Transcript Saltol - Confex
Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties
Isaac Kofi Bimpong
1
, Baboucarr Manneh
1
, Bathe Diop
1
1
Africa Rice Centre, Sahel station, B.P 96, Saint Louis, Senegal,
2
and Glenn B. Gregorio
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 transporters.
SKC1
gene encodes a member of HKT-type 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
Materials and methods
4 Nericas-L9, -L23, -L24 & L27: tolerant & different genes from Saltol
Genotype
NERICA-L9 NERICA-L23 NERICA_L24 NERICA_L27 FL 478(Tolerant check) IR 29 (Sensitive check)
Mean salt injury at EC 12 dSm -1
Saltol (control)
3 3 5 3 5 9
CG14
0
NL23 NL4 NL1 NL2 NL3 NL5 IR64 NL25 NL20 NL30 NL29
0.2
NL34 NL13 NL15 NL16 NL14 NL9 NL26 NL12 NL18 NL19 NL11 NL17 NL6 NL10
Allelic diversity for
Saltol
QTL with 34 lowland NERICAs
Comparison of 15 major QTL/genes published as tolerant to salinity other than Saltol with identified tolerant germplasm qNa+S V-1-1
QSst2 qNa+/ K+SV 2.2 qNa+L V-3.1 Trait based QTL
QPh4 chrm6
qNa+/ K+ SV 8-1 QSds8 qDWS 9/ qSTR 9
FL478
chrm 10
Evaluation of physiological traits for salt tolerance
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.
Name
Jarmissa Camaro Codeh mano RM 10843 RM 572 RM 208 RM 145 RM 563 RM 551 RM 273 n.a
RM 336 RM 281 RM 38 RM 215 RM 311 n.a
MABC to introgress Saltol in African Varieties
African variety/FL478 // African variety
Madina koyo Gold coast fingo RAM121 TOG6224 TOG7230 NERICA L9 n.a
n.a
BC
1
F
1
NERICA L23 n..a.
Selected BC
1
F
1
NERICA L24 n.a
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
•
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
1
Gambia
WAR 1
Mali
WAS 201-B-2
Senegal
IR 66946-3R-178-1-1 2 3 IR 1907-3R-2-1-2-B
IR 59418-7-B-27-3
IR 63275-B-1-1-1-3-3-2 WAS 202-B-1 IR 72593-B-3-2-1-2-B
IR 59418-7B-21-3
Results Current status of MABC Cross combination Mapping popn used Lines with Saltol identified Seeds produced with Saltol background Rassi x FL478 Rassi x FL478 BC2F1 BC3F2 7 out of 29 5 out of 23 BC2F2 & BC3F1 BC3F3 & BC4F2
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
Sahel 108 x POKKALI BC2F1 6 out of 37 BC2F2 & BC3F1 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
Variety
Jarmissa Many Fingo Camaro Condeh Mano Madina Koyo Gold Coast Fingo Nafisatu FL 478 (Tolerant Ck) IR 29 (Sensitive Ck)
Tolerance to Salinity
5 3 5 5 5 3 5 4 9
Country of Origin
Gambia Gambia Gambia Gambia Senegal Gambia Gambia IRRI IRRI 4 5 WAS 73-B-B-84-2 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 6 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 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