Allelic variants in the PRR37 gene and the human-mediated dispersal and diversification of sorghum

Abstract

Allele phylogenetic analysis of the sorghum flowering-time gene PRR37 provided new insight into the human-mediated selection of a key adaptive gene that occurred during sorghum's diversification and worldwide dispersal. The domestication and spread of the tropical cereal sorghum is associated with the historic movement of humans. We show that an allelic series at PRR37 (pseudo-response regulator 37), a circadian clock-associated transcription factor, was selected in long-day ecosystems worldwide to permit floral initiation and grain production. We identified a series of loss-of-function (photoperiod-insensitive) alleles encoding truncated PRR37 proteins, alleles with key amino acid substitutions in the pseudo-receiver domain, and a novel splice variant in which the pseudo-receiver domain is truncated. Each PRR37 allelic variant was traced to a specific geographic location or specialized agronomic type. We present a graphical model that shows evidence of human selection and gene flow of the PRR37 allelic variants during the global dispersal and agronomic diversification of sorghum. With the recent identification of the Ghd7 gene as an important regulator of flowering date in sorghum, we briefly examine whether loss-of-function Ghd7 allelic variants were selected prior to the human-mediated movement of sorghum from its equatorial center of origin to temperate climates worldwide.

High-depth resequencing of 312 accessions reveals the local adaptation of foxtail millet

“…The PRR gene family was first discovered in Arabidopsis, in which three of five members play redundant roles in flowering under long-day conditions (Nakamichi et al 2007). PRR genes also influence geographical adaptation in several crops (Klein et al 2015;Koo et al 2013;Turner et al 2005). Recent study suggested two homologous PRR3 genes controlling flowering and maturity were sequentially selected during soybean domestication (Lu et al 2020).…”

Positional Cloning of the Flowering Time QTL qFT12-1 Reveals the Link Between the Clock Related PRR Homolog With Photoperiodic Response in Soybeans

“…In sorghum, there are many loss-of-function alleles encoding truncated PRR37 protein. Each PRR37 allelic variant could be traced to specific geographic location or specialized agronomic type (Klein et al, 2015), indicative of human selection. In this study, when we analyzed the variation of Glyma.12G073900 at nucleotide 2088 in 642 soybean accessions, it was found that JLCLH homologous type mostly exists in wild soybeans and landrace, whereas CN homozygous type are mostly distributed in improved cultivar.…”

Genomic and environmental determinants and their interplay underlying phenotypic plasticity

“…Sequence analysis revealed that the most significant QTL corresponds to the known Ma 1 gene on chromosome 6 ( PRR37 , Sobic.006G057866), encoding a pseudoresponse regulator protein ( 28 ). A single adenine insertion in the third exon of Tx430 allele was identified that led to a premature stop codon and nonfunctional protein ( prr37 Feterrita ) ( 29 ) ( Fig. 5 and SI Appendix , Fig.…”