Genome Scan of Rice Landrace Populations Collected Across Time Revealed Climate Changes' Selective Footprints in the Genes Network Regulating Flowering Time.

The Tajima’s D test detected significant deviations from neutrality in Og -1 and Og -2 (Mean D = − 2.01, p value = 0.0010), almost significant deviation in Osj -1 and Osj -2 (Mean D = − 1.29, p value = 0.0575), and non-significant deviation in Osi -1 and Osi -2 (Additional file 5 : Table S3).

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The ontology analysis of the 2038 MSU-TIGR genes, on the pseudo-chromosomic segment bearing the 24 M2 type ILUS , with the Agri-GO tool, detected highly significant enrichment in genes involved in several biological processes (Additional file 9 : Table S6A) including “reproductive processes”, “response to light and radiation” and “response to stimulus” (Table 2 ).

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