A research team led by New York University scientists has sequenced and analyzed the genomes of two members of the basmati rice group: a variety of basmati rice called Basmati 334 and the sadri rice variety Dom Sufid.
Basmati rice. Image credit: Republica.
The Asian rice (Oryza sativa) is an agriculturally important crop that feeds one-half of the world’s population and supplies 20% of people’s caloric intake.
Historically, the species has been classified into two major variety groups, japonica and indica, based on morphometric differences and molecular markers. These variety groups can be considered as subspecies, particularly given the presence of reproductive barriers between them.
Archaeobotanical remains suggest japonica rice was domesticated 9,000 years ago in the Yangtze basin of China, while indica rice originated 4,000 years ago when domestication alleles were introduced from japonica into either Oryza nivara or a proto-indica in the Indian subcontinent.
More recently, two additional variety groups have been recognized that are genetically distinct from japonica and indica: the aus/circum-aus and aromatic/circum-basmati rice.
Among its members, the circum-basmati group boasts the iconic basmati rice from southern Asia and the sadri rice from Iran.
Despite its economic and cultural importance, a high-quality reference genome is currently lacking, and the group’s evolutionary history is not fully resolved.
“Rice is one of the most important staple crops worldwide, and the varieties in the basmati group are some of the most iconic and prized rice varieties,” said Dr. Jae Young Choi, a postdoctoral researcher in the Center for Genomics and Systems Biology and the Department of Biology at New York University.
“However, until recently, a high-quality reference genome for basmati rice did not exist.”
Dr. Choi and colleagues from New York University, Oxford Nanopore Technologies and the New York Genome Center sequenced the genomes of two basmati rice varieties using nanopore sequencing technology.
The researchers focused on Basmati 334 from Pakistan, known to be drought tolerant and resistant to rice-killing bacterial blight, and Dom Sufid from Iran, an aromatic long-grain rice that is one of the most expensive on the market.
Using long reads from nanopore sequencing, the scientists assembled high-quality, complete genomes of Basmati 334 and Dom Sufid that were a significant improvement over earlier genome sequences assembled using short reads.
The sequencing also confirmed that basmati rice is a hybrid of two other rice groups. Most genetic material in basmati comes from japonica, followed by the rice group aus.
The study authors now plan to work with the scientific and rice breeding communities to identify important genes, see what makes the basmati group unique, and even develop molecular markers to help breed new varieties.
“By having the sequence of rice varieties like Basmati 334, which can withstand drought conditions and resist bacterial blight, we can start to identify genes that give rise to these valuable traits,” said New York University’s Michael Purugganan.
“Drought tolerance is something we are particularly interested in, given the challenges we face due to climate change and the implications for food security worldwide.”
The team’s results were published in the journal Genome Biology.
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J.Y. Choi et al. 2020. Nanopore sequencing-based genome assembly and evolutionary genomics of circum-basmati rice. Genome Biol 21 (21); doi: 10.1186/s13059-020-1938-2
