Analysis of agronomic and domestication traits in a durum × cultivated emmer wheat population using a high-density single nucleotide polymorphism-based linkage map

Abstract

Development of a high-density SNP map and evaluation of QTL shed light on domestication events in tetraploid wheat and the potential utility of cultivated emmer wheat for durum wheat improvement. Cultivated emmer wheat (Triticum turgidum ssp. dicoccum) is tetraploid and considered as one of the eight founder crops that spawned the Agricultural Revolution about 10,000 years ago. Cultivated emmer has non-free-threshing seed and a somewhat fragile rachis, but mutations in genes governing these and other agronomic traits occurred that led to the formation of today's fully domesticated durum wheat (T. turgidum ssp. durum). Here, we evaluated a population of recombinant inbred lines (RILs) derived from a cross between a cultivated emmer accession and a durum wheat variety. A high-density single nucleotide polymorphism (SNP)-based genetic linkage map consisting of 2,593 markers was developed for the identification of quantitative trait loci. The major domestication gene Q had profound effects on spike length and compactness, rachis fragility, and threshability as expected. The cultivated emmer parent contributed increased spikelets per spike, and the durum parent contributed higher kernel weight, which led to the identification of some RILs that had significantly higher grain weight per spike than either parent. Threshability was governed not only by the Q locus, but other loci as well including Tg-B1 on chromosome 2B and a putative Tg-A1 locus on chromosome 2A indicating that mutations in the Tg loci occurred during the transition of cultivated emmer to the fully domesticated tetraploid. These results not only shed light on the events that shaped wheat domestication, but also demonstrate that cultivated emmer is a useful source of genetic variation for the enhancement of durum varieties.

QTL Analysis of Spike Morphological Traits and Plant Height in Winter Wheat (Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map

“…Traits alongside the double headed arrows are spike length (SL), fertile spikelet number per spike (FSN), sterile spikelet number per spike (SSN), total spikelet number per spike (TSN), spikelet compactness (SC), and plant height (PHT). The known positions of the 1RS/1BL translocation (T1RS/1BL), Rht8, Ppd-B1, Vrn-A1 , and Q loci are presented in blue arrows (Korzun et al, 1998; Liu et al, 2008; Cavanagh et al, 2013; Wang et al, 2014; Faris et al, 2014a). …”

microRNA172 plays a critical role in wheat spike morphology and grain threshability

“…The primary genetic determinants of the free-threshing habit are recessive mutations at the Tg ( tenacious glume ) gene and a hypermorphic mutation at the Q gene (Faris et al, 2014). Q also controls the subcompact spike phenotype and influences other domestication-related traits such as rachis fragility, glume toughness, plant height and flowering time (Faris et al, 2005).…”

Candidate loci involved in domestication and improvement detected by a published 90K wheat SNP array

“…With the millions of SNPs now discovered by next generation sequencing technology, it is possible to screen for genomic regions in wheat that have undergone selection during evolution. Currently, several wheat SNP arrays are publically available2526 and some selected regions, or QTLs, have been identified using these SNP chips2527.…”