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African Rice SNP Map Reveals Geographical Adaptation Through Salt Tolerance

NEW YORK (GenomeWeb) – A new study of African rice (Oryza glaberrima Steud.), a close relative of Asian rice (Oryza sativa L.), has yielded a map of its 2.32 million SNPs and shed new light on its domestication history and adaptation to different geographies.

In the study, published today in Nature Genetics, an international team of researchers led by investigators at New York University used paired-end Illumina sequencing to resequence the genomes of 93 traditional O. glaberrima landraces — domesticated, regional ecotypes — from across the species range in West and Central sub-Saharan Africa, where it is mainly grown.

Most of the samples they used originated from a coastal region spanning Senegal to Liberia, as well as from inland areas in Nigeria, Niger, Cameroon, Chad, Mali, and Burkina Faso. They sequenced four of the landraces to between 30x and 73x mean nuclear genome coverage depth, and sequenced the remaining accessions to an average depth of 14.61x. The researchers then aligned these sequences to the O. glaberrima CG14 reference genome sequence, and identified more than 2.3 million SNPs.

They then performed principal-component analysis of SNP variation and found that they were "strongly correlated" with geography: either an east-west cline or a north-south cline. This allowed them, in turn, to deduce that all the landraces predominantly belonged to one cluster, with various levels of genomic contribution from five other ancestral populations.

"Using the wild progenitor Oryza barthii A. Chev as an outgroup, we observed an older split between coastal and inland populations and a more recent separation of northern and southern populations," the authors wrote. "Even without migration, this topology accounted for more than 99 percent of the variance in SNP data."

They also found that the species underwent a population bottleneck starting around 13,000 to 15,000 years ago, similar to what has been observed in other annual crop species, and coinciding with an increase in precipitation in West Africa after deglaciation leading into the start of the early Holocene African Humid Period.  

Post-domestication, the SNP map revealed that the trait in African rice most likely associated with geographical adaptation is salinity tolerance. "Arid regions of northern West Africa have higher salinity levels, associated with saltwater intrusion into rivers that can reach up to 250 kilometers inland," the researchers wrote. They also interviewed African farmers about how they mitigate salt stress on their plants, and found that in Senegal, the major strategy was to farm salt-tolerant varieties. About 25 percent of the O. glaberrima varieties used by farmers in this area were salt tolerant, according to the researchers.

To examine phenotypic variation in salt tolerance, the team measured several salinity-associated fitness traits in 121 landrace seedlings at early and late stages of salt exposure, and found significant differences in the phenotypes across the four West African populations, except for the phenotypes corresponding to sodium and potassium content.

They also performed GWAS mapping with the 93 landrace sequences and found 28 SNPs in 11 unique genomic regions linked to salt-tolerance traits, four of which were within 300 kb of genomic regions that possess signatures of positive selection.

"Our analysis of African rice provides genetic evidence that may point to an extended period of low-intensity cultivation or management of a wild species before its domestication," the team wrote. "There have been two competing hypotheses for the timescale of domesticated crop origins — the rapid and protracted transition models of domestication. Our work provides support for the latter hypothesis, and, although other extrinsic (for example, climatic) factors cannot be ruled out, further archaeological and genetic work may help to establish the tempo and mode of the domestication process."

The researchers further added that the SNP map they described not only identified genomic regions associated with geographical differentiation and adaptation to a major abiotic stress factor like salinity, but could also offer other researchers new tools for mapping agriculturally important genes.