang T, Wang Y, Fan D, Zhao Y, Wang Z, Zhou C, Chen J, Zhu C, Li W, Weng Q, Xu Q, Wang Z-X, Wei X, Han B, Huang X (2018) Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice. Nat Genet 50(2):278–284. https://doi.org/10.1038/s41588-018-0041-z
Zhou Y, Chebotarov D, Kudrna D, Llaca V, Lee S, Rajasekar S, Mohammed N, Al-Bader N, Sobel-Sorenson C, Parakkal P, Arbelaez LJ, Franco N, Alexandrov N, Hamilton NRS, Leung H, Mauleon R, Lorieux M, Zuccolo A, McNally K, Zhang J, Wing RA (2020) A platinum standard pan-genome resource that represents the population structure of Asian rice. Sci Data 7(1):113. https://doi.org/10.1038/s41597-020-0438-2
Haberer G, Kamal N, Bauer E, Gundlach H, Fischer I, Seidel MA, Spannagl M, Marcon C, Ruban A, Urbany C, Nemri A, Hochholdinger F, Ouzunova M, Houben A, Schön C-C, Mayer KFX (2020) European maize genomes highlight intraspecies variation in repeat and gene content. Nat Genet 52(9):950–957. https://doi.org/10.1038/s41588-020-0671-9
Sansaloni C, Franco J, Santos B, Percival-Alwyn L, Singh S, Petroli C, Campos J, Dreher K, Payne T, Marshall D, Kilian B, Milne I, Raubach S, Shaw P, Stephen G, Carling J, Pierre CS, Burgueño J, Crosa J, Li H, Guzman C, Kehel Z, Amri A, Kilian A, Wenzl P, Uauy C, Banziger M, Caccamo M, Pixley K (2020) Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nat Commun 11(1):4572. https://doi.org/10.1038/s41467-020-18404-w
Pont C, Leroy T, Seidel M, Tondelli A, Duchemin W, Armisen D, Lang D, Bustos-Korts D, Goué N, Balfourier F, Molnár-Láng M, Lage J, Kilian B, Özkan H, Waite D, Dyer S, Letellier T, Alaux M, Russell J, Keller B, van Eeuwijk F, Spannagl M, Mayer KFX, Waugh R, Stein N, Cattivelli L, Haberer G, Charmet G, Salse J, Wheat, Barley Legacy for Breeding Improvement c (2019) Tracing the ancestry of modern bread wheats. Nat Genet 51(5):905–911. https://doi.org/10.1038/s41588-019-0393-z
He F, Pasam R, Shi F, Kant S, Keeble-Gagnere G, Kay P, Forrest K, Fritz A, Hucl P, Wiebe K, Knox R, Cuthbert R, Pozniak C, Akhunova A, Morrell PL, Davies JP, Webb SR, Spangenberg G, Hayes B, Daetwyler H, Tibbits J, Hayden M, Akhunov E (2019) Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome. Nat Genet 51(5):896–904. https://doi.org/10.1038/s41588-019-0382-2
Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P, Hasterok R, Routledge APM (2001) Brachypodium distachyon;. A new model system for functional genomics in grasses. Plant Physiol 127(4):1539. https://doi.org/10.1104/pp.010196
Huala E, Dickerman AW, Garcia-Hernandez M, Weems D, Reiser L, LaFond F, Hanley D, Kiphart D, Zhuang M, Huang W, Mueller LA, Bhattacharyya D, Bhaya D, Sobral BW, Beavis W, Meinke DW, Town CD, Somerville C, Rhee SY (2001) The Arabidopsis Information Resource (TAIR): a comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant. Nucleic Acids Res 29(1):102–105. https://doi.org/10.1093/nar/29.1.102
Zou C, Li L, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Jia W, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable PS, Chang Y, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu J-K, Zhang H (2019) The genome of broomcorn millet. Nat Commun 10(1):436. https://doi.org/10.1038/s41467-019-08409-5
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Walkowiak, S., Pozniak, C.J., Nilsen, K.T. (2022). Recent Advances in Sequencing of Cereal Genomes. In: Bilichak, A., Laurie, J.D. (eds) Accelerated Breeding of Cereal Crops. Springer Protocols Handbooks. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1526-3_1
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