Markers for Altsb, a major QTL for aluminum tolerance in sorghum

Product Description/Background:

Al toxicity is the primary limitation on crop production for 38% of farmland in Southeast Asia, 31% of Latin America and approximately 20% of East Asia, Sub-Saharan Africa and North America (Wood et al. 2000). On acid soils, toxic levels of Al ions are released into soil solution, where they damage roots and impair their growth and function. This results in reduced nutrient and water uptake, with concomitant reductions in crop yield.In sorghum, although genetic tolerance to aluminum toxicity is very rare, extensive screening and association analysis research has focused on AltSB, a major aluminum tolerance QTL providing significant protection and yield gains in acid soils. Nutrient solution studies have indicated a gain of 0.5 tonnes/Ha (Jurandir Magalhaes, unpublished ).  Field studies in Brazil and West Africa are on-going.  The gene, SbMATE, conferring the tolerance to aluminum and underlying the Altsb QTL was isolated, cloned, and determined to account for the majority of variation in tolerant genotypes. This gene is now protected under a USA patent filed by the USDA and Embrapa. The gene specific and flanking markers cited below in Table 1 were developed in most part through GCP research project G3007.04 cited above.  These are currently being used for introgression of aluminum tolerance in elite Brazilian and African sorghum lines. Markers for the QTL continue to be developed. Haplotype specific SNP markers have also been developed and validated for a follow-up field project in West Africa.  These will soon be published and made available. Current and future SNP marker information will be maintained and made available through the Genotyping Data Management System soon to be deployed on the IBP and by KBiosciences (see Access/Availability below for details).

Table 1. Diagnostic STS markers for the Altsb locus accounting for the majority of the variation for tolerance to aluminum toxicity in tolerant sorghum genotypes.

Diagnostic SNP markers (ID codes) for the Altsb locus on the KASPar (KBiosciences) platform: AltSB_836, AltSB_248, AltSB_199, AltSB_594, AltSB_598, AltSB_608, AltSB_842, AltSB_25094, SNP 5519

Phenotypic expression of Altsb on sorghum grown on acid soils in Brazil.

From the originating GCP project, “G3007.04 Tailoring Superior Alleles for Abiotic Stress Genes for Deployment into Breeding Programs: A Case Study Based on Association Analysis of AltSB, a Major Aluminum Tolerance Gene in Sorghum (ALTSORGHUM)”

“We constructed a genetic map with nearly 400 loci (SSRs and DArTs) and phenotyped 100 accessions from a SC283 (Al tolerance provided by AltSB) x BR007 (Al sensitive) RIL population for grain yield on acid soils with approximately 50% Al saturation at Embrapa Maize and Sorghum. The population was also phenotyped for Al tolerance in hydroponics. We detected a major QTL for grain yield on acid soils which co-localized with AltSB on chromosome 3 (Magalhaes et al., 2004). This indicates that AltSB does provide grain yield advantage on acid soils, which was approximately 0.5 ton/ha in our conditions according to our QTL model. “ – Jurandir Magalhaes, Embrapa, Principal Investigator

Figure 1.  Results of allele substitution effect for AltSB in terms of grain yield on acid soils in this study. TT stands for the phenotypic mean for RILs that are homozygous for the AltSB allele coming from the Al tolerant parent, SC283, whereas tt represents the mean for RILs that are homozygous for the Al sensitive parent, BR007, allele.

Access to markers

The above marker information can be used freely to generate markers and used to genotype germplasm.  For SSR and STS marker services in Africa and Asia  we suggest BecA, Nairobi, Kenya and ICRISAT, Patancheru, India. SNP markers can be accessed through KBiosciences, Hoddesdon, Herts, UK. Click here for a list and description of laboratories and services.  In addition, the Integrated Breeding Platform Genotyping Service provides a set of options for users to access different marker service laboratories in the public and private sector with clear contractual conditions. The service identifies laboratories able to provide services for genetic diversity analysis and plant breeding applications and negotiates favourable terms for IBP clients. Laboratories are selected on the basis of competitive cost, fit with quality control requirements and expeditious delivery.  Click on  Service request for details of how to access genotyping services through the platform. For additional information and help on using the IBP Marker Service, contact Chunlin He.

If you need assistance in the use of these markers refer to  IBP Breeding Services or for more information contact Mark Sawkins or Chunlin He.

Source:

These markers were validated in part through GCP Project G3007.04 Tailoring Superior Alleles for Abiotic Stress Genes for Deployment into Breeding Programs: A Case Study Based on Association Analysis of AltSB, a Major Aluminum Tolerance Gene in Sorghum (ALTSORGHUM).  Jurandir Malgalhaes, Embrapa, Siete Lagoas, Brazil ( jurandir@cnpms.embrapa.br ) was the Principal Investigator.

Supporting Germplasm Resources:

If it is determined that the local collection contains none or insufficient aluminum tolerance, introgression of the Altsb allele from outsourced germplasm may be necessary. Table 2 lists verified accessions with Al tolerance alleles extracted from a supplementary table for the publication, Caniato FF, Guimarães CT, Hamblin M, Billot C, Rami J-F, Maciel BH, Kochian LV, Liu J, Garcia AAF, Hash CT, Ramu P, Mitchell S, Kresovich S, Oliveira AC, Avelar G, Borém A, Glaszmann J-C, Schaffert RE, Magalhaes JV. 2011. The relationship between population structure and aluminum tolerance in cultivated sorghum. PLoS One 6(6): e20830.  The full table may be viewed by downloading the file attachment at the end of this page (Aluminum tolerant germplasm supplementary table.xlsx).  Selection was based largely on the recommendation of Jurandir Magalhaes, Embrapa, Brazil to include only those exhibiting relative net root growth values of at least 80 after 5 days exposure to 27 µM of Al3+ in hydroponic solution (RNRG5d).  Further, only those accessions that can be procured from GRIN, USA  and/or ICRISAT, India are indicated.

Several accessions should be chosen as the genetic background will play a major role in the expression of the tolerant phenotype.  However, genetic background effects do not seem to be strong in SC283 and SC566 (Jurandir Malgalhaes, personal communication).  Photoperiod sensitivity may well be important and it should be noted that the listed accessions with an “IS” prefix are photoperiod sensitive while the three accessions with an “SC” prefix have been backcrossed to reduce plant height and neutralize photoperiod sensitivity.  Nevertheless, each of the “SC” accessions should also have a photoperiod-sensitive “IS” counterpart at ICRISAT and can be requested.  In any case, breeders should test several phenotypes in order to determine which lines will fit best into their programs.

Table 2. Verified sorghum accessions with the Altsb allele and exhibiting a high degree of aluminum tolerance as measured by relative net root growth values of at least 80 after 5 days exposure to 27 µM of Al3+ in hydroponic solution.

Altsb germplasm

 

 

 

 

 

 

 

 

 

 

The availability of accessions at GRIN and ICRISAT is indicated in Table 2.   Accessions distributed by GRIN can be requested on-line at http://www.ars-grin.gov/  Accessions from ICRISAT may be requested by contacting:

Dr H D Upadhyaya
Assistant Research Program Director-Grain Legumes 
and Principal Scientist and Head Gene Bank
ICRISAT-Patancheru 
Andhra Pradesh, India 
H.Upadhyaya@cgiar.org

Supporting Information:

For gene-specific STS markers for Altsb refer to:

Caniato FF, Guimarães CT, Schaffert RE, Alves VMC, Kochian LV, Borém A, Klein PE and Magalhaes JV. 2007. Genetic diversity for aluminum tolerance in sorghum.  Attachment below.

For gene-specific STS flanking markers for Altsb refer to:

Caniato FF, Guimarães CT, Hamblin M, Billot C, Rami J-F, Maciel BH, Kochian LV, Liu J, Garcia AAF, Hash CT, Ramu P, Mitchell S, Kresovich S, Oliveira AC, Avelar G, Borém A, Glaszmann J-C, Schaffert RE, Magalhaes JV. 2011. The relationship between population structure and aluminum tolerance in cultivated sorghum. PLoS One 6(6): e20830. Attachment below. 

For additional markers and a genetic map refer to:

P. K. Sabadin, M. Malosetti, M. P. Boer, F. D. Tardin, F. G. Santos, C. T. Guimarães, R. L. Gomide, C. L. T. Andrade,  P. E. P. Albuquerque, F. F. Caniato, M. Mollinari, G. R. A. Margarido, B. F. Oliveira, R. E. Schaffert, A. A. F. Garcia, F. A. van Eeuwijk, J. V. Magalhaes. Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phonological and plant height differences Theor Appl Genet. 2012 May;124(8):1389-402. doi: 10.1007/s00122-012-1795-9. Attachment below.

Originating Project Final Technical Report 

Final Technical Report of GCP GCP Project G3007.04 Tailoring Superior Alleles for Abiotic Stress Genes for Deployment into Breeding Programs: A Case Study Based on Association Analysis of AltSB, a Major Aluminum Tolerance Gene in Sorghum (ALTSORGHUM). Attachment below.

Supplementary Resources:

Publications

Magalhaes JM, Liu J, Guimares CT, Lana UGP, Alves VM, Wang Y-H, Schaffert RE, Hoekenga OA, Shaff JE, Pineros MA, Klein PE, and LV Kochian. 2007. A gene in the multidrug and toxic compound extrusion (MATE) family confers aluminum tolerance in sorghum. Nature Genetics 39: 1156-1161. Attachment below.

Magalhaes, J.V., Garvin, D.F., Wang, Y.H., Sorrells, M.E., Klein, P.E., Schaffert, R.E., Li, L. and Kochian, L.V. (2004) Comparative mapping of a major aluminum tolerance gene in sorghum and other species in the Poaceae. Genetics, 167, 1905–1914. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1471010/

http://www.readcube.com/articles/10.1038/ng2074

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