molecular marker application to incorporate salinity tolerance to west africa rice varieties

1
Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties Isaac Kofi Bimpong 1 , Baboucarr Manneh 1 , Bathe Diop 1 and Glenn B. Gregorio 2 1 Africa 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 Varieties MABC to introgress Saltol in African Varieties Conclusions Materials and methods 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. New Germplasm Tolerant to Salinity Results African variety/FL478 African variety // BC 1 F 1 Selected BC 1 F 1 BC 1 F 1 BC 2 F 1 Selected BC 2 F 1 African variety / BC 2 F 1 African variety / BC 3 F 2 X BC 3 F 1 Selected BC 3 F 1 BC 3 F 1 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 Toleranc e 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 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 Mappin g 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 (contro l) qNa+ SV- 1-1 QSst2 qNa+ / K+SV- 2.2 qNa+ LV-3.1 Trait based QTL QPh4 chrm 6 qNa+/ K+ SV 8-1 QSds8 qDWS- 9/ qSTR-9 chrm 10 Name RM 10843 RM 572 RM 208 RM 145 RM 563 RM 551 RM 273 RM 336 RM 281 RM 38 RM 215 RM 311 Jarmissa Camaro n.a Codeh mano n.a Madina koyo Gold coast fingo n.a n.a RAM121 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/gene n.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 3 NERICA-L23 3 NERICA_L24 5 NERICA_L27 3 FL 478(Tolerant check) 5 IR 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 NL1 NL2 NL3 NL4 NL5 NL6 NL7 NL8 NL9 NL10 NL11 NL12 NL13 NL14 NL15 NL16 NL17 NL18 NL19 NL20 NL21 NL22 NL23 NL24 NL25 NL26 NL27 NL28 NL29 NL30 NL31 NL32 NL33 NL34 FL478 CG14 IR64

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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 Presentation

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Page 1: Molecular Marker Application to Incorporate Salinity Tolerance to West Africa Rice Varieties

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