Abstract

BackgroundMonitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. The tertiary gene pool of wheat is a very important source of genetic variability for wheat improvement against biotic and abiotic stresses. By exploring the 5Mg short arm (5MgS) of Aegilops geniculata, we can apply chromosome genomics for the discovery of SNP markers and their use for monitoring alien introgressions in wheat (Triticum aestivum L).ResultsThe short arm of chromosome 5Mg of Ae. geniculata Roth (syn. Ae. ovata L.; 2n = 4x = 28, UgUgMgMg) was flow-sorted from a wheat line in which it is maintained as a telocentric chromosome. DNA of the sorted arm was amplified and sequenced using an Illumina Hiseq 2000 with ~45x coverage. The sequence data was used for SNP discovery against wheat homoeologous group-5 assemblies. A total of 2,178 unique, 5MgS-specific SNPs were discovered. Randomly selected samples of 59 5MgS-specific SNPs were tested (44 by KASPar assay and 15 by Sanger sequencing) and 84% were validated. Of the selected SNPs, 97% mapped to a chromosome 5Mg addition to wheat (the source of t5MgS), and 94% to 5Mg introgressed from a different accession of Ae. geniculata substituting for chromosome 5D of wheat. The validated SNPs also identified chromosome segments of 5MgS origin in a set of T5D-5Mg translocation lines; eight SNPs (25%) mapped to TA5601 [T5DL · 5DS-5MgS(0.75)] and three (8%) to TA5602 [T5DL · 5DS-5MgS (0.95)]. SNPs (gsnp_5ms83 and gsnp_5ms94), tagging chromosome T5DL · 5DS-5MgS(0.95) with the smallest introgression carrying resistance to leaf rust (Lr57) and stripe rust (Yr40), were validated in two released germplasm lines with Lr57 and Yr40 genes.ConclusionThis approach should be widely applicable for the identification of species/genome-specific SNPs. The development of a large number of SNP markers will facilitate the precise introgression and monitoring of alien segments in crop breeding programs and further enable mapping and cloning novel genes from the wild relatives of crop plants.

Highlights

  • Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives

  • Flow-sorting and sequencing of the 5Mg short arm The analysis of DAPI-stained, chromosome suspensions prepared from a wheat–Ae. geniculata t5MgS telocentric addition line resulted in histograms with five peaks of fluorescence intensity (Figure 1)

  • Mapping of reads and Single-nucleotide polymorphism (SNP) calling For mapping the 5MgS reads, we used 5AS, 5BS and 5DS chromosome shotgun sequence assemblies provided by the International Wheat Genome Sequencing Consortium

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Summary

Introduction

Monitoring alien introgressions in crop plants is difficult due to the lack of genetic and molecular mapping information on the wild crop relatives. Bread or hexaploid wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD genome), which accounts for 95% of the harvested wheat crop, traces its origin to a rare hybridization event ~6,000 years ago Tetraploid, emmer wheat T. turgidum L. arose ~350,000 years ago from a hybridization between T. urartu Tuanian ex Gandilyan (2n = 2x = 14, AA) and a B-genome species, whose closest living relative is Ae. speltoides Tausch (2n = 2x = SS) [14,15,16]. These two species, together with the A-genome species T. monococcum L. subsps. Wheat marker systems can be used to map alien introgressions from secondary gene pool

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