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The National Barley Molecular Marker Program – achievements and future directions

Andrew Barr and Peter Langridge

Coordinators, On behalf of the NBMMP
Dept. of Plant Science, University of Adelaide, Waite Campus, Glen Osmond, S.A..

Aims

The program has three major aims – a) identify markers linked to traits of importance for barley improvement; b) apply markers within the barley improvement programs; and c) ensure the most efficient utilisation of resources available to the program.

Partners

The NBMMP involves the following organisations - Adelaide University, SARDI, Southern Cross University, Murdoch University, NSW Agriculture, QDPI, DNRE Victoria, Ag WA, University of WA. The program is funded by GRDC with substantial contributions from the host organisations.

Components

The program is divided into 10 components: 1. Coordination, 2. Disease/pest resistance, 3. Quality Evaluation, 4. Map Construction, 5. Marker and Mapping technologies, 6, 7, 8, 9, 10. Implementation of markers in breeding programs- Qld, NSW, Vic, SA, WA.

Major research projects

1. Population construction, mapping and phenotyping “Major Mapping Populations”.

Two major populations are to be constructed each year (Table 1). These populations have been chosen to map the genes / QTLs controlling the traits of greatest importance to the Australian barley industry including tolerance to abiotic and biotic stress, malting, yield and adaptation. “Full” linkage maps are being constructed using a combination of RFLP, AFLP and SSR markers.

Table 1. First eight major populations in the NBMMP – rationale and status.

Cross

Rationale

Population const- ruction

Field trials

Map constr- uction

Quality testing

QTL analysis

Tallon * Kaputar

High malt quality adapted to Northern Region

1996

1998, 1999

1999

1999

1999

Alexis * Sloop

European malt quality adapted to southern Australia

1997

1999

1998/99

Limited 1999

Limited 1999

Franklin * Arapiles

Malt quality adapted to southern Australia

1998

1999

1999

   

Halcyon * Sloop

European winter malt quality & foliar disease resistance

1998

Limited 1999

1999

   

VB9524 * ND11231

Genetics of low grain protein

1998

Limited 1999

     

Dash * VB9104

High yielding feed types

1998 - 99

       

Gairdner * Unicorn

Australian malt quality by Japanese type

1999

       

Tallon * Scarlett

German high quality, adapted to Northern region

1999

       

The NBMMP inherited three populations constructed at the Waite Campus and in its two years has continued phenotyping these populations (Chebec * Harrington, Galleon * Haruna nijo, Clipper * Sahara 3771). The first of the NBMMP populations to enter field trials was Tallon*Kaputar in 1998 while the Alexis*Sloop population has now been mapped and is in field trials in 1999.

2. Population construction, phenotyping and bulk segregant analysis of up to 30 “Minor” Populations.

This program aims to develop molecular markers for simply inherited traits of importance to the barley industry in Australia. Crosses have been made by many participants and usually around 50 individuals from a doubled haploid, recombinant inbred or F2 population have been phenotyped. The DNA of the “best” and “worst” individuals (usually around five individuals) is pooled. Molecular markers polymorphic between the pools are sought and then validated in an independent population. This technique is called “bulked segregant analysis”. The following traits and donor varieties (in parentheses) are included in this program; Scald (Osiris, Waveney, Sultan, B87-14, Forrest etc); Net Blotch (Patty, Pompadour, TR129, WPG); Spot form net blotch (Galleon, WI 2976); Grain staining (TR118, Kino nijo 7); Acid soil tolerance (Brindabella, OR 375); Common root rot (B1602); Pre - harvest sprouting (Nomad); Stripe rust (CIMMYT lines, European varieties); Leaf rust (Alexis * Patty); Boron tolerance (CM72); Russian wheat aphid (); Water sensitivity (Harrington/Stirling); Pro-anthocyanidin gene ant28.

3. Establishment and operation of five implementation laboratories.

The NBMMP aims to develop a research program and collaborative linkages to ensure rapid adoption of marker technology by the five mainland breeding programs. The NBMMP supplemented the infrastructure provided by the host organisations with items such as PCR machines, -80C freezers and gel tanks to remove physical barriers from adoption. Implementation laboratories are now providing services to breeding programs at Horsham, Wagga, Warwick, Adelaide and Perth.

Major achievements

The NBMMP began in July 1997 and already has made a major impact on breeding programs in Australia. Major achievements include:

  • Malt extract QTLs mapped in two populations – opening the real possibility of marker assisted selection (MAS) to improve malt.
  • Diastatic power and alpha amylase QTLs mapped in Chebec * Harrington.
  • New populations constructed, mapped and field tested.
  • Spot form net blotch marker developed, validated and implemented.
  • MAS used to fast track a Sloop – type with CCN resistance, from an initial cross in 1994 to Stage 4 trials in 1998 and seed production beginning in 1999.
  • Implementation into breeding programs of markers for B tolerance, Mn efficiency, diastatic power, malt extract, resistance to leaf rust, stripe rust, scald, Russian wheat aphid, CCN and barley yellow dwarf virus. In 1998, over 10,000 marker assays were performed in implementation laboratories servicing Australian breeding programs with a further increase likely for 1999 as more markers become available (Table 2).
  • An understanding of the genetic basis of genotype x environment interaction for yield differences between northern and southern barley growing regions. QTL analysis of the Chebec*Harrington yield data showed that genotypes with “long basic vegetative phase” were favoured in the north (ie the Harrington type) while the “short basic vegetative phase” types (ie the Chebec type) were favoured in the south.
  • Establishment of a NBMMP website.

Problems and challenges

The NBMMP is a large and ambitious project. It has challenged all of the participants and, in particular, our joint ability to keep each other informed and involved in the program. The GRDC commissioned a major review of the NBMMP in April, 1999. The review team included Professor Pat Hayes, Oregon State University and GRDC program leaders / consultants Mr. Ian Muirhead, Ms. Deirdre Davis and Mr. Andrew Parratt. Their recommendations have not been formally released at the time of writing this paper but they also identified communications as a major focus. To this end, we plan to supplement our current strategies of an annual two day workshop (modified format in future), annual teleconference for field program and web site with an upgraded web site distribution of the annual GRDC reports and more regular teleconferences especially for the implementation laboratories.

On the technical side, the most serious limitations have been delays in the construction of some mapping populations (which, in turn, has delayed the map construction components) and more seriously, the lack of polymorphic markers for implementation. For instance, in the screening of topcross F1’s in SA in 1998 and 1999 the proportion of crosses where polymorphic markers were successfully used was 65% and less than 40%, respectively. The microsatellite or SSR markers (around 500 in total) generously supplied by Scottish Crops Research Institute have not been placed on our maps and many of those that have are not polymorphic in the germplasm used in Australian programs.

One staffing issue has bedeviled the program. It has proven difficult to attract and secure skilled molecular biologists to the implementation laboratories. A rapid increase in opportunities in plant biotechnology in several states and territories in 1999 is unlikely to ease this situation.

All of the breeders involved have debated the pros and cons of MAS and the most appropriate way to employ it in their breeding program. Given that the programs have different breeding strategies and systems, the optimum use varies but most breeders would agree that MAS has extended the range of useful tools in their programs.

New traits, projects and hopes ……..

The NBMMP has been the launching pad for several other projects within the GRDC portfolio. For instance, VIDA at Horsham have just begun a project on the genetics and mapping of low grain protein in barley, which is strongly linked to NBMMP. A GRDC international collaboration between the Waite Campus partners and ICARDA seeking barley varieties adapted to low rainfall areas, builds on the expertise of the NBMMP. Student projects in the validation of markers for diastatic power, the mapping and trait dissection of malt extract QTLs and the genetics of the performance of barley on sand also use the resource base from the NBMMP.

Table 2. Markers implemented in NBMMP labs by Sept. 1999.

Type

Traits

Gene

Chrom.

Useful

Implemented

     

location

markers

by

Diseases

CCN

Ha2 locus

2H

AWBMA 21

SA, VIC

And

CCN

Ha4 locus

5H

XYL

SA, VIC

Pests

Scald

AB208 – Rrs14

1H

Hor 2, PCR marker

NSW

 

Scald

AB6 (Tantangara) Rrs13

6HS

MWG916

NSW

 

Scald

AB35 – gene undesignated

7H

SSR 807.12, PCR marker

NSW

 

Mildew

mlo

4HL

?

WA

 

BYDV tolerance

Yd 2

3HL

PCR - YLM

SA, WA, VIC, NSW

 

Leaf rust

RphQ (possibly allelic to Rph2)

5H

OPU-02

Qld

 

Stem rust

Rpg1

7H

ABG704, Allele specific PCR marker derived from ABG704

Qld

 

Stem rust

rpg4

5H

Allele specific PCR marker

Qld

 

Spot form net blotch

Rpt 4

7H

PSR117,AWBMA 11

SA

 

Russian wheat aphid

Undesignated

2H

ABG8, PCR marker

VIC, NSW

   

Undesignated

1H

KVI/KV2, Hor2

VIC, NSW

Malt

Diastatic Power

Amy1

6H

 

SA (research projects only)

Quality

 

Amy2

7H

Xcdo358

SA (research projects only)

   

Undesignated

5H

Xabg463 / Xabg057

SA (research projects only)

   

Bmy1

4H

Bmy 1 Intron III

SA, WA, VIC, NSW

   

Bmy2

2H

 

SA (research projects only)

 

Malt extract

Undesignated

5H

ABG 057

SA

Agronomic

Boron tolerance

Undesignated

2H

CDO370, WG996

SA, VIC

   

Undesignated

3H

AWBMA15, WG405

SA, VIC

   

Undesignated

4H

WG114, KSUG10

SA, VIC

 

Mn efficiency

Mnel

4HS

ABG714

SA

 

Basic vegetive

bvp

2H

ABC156E

WA

 

stage/flowering time

 

2H

PSR108

 
     

2H

PSR108A

 
     

2H

BCD221

 
     

2H

BCD339F

 
   

ppd

1HL,2HS

PSR162,WG858 respectively

WA

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