Genetic improvement of rice seed vigour for dry direct-seeded conditions

Rice is the most important staple crop in the developing world. It has been estimated that over three billion people in Asia rely on rice to provide 30 to 75% of their calories. The most widely used method for cultivating rice involves germinating the seeds in nurseries and transplanting the seedlings to flooded 'paddy' fields. This puddled transplanted rice (PTR) method accounts for ~55% of global rice cultivation and ~75% of world production. However, in many parts of South and Southeast Asia, farmers are switching to direct seeded rice (DSR) because the availability of labour and water is in decline and their associated costs are rising. A similar transition is also occurring in West Africa. To obtain a good crop using DSR it is imperative that the seeds germinate quickly in the soil and that the seedlings grow vigorously. However, because breeders have focused on developing varieties for PTR there has been little or no selection for seed vigour. Agronomists have highlighted a need for the development of new rice varieties with improved seed vigour so that they perform better in dry direct seeded conditions. The first aim of this project is to identify which genes are responsible for controlling seed vigour in rice by filming the germination of ~1000 different rice varieties that have had their genomes sequenced and identifying the key genetic differences that are associated with strong vigour. This knowledge can be used by breeder to develop new varieties. The second aim of this project is to determine whether the shoot growth of existing elite semi-dwarf rice varieties can be improved by enhancing the production of the plant growth regulator gibberellin in a specific seedling tissue called the mesocotyl. The increase in mesocotyl elongation could help seedlings to emerge from the soil when the seed has been planted at a greater depth. This is a key weakness of current varieties.

Rice forms part of the staple diet of more than half the world's population. 18 of the top 20 rice producing countries are Lower and Middle Income Countries (LMICs) on the DAC list of ODA recipients. Together they account for ~95% of world production. The majority of the rice is consumed in the country of origin and only ~5% is traded internationally. The predominant method of rice production is Puddled Transplanted Rice (PTR), accounting for ~55% of cultivated area and ~75% of yield. PTR is productive but highly intensive in its requirements for water, labour and energy. It is also responsible for between 10 and 20% of global methane emissions. Dry Direct Seeded Rice (DSR) is a more sustainable alternative to PTR, particularly where low or zero tillage is employed. DSR is becoming more widely practiced in many LMICs owing to a combination of social, environmental and economic drivers. In order to achieve the best yield using DSR, strong early seedling establishment is required to overcome adverse conditions in the soil and greater weed pressure. However, current high-yielding semi-dwarf rice varieties have not been bred for seed vigour because this trait is not critical for PTR. The aim of this project is to help in the development of new DSR varieties with enhanced seed vigour. Automated high-throughput imaging technologies will be used to measure multiple component traits associated with seed vigour in a diversity set of ~1000 re-sequenced rice accessions and establishment will also be scored in small-scale field experiments. The data will be used to determine trait relationships and to perform a Genome Wide Association Study. This will identify genes and alleles that confer stronger seed vigour and can be used for molecular breeding. A targeted metabolic engineering approach will also be used to determine whether shoot growth can be enhanced in current elite semi-dwarf varieties by increasing the levels of active gibberellins in the mesocotyl.

The ultimate beneficiaries of this project will be farmers in Asia and the people who rely on the food they produce. Rice is the most important staple crop in Asia, where it has been estimated that over 3 billion people rely on it to provide between 30 and 75% of their calories. The dominant method of rice cultivation is puddled transplanted rice (PTR), which accounts for about 55% of global crop area and around 75% of world production. However, many farmers are transitioning to dry direct seeded rice (DSR) owing to a combination of social, environmental and economic factors. In South Asia this transition is occurring fastest in India, Nepal and Bangladesh, and in Southeast Asia in the Philippines, Cambodia, Vietnam, Laos and Myanmar. Rice plants use between 1500-2500 litres of water to produce one kilogram of seed. The availability of water for agriculture in general (and rice cultivation in particular) is decreasing due to a shift in rainfall patterns, with less rain at the beginning of the season making irrigation for PTR less reliable. Furthermore, due to increased industrialisation and rural-urban migration, the availability of labour for agriculture has also reduced drastically in most rice-growing countries. Mechanised dry DSR is becoming a more attractive alternative to PTR. However, DSR has yet to be adopted in many countries and regions because suitable rice varieties are not available.

The research carried out in this project is in collaboration with the International Rice Research Institute (IRRI). More than half the area of rice grown in Asia is planted to IRRI-bred varieties or their progenies. The project will therefore directly help breeders to develop better varieties for dry direct seeded conditions. These varieties require improved seed vigour so that they can germinate and emerge rapidly from deeper soil depth, where even in the event of reduced rainfall there is more moisture available. This is currently a major weakness of elite rice varieties, which have been bred for the PTR system where seed vigour is much less important. It has been estimated that PTR contributes between 10 and 20% of all methane emission and so the continued transition to dry DSR will have an environmental benefit in combating global warming. Due to the fact that DSR matures approximately 10-15 days earlier than PTR, it also provides better opportunities to farmers to grow a second crop and increase their income. DSR rice varieties with improved seed vigour will have a large-scale impact. Researchers at IRRI have estimated that they could increase rice yields by ~0.5 t/ha, reduce the need for irrigation by ~40 cm of water/ha, allow labour savings of ~25 person-days/ha, make energy savings of ~1,500 Mj/ha, reduce greenhouse gas emissions by ~1,500 kg of CO2 equivalent/ha and increased net economic returns by USD 50/ha in most of the rice growing countries in Asia.