Targeted Musa Genome Sequencing and Frame Map
Construction (SP2)
Collaborators: F. Bakry (CIRAD), F.C. Baurens (CIRAD), J. Dolezel (IEB),
P. Heslop–Harrison (University of Leicester), I. Hippolyte (CIRAD), T. Matsumoto (NIAS),
R.N.G Miller (UCB), M. Rouard (Bioversity International), N. Roux (Bioversity International),
S. Sidibe-Bocs (CIRAD), M. Souza (EMBRAPA), T. Sasaki (NIAS)
Genetic Map
Genomic Resources and Sequencing
144x384 well plates of an A genome (MA4) and 96x384 well plates of the B
genome (MBP PKW) BAC library have been pooled.
41 BACs bearing genes mainly related to abiotic and biotic stresses have
been sequenced, a total of 3.303Mbp. ESTs have been used as probes to
identify the BACs to sequence (cf. figure below).
2 cDNA libraries from PKW leaves and roots were produced. 5760 ESTs
clones from these libraries have been sequenced.
Additional 6132 ESTs from a previously developed cDNA library from
Mycosphaerella fijiensis infected leaves of ‘Calcutta 4’ were produced.
614 repetitive DNA sequences, isolated from ‘Calcutta 4’, were analyzed.
The A and B genomes are being compared, using abiotic stress related and
RGA (Resistant Gene Analogue) loci to identify BACs for sequencing.
Comparative Genomics
Bananas (Musa spp.) are one of the developing
world’s most important food crops and are grown
in more than 100 countries throughout the tropics
and sub-tropics.
Productivity is declining in many regions. Moreover
the
production
systems
that
depend
on
agrochemicals and irrigation are not sustainable.
Cultivars are mostly sterile and parthenocarpic
triploids (2n=3x=33), originating from two wild diploid
species: Musa acuminata (A genome) and Musa
balbisiana (B genome).
Despite the importance of this crop, basic genetic
and genomic tools are lacking.
Objectives:
Consolidate and characterize existing publicly available Musa genomic
resources and make new resources available
Selective sequencing of BACs (Bacterial Artificial Chromosome) bearing
genes potentially involved in important traits
Establishment of international mapping populations with a view to precision
genetic mapping
Anchor BACs, maps, SSR and others markers with reference to gene and
genome sequences from rice and other models
Establishment
of
public
databases
(http://www.musagenomics.org);
distribution of clones; training and dissemination of information
The BORLI population ( M.a. ‘Borneo’ x M.a. ‘Pisang Lilin’) was chosen as
the mapping population mainly because of the great heterozygosity of both
parents (76% each) and the population size.
BAC Filter hybridization
with selected cDNA probes
EST selection through
bioinformatic analysis
BAC Fingerprint
analysis
Re-Hybridization
with selected cDNA
probes
Selection (size,
hybridization
profile…) and
sequencing
Fig. 1: Defining BACs for sequencing through EST
hybridization approach
The Project
The map is based on 180 individuals. SSR markers were analysed on all
the population, DArT markers on half on the population. 180 SSR and 380
DArT markers are distributed on 11 main linkage groups for Borneo and
9 linkage groups for ‘Pisang lilin’. A consensus map was drawn for 6
linkage groups, for the other ones, translocation breakpoints and/or
chromosome rearrangements did not allow map reconstruction. Analysis
on these groups will be refined.
Developing basic genomic tools to assist germplasm exploitation is important for Musa (banana), especially in the context of the use of Musa
genomic diversity. Moreover, it is also a top priority in the vision of the whole genome sequencing. The initiation of genomic sequencing to
identify genes will allow exploitation of breeding-relevant genetic variation within Musa. The GCP has promoted the development of publicly
available, well characterized genomic resources in order to integrate them with ongoing trait-based research in Musa.
Fig. 3: Comparison of homologous regions containing clusters of duplicated
RGAs within Musa species and with rice. Micro-synteny appears between
Ma4052E23 and a region of the rice chromosome 6
Fig. 4: Musa/Oryza NSB-LRR homology relationships. Banana/rice NBS
phylogeny suggests that the rice chromosome 11 RGA and MARGA08
tandem duplications occured after banana/rice divergence (MARGA08 cluster
younger than Os11RGA cluster)
Several annotation studies are ongoing, especially on biotic and abiotic
stress. BACs showing micro-synteny (based on BAC-ends) with rice are being
analysed. The most advanced study is related to RGAs and is illustrated
below:
Further information can be found online on the Global Musa Genomics Consortium website :
http://www.musagenomics.org
Fig. 2: Borli genetic map built from an F1 progeny of Musa acuminata ‘Borneo’ x Musa
acuminata ‘Pisang lilin’. Join map4 software was used at LOD 6 with Kosambi function.
Linkage groups numbered according to Vilarhinos et al., 2006
300221-np Cir20 0.0 302046-np 2.3 CIR301 3.1294420-np 4.5 Ecir623-np 7.7 Ecir504 8.9Ecir610-np 14.6 302225-np 21.4 282897-np 21.5Ecir629-np 29.0ECIR633 34.7 299320-np 37.3cIR102 39.9292676-np 40.5 291893-np 41.8 291858-np 41.9300914-np 51.4 283019-np 301168-np 51.7 Ecir622-np 52.8 CIR130-np 52.9 CIR261 53.0290819-np 55.8 CIR105 58.5 ECIR579 61.1Ma3-90 62.3CIR21 65.8 CIR13 65.9292151-np 76.8284699-np 77.0 295151-np 77.3 ECIR549 81.6294293-np 82.0 CIR111 88.4 292284-np 106.9292027-np 108.1 299742-np 110.2
P. Lilin 3+12
298729-lm 303341-lm 301219-lm 0.0 299809-lm 10.4 Cir20 13.7 CIR301 19.6 294224-lm 22.8 Ecir504 32.9 291757-lm 36.3 ECIR633 49.0 298545-lm 302454-lm 282985-lm 301356-lm 299796-lm 298763-lm 301610-lm 298692-lm 282859-lm 50.5 299555-lm 300679-lm 50.8 CIR102 53.1 295835-lm 54.0 CIR105 54.6 CIR261 54.7 Ma3-90 56.3 CIR21 CIR13 56.9 295850-lm 57.7 302982-lm 290809-lm 57.8 CIR111 69.7 295017-lm 76.7Borneo3+12
0 CIR189 7 , 6 8 Ecir551 11 , 5 5 2 ECIR571 1 2 , 0 3 4 293412-np 1 3 , 2 8 6 290800-np 1 6 , 6 1 5 Ma1_17 1 6, 7 1 3 292409-np 1 8 , 2 1 6 301453-np 2 0 , 5 6 1 CIR39 2 2 , 9 9 9 Ecir583 2 5 , 3 8 6 CIR174 2 5 ,9 8 4 303077-np 2 6 , 5 4 3 Ecir619-np 27 , 4 2 2 Ecir618-np 3 1 , 2 5 4 292849-np 3 1 , 79 4 291116-np 3 3 , 6 1 7 291330-np 3 4 , 5 0 2 291199-np 3 5 , 1 7 2 CIR285 3 6 , 6 1 5 291390-np 3 7 , 47 5 299129-np 3 7 , 9 8 3 CIR109 3 9 ,6 5 1 291481-np 39 , 6 5 4 Ma1_32 4 1 , 0 8 3 JARRET132 4 2 , 0 0 8 294443-np 4 3 , 0 6 CIR28 4 5, 1 9 3 301864-np 4 6 , 0 5 6 293082-np 5 0 , 0 73 Ecir617-np 5 1 , 3 4 9 CIR01 5 1 , 6 16 CIR29 5 2, 0 7 4 291371-np 5 4 , 4 4 2 CIR185-np 5 5 , 9 4 4 Ecir584 6 1 , 3 9 4 CIR286 6 2 ,9 7 1 291314-np 6 3 , 9 6 4 290857-np 6 4 , 4 7 5 302553-np 65 , 5 6 2 CIR154 6 5 , 6 7 8 295681-np 6 8 , 02 6 293894-np 6 9 , 6 5 299313-np 7 0, 2 7 4 300588-np 7 0 , 3 8 3 298188-np 7 4 , 58 4 CIR256-np 7 5 , 7 9 5 300167-np 7 6 , 8 4 3 CIR249 78 , 0 6 2 CIR252 7 8 , 1 Ecir516 7 9 , 50 9 299512-np 8 1 , 0 9 9 ECIR519 8 2, 0 8 7 CIR180 82 , 4 3 8 Ecir599 8 2 , 6 11 CIR11-np 8 2 , 8 1 7 293353-np 8 2 , 8 2 8 293665-np 8 2 ,8 6 5 295014-np 8 3 , 1 4 6 ECIR554-np 8 3 , 3 1 7 285105-np 8 3 , 4 4 2 CIR167 8 3 , 68 7 CIR163 8 3 ,8 4 Ecir546 8 4 , 5 6 8 Ecir609 86 , 1 1 7 CIR215 8 7 , 6 9 5 Ecir556 8 8 , 81 ECIR0496 8 9 , 6 3 8 301390-np 9 0 , 0 9 291192-np 91 , 4 5 5 CIR264 9 3 , 5 1 282556-np 9 4 , 40 3 CIR172 9 5 , 6 7 2 295688-np 96 , 9 5 3 UCb92 1 0 1 , 4 0 3 CIR152 1 0 7 , 83 5 CIR07 1 0 7 , 9 1 5 ECIR575 1 0 8 , 8 2 8 ECIR0499 1 09 , 4 1 6 295000-np 1 0 9 , 5 1 5 294284-np 1 1 1 , 11 5 291694-np 1 1 1 , 8 2 4 293444-np 1 1 4, 8 9 5 301032-np 1 1 5 , 1 2 2 301905-np 1 1 6 , 8 65 CIR03 1 2 3 , 1 9 2 292033-np 1 2 6 , 2 6 3 291993-np 1 3 3, 4 8 6 CIR08 1 3 4 , 9 8 1 292488-np 1 3 5 , 0 4 292918-np 1 3 5 , 1 9 4 299179-np 1 3 5 ,3 3 291546-np 1 38 , 8 7 5 296030-np 1 4 5 , 9 5 5 293814-np 1 53 , 4 4 6 CIR137-np 1 5 6 , 7 4 1 CIR280-np 1 6 8 , 75 300203-np 293128-lm 0.0 CIR109 9.7 CIR154 18.8 Ecir516 30.0 CIR252 30.1CIR249 31.5 284911-lm 45.1293523-lm302413-lm 48.8Ecir539-lm 51.0299191-lm 52.7CIR264 54.8 292163-lm 62.3293669-lm 63.5 301169-lm 70.7 CIR280-lm 78.0Borneo15
P. Lilin 1+2a+4+15
300487-lm 0.0 294264-lm 3.2291415-lm 3.6 302676-lm 4.8Ecir535-lm 8.8 CIR189 10.5301679-lm 10.8Ecir551 12.8 298606-lm 13.2ECIR571 14.2 Ma1_17 19.2CIR39 22.2 Ecir583 23.1CIR174 25.7 CIR285 32.2 CIR108-lm 41.8 CIR28 43.4 CIR235lm 49.2292320-lm 55.5 303145-lm 56.4300186-lm 56.7292935-lm 59.0CIR01 CIR29 60.0 292810-lm 60.2284900-lm 60.3 Ecir584 60.4Borneo 2a
300831-lm 0.0 Ecir557 4.6 CIR180 8.6 CIR167 9.6 301793-lm 14.0 302647-lm 14.1 300166-lm 15.0 301919-lm 15.6 CIR163 16.6 Ecir599 22.0 Ecir546 23.1 300750-lm 24.4 ECIR519 40.3 298410-lm 42.3 CIR172 52.1 295703-lm 52.7 UCb92 57.5 291324-lm 64.6 CIR03 66.6 CIR07 67.2 CIR08 67.9borneo1
JARRET 1_32 0.0 Ma1_32 2.9Borneo4
Ecir612 0.0 CIR282 6.4 CIR182 7.5 291518-lm 19.8CIR45 20.6 CIR273 25.8 292385-lm 29.5CIR124 35.6 ECIR560 56.6 294465-lm 65.1 292136-lm300608-lm 80.7Borneo 16
301177-np 0.0 Ecir612 1.3 CIR282 28.3 CIR182 32.2 CIR193 48.0 CIR124 53.3CIR45 58.0299332-np 60.6 298571-np 60.7293379-np 61.3 CIR254 64.8 CIR273 70.9299189-np 79.4 Ecir508 81.5 295013-np 91.5290851-np 98.5 300582-np 102.5ECIR560 103.7291124-np 103.9 294583-np293571-np 114.4302416-np 115.2 295426-np 115.3 300920-np284980-np 116.2Ecir565 117.1 302606-np 119.8301708-np 121.4CIR257 130.3 Ecir505 133.6Plili 16
Consensus linkage groups
299355-lm 0.0 ECIR544 12.6 295909-lm 18.5 298946-np 36.3 CIR17 38.7 298892-np 40.0 295671-lm 40.9 295674-lm 41.0 294576-lm 44.2 CIR274 49.8 291624-np 50.7 295856-np 51.0 302085-np 302090-np 51.8 293338-lm 54.9 301308-np 56.9 ECIR561-np 58.0 295639-np 58.8 ECIR507-np 61.5 ECIR515-np 63.7 CIR247-np 77.4 296063-np 89.0 298954-np 89.1 302620-np 103.2 302899-np 302621-np 104.0 303066-np 104.1 299731-np 104.2 CIR277 105.2 294553-lm 110.3 CIR129-lm 112.0 CIR139 113.0 CIR228 114.0 294469-np 115.9 CIR195 127.4 299016-np 129.2 301498-np 134.1 ECIR506-np 136.0
