molecular marker application to incorporate salinity tolerance to west africa rice varieties
DESCRIPTION
African variety. //. African variety/FL478. BC 1 F 1. Selected BC 1 F 1. /. BC 1 F 1. African variety. BC 2 F 1. Selected BC 2 F 1. BC 2 F 1. /. African variety. BC 3 F 1. Selected BC 3 F 1. BC 3 F 1. X. BC 3 F 2. - PowerPoint PPT PresentationTRANSCRIPT
Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties
Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties
Isaac Kofi Bimpong1, Baboucarr Manneh1, Bathe Diop1 and Glenn B. Gregorio2
1Africa Rice Centre, Sahel station, B.P 96, Saint Louis, Senegal, 2 International Rice Research Institute (IRRI), DAPO Box 7777, Manila, Philippines
Salinity is a serious constraint for rice production in West Africa. Molecular markers are now routinely being used to identify and transfer useful genes/QTLs for salinity tolerance. One of the major QTL (Saltol) derived from the salt-tolerant Indian landrace Pokkali, has been mapped on chromosome 1.The QTL for salt tolerance (SKC1), maintains K+ homoeostasis in the salt-tolerant cultivars under salt stress, and the SKC1 gene encodes a member of HKT-type transporters. Fine-mapping of the Saltol QTL and the development of indel markers based on candidate genes in this region is being pursued at IRRI. Marker-assisted backcrossing (MABC) has been used to transfer the Saltol QTL into popular varieties such as IR64, BR28, and BR11. A diverse set of germplasm including the NERICAs (New Rice for Africa), collection from Cassamance regions in Senegal and Gambia are being characterized for physiological traits underlying salinity tolerance to identify new sources of tolerance for use as donors in breeding and identification of novel QTLs. Besides, MABC is currently being used to introgress Saltol into few varieties popular in West Africa. The long term goal is to identify and combine genes/QTLs controlling different physiological mechanisms to achieve a higher level of salt tolerance in high yielding West African rice varieties.
Objectives To use MABC approach to introgress Saltol into several African varieties that will
subsequently be deployed for commercial cultivation
Identify new source of suitable donors of major QTLs/genes other than Saltol
Identify new salt tolerance breeding lines using the participatory varietal selection (PVS) approach
MABC to introgress Saltol in African VarietiesMABC to introgress Saltol in African Varieties
Conclusions
Materials and methods
Evaluation of physiological traits for salt toleranceA total of 348 germplasm comprising of NERICAs, O. glaberrimas
and O. sativas were evaluated for salinity tolerance under controlled conditions. Salt stress was imposed 5 d after germination by adding
NaCl to an EC of 12 dS m-1 in Yoshida nutrient solution. IR29 (sensitive) and FL 478 (highly tolerant) were used as checks. Entries
were scored based on visual symptoms using IRRI’s Standard evaluation system (SES) scores.
New Germplasm Tolerant to Salinity
Results
African variety/FL478 African variety//
BC1F1
Selected BC1F1
BC1F1
BC2F1
Selected BC2F1
African variety/
BC2F1 African variety/
BC3F2
X
BC3F1
Selected BC3F1
BC3F1
Recipient varieties:– IR64, Sahel 108, Sahel 201, BG90-2, Kogoni
91-1, Bouake189, Rassi, NERICA L-19, ITA212
Donors:– Pokkali, FL478 (salt tolerance)
• Routine use of MAB to transfer Saltol : using flanking SSRs: 11-13 Mb on chrom1– Foreground (36 markers)– & recombinant markers used for selection
after each cross– SSRs for background selection (179
markers)
Variety Tolerance to Salinity
Country of Origin
Jarmissa 5 Gambia
Many Fingo 3 Gambia
Camaro 5 Gambia
Condeh Mano 5 Gambia
Madina Koyo 5 Senegal
Gold Coast Fingo 3 Gambia
Nafisatu 5 Gambia
FL 478 (Tolerant Ck) 4 IRRI
IR 29 (Sensitive Ck) 9 IRRI
8 Salt tolerant landraces from 188 identified from hydroponic and field screening
Molecular analysis show 5 of 8 appear to have different genes from Saltol
4 out of 104 accession of O. glaberrima;
(TOG7230, RAM26, RAM121) tolerant
Cross combination Mapping popn used
Lines with Saltol identified
Seeds produced with Saltol background
Rassi x FL478 BC2F1 7 out of 29 BC2F2 & BC3F1
Rassi x FL478 BC3F2 5 out of 23 BC3F3 & BC4F2
Sahel 108 x POKKALI
BC2F1 6 out of 37 BC2F2 & BC3F1
Current status of MABC
Saltol (control)
qNa+SV-1-1 QSst2
qNa+/K+SV-
2.2
qNa+LV-3.1
Trait based QTL
QPh4 chrm6
qNa+/K+ SV
8-1
QSds8
qDWS-9/
qSTR-9
chrm 10
NameRM10843
RM572
RM208
RM145
RM563
RM551
RM273
RM336
RM281
RM38
RM215
RM311
Jarmissa Camaro n.a
Codeh mano n.a
Madina koyo Gold coast fingo n.a n.aRAM121 TOG6224 TOG7230 NERICA L9
NERICA L23 n..a.
NERICA L24 n.a
NERICA L27 HASAWI n.a n.a Pokkali FL478 n.a
To genotype for Saltol (10 markers used;
3 each at the upper & lower flanking region
4 Saltol specific markers Background genotyping using
151 polymorphic markers
Comparison of 15 major QTL/genes published as tolerant to salinity other than Saltol with identified tolerant germplasm
Blue = tolerance in germplasm is different from the already identified & published QTLs/gene. Yellow = alleles is similar to the already identified & published QTLs/genen.a= not clear or poor amplification
New source of tolerance have been identified in both O. sativa & O. glaberrima Saltol gene/QTL have been introgressed into the background of 3 African mega varieties More than 5 breeding & mapping populations at different stages have been developed 10 salt tolerant lines/varieties identified by NARs after 2 season of PVS
Allelic diversity for Saltol QTL with 34 lowland NERICAs
Genotype
Mean salt injury at
EC 12 dSm-
1
NERICA-L9 3NERICA-L23 3
NERICA_L24 5
NERICA_L27 3FL 478(Tolerant
check) 5IR 29 (Sensitive
check) 9
4 Nericas-L9, -L23, -L24 & L27: tolerant & different genes from Saltol
Gambia Mali Senegal
1 WAR 1 WAS 201-B-2 IR 66946-3R-178-1-1
2 IR 1907-3R-2-1-2-B IR 59418-7-B-27-3 IR 72593-B-3-2-1-2-B
3 IR 63275-B-1-1-1-3-3-2 WAS 202-B-1 IR 59418-7B-21-3
4 WAS 73-B-B-84-2 WAS 197-B-8-2 IR 1829-3R-89-1-1
5 CT6163-8-9-5-2-M-134M IR 76393-2B-7-1-13-1
6 WAS 73-B-B-231-4 & WAS 236
PVS for Salt Tolerant in 3 countries
After 2 phases of PVS 4-6 promising lines have been selected by farmers Selected lines being validated in final round of PVS Main selection criteria :Earliness, plant height, tillering ability, panicle length and weight,
resitance to birds,
0 0.2
NL1NL2
NL3
NL4
NL5
NL6
NL7NL8NL9
NL10
NL11
NL12
NL13NL14NL15
NL16
NL17
NL18
NL19
NL20NL21
NL22NL23NL24
NL25
NL26
NL27NL28
NL29NL30
NL31
NL32NL33
NL34
FL478
CG14 IR64