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 salttolerant 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.
 4 Nericas-L9, -L23, -L24 & L27: tolerant & different genes from Saltol
NL25
Genotype
Mean salt
injury at EC
12 dSm-1
NERICA-L9
NERICA-L23
3
3
NL23
NL34
NL28
NL27
NL30
NL13
NL29
NL20NL31
NL21
NL15
NL24
NL22
NL16
NL14
NL7
NL8
NL9
NL4
NL1
NL2
NL33
NL32
NL5
NL3
NERICA_L24
5
NERICA_L27
FL 478(Tolerant
check)
IR 29 (Sensitive
check)
3
NL10
NL26
NL12
NL18
NL11
NL19
5
FL478
NL17
NL6
9
IR64
CG14
0
Objectives
0.2
Allelic diversity for Saltol QTL with 34 lowland NERICAs
 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
Comparison of 15 major QTL/genes published as tolerant to salinity
other than Saltol with identified tolerant germplasm
qNa+/
Trait
qNa+/
qDWSchrm
Saltol qNa+S
K+SV- qNa+L based
K+ SV
9/ qSTRQSst2
QPh4 chrm6
QSds8
10
(control) V-1-1
2.2 V-3.1 QTL
8-1
9
Materials and methods
Evaluation of physiological traits for salt tolerance
RM
10843
Name
Jarmissa
Camaro
A 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.
RM
572
RM
208
RM
145
RM
563
RM
551
RM
273
RM
336
RM
281
RM
38
RM
215
n.a
Codeh mano
n.a
Madina koyo
Gold coast
fingo
RAM121
TOG6224
TOG7230
NERICA L9
MABC to introgress Saltol in African Varieties
African variety/FL478 // African variety
RM
311
n.a
n.a
BC1F1
NERICA L23
n..a.
Selected BC1F1
NERICA L24
n.a
BC1F1 / African variety
BC2F1
Selected BC2F1
BC2F1 / African variety
BC3F1
Selected BC3F1
BC3F1
X
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)
NERICA L27
HASAWI
Pokkali
FL478
n.a
n.a
n.a
Blue = tolerance in germplasm is different from the already identified & published QTLs/gene.
Yellow = alleles is similar to the already identified & published QTLs/gene
n.a= not clear or poor amplification
PVS for Salt Tolerant in 3 countries
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
4
5
WAS 73-B-B-84-2
BC3F2
Results
Current status of MABC
Cross combination Mapping
popn
used
Rassi x FL478
BC2F1
Lines with
Seeds produced
Saltol identified with Saltol
background
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
 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
WAS 197-B-8-2
IR 1829-3R-89-1-1
CT6163-8-9-5-2-M-134M IR 76393-2B-7-1-13-1
WAS 73-B-B-231-4 & WAS 236
 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,
Conclusions
New Germplasm Tolerant to Salinity
 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
6
IR 59418-7B-21-3
Variety
Tolerance
to Salinity
Country
of Origin
Jarmissa
Many Fingo
Camaro
Condeh Mano
Madina Koyo
5
3
5
5
5
Gambia
Gambia
Gambia
Gambia
Senegal
Gold Coast Fingo
3
Gambia
Nafisatu
FL 478 (Tolerant Ck)
5
4
Gambia
IRRI
IR 29 (Sensitive Ck)
9
IRRI
 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