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PAG XXVI - CROP GENOMICS FOR GLOBAL FOOD SECURITY Brassicaceae 2:30 PM TUESDAY 16TH JANUARY 2018 Genome-Wide Analysis of NBS-LRR Genes in the • ~340 genera and 3350 species Brassicaceae and Applications for Breeding • Economically important edible and industrial oilseed, vegetable, condiment, and fodder crops • New and underutilised crucifer crop species • Rich source of agronomic and economic traits in its highly diverse wild species and germplasm

FABIAN C. INTURRISI UNIVERSITY OF WESTERN AUSTRALIA [email protected]

Brassica species More than Brassica species Triangle of U • Brassica rapa • Vegetables – Rocket/ arugula (Eruca sativa) – Chinese cabbage, turnip, Pak choi, bok choi – Wild rocket (Diplotaxis tenuifolia) • Brassica nigra – Garden cress (Lepidium sativum) – Radish (Raphanus sativus) – Black mustard – Maca (Lepidium meyenii) • Brassica oleracea • Condiment/ spice – Horseradish (Armoracia rusticana) – Cabbage, brussels sprouts, cauliflower, – Wasabi (Eutrema japonicum) Horseradish Radish broccoli, kohl rabi, kale – White mustard (Sinapis alba) Garden Cress • Ornamentals • Brassica napus – Aethionema, Alyssum, Arabis, Erysimum, Iberis and Matthiola – Canola/rapeseed, Rutabaga/ swede • Wild crucifers – Arabidopsis thaliana - Most widely used plant model • Brassica juncea – Arabidopsis halleri - Heavy metal tolerance and – Indian mustard hyperaccumulation – Lepidium meyenii - Floral structure • Brassica carinata – Eutrema salsugineum - Salinity stress – Ethiopian mustard – Barbarea vulgaris - Insect resistance Rocket Wild Rocket

Global Food Security Brassicaceae and disease

Arable land World Pathogen Disease • Projected world population Albugo candida White rust – 9.1 billion in 2050 Developing countries Alternaria brassicae Alternaria (brassicae) blight Alternaria brassicicola Alternaria (brassicicola) blight Developed countries • Projected food demand Alternaria raphani Alternaria (raphani) blight – Increase by 70% by 2050 Leptosphaeria maculans Blackleg/ Stem canker Sclerotinia sclerotiorum Sclerotinia stem rot World population Food demand Crop productivity Rhizoctonia solani Hypocotyl rot, Damping root, Root rot Hyaloperonospora parasitica Downy mildew Plasmodiophora brassicae Clubroot Pseudocercosporella capsellae White leaf spot Pseudomonas syringae Leaf blight Xanthomonas campestris Black rot Beet western yellow virus (Turnip Beet western yellow virus (Turnip yellows Climate change Biotic factor Yellows virus) virus) Turnip mosaic virus Turnip mosaic virus Poor soil nutrition Abiotic factor Cauliflower mosaic virus Cauliflower mosaic virus

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Resistance genes Objectives • R genes characteristics – Gene-for-gene interaction • Comprehensive genome–wide analysis of R genes in – Responsible for specific Brassicaceae recognition of pathogen Avr • Comparative analysis of R genes (NBS-LRRs, RLKs and RLPs) in proteins Brassicaceae genomes – Three main classes: NBS-LRRs, RLPs and RLKs • Further understanding of R gene evolution in Brassicaceae

Methodology Collection of genomic resources

• Collection of genomic 35 sequenced and annotated resources Brassicaceae genomes Species Reference Species Reference Arabidopsis halleri Briskine et al 2016 Arabis alpine Willing et al 2015 Arabidopsis lyrata Rawat et al 2015 Brassica juncea Yang et al 2016 Arabidopsis thaliana ARAPORT Cheng et al 2017 Brassica napus cv. Darmor v4 Chalhoub et al 2014 Arabidopsis thaliana TAIR AGI 2000 Brassica napus cv. Darmor v8 Bayer et al 2017 Identification and Boechera stricta Lee et al 2017 Brassica napus cv. Tapidor Bayer et al 2017 classification of R Capsella grandiflora Slotte et al 2013 Brassica napus cv. ZS11 Sun et al 2017 Capsella rubella Slotte et al 2013 Brassica napus pangenome Hurgobin et al 2017 genes Lepidium meyenii Zhang et al 2016a Brassica nigra Yang et al 2016 Brassica oleracea pangenome Golicz et al 2016 Species Reference Brassica oleracea V2.1 Parkin et al 2014 Aethionema arabicum Haudry et al 2013 Brassica rapa Cai et al 2017 Barbarea vulgaris Byrne et al 2017 Brassica rapa JGI 2017 Camelina sativa Kagale et al 2014 Brassica rapa Wang et al 2011 Phylogenetic analysis Cardamine hirsute Gan et al 2016 Eutrema salsugineum Wu et al 2012 Leavenworthia alabamica Haudry et al 2013 Eutrema salsugineum Yang et al 2013 of R genes Raphanus raphanistrum Moghe et al 2014 Thellungiella parvula Dassanayake et al 2011 Raphanus sativus Kitashiba et al 2014 Sisymbrium irio Haudry et al 2013 Raphanus sativus Mitsui et al 2015 Tarenaya hassleriana Cheng et al 2013 Thlaspi arvense Dorn et al 2015

Genome TNL TN CNL CN RNL RN NL NBS OTHER TX RLK RLP TM-CC Total Aethionema_arabicum_Haudry_et_al_2013 31 13 34 3 2 0 29 6 24 30 470 39 269 37839 Arabidopsis_halleri_Briskine_et_al_2016 47 16 25 4 1 0 36 10 13 39 451 77 93 26911 Identification and characterisation of R genes Arabidopsis_lyrata_Rawat_et_al_2015 84 22 32 4 3 0 38 17 22 50 552 80 156 33132 Arabidopsis_thaliana_Araport_Cheng_et_al_2017 194 27 78 2 5 1 72 14 45 58 989 124 256 79554 Arabidopsis_thaliana_TAIR_AGI_2000 77 13 38 1 4 1 17 4 17 33 517 75 147 37513 Arabis_alpina_Willing_et_al_2015 97 27 25 8 5 3 36 10 16 70 516 90 135 34220 Barbarea_vulgaris_Byrne_et_al_2016 67 25 31 7 2 0 52 15 19 71 505 95 150 25350 The identified NBS LRRs were grouped based on the domain structure Boechera_stricta_Lee_et_al_2017 156 32 49 4 1 0 78 12 39 89 561 111 159 29812 Brassica_juncea_v1.5_Yang_et_al_2016 42 23 60 17 11 2 71 56 26 82 1225 228 399 79644 Brassica_napus_cv._Darmor_v4_Chalhoub_et_al_2015 169 58 56 26 9 2 92 48 31 136 1503 276 419 101040 Brassica_napus_cv._Darmor_v8_Bayer_et_al_2017 30 15 14 19 7 3 70 32 20 83 1010 78 321 94765 Brassica_napus_cv._Tapidor_Bayer_et_al_2017 20 9 14 13 7 3 59 27 10 54 704 228 302 84347 • Typical or regular NBS LRR gene Brassica_napus_cv._ZS11_Sun_et_al_2017 154 59 60 19 10 1 97 41 29 130 1556 272 443 101942 Brassica_napus_Pangenome_Hurgobin_et_al_2017 13 12 17 10 0 2 76 49 6 50 89 73 10 16518 Brassica_nigra_Yang_et_al_2016 112 30 35 8 5 1 57 20 30 74 776 176 256 47953 TIR NBS LRR CC NBS LRR RPW8 NBS LRR Brassica_oleracea_Pangenome_Golicz_et_al_2016 8 4 9 9 0 1 42 24 6 18 79 54 6 7078 Brassica_oleracea_v2.1_Parkin_et_al_2014 121 33 43 14 6 2 71 38 20 105 822 159 295 59220 Brassica_rapa_Cai_et_al_2017 11 5 7 20 7 1 26 12 6 29 670 65 251 48826 Brassica_rapa_FPsc_JGI_2017 94 20 37 2 7 0 32 8 17 43 824 122 199 43370 Brassica_rapa_Wang_et_al_2011 88 18 37 5 5 0 33 6 18 40 746 111 211 41020 Camelina_sativa_Kagale_et_al_2014 77 32 69 14 6 1 179 46 32 95 1636 319 489 94495 • Non–regular NBS LRR genes- absence of specific domains Capsella_grandiflora_Slotte_et_al_2013 41 14 11 4 4 0 29 6 7 32 511 72 147 26561 Capsella_rubella_Slotte_et_al_2013 35 11 39 3 5 0 42 6 13 46 571 99 168 28447 Cardamine_hirsuta_Gan_et_al_2016 109 44 70 19 2 0 80 60 21 119 742 134 165 38094 Eutrema_salsugineum_Wu_et_al_2012 50 9 27 3 2 0 26 10 8 42 522 84 157 29284 TIR NBS CC NBS RPW8 NBS Eutrema_salsugineum_Yang_et_al_2013 50 9 27 3 2 0 26 10 8 42 521 85 155 29485 Leavenworthia_alabamica_Haudry_et_al_2013 40 20 21 3 7 0 20 6 13 57 574 54 294 38676 Lepidium_meyenii_Zhang_et_al_2016 18 11 86 27 7 1 104 50 18 44 1424 214 535 96417 NBS LRR Raphanus_raphanistrum_Moghe_et_al_2014 18 11 20 14 4 2 72 32 4 45 645 154 177 50972 NBS TIR Raphanus_sativus_Kitashiba_et_al_2014 91 26 38 4 4 2 46 24 31 83 774 176 431 80521 Raphanus_sativus_Mitsui_et_al_2015 90 24 37 4 5 2 42 14 30 65 776 162 418 64657 Schrenkiella_parvula_Dassanayake_et_al_2011 37 7 12 4 3 1 14 7 7 29 512 50 165 28178 Sisymbrium_irio_Haudry_et_al_2013 73 15 47 4 3 0 42 13 31 62 608 130 321 49956 Tarenaya_hassleriana_Cheng_et_al_2013 42 15 30 2 2 0 23 9 4 25 728 40 250 41094 Thlaspi_arvense_Dorn_et_al_2015 20 5 17 7 1 0 53 16 14 50 474 120 145 27390 Total 2406 714 1252 310 154 32 1882 758 655 2120 25583 4426 8494 1754281

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Example of R gene position and density: Example of R gene position and density: B. napus pangenome –A genome B. oleracea pangenome

Orthologous grouping of R genes in B. juncea, B. Phylogeny of Brassicaceae genome assemblies rapa and B. nigra OG0000067 Phylogenetic tree Absolute values of R genes Relative values of R genes

OG0000724

OG0003753 R genes R genes Domains Intron-exon boundaries

Application of novel R genes in breeding for future Acknowledgements food security • Professor Jacqueline Batley This analysis provides a valuable resource for the identification of R • Professor David Edwards genes for enhanced crop protection by developing elite resistant • Batley Lab cultivars where by the R gene functionality is studied against particular – Soodeh Tirnaz – Ting Xiang Neik diseases and bred into commercial cultivars. – Aria Dolabatian • – Hua Yang Introgression of novel R genes into crop species – Fangning Zhang • Development of wild crucifers showing novel resistance into crop – Aria Dolatabadian species – Muhammad Ishaq Ibrahim – Anita A. Severn-Ellis • Identification of orthologs in developed species for genome editing – Dhwani A. Patel based breeding – Aneeta Pradhan • Edwards Lab – Philipp E. Bayer – Kenneth Chan – HueyTyng Lee

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Thank you for your attendance Questions

• Poster in lower level –Brassicas, Arabidopsis, and related –P0551 Genome-wide analysis of NBS-LRR genes in the Brassicaceae and applications for breeding

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