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MAGIC map and go: deploying MAGIC populations for rapid development and dissemination of genetic markers for yield improvement in elite UK winter wheat

Project Report No. PR610

MAGIC map and go: deploying MAGIC populations for rapid development and dissemination of genetic markers for yield improvement in elite UK winter wheat


Keith Gardner (1), Benedetta Sacommanno (1), Phil Howell (1), Ian Mackay (1), Anna Sanchez (1), John Jacobs (2), Steve Smith (3), Charlotte Hayes (3), Nicholas Bird (4), Ed Byrne (4), Jacob Lage (4), Simon Berry (5), Edward Flatman (5), Peter Jack (6), Chris Burt (6), and James Cockram (1)

(1) NIAB, Huntingdon Road, Cambridge, CB3 0LE,
(2) BASF, Technologiepark-Zwijnaarde 38, 9052 Gent
(3) Elsoms Seeds Ltd, Pinchbeck Road, Spalding, Pe11 1QG
(4) KWS UK Ltd, 56 Church Street, Thriplow, SG8 7RE
(5) Limagrain UK Ltd, Market Raisen, LN7 6DT
(6) RAGT Seeds Ltd, Grange Road, Saffron Walden, CB10 1TA

Abstract

The genetic improvement of grain yield in bread wheat was targeted by this project. In collaboration with five wheat breeding companies, the high-density genotyping of a wheat multi-founder advanced generation inter-cross (MAGIC) population was exploited. This population captures high levels of genetic recombination and diversity. It was used to:

1. Identify the genetic regions in wheat controlling yield and stability.

2. Provide a molecular toolkit to track, within breeding programmes, regions of the wheat genome that confer increased yield/yield stability.

3. Provide the participating breeders with analysis pipelines and resources to carry out analysis of MAGIC datasets.

4. Exploit the structure of the MAGIC population to rapidly ‘Mendelise’ QTL for multiple yield/yield component traits, providing precise genetic and molecular resources for subsequent studies to fine-map to the gene/causative polymorphism level.

5. Use the molecular breeding methodology, genomic prediction (GP), to allow selection for yield/yield stability in MAGIC lines, based on molecular data alone.

MAGIC lines (1109) were grown at five UK sites over two seasons. This delivered 4,996 2x6m plots on which 18 yield, yield component and agronomic traits were measured. This generated ~90,000 phenotypic data points. Phenotypic information was combined with genotypic data for ~20,000 SNPs for genetic analysis. This identifed 376 QTL, with genetic intervals for most QTL <10 cM. A subset of 20 QTLs was prioritised for the development of ‘KASP’ genetic markers, based on QTL significance, allelic effect and stability across years and sites. This resulted in the design and validation of 58 co-dominant KASP markers for the 20 target QTL. We developed/initiated 31 near isogenic lines (NILs) for 17 traits, along with genetic markers with which to further exploit these materials. Additionally, we determined the gene content from the variety Chinese Spring and identified candidate genes. For one QTL, we identified a single candidate gene controlling spikelet number per ear on chromosome 7A. We searched for artificial mutants using wheat ‘TILLING’ populations for the tetraploid and hexaploid varieties Kronos and Cadenza, respectively. Highly deleterious mutations across multiple homoeologues in 23 candidate genes were identified. These TILLING resources will be used to help determine the specific genes and genetic variants underlying the QTLs identified. Finally, we used pre-project MAGIC phenotypic data for yield, in combination with phenotypic data collected in this project, to investigate GP for predicting phenotypic performance in a given generation, based on markers for plant height.

MAGIC reliably delineates QTL to relatively precise genetic and physical intervals. Tightly linked co-dominant genetic markers, that tag yield and yield component QTL, have been delivered to our industry partners for potential use in their breeding programmes. The work allowed candidate genes within QTL to be identified, and extensive biological (NILs, TILLING lines) and molecular (KASP markers) materials to be generated with which to further investigate phenotypic effects of QTL and genes in isolation.

MAGIC Field Trial

A MAGIC field trial. Located at NIAB Cambridge in 2015, this trial consisted of 504 plots. 

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