Abstract Detail

Crops and Wild Relatives

Meyer, Rachel [1], Gross, Briana [2], Flowers, Jonathan [3], Purugganan, Michael [4].

Did two rice species go through parallel domestication via changes to the same genes?

Two species of Oryza (Poaceae) underwent gradual domestication to become a staple food: O. sativa L. in China, and O. glaberrima Steud. in sub-Saharan West Africa. Recent studies have revealed a surprisingly parallel story to both species. The wild progenitors of both crops were widespread. In both, domestication was protracted, beginning early in the Holocene, and requiring thousands of years to fix key mutations. Crop domestication literature often points to Vavilov’s Law of Homologous Series of Evolution, stating that related species will often undergo parallel genetic change as the environment (including humans) selects on phenotype. In cereals, several QTL and genes have orthologs in multiple species that all were implicated in playing a role in the domestication process that altered, for example, seed shattering, seed color, early germination, and determinacy. AIM: We tested the extent of parallelism in domestication genes and in whole genome patterns of selection, hypothesizing that over half of the loci would be under selection or show functional change of the same effect, whilst not requiring the same particular mutations. The null hypothesis is that few or no genes show parallel selection or functional change, which would defy Vavilov’s law. METHODS: We made whole genome alignments and SNP maps of 102 accessions of O. glaberrima and 17 accessions wild progenitor O. barthii, using the O. glaberrima reference genome. We did the same for 101 accessions of O. sativa subsp. tropical japonica and 16 accessions wild progenitor O. rufipogon, using the tropical japonica reference genome. We mined the literature for 42 functionally characterized domestication genes that show evidence of selection in O. sativa, found their ortholog in O. glaberrima, and explored genetic diversity, SNPs, and INDELS of these genes and 5kb flanking either side. We used ANGSD to calculate genome wide diversity statistics and sliding window selection patterns including Fst and XP-CLR. We examined parallel patterns in O. sativa domestication loci against the background parallelism of ‘neutral’ loci. RESULTS: While some parallelism occurs on the genome-wide level, evidence of homologous evolutionary patterns from domestication affecting the 42 genes were not extensive. While methylation and regulatory patterns affecting transcriptional and post-transcriptional processes cannot be ruled out, it appears the mechanism of achieving parallel phenotypic change in the two rice species has only scantily stemmed from orthologous genetic change, rather, parallel pathways may be the level of the homologous feature Vavilov’s law should point to.

1 - University of California Los Angeles, Ecology and Evolutionary Biology, 610 Charles E Young Drive E, Los Angeles, CA, 90095, USA
2 - University of Minnesota Duluth, Biology, 207 Swenson Science Building, 1035 Kirby Drive, Duluth, MN, 55812, USA
3 - New York University, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY, 10003, USA
4 - New York University, Center for Genomics and Systems Biology, 12 Waverly Place, New York, NY, 10003, United States

Keywords:
none specified

Presentation Type: Oral Paper
Session: 39, Crops and Wild Relatives
Location: Sundance 2/Omni Hotel
Date: Wednesday, June 28th, 2017
Time: 3:00 PM
Number: 39007
Abstract ID:520
Candidate for Awards:None