Abstract
Eragrostis tef (Zucc.), a member of the Chloridoideae subfamily of grasses, is one of the most important food crops in Ethiopia. Lodging is the most important production problem in tef. The rht1 and sd1 dwarfing genes have been useful for improving lodging resistance in wheat and rice, respectively, in what has been known as the “Green Revolution.” All homologs of rht1 and sd1 were cloned and sequenced from 31 tef accessions collected from across Ethiopia. The allotetraploid tef genome was found to carry two rht1 homologs. From sequence variation between these two putative homologs, an approximate ancestral divergence date of 6.4 million years ago was calculated for the two genomes within tef. Three sd1 homologs were identified in tef, with unknown orthologous/paralogous relationships. The genetic diversity in the 31 studied accessions was organized into a relatively small number of haplotypes (2−4) for four of these genes, whereas one rht1 homeologue exhibited 10 haplotypes. A low level of nucleotide diversity was observed at all loci. Linkage disequilibrium analysis demonstrated strong linkage disequilibrium, extending the length of the five genes investigated (2−4 kb), with no significant decline. There was no significant correlation between haplotypes of any of these genes and their recorded site of origin.
Highlights
Eragrostis tef (Zucc.), a member of the Chloridoideae subfamily of grasses, is one of the most important food crops in Ethiopia
The Central Statistical Authority (2010) reported that tef constitutes 19% of the gross grain production of all the major cereal cultivated in the country and 24% of the total acreage of cereals planted in Ethiopia
Five varieties were the result of direct selection on the basis of their performance in farmers’ fields, and five were developed through intraspecific hybridization of varieties selected from the tef germplasm collection maintained at the Debre Zeit Agricultural Research Center in Ethiopia
Summary
Plant material A total of 31 E. tef germplasm accessions were obtained from the U.S D.A. Several degenerate primers were designed from the most conserved regions among the rht and sd n Table 1 Region of origin of Eragrostis tef accessions collected from Ethiopia. PCR amplification products with high identify to rht and sd orthologs were gel purified (QIAGEN, Valencia, CA) and used as probes to screen tef genomic libraries for cross-hybridizing clones. Separate sd and rht probes amplified with degenerate primers designed from rice and wheat orthologs, respectively, were used to screen each tef genomic library for cross-hybridizing clones. To amplify the sd and rht genes from 30 tef accessions, gene-specific primers were designed from the 59 UTR and 39 end of each gene by aligning the sequences and scrutinizing them for nucleotide substitutions unique to each gene. Sequences obtained from genomic subclones, cloned PCR products and PCR-amplified probes were analyzed using BLASTN to verify cloning or amplification of the correct gene. Sampled trees were summarized in TreeAnnotator version 1.6.1 (Rambaut and Drummond 2007b) and visualized in Figtree version 1.3.1 (Rambaut and Drummond 2007c)
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