Reinventing salt-tolerant rice breeding on ground zero

Salinity is an agricultural problem that significantly affects rice production and is spreading in fields across the world. Poor irrigation practices, insufficient irrigation water during cropping seasons with low rainfall, high evaporation, increasing saline groundwater levels, and saltwater intrusion in coastal areas are among the significant causes of salinity.

Salinity cuts rice production by 30–50%. Because this growing environmental crisis plagues the world's largest rice-producing and exporting countries, such as Vietnam, Thailand, Bangladesh, and India, it threatens the future of agri-food systems that feed billions of people.

But millions of smallholder rice farmers living along the coastal areas of Asia and Africa are already feeling the brunt of this ever-spreading scourge.

A vast and lasting damage

Salinity inflicts long-lasting damage that affects generations of farmers. In October 1999, a tropical depression in the Andaman Sea gradually developed into a superstorm, the Paradip Cyclone, barrelling towards India. It became the most severe weather system to strike Odisha in the 20th century.

For most, the damages caused by the cyclone are only a memory. The floods have receded, ruins have been rebuilt, and lives so violently interrupted have resumed.

However, more than two decades later, rice farmers in the state's coastal region along the Bay of Bengal continue living with the cyclone's aftermath.

Recently developed germplasm that exhibits tolerance to high-salinity levels using cutting-edge breeding techniques and a novel method of seawater irrigation for screening. (Photo: IRRI)

Waseem Hussain, who leads the Global Rice Salinity and Flooding Breeding Program at the International Rice Research Institute (IRRI), visited the area recently and spoke with the rice farmers.

"They told us that they used to grow rice in every field before 1999," Dr. Hussain said. "But the cyclone converted their farms into salt lands, and they said that they could not grow anything since. The salinity level goes very high during the dry season because it doesn't rain here."

De-salting the earth

There are several ways to manage salinity in the soil, but most are costly and beyond the reach of poor rice farmers. Developing salt-tolerant crop varieties is the most economical solution because it entails less resource use and is both practical and socially acceptable.

Rice is more susceptible to salinity than other crops, and breeders worldwide have been working to develop varieties that can grow in afflicted soils. IRRI has accomplished much in this regard over the past 40 years, and various countries have released salt-tolerant rice varieties originating from IRRI's germplasm.

Genetic history fails  to repeat itself

One of the most impactful milestones in rice breeding occurred in 1991 when researchers discovered the SUB1 gene from an unheralded Indian landrace designated FR13A (FR stands for "flood resistant").

The SUB1 gene, which enables rice to survive underwater for 14 days, has been introduced into several popular and high-yielding varieties for the millions of poor farmers in flood-prone areas worldwide that are rendered useless for rice production during the rainy season.

In 2015, one of these varieties, Swarna-Sub1, was hailed as a significant innovation for helping rice farmers in flood-prone areas of India.

The milestone gene for developing salt-tolerant rice is Saltol. The gene confers salinity tolerance, particularly during the seedling stage. Like SUB1, breeders have incorporated the Saltol gene into various rice varieties. However, a single gene like Saltol cannot provide a reasonable salinity tolerance and can grow in farmers' fields like SUB1 varieties. 

"We sent salt-tolerant germplasm materials to Bangladesh and India for testing," Dr. Hussain said. "In 2021, I visited some of the sites on farmers' fields in Bangladesh to see how the materials are performing. To my surprise, all of the materials were completely dead. None survived. I went to the other location, and the same thing happened. They were supposed to be salt-tolerant but didn't survive under those conditions in coastal belts. "

One thing that caught Dr Hussain's attention during his visit to Odisha was the rice plants growing in small pockets. But they were farmers' landraces. He asked the farmers about the released varieties by public institutes. They said they don't grow or survive here, or if they grew, they produced very low yields.  

"It was pretty shocking to hear this from the farmers," Dr. Hussain said. "If we continue breeding salt-tolerant rice in the same manner we have been doing for the past 40 years, we will have the same story."

Manufactured stress vs. real-world stress

IRRI researchers developed screening techniques for rice salt tolerance conducted in a phytotron, a type of greenhouse where the temperature and relative humidity can be manipulated to minimize environmental interactions.

The plants are screened at the seedling, vegetative, and reproductive stages. They are placed in styrofoam floats inside a plastic box containing a carefully formulated saline nutrient solution. The saline nutrient solution is carefully prepared, every ingredient precisely measured, and strictly maintained to ensure uniformity.

Unlike the environment inside a phytotron, nature rules the real world. There are no knobs and switches to bend its forces to desired settings.

IRRI breeders used artificial salts in salinity screening experiments under managed conditions. Artificial salts do not mimic the real condition of salinity stress in the farmer's field.

"Conditions in farmers' fields are very dynamic and complex," Dr. Hussain explained. "The salinity level is highly unpredictable. Sometimes it will be low. Sometimes it will be high. When it rains, the level of salinity decreases. When it doesn't rain, the salinity level goes up.

"Salinity can come at any time. It's not within the control of the farmers. It can happen at any stage of crop growth. Under experimental conditions, the plants are given very short treatment periods, for one or two weeks, and then evaluated to see how they responded."

"An idea struck in my mind that to develop salt-tolerant rice varieties that can grow in these fields,  we have to match the conditions in the fields," said Dr. Hussain. "Controlled or managed experiments do not reflect the true story of the farmers' fields."

That's where Dr. Hussain and his team came up with the idea of establishing screening plots where the plants can experience the harsh realities of coastal environments. 

Ground zero for salt-tolerant rice breeding

About 132 kilometers east of Manila, the Municipality of Infanta in Quezon Province, Philippines, is known for its traditional Filipino distilled palm liquor, lambanog. Its eastern border is coastal, touching Polilo Strait, and it has numerous seaside resorts.

According to the Department of Agriculture, rice is cultivated in the municipality, where the average harvest is 2,932 kilograms per hectare.

Infanta's climate rains throughout the year, with a pronounced rainy season from November to April. However, it is no stranger to natural calamities, particularly typhoons that form thousands of kilometers away in the heart of the Pacific Ocean.

In 2004, Infanta suffered a fate similar to Odisha five years earlier. The town was heavily affected by four successive weather systems: two tropical depressions and two typhoons. These triggered flooding, landslides, and storm surges. 

Storm surges are the bane of coastal agricultural lands. Strong winds push seawater further inland, blighting the soil.

The 2020 National Mapping, Characterization and Coastal Areas Affected by Salinity Development of Spatial Database for the Coastal Areas Affected by Salinity by the Bureau of Soils and Water Management reports that Infanta's coastal areas vary from non-saline to severely saline with more than 5,300 hectares exhibit moderately saline soil.

From the perspective of salt-tolerant rice breeding, Infanta is ground zero. Dr. Hussain and his team set out to transform rice breeding using a radical approach that has never been done before.

Reinventing conventional wisdom

Although it seems counterintuitive, countless published scientific works using the standard screening protocol helped shape Dr. Hussain's revisionist approach to salt-tolerant rice breeding.

He and his team reviewed the literature at IRRI and globally and found tremendous amounts of published research on various rice genes associated with salt tolerance.

"Breeders have acquired an understanding of the biological mechanisms inside plants, Dr. Hussain said. "But whatever genes identified through ideal-conditions screening or greenhouse experiments have 0% translation in the field."

So, Dr. Hussain and his team abandoned the established protocol of subjecting plants to short salinity periods and classified them as tolerant if they did not die.

They set up the experimental site 200 meters from the coast, where seawater inundates the field during high tides. During low tides, they use a pump to draw water from the sea to irrigate the plants.

Their inventive screening method subjected thousands of rice germplasm from previous breeding efforts at IRRI to salinity treatments not at a particular stage but throughout their life cycle up to the harvesting stage.

"IRRI researchers have done a tremendous job of creating salt-tolerant germplasm from the International Rice Genebank," Dr. Hussain said. "I think that is our biggest advantage. The germplasm was already there. The only thing to do was to put them in real conditions and identify the best salinity-tolerant genotypes. It is like finding a needle in a haystack.″

A genotype refers to an organism’s complete set of genes, which, in combination with environmental factors, determine its appearance and behavior.

"It took us over three years to optimize their innovative screening experiment protocol in Infanta because it's not easy to do it in the field," he said. "But we have a very robust screening facility there now. When we want to identify salt-tolerant rice plants, we screen them in Infanta."

Scientific heresy or the protocol of the future?

This kind of out-of-the-box thinking made other breeders shake their heads in disbelief. Challenging any dogma will always elicit blowback and comes with a price for those with dissenting standpoints.

But irrigating rice with seawater?

"We were told our approach is very wrong," Dr. Hussain said. "We received much criticism from people telling us we cannot grow rice in the seawater because we will kill the plants. Rice is not halophyte (salt-tolerant), and it is impossible to grow rice in seawater.  But our aim was not to grow the rice in seawater. We were trying to identify which genotype would respond with appropriate tolerance when we put them under real saline stress. We use the plants that endure in our breeding program to develop new varieties."

The first lines the team identified and created new germplasm through crossing are in the testing stage of ongoing trials in India and Bangladesh.

"I think they will perform," Dr Husain said. ″In three or four years, I expect suitable salt-tolerant varieties for coastal ecologies of Asia and Africa emanating from our newly identified germplasm at infanta. But the real test will begin in farmers' fields."

References:

Screening rice for salinity tolerance

https://www.researchgate.net/publication/281497630_Screening_rice_for_sa...

2020 National Mapping, Characterization and Coastal Areas Affected by Salinity Development of Spatial Database for the Coastal Areas Affected by Salinity

http://bswm.da.gov.ph/wp-content/uploads/Salinity-2020-Technical-Report-...