NEW YORK – A new basmati rice genome assembly using nanopore sequencing reads gives insight into the crop's origins.
Oryza sativa is a key agricultural crop that provides about 20 percent of people's caloric intake, according to the Food and Agriculture Organization of the United Nations. While O. sativa is typically split into two major varieties — japonica and indica — two other genetically distinct variety groups — aus/circum-aus and aromatic/circum-basmati — have recently been recognized.
Researchers from New York University used nanopore sequencing to generate the genomes of two basmati rice landraces, the drought-tolerant Basmati 334 from Pakistan and the expensive Dom Sufid from Iran. By analyzing these genomes, the researchers identified variants not found in japonica rice, found evidence of admixture between the circum-basmati and circum-aus varieties, and uncovered three geographic groups among the basmati varieties, as they reported Wednesday in Genome Biology. The assemblies could further help develop rice with desired traits such as drought or disease resistance.
"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," first author Jae Young Choi, a postdoc at New York University, said in a statement.
The researchers sequenced the two basmati rice varieties using Oxford Nanopore Technologies' long-read sequencing platform to about 62X coverage for the Basmati 334 genome and about 51X coverage for the Dom Sufid genome. After polishing the genome assemblies using nanopore and short Illumina sequencing reads, the researchers generated a 386.5 Mb assembly across 188 contigs for Basmati 334 and 383.6 Mb across 116 contigs for Dom Sufid.
Aligning these draft genome assemblies to the japonica reference genome — a rice from East Asia — uncovered a high level of macrosynteny among the three rice varieties, with the exception of an inversion on chromosome six among the basmati varieties. However, they also found single nucleotide changes, insertions and deletions, and repeat expansions that varied among the rice. For instance, the Dom Sufid variety carried an eight-base-pair deletion affecting the BADH2 sequence region, an alteration associated with fragrance among rice varieties. Basmati 334 and the japonica reference, both non-fragrant varieties, did not have this deletion.
By comparing the rice genomes, the researchers traced the origins of the basmati variety. Through their modeling, the researchers found that the origins of circum-basmati rice was primarily rooted to japonica rice, but with gene flow from circum-aus rice, a rice from Bangladesh. In particular, their analysis suggests there was a period of time during which the circum-aus, circum-basmati, and japonica rice varieties were isolated, but then with gene flow occurring after the split.
They noted, though, that the history of chromosome 10 differed. In basmati rice, this chromosome appears to have had higher levels of circum-aus introgression, but it is unclear why this occurred, the researchers noted.
Within basmati rice, the analysis indicated there were three genetic sub-groups that largely aligned with geography: Bhutan/Nepal, Iran/Pakistan, and India/Bangladesh/Myanmar. Both the Bhutan/Nepal and Iran/Pakistan groups had genetic signature indicative of an admixed population, but the India/Bangladesh/Myanmar group was more distinct and may have experienced more gene flow from circum-aus rice, the researchers noted.
Following their sequencing of these two basmati rice strains, the researchers plan to work with breeders and others to identify key genes and molecular markers to aid in the development of new rice 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," senior author Michael Purugganan, a biology professor at NYU, said in a statement. "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."