In Kashmir's traditional rice, clues to a journey from East Asia

Kashmir's traditional varieties carry cold-tolerance and other locally adapted genes that modern varieties have partly lost, making them potentially valuable as climate change increases stress on crops, new research has found. The analysis also indicated the varieties are more closely related to those from the Korean Peninsula and Northeast China

For many generations, Kashmir's farmers have cultivated traditional varieties of rice -- and a new study by researchers at the Sher-e-Kashmir University of Agricultural Sciences and Technology (SKUAST-Kashmir), Srinagar, has found that these varieties carry a unique genetic history.

According to the study, published in The Plant Genome, Kashmir's traditional varieties carry cold-tolerance and other locally adapted genes that modern varieties have partly lost, making them potentially valuable as climate change increases stress on crops.

The genetic analysis also indicated the varieties are more closely related to those from the Korean Peninsula and Northeast China.

3K rice panel

The SKUAST-Kashmir team began by placing Kashmir's rice on a larger genetic map.

In a 2018 study, Chinese researchers had collected rice germplasm -- genetic material from seeds -- from around the world and created the so-called 3K rice panel. Their 3,010 samples represented cultivated rice diversity from different parts of the world, including the Oryza sativa cultivated in Asia.

However, SKUAST-Kashmir genetics and plant breeding professor Asif Bashir Shikari said the 3K panel didn't include germplasm from Kashmir's traditional varieties.

"That was the primary reason we sequenced 142 rice germplasm accessions from Kashmir region and compared them with the 3K panel in our study," he said.

The team also looked beyond the overall genome. According to Dr. Shikari, rice has roughly 30,000 to 40,000 genes but not all of them are directly related to traits important for agriculture. So the team focused on 21 traits that were relevant and relatively easy to observe, including grain characteristics, starch content, aroma, and those related to adaptation.

They compared the Kashmir germplasm with that from other parts of the world -- including China, India and Bangladesh -- in the 3K panel on these traits. Thus they found that the Kashmir germplasm showed greater genetic affinity with rice from Korea and Northeast China.

"This was particularly interesting in the case of genes HAN1 and CTB4a, associated with cold tolerance, because Kashmir's traditional rice is distinct from the rest of the country as it is cultivated under relatively cold conditions," Dr. Shikari said.

"If such traits were introduced through gene flow or the movement of germplasm, it could also provide clues about the historical movement of rice and help us investigate the possible routes through which these genetic characteristics reached Kashmir," he added.

Tracing the journey

According to Gaurav Zinta, principal scientist in the biotechnology division at the CSIR-Institute of Himalayan Bioresource Technology, Palampur, the distinction "suggests Kashmir's traditional rice likely descends from temperate East Asian rice, similar to that grown in Korea and Japan, and was later shaped by the valley's short, cool growing season".

Dr. Zinta added that, on the other hand, modern varieties grown in the region tell a different story.

"Many were bred using lowland Indian rice to improve yield and grain type, and in the process, they lost much of the cold tolerance," he said. "So the landraces are more than a piece of history. They are a reservoir of useful genes that modern breeding has partly left behind, and they deserve active conservation."

That said, the landraces are not purely East Asian: "Some of their genes, such as those affecting starch and cooking quality, resemble those of tropical rice, suggesting they also mixed with other rice types over time," Dr. Zinta explained. "Their history is best seen as layered rather than a single straight line."

"Shared genes show that Kashmir rice and East Asian rice are related, [but] not the path the rice took," he continued. "It could have crossed the Himalaya directly or come through Central Asia along early trade routes that later formed part of the Silk Road. The paper mentions both possibilities without clearly separating them."

To confirm the route, he suggested that researchers compare Kashmir rice with rice from regions along the way, including from Nepal and Tibet. "Ancient rice grains found in Kashmir should also be dated and, where possible, their DNA analysed. This would show when rice reached Kashmir and where it originated."

He also said the study has some limitations, including studying a "fairly small" number of local landraces and the team not testing the varieties for cold tolerance, aroma or grain quality. As a result, "the link between genes and traits is predicted rather than demonstrated," Dr. Zinta added.

He said the effort nonetheless provided a strong foundation for future work.

Archaeology of rice

The research team also considered the fact that wheat, barley, and some millets were among the region's earliest cultivated crops.

Anil Pokharia, scientist at Birbal Sahni Institute of Palaeosciences, Lucknow, said there is no clear archaeological evidence of rice being cultivated in the Neolithic period, around 3,000 years ago.

"Wheat and barley appear to have been the dominant crops, with wheat cultivated as a long-duration crop, sown around October and harvested the following July or August. Rice appears to have been introduced later, possibly around 1000-1500 BC, during the megalithic period, although the exact timing remains uncertain," he said.

"With the introduction of rice as a summer crop, shorter-duration forms of wheat and other crops would also have been needed to fit the changing agricultural cycle."

That said, he added that the archaeological record at Burzahom and Gufkral are limited by the fact that rice grains could not be directly radiocarbon dated, increasing the uncertainty as to their precise age.

According to Dr. Shikari, the genomic evidence provides another line of evidence -- and that genetic patterns in present-day Kashmir rice are consistent with the possibility that the region has a distinct history of rice cultivation.

The authors discuss in their paper that the evolutionary history of japonica rice appears to have been closely associated with climate changes during the mid-to-late Holocene, in a period characterised by cooling and unstable weather.

"The onset of cooler environmental conditions may have imposed strong selection pressure on rice populations, favouring genetic variants associated with cold tolerance," Dr. Shikari said.

Dr. Pokharia suggested Kashmir could be an important region for future archaeological research because of its position as a potential junction between influences from East and West Asia.

"The excavations carried out with a broader research perspective, combined with multidisciplinary approaches involving archaeology, genetics and other fields, could help researchers better understand the movement of crops, people and cultural influences into the region," he said.