Exploiting novel genes to improve resource use efficiency in wheat.

Lead Research Organisation: John Innes Centre
Department Name: Crop Genetics

Abstract

Resource use efficiency can be improved by either maintaining yield with lower crop inputs (e.g. fertiliser or pesticides) or increasing yield with the same, or reduced, crop inputs. Increasing yield is likely to be the most sustainable approach given the need to ensure global food security and the limited scope for expanding the cropped area. A recently completed LINK project (LK0958) identified regions of chromosomes 3A and 7D (known as quantitative trait loci or QTL) that were associated with increased resource use efficiency resulting from yield increases of 0.3 to 0.4 t/ha (at a given level of crop inputs). A smaller yield effect QTL was also found on chromosome 6A. These QTL were also associated with a lower resistance to lodging primarily as a result of greater height, and also due to a smaller stem wall width and root plate spread. Several other height QTL were found which did not affect yield. It was also shown that some height QTL were twice as responsive as others to shortening by plant growth regulator (PGR) chemicals. These discoveries offer the prospect of increasing resource use efficiency by combining QTL for increased yield (at a given level of inputs) with QTL for increased lodging resistance (through crop shortening), as well as by improving lodging control through better targeting of PGRs. However this is not currently possible because the genetic markers identified in LK0958 are not close enough to the specific genes located within the QTL region for the breeders to reliably identify the presence of the positive genes in a range of genetic backgrounds. This project aims to increase resource use efficiency by developing reliable genetic markers and a physiological understanding for QTL that increase yield and lodging resistance without increasing the crop's requirement for inputs. This will be achieved by: 1) Developing varieties that differ only for the region of chromosome with the QTL for resource use efficiency (near isogenic lines) which will be used to achieve objectives 2 and 3, 2) Identifying more reliable genetic markers for these QTL, 3) Understanding the physiological mechanisms by which these QTL act and quantifying effects on resource use efficiency and greenhouse gas emissions, 4) Investigating which yield and height QTL are in current varieties and the scope for combining them to increase resource use efficiency through greater yield and reduced lodging risk, and 5) Quantifying the responsiveness of the different height QTL to different PGR active ingredients. A major component of this project will involve cloning the gene within the height/yield QTL on chromosome 3A to produce a 'perfect' genetic marker. New markers will be developed for the other QTL which will have much greater reliability due to their closer proximity. This will allow breeders to design crosses to achieve the optimum combination of height and yield QTL in a given cross. Understanding the physiological mechanisms by which the QTL affect yield (e.g. is sink (grains/m2) or source (supply of assimilate) increased) will help to identify the crop management practices required to achieve these greater yields with minimum crop inputs, and thereby increasing resource use efficiency. Genetic markers for the height QTL will also be used to predict which varieties will respond most to PGRs with different modes of action. As PGRs are used prophylactically on the majority of wheat crops this will allow their use to be avoided on unresponsive varieties. It is estimated that the project will increase resource use efficiency by 10% through greater yields and better lodging control. The project will also complement the Defra funded Wheat Genetic Improvement Network (WGIN) by phenotyping the near isogenic lines (NILs) produced within the network and producing new NILs that can be added to the network's genetic resources.

Technical Summary

Aim - to increase resource use efficiency by 10% by developing reliable genetic markers and a physiological understanding for QTL that increase yield and lodging resistance without increasing the crop's requirement for inputs. This will be achieved by: 1) Developing near isogenic lines (NILs) for QTL that increase resource use efficiency. NILs for height/yield QTL on chromosomes 2A, 2D, 3A, 3B and 6A developed within WGIN will be multiplied in years 1/2 to provide sufficient seed for field experiments in years 3/4. NILs will also be developed for the QTL on 7D. 2) Identifying more reliable genetic markers for these QTL A major component of this project will involve cloning the height/yield QTL on chromosome 3A to produce a 'perfect' genetic marker. New markers will be developed for the other QTL which will have much greater reliability due to their closer proximity. 3) Understanding the physiological mechanisms by which these QTL act and quantifying effects on resource use efficiency and greenhouse gas (GHG) emissions. Field plots of the NILs with different N fertiliser levels will be used to understand how yield is increased and whether the requirement for crop inputs is affected. Published models will be used to estimate the effects of the QTL on GHG emissions. 4) Investigating which yield and height QTL are in current varieties and the scope for combining them to increase resource use efficiency through greater yield and reduced lodging risk. A double dwarf cross (Rht1 and Rht2) with the QTL for increased height and increased yield (3A, 6A, 7D) will be made to assess the effect of combining all the QTL for high yield. A wide range of current varieties will be screened with the genetic markers. 5) Quantifying the responsiveness of the different height QTL to different PGR active ingredients. The effect of PGRs which inhibit gibberellin biosynthesis or stimulate ethylene production will be investigated on the NILs

Planned Impact

Plant breeding companies The development of reliable genetic markers will enable breeders to design crosses to achieve the optimum combination of height and yield QTL for increasing resource use efficiency. It is estimated that this project will enable breeders to produce new varieties which have about 10% more yield than current varieties. This technology will be immediately available to Limagrain whose varieties currently account for a significant proportion of the UK wheat area and after the project the technology will be made available to other breeding companies. Farming industry Breeding new varieties with 10% more yield than current varieties and which do not require additional crop inputs will significantly increase the profitability of the wheat crop. Across the UK this will result in about 1.5 million extra tonnes of wheat worth about £150M.Greater straw yields will further enhance profitability especially if large scale methods for converting straw to biofuels are developed. Reliable genetic markers will also be used to identify which height QTL are in commercial varieties from which it will be possible to predict their responsiveness to PGRs with different modes of action. This will enable farmers to target specific PGRs at specific varieties to achieve the maximum reduction in lodging risk. It is anticipated that better targeting of PGRs will improve lodging control by 10 to 20%, which will reduce lodging costs by about £10 million per year (Berry et al., 1998). Environment and wheat consumers The average rate of nitrogen (N) fertiliser applied to wheat works out at approximately 25 kg N per tonne of grain produced (assuming a yield of 8 t/ha). It is expected that this project will reduce the N requirement to 22 kg N per tonne of grain by producing new varieties with a 10% improvement in N use efficiency. If greater N uptake efficiency is proven to be the mechanism then this will result in fewer N residues at risk to nitrate leaching. lant growth regulators are applied to 89% of winter wheat in the UK which amounts to 2270 t of active substance. It is anticipated that this project will reduce the requirement for PGRs by 20% which will reduce the amount of PGR active substance applied by 454 t per year. This will also reduce the proportion of grain contaminated with chlormequat residues. The yield increases anticipated from this project are not expected to alter the total requirement for pesticides (other than less PGRs). This indicates that pesticide usage will decrease from 0.57 to 0.49 kg per tonne of grain. Reducing lodging will help to reduce the incidence of mycotoxin contamination of grains. Achieving greater yields with similar or reduced inputs of fertiliser and pesticides is estimated to reduce greenhouse gas (GHG) emissions per tonne of grain from 325 kg CO2e to 292 kg CO2e (Berry et al., 2008). Achieving greater yields is also likely to reduce the area of uncropped land converted to arable production which will result in significant additional reductions in GHG emissions, e.g. converting temperate grassland to arable is estimate to release 6000 kg CO2e per year for 20 to 30 years (Searchinger et al., 2008). By increasing yield this project will allow current productivity to be maintained using less cultivated land, or will help meet the growing global demand for food with a reduced requirement for expanding the cropped area. It would be expected that reducing the area of arable land that is cropped will help biodiversity indicators such as farmland birds. Science base The project will develop and multiply NILs for height QTL which will be made publicly available through WGIN and will be important resources for other scientists. The DNA sequence of the height QTL on 3A will provide an understanding of the biochemical/hormonal mechanisms by which this locus affects height and whether it could have pleiotropic effects on other traits such as yield
 
Description A narrowing down of the genetic regions involved in plant height determination for the 5 major loci under investigation was achieved. For three of the 5 regions, candidate genes were suggested. For the 3A locus we have separated genetic effects of height and heading date and shown that yield benefit is likely related to phenology and fertility effects.
Exploitation Route New genetic markers for plant height developed can be used for marker assisted selection of height loci in breeding material.
Sectors Agriculture, Food and Drink

 
Description New genetic markers for plant height and yield used for wheat breeding particularly on chromosomes 2D and 3A.
First Year Of Impact 2016
Sector Agriculture, Food and Drink
Impact Types Societal,Economic,Policy & public services