Objective 2 - Simon Griffiths (JIC)

Production of Near Isogenic Lines (NILs)


The traits for detailed study for WGIN include resource use efficiency, drought tolerance, yield stability, and durable disease resistance. These traits are controlled by many genes, which, initially, can only be identified as Quantitative Trait Loci (QTL). A QTL assigns a gene to a large chromosomal region. Work proposed in WGIN 2 will provide the materials that will allow genes to be defined as single points on a chromosome. The future genetic improvement of wheat will depend on the availability of genetic markers that are diagnostic for alleles of interest, the resolution of a QTL location does not allow the identification of diagnostic markers.

Apart from this genetic complexity, the WGIN traits of interest are also complex at the physiological level. That is, they integrate multiple aspects of plant development and physiology. It is important to understand which aspect of plant biology is affected by a gene underlying a trait, but again, the description of genes only as QTL hinders the dissection of traits in this way.

The proven approach to answering these questions is to produce pairs of lines that only differ in the genomic region of interest so that all other genes affecting the trait of interest are the same in both lines, so any difference can be assigned to a single gene by ‘Medelizing’ the locus. These types of material are known as Near Isogenic Lines (NILs). They allow a detailed study of specific gene action at the physiological and developmental level, and the precise genetic mapping of the gene. They are essential for the development of genetic markers which are close enough to a gene to allow wheat breeders to track the desirable alleles of that gene in different breeding pedigrees. They also pave the way for isolation of the gene by a positional cloning approach, a process which is increasingly tractable and will become facile with the availability of the wheat genome sequence and next generation sequencing technologies, as long as we have the appropriate germplasm in place. The limited developmental of this type of material is a major weakness in current UK wheat research. This is partly due to the fact that NILs require at least three years development and therefore not fall easily into the timescale of most grant applications.


Table 1 summarises targets for the backcrossing programme proposed for WGIN 2. These targets have been specifically chosen to address the policy objectives of defra and the trait Activities of WGIN. The Near Isogenic Lines developed in this programme would deliver a competitive advantage to UK wheat research into the genetic mechanisms controlling yield stability and resource use efficiency. This understanding is the most direct way in which academic understanding of these traits can be translated into the delivery of sustainable internationally competitive UK agriculture. Because yield, plant stature, and flowering time are fundamental agronomic traits they are not placed under a particular Activity heading in Table 1. This is because the pleiotropic effects of these traits are likely to impinge on all of the Activities described. The backcrossing programme for these traits is already ongoing in WGIN so these lines will be available for field trials as part of the work proposed here.


Two donor parents such, as two doubled haploid lines from the population in which the QTL was discovered, will be crossed with recipient parents to produce two F1 plants and independent crossing streams. Two more backcrosses will be carried out with selection of flanking genetic markers (usually SSRs) at each generation. BC2 individuals will then be selfed and sixteen lines (eight of each parental allele) selected from each crossing stream. The thirty two BC2 derived NILs each contain a recurrent parent genomic background of at least 87.5%.

For the yield, height, and heading date NILs the last two years of the work will be used to carry out replicated field trials of 6m2 plots. The NIL populations will be phenotyped for yield, height, and flowering time.

Table 1

Activity and trait

QTL or major gene

Recipient lines

5 AE Watkins and Gediflux Germplasm Collections

New alleles from allele mining experiments will be backcrossed into Paragon


7  Insect Resistance

Major alleles or new QTL for  insect resistance

Paragon (or another  suitable susceptible)

8.  Nitrogen use efficiency (NUE) and Quality QTLs linked to NUE

QTL for NUE identified in Activity 8, the Wheat Functionality LINK project, and QTL identified in the BBSRC-INRA NUE project.

Avalon, Cadenza, Rialto, Savannah, and Paragon

9 Drought tolerance

QTL for WUE  identified in Activity 9

Parents of doubled haploid population chosen for phenotyping and Paragon.

10 Take-all disease

QTL for resistance identified in activity 10
QTL for low take-all inoculum build-up identified in activity 10

Paragon and Hereward (or another nabin 1 wheat)
Hereward  (or another nabin 1 wheat)

11 Introgression of resistance to Septoria leaf blotch from Triticum monococcum into hexaploid wheat

TmStb1 introgression with linked markers

Cadenza, Chinese Spring and Riband

Plant  architecture and stature

2A, 2D, 3A, 3D and 6A

Avalon, Cadenza, and Paragon


Spark, Rialto, and Paragon

3A,, 7A

Charger, Badger, and Paragon


Savannah, Rialto, and Paragon

Heading data

1D, 3A, 6A and 7D

Avalon, Cadenza, and Paragon

Yield components and biomass

 3A, 2D,S and 6A

Avalon, Cadenza, and Paragon


Spark, Rialto, and Paragon

2A, 2B, 5A

Charger, Badger, and Paragon


Savannah, Rialto, and Paragon

Yield benefit associated with Lr19 (Agropyron elongatum segment) (Reynolds et al., 2001) in the CIMMYT varieties Oasis and Wheatear

Paragon, Claire, Hereward

February 2011:
The development of the Avalon x Cadenza NIL population is now completed and details on its development are available here: Development of the Avalon x Cadenza NIL population