Haplotype Analysis and Linkage Disequilibrium at Five Loci inEragrostis tef

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.

High-Throughput Discovery of Mutations in Tef Semi-Dwarfing Genes by Next-Generation Sequencing Analysis

“…For the two apparent rht1 homeologues used in this study, Smith and colleagues (Smith et al 2012) calculated a divergence time of 4-5 MYA. Given the significant variation that exists in the rates of divergence for different plant nuclear genes (Zhang et al 2002), it is clear that many more homeologous pairs need to have their divergence date ascertained in tef, so a relatively robust number can be derived.…”

“…Exonic segments of four dwarfing candidate genes, dw3a, dw3b, rht1a, and rht1b (Smith et al 2012) were chosen for 454 sequencing. Seven pairs of primers for the dw3/br2 genes and 1 pair of primers for the rht1 homeologues were designed to cover the appropriate coding regions (Figure 1) for initial PCR and sequencing.…”

“…Array-enriched whole-exome sequencing has been widely used to identify candidate causative genes for human disease. For example, SNPs in genes DHODH and MLL2 were respectively identified as causal agents for Miller syndrome and Kabuki syndrome by this approach (Ng et al 2010a,b).Recently, Smith et al (2012) cloned and sequenced homologs of the sd1 and rht1 genes from tef. Two rht1 homeologues, apparent orthologs of the wheat genes, were sequenced across 31 tef accessions, as were three tef sd1 homologs of unknown paralogous/orthologous relationship.…”

“…Recently, Smith et al (2012) cloned and sequenced homologs of the sd1 and rht1 genes from tef. Two rht1 homeologues, apparent orthologs of the wheat genes, were sequenced across 31 tef accessions, as were three tef sd1 homologs of unknown paralogous/orthologous relationship.…”

“…TILLING (targeting induced local lesions in genomes) and EcoTILLING (Comai et al 2004) have been applied to a variety of plants, resulting in identification of mutations in specific target genes in Arabidopsis Till et al 2003;Martin et al 2009), rice (Till et al 2007;Suzuki et al 2008), wheat (Slade et al 2005), maize , sorghum (Xin et al 2008), pea (Dalmais et al 2008), soybean (Cooper et al 2008), tomato (Minoia et al 2010), and other plant species. However, TILLING is a time-consuming, expensive, and labor-intensive approach when applied to either large populations or large genomes and might be particularly challenging in a recent tetraploid like tef (Smith et al 2012) where homeologues have not yet differentiated greatly in sequence.…”