An average (~1t/ha) wheat grain yield in Kazakhstan, which is the lowest across the world, has not changed since the reclamation of fallow land (1950-60’s). Moreover, country’s wheat breeding is mainly based on conventional methods compared to the UK’s, which takes advantage of using the most advanced genomic techniques. The genomic approach with combination of other intensive agricultural practices has had a significant positive effect on enhancing the average wheat yield in the UK which doubled from 4 to almost 9 t/ha in the last 60-70 years.

Thus, the aim of this grant proposal is to use such a genetic strategy to develop four bi-parental wheat populations, through crossing the Kazakh and UK commercial wheat varieties, and constructing their high-density genetic maps. Therefore, four wheat varieties from Kazakhstan were crossed with the UK wheat. Consequently, four bi-parental populations, consisted of 384 samples in total, were developed. Each population were taken five rounds of SSD (Single Seed Descent) purification providing >94% homozygosity with the remaining >6% heterozygosity in F5 generation. This shows that the proposed project have a scientific background.

Therefore, objectives of this proposal are:

1. To reduce the heterozygosity level >3% in populations.
2. To fingerprint four populations genetically.
3. To construct high-density genetic maps per each population.

These objectives will be addressed in this proposal as follows:

1. The heterozygosity level in each population will be reduced >3% by using SSD method. So, each population will be taken one more round of SSD purification.
2. Each bi-parental population will be genetically fingerprinted based on the 35K AXIOM Genotyping Microarray. Before genotyping, high-quality DNA will be isolated from F6 plants.
3. The high-density genetic maps per population based on 35000 SNP DNA-markers will be constructed using software programs such as R, Phyton, PLINK and TASSEL.

The results of this project will be used as a background to conduct QTL mapping studies in the next project.

Targets

The development of four bi-parental populations for Kazakh bread wheat and construction of their heigh-density genetic maps towards dissecting and mapping the type of genetic variation that is fixed in the elite breeding pools of Kazakh wheat breeders.

Tasks

In quantitative genetics, prior to identify and map the genes/genomic regions which have a potential to increase crop yield, the recombinant lines and their genetic maps need to be developed and constructed respectively. This will be achieved through three main objectives:

1. Develop four bi-parental recombinant lines for Kazakh bread wheat and their seed multiplication.

We used four commercial wheat varieties from Kazakhstan to cross with the UK wheat to generate bi-parental populations. However, these four populations still possess higher rate of heterozygosity as each of them were taken only five rounds of SSD purification. To reduce the level of heterozygosity and make >97% loci fixed, each population will be taken one extra round of SSD purification in the automated glasshouses of John Innes Centre (JIC), UK, during this proposed work. In the same year, the controlled environment facilities available at JIC will allow us to grow these populations again to have their seeds multiplied which then will be sent to Kazakhstan.

1. Genotype all four bi-parental populations using the 35K AXIOM high throughput genotyping microarray.

While plants are being grown for the seed multiplication, the young leave tissues will be collected at the early tillering stage from each sample (384 individual) for the isolation of high-quality DNA. Once the qualities and quantities of DNAs of each sample are standardised, they will be sent to Bristol University for genotyping with 35000 DNA markers. The multiplied seeds will be sent to Kazakhstan for further genetic and field assessments for integrating the genotypic and phenotypic data aimed at finding the loci associated with the adaptation and yield in different Kazakh wheat growing environments.

1. Construct high-density genetic maps.

Prior to integrating genotypic data with phenotypic, the genetic map needs to be constructed. Therefore, the genetic maps are critical tool for gene mapping. However, the genetic maps cannot be used in genetic analysis straightaway. It is critical to scrutinise their accuracy such as ordering the markers, omitting the duplicated genotypes and markers, before integrating into genetic analysis. In this grant proposal, we will construct high quality genetic maps.

Given the strong and long experience of the scientific consultant and the applicant respectively in the field of wheat genetics, the proposed work is achievable.

Expected results

The main results of the proposal

The four bi-parental populations, consisted of 384 genotypes in total, for Kazakh bread wheat and their individual genetic maps, comprised of 35000 SNP DNA markers, will be the main outcomes the project.

1) publication of papers in foreign peer-reviewed scientific journals

Two papers will be published in journals with Q1, Q2 and Q3 impact factor in the Web of Science or with a CiteScore percentile of at least 50 in the Scopus.

The first paper will focus on constructing the genetic maps for specifically Kazakh bread wheat while comparing and contrasting essential genetic aspects such as recombination and duplication events within and between the populations.

The second paper will discuss the genetic and phenotypic diversity within and between populations and compared to other wheat panels such as NILs developed by the applicant during his PhD research which was dedicated to understanding the genetic control of adaptation and yield for Kazakh bread wheat.

2) publication of monographs, books and (or) chapters in the books;

Not planned

3) receipt of patents in foreign patent offices;

Not planned

4) development of scientific and technical documentation;

Not planned

5) dissemination of results among potential users, the scientific community and the general public;

Both plant recourse and genetic dataset developed by the proposed project will be available for local and international wheat breeders and scientists. These genetic resources will lay the foundation for much future studies aiming to release new improved wheat varieties in Kazakhstan.

6) other measurable results in accordance with the requirements of the tender documentation and the specifics of the project. Additionally in the section are indicated:

6.1) area of application and target consumers of each of the expected results.

We believe that alleles of the fixed genes in Kazakh wheat gene pool should be detectable in these four bi-parental populations as they were developed as a result of crossing wheats adapted to different growing environments. Therefore, they are especially beneficial for Kazakh wheat breeders as each population will enable them to pinpoint important genetic factors that they could not segregate through the crossing of highly related local wheat varieties.

The genetic maps will provide Kazakhstani wheat geneticists with a great opportunity to identify and map those genetic factors of important traits to the wheat genome. Thus, the next studies relying on the outcomes of this work will benefit using the developed germplasm resources and their genetic fingerprints for the marker-trait association studies in Kazakh bread wheat based on quantitative genetics methods.

6.2) the impact of expected results on the development of basic scientific directions and related areas of science and technology

Besides local and international wheat geneticists and breeders, next potential consumers of the project results would be undergraduate, MSc and PhD students. They will benefit from the ready-to-use plant materials and their genetic maps. So, there is a great potential that the project results seem to facilitate the development of NIL and NAM (Nested Association Mapping) populations through these masters and postgraduate research studies which is important for training the next generation wheat geneticists in the country. If the project gets funded, it will support the development of NAM populations for the first time with involvement of commercial wheat varieties from Kazakhstan.

3) applicability and (or) the possibility of commercialization of the results

The results of the project could be commercialised once the new improved wheat varieties are released.

4) social, economic, ecological, scientific-technical effect of project results;

In the short term, the project results will affect Kazakh wheat breeders’ thinking about using more sophisticated crossing and selection strategies in which they could benefit from. In the longer term, there could be direct impacts on combining the traditional breeding methods in Kazakhstan with the genomic selection.

Taken together, the genetic knowledge acquired from this and future projects, relaying on the results of the current study, should support the delivery of positive economic and social impact through plant breeding and training the next generation wheat geneticists in Kazakhstan.

5) other direct and indirect results of the project.

The importance of computational biology or next generation plant breeding methods for plant improvement will be popularised among wheat breeders, University students and school children in Kazakhstan through organising courses and workshops with hands-on activities. For more information on this, please refer to section 3 “Scientific novelty and significance of the project”.